Articles related to genetics 03/18

List provided by
Ishwarappa KATAGERI katageriis@uasd.in

Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations
Chandnani R et al.
Plant Genome. 2018 Mar; 11(1). doi: 10.3835/plantgenome2017.06.0057
Corresponding author: paterson@uga.edu

In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. ‘Acala Maxxa’ (GH) and G. barbadense L. ‘Pima S6’ (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments. Totals of 3186 and 3026 polymorphic single-nucleotide polymorphisms (SNPs) in GH and GB backgrounds, respectively, were identified and used for trait mapping. Small-effect QTL (<10% variance explained) made up 87 and 100% of QTL in GH and GB backgrounds, respectively

 Genetic Map Construction and Fiber Quality QTL Mapping Using the Cotton SNP80K Array in Upland Cotton
Zhaoyun Tan et al.
Front. Plant Sci. 9:225. (2018)
Corresponding author: zhangzs@swu.edu.cn

Cotton fiber quality traits are controlled by multiple quantitative trait loci (QTL), and the improvement of these traits requires extensive germplasm. Herein, an Upland cotton cultivar from America, Acala Maxxa, was crossed with a local high fiber quality cultivar, Yumian 1, and 180 recombinant inbred lines (RILs) were obtained. In order to dissect the genetic basis of fiber quality differences between these parents, a genetic map containing12116 SNP markers was constructed using the CottonSNP80K assay, which covered 3741.81 cM with an average distance of 0.31 cM between markers. Based on the genetic map and grow outs in three environments, we detected a total of 104 QTL controlling fiber quality traits. Among these QTL, 25 were detected in all three environments and35 in two environments.

Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton.
unji Su et al.
Theor Appl Genet. 2018 Mar 1. doi: 10.1007/s00122-018-3079-5
Corresponding author: ysx195311@163.com

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block.

Expression of cry2Ah1 and two domain II mutants in transgenic tobacco confers high resistance to susceptible and Cry1Ac-resistant cotton bollworm
Li S et al.Sci Rep. 2018 Jan 11;8(1):508.
doi: 10.1038/s41598-017-19064-5.
Corresponding author: langzhihong@caas.cn

To improve the novel Bacillus thuringiensis insecticidal gene cry2Ah1 toxicity, two mutants cry2Ah1-vp (V354VP) and cry2Ah1-sp (V354SP) were performed. SWISS-MODEL analysis showed two mutants had a longer loop located between β-4 and β-5 of domain II, resulting in higher binding affinity with brush border membrane vesicles (BBMV) of Helicoverpa armigera comparing with Cry2Ah1

Genetic dissection of the fuzzless seed trait in Gossypium barbadense.
Zhu QH et al.
J Exp Bot. 2018 Jan 17. doi: 10.1093/jxb/erx459.
Corresponding author: qianhao.zhu@csiro.au and  iain.wilson@csiro.au

Cotton fibres are single-celled trichomes arising from the epidermal cells of the seed coat and may be either long (lint) or very short (fuzz). The dominant fuzzless N1 of Gossypium hirsutum is a defective allele of the At-subgenome homoeolog of MYB25-like, but the genetic components underlying the recessive fuzzless trait from G. barbadense (Gb) are unknown. We have identified five genetic loci, including a major contributing locus containing MYB25-like_Dt, associated with Gb fuzzless seeds based on genotyping of fuzzy and fuzzless near isogenic lines (NILs) from an interspecies cross (G. barbadense × G. hirsutum).

Genome-Wide Characterisation of DNA Methylation in an Invasive Lepidopteran Pest, the Cotton Bollworm Helicoverpa armigera
Jones CM, Lim KS, Chapman JW, Bass C
G3 (Bethesda). 2018 Mar 2;8(3):779-787.
doi: 10.1534/g3.117.1112.
Corresponding author: chris.jones@lstmed.ac.uk.

The genes and genomes of insect pests are shaped by the wide array of selective forces encountered in their environments. While the molecular adaptations that evolve are beginning to be understood at the genomic and transcriptomic level they have been less well characterised at an epigenetic level. Here, we present a genome-wide map of DNA methylation, at single-nucleotide resolution for the cotton bollworm moth, Helicoverpa armigera; a globally invasive pest of agriculture. We show that methylation is almost identical in the larvae and adults of H. armigera and that, through whole genome bisulfite sequencing, at the most ~0.9% of CpG sites in this species are methylated.

 

Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum.
Wang Y et al.
BMC Genomics. 2018 Jan 4; 19(1):15.
doi: 10.1186/s12864-017-4398-7.
Corresponding author: baoliangzhou@njau.edu.cn

We previously reported the development of a set of Gossypium hirsutumG. australe alien chromosome addition lines. Naturally, however, G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G2G2 genome) into the most cultivated cotton, G. hirsutum (AADD)

In-field High Throughput Phenotyping and Cotton Plant Growth Analysis Using LiDAR
Sun S et al.
Front Plant Sci. 2018 Jan 22; 9: 6.
doi: 10.3389/fpls.2018.00016. eCollection 2018
Corresponding author: cyli@uga.edu

Plant breeding programs and a wide range of plant science applications would greatly benefit from the development of in-field high throughput phenotyping technologies. In this study, a terrestrial LiDAR-based high throughput phenotyping system was developed. A 2D LiDAR was applied to scan plants from overhead in the field, and an RTK-GPS was used to provide spatial coordinates. Precise 3D models of scanned plants were reconstructed based on the LiDAR and RTK-GPS data. The ground plane of the 3D model was separated by RANSAC algorithm and a Euclidean clustering algorithm was applied to remove noise generated by weeds. After that, clean 3D surface models of cotton plants were obtained, from which three plot-level morphologic traits including canopy height, projected canopy area, and plant volume were derived. Canopy height ranging from 85th percentile to the maximum height were computed based on the histogram of the z coordinate for all measured points; projected canopy area was derived by projecting all points on a ground plane; and a Trapezoidal rule based algorithm was proposed to estimate plant volume

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum).
Wen T et al.
Plant Biotechnol J. 2018 Feb 24. doi: 10.1111/pbi.12902.
Corresponding author: linzhongxu@mail.hzau.edu.cn and xjycy99@126.com

Brown fibre cotton is an environmental-friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine-mapped the brown fibre region, Lc1, and dissected it into two loci, qBF-A07-1 and qBF-A07-2.

Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton.
Zhao C et al.
BMC Genomics. 2018 Jan 2; 19(1):6. doi: 10.1186/s12864-017-4406-y.
Corresponding author: guobaosheng111@126.com.  And gengjunyi66@126.com.

Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton.

QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population.
Jia X et al.
Mol Genet Genomics. 2018 Feb 8. doi: 10.1007/s00438-018-1424-7.
Corresponding author: ysx195311@163.com

Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0.63 cM, 186 additive QTLs were obtained for five fiber quality traits over five consecutive years, including 39 for fiber length (FL), 36 for fiber strength (FS), 50 for fiber uniformity (FU), 33 for micronaire (MC) and 28 for fiber elongation (FE). Three stable QTLs, qMC-A4-1, qMC-D2-3 and qFS-D9-1, were detected in four datasets, and another eight stable QTLs, qMC-A4-2, qMC-D11-2, qFU-A9-1, qFU-A10-4, qFS-D11-1, qFL-D9-2, qFL-D11-1 and qFE-A3-2, were detected in three datasets

QTL Mapping for Fiber Quality and Yield Traits Based on Introgression Lines Derived from Gossypium hirsutum × G. tomentosum
Keerio AA et al.
Int J Mol Sci. 2018 Jan 14; 19 (1). pii: E243. doi: 10.3390/ijms19010243
Corresponding author: linzhongxu@mail.hzau.edu.cn

The tetraploid species Gossypium hirsutum is cultivated widely throughout the world with high yield and moderate fiber quality, but its genetic basis is narrow. A set of 107 introgression lines (ILs) was developed with an interspecific cross using G. hirsutumacc. 4105 as the recurrent parent and G. tomentosum as the donor parent. A specific locus amplified fragment sequencing (SLAF-seq) strategy was used to obtain high-throughput single nucleotide polymorphism (SNP) markers. In total, 3157 high-quality SNP markers were obtained and further used for identification of quantitative trait loci (QTLs) for fiber quality and yield traits evaluated in multiple environments. In total, 74 QTLs were detected that were associated with five fiber quality traits (30 QTLs) and eight yield traits (44 QTLs), with 2.02-30.15% of the phenotypic variance explained (PVE), and 69 markers were found to be associated with these thirteen traits

Pollen-mediated gene flow from transgenic cotton is constrained by physical isolation measures
Yan Set al.
Sci Rep. 2018 Feb 12;8(1):2862. doi: 10.1038/s41598-018-21312-1.
Corresponding author:  liuxiaoxia611@cau.edu.cn

The public concern about pollen-mediated gene flow (PGF) from genetically modified (GM) crops to non-GM crops heats up in recent years over China. In the current study, we conducted greenhouse and field experiments to measure PGF with various physical isolation measures, including 90, 80, 60 and 40 holes/cm2 separation nets and Sorghum bicolor, Zea mays and Lycopersicon esculentum separation crops between GM cotton and non-GM line (Shiyuan321) by seed DNA test during 2013 to 2015, and pollen grain dyeing was also conducted to assess the pollen flow in greenhouse during 2013. Our results revealed that (1) PGF varied depending on the physical isolation measures. PGF was the lowest with 90 holes/cm2 separation net and S. bicolor separation crop, and the highest with 40 holes/cm2 separation net and no isolation measure. (2) Similar to PGF results, 90 holes/cm2 separation net and S. bicolor separation crop could minimize the pollen dispersal. (3) PGF declined exponentially with increasing distance between GM cotton and Shiyuan321. Because of the production mode of farm household (limited cultivated area) in China, our study is particularly important, which is not only benefit for constraining PGF, but also has potential application value in practical production and the scientific researches.

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii.
Zhu G, Li W, Zhang F, Guo W
BMC Genomics. 2018 Jan 23;19(1):73. doi: 10.1186/s12864-018-4449-8.
Corresponding author: moelab@njau.edu.cn

Using a diploid D genome wild salinity-tolerant cotton species, Gossypium davidsonii, we analyzed alternative splicing (AS) of genes related to salt stress by comparing high-throughput transcriptomes from salt-treated and well-watered roots and leaves. A total of 14,172 AS events were identified involving 6798 genes, of which intron retention (35.73%) was the most frequent, being detected in 3492 genes. Under salt stress, 1287 and 1228 differential alternative splicing (DAS) events were identified in roots and leaves, respectively. These DAS genes were associated with specific functional pathways, such as “responses to stress”, “metabolic process” and “RNA splicing”, implying that AS represents an important pathway of gene regulation in response to salt stress. Several salt response genes, such as pyrroline-5-carboxylate synthase (P5CS), K+ channel outward (KCO1), plasma membrane intrinsic protein (PIP) and WRKY33 which were involved in osmotic balance, ion homeostasis, water transportation and transcriptional regulation, respectively, were identified with differential alternative splicing under salt stress. Moreover, we revealed that 13 genes encoding Ser/Arg-rich (SR) proteins related to AS regulation were differentially alternatively spliced under salt stres.

Simple Sequence Repeat (SSR) Genetic Linkage Map of D Genome Diploid Cotton Derived from an Interspecific Cross between Gossypium davidsonii and Gossypium klotzschianum.
Kirungu JN et al.
Int J Mol Sci. 2018 Jan 11;19(1). pii: E204. doi: 10.3390/ijms19010204.
Corresponding author: joynk@cricaas.com.cn. And dengyf@cricaas.com.cn

The challenge in tetraploid cotton cultivars is the narrow genetic base and therefore, the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars. Construction of genetic maps has provided insight into understanding the genome structure, interrelationships between organisms in relation to evolution, and discovery of genes that carry important agronomic traits in plants. In this study, we generated an interspecific hybrid between two wild diploid cottons, Gossypium davidsonii and Gossypium klotzschianum, and genotyped 188 F2:3 populations in order to develop a genetic map. We screened 12,560 SWU Simple Sequence Repeat (SSR) primers and obtained 1000 polymorphic markers which accounted for only 8%. A total of 928 polymorphic primers were successfully scored and only 728 were effectively linked across the 13 chromosomes, but with an asymmetrical distribution. The map length was 1480.23 cM, with an average length of 2.182 cM between adjacent markers.

SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population
Huang C et al.
Mol Genet Genomics. 2018 Feb 1. doi: 10.1007/s00438-018-1419-4.
Corresponding author:  linzhongxu@mail.hzau.edu.cn

The quality of fiber is significant in the upland cotton industry. As complex quantitative traits, fiber quality traits are worth studying at a genetic level. To investigate the genetic architecture of fiber quality traits, we conducted an association analysis using a multi-parent advanced generation inter-cross (MAGIC) population developed from eight parents and comprised of 960 lines. The reliable phenotypic data for six major fiber traits of the MAGIC population were collected from five environments in three locations. Phenotypic analysis showed that the MAGIC lines have a wider variation amplitude and coefficient than the founders. A total of 284 polymorphic SSR markers among eight parents screened from a high-density genetic map were used to genotype the MAGIC population. The MAGIC population showed abundant genetic variation and fast linkage disequilibrium (LD) decay (0.76 cM, r2 > 0.1), which revealed the advantages of high efficiency and power in QTL exploration. Association mapping via a mixed linear model identified 52 significant loci associated with six fiber quality traits.

Transcriptomic profiling of developing fiber in levant cotton (Gossypium herbaceum L.)
Parekh MJ et al.
Funct Integr Genomics. 2018 Mar;18(2):211-223. doi: 10.1007/s10142-017-0586-4. Epub 2018 Jan 13
Corresponding author:  sushil254386@yahoo.com

Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but produce coarse lint. This undesirable characteristic strongly needs the knowledge of fiber development at molecular basis. The present study reported the transcriptome sequence of the developing fiber of G. herbaceum on pyrosequencing and its analysis.

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation.
He Pet al.
New Phytol. 2018 Apr;2018(1):167-182. doi: 10.1111/nph.14999. Epub 2018 Feb 8.
Corresponding author:  jnyu@snnu.edu.cn

RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule. Biochemical and genetic analyses revealed that the two vital editing sites were important for the interaction between the α and β subunits of ATP synthase, which resulted in ATP accumulation and promoted cell growth in yeast. Ectopic expression of C1292, C1415, or doubly edited Ghatp1 in Arabidopsis caused a significant increase in the number of trichomes in leaves and root length

Advanced Backcross QTL Analysis of Fiber Strength and Fineness in a Cross between Gossypium hirsutum and G. mustelinum.
Wang B et al.
Front Plant Sci. 2017 Oct 25;8:1848. doi: 10.3389/fpls.2017.01848.
Corresponding author: paterson@uga.edu and pwchee@uga.edu

The molecular genetic basis of cotton fiber strength and fineness in crosses between Gossypium mustelinum and Gossypium hirsutum(Upland cotton) was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. The BC3F2 families were genotyped with simple sequence repeat markers from a G. hirsutum by G. mustelinum linkage map, and the three generations of BC3-derived families were phenotyped for fiber strength (STR) and fineness (Micronaire, MIC). A total of 42 quantitative trait loci (QTLs) were identified through one-way analysis of variance, including 15 QTLs for STR and 27 for MIC, with the percentage of variance explained by individual loci averaging 13.86 and 14.06%, respectively. Eighteen of the 42 QTLs were detected at least twice near the same markers in different generations/families or near linked markers in the same family, and 28 of the 42 QTLs were identified in both mixed model-based composite interval mapping and one-way variance analyses.

Physiological and molecular mechanism of defense in cotton against Verticillium dahlia
Shaban M et al.
Plant Physiol Biochem. 2018 Feb 13; 125:193-204. doi: 10.1016/j.plaphy.2018.02.011
Corresponding author: lfzhu@mail.hzau.edu.cn

Cotton, a natural fiber producing crop of huge importance for textile industry, has been reckoned as the backbone in the economy of many developing countries. Verticillium wilt caused by Verticillium dahliae reflected as the most devastating disease of cotton crop in several parts of the world. Average losses due to attack of this disease are tremendous every year. There is urgent need to develop strategies for effective control of this disease. In the last decade, progress has been made to understand the interaction between cotton-V. dahliae and several growth and pathogenicity related genes were identified. Still, most of the molecular components and mechanisms of cotton defense against Verticillium wilt are poorly understood. However, from existing knowledge, it is perceived that cotton defense mechanism primarily depends on the pre-formed defense structures including thick cuticle, synthesis of phenolic compounds and delaying or hindering the expansion of the invader through advanced measures such as reinforcement of cell wall structure, accumulation of reactive oxygen species (ROS), release of phytoalexins, the hypersensitive response and the development of broad spectrum resistance named as, systemic acquired resistance (SAR)

Multivariate Analysis of the Cotton Seed Ionome Reveals a Shared Genetic Architecture
Pauli D et al.
G3 (Bethesda). 2018 Feb 1. pii: g3.300479.2017. doi: 10.1534/g3.117.300479.
Corresponding author: mag87@cornell.edu

To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the population were profiled in addition to those of soil samples taken from throughout the field site to better model environmental variation. The elements profiled in seeds exhibited moderate to high heritabilities, as well as strong phenotypic and genotypic correlations between elements that were not altered by the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton
Wang M et al.
Nat Plants. 2018 Feb; 4(2):90-97. doi: 10.1038/s41477-017-0096-3. Epub 2018 Jan 29
Corresponding author: xlzhang@mail.hzau.edu.cn

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes.

Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress.
Deng Fet al.
BMC Plant Biol. 2018 Jan 25;18(1):23. doi: 10.1186/s12870-018-1238-0
Corresponding author: ffshen@sdau.edu.cn

Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation.

Genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species.
Zou X et al.
Gene. 2018 Mar 10; 646:28-38. doi: 10.1016/j.gene.2017.12.043.
Corresponding author: yuanyoulu@caas.cn

The cellulose synthase gene superfamily, which includes the cellulose synthase (Ces) and cellulose synthase-like (Csl) families, is involved in the synthesis of cellulose and hemicellulose. This superfamily is critical for cotton fiber development in Gossypium species. Applying a series of bioinformatic methods, we identified 228 Ces/Csl genes from four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii). These genes were then grouped into 11 subfamilies based on phylogenetic relationships. A subsequent analysis of gene evolution revealed sites in CSLG and CSLJ genes that were under long-term positive selection pressure, with a posterior probability >0.95. Moreover, the dN:dS value for the CSLJ clade was 1.305, suggesting this subfamily was under positive selection pressure.

High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system.
Wang Pet al.
Plant Biotechnol J. 2018 Jan; 16(1):137-150. doi: 10.1111/pbi.12755
Corresponding author: xlzhang@mail.hzau.edu.cn and jsx@mail.hzau.edu.cn

Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologues. To efficiently achieve site/gene-specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system has exerted broad site-specific genome editing from prokaryotes to eukaryotes. In this study, we utilized a CRISPR/Cas9 system to generate two sgRNAs in a single vector to conduct multiple sites genome editing in allotetraploid cotton. An exogenously transformed gene Discosoma red fluorescent protein2 (DsRed2) and an endogenous gene GhCLA1 were chosen as targets. The DsRed2-edited plants in T0 generation reverted its traits to wild type, with vanished red fluorescence the whole plants.

Genome wide identification of cotton (Gossypium hirsutum)-encoded microRNA targets against Cotton leaf curl Burewala virus
Shweta, Akhter Y and Khan JA.
Gene. 2018 Jan 5; 638: 60-65. doi: 10.1016/j.gene.2017.09.061.
Corresponding author: jkhan1@jmi.ac.in

Cotton leaf curl Burewala virus (CLCuBV, genus Begomovirus) causes devastating cotton leaf curl disease. Among various known virus controlling strategies, RNAi-mediated one has shown potential to protect host crop plants. Micro(mi) RNAs, are the endogenous small RNAs and play a key role in plant development and stress resistance. In the present study we have identified cotton (Gossypium hirsutum)-encoded miRNAs targeting the CLCuBV. Based on threshold free energy and maximum complementarity scores of host miRNA-viral mRNA target pairs, a number of potential miRNAs were annotated. Among them, ghr-miR168 was selected as the most potent candidate, capable of targeting several vital genes namely C1, C3, C4, V1 and V2 of CLCuBV genome. In addition, ghr-miR395a and ghr-miR395d were observed to target the overlapping transcripts of C1 and C4 genes. We have verified the efficacy of these miRNA targets against CLCuBV following suppression of RNAi-mediated virus control through translational inhibition or cleavage of viral mRNA.

A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation.
Wang M et al.
New Phytol. 2018 Jan; 217(1):163-178. doi: 10.1111/nph.14762.
Corresponding author: xlzhang@mail.hzau.edu.cn

Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high-throughput next-generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity between coexisting subgenomes. Here we characterize AS in the polyploid species cotton. Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an integrated pipeline for Iso-Seq transcriptome data analysis (https://github.com/Nextomics/pipeline-for-isoseq).

GPhenoVision: A Ground Mobile System with Multi-modal Imaging for Field-Based High Throughput Phenotyping of Cotton
Yu Jiang et al.
Scientific Reports volume 8, Article number: 1213 (2018)

Imaging sensors can extend phenotyping capability, but they require a system to handle high-volume data. The overall goal of this study was to develop and evaluate a field-based high throughput phenotyping system accommodating high-resolution imagers. The system consisted of a high-clearance tractor and sensing and electrical systems. The sensing system was based on a distributed structure, integrating environmental sensors, real-time kinematic GPS, and multiple imaging sensors including RGB-D, thermal, and hyperspectral cameras. Custom software was developed with a multilayered architecture for system control and data collection. The system was evaluated by scanning a cotton field with 23 genotypes for quantification of canopy growth and development. A data processing pipeline was developed to extract phenotypes at the canopy level, including height, width, projected leaf area, and volume from RGB-D data and temperature from thermal images.

Upregulation of GhTT2-3A in Cotton Fibers during Secondary Wall Thickening Results in Brown Fibers with Improved Quality.
Yan Q et al.
Plant Biotechnol J. 2018 Mar 6. doi: 10.1111/pbi.12910

Brown cotton fibers are the most widely used naturally colored raw materials for the eco-friendly textile industry. Previous studies have indicated that brown fiber pigments belong to proanthocyanidins (PAs) or their derivatives, and fiber coloration is negatively associated with cotton productivity and fiber quality. To date, the molecular basis controlling the biosynthesis and accumulation of brown pigments in cotton fibers is largely unknown. In the present study, based on expressional and transgenic analyses of cotton homologs of Arabidopsis PA regulator TRANSPARENT TESTA 2 (TT2) and fine mapping of the cotton dark brown fiber gene (Lc1), we show that a TT2 homolog, GhTT2-3A, controls PA biosynthesis and brown pigmentation in cotton fibers.

 

Cotton-innovation website

Cotton-innovation website:

A site dedicated to cotton innovations for West and Central Africa, an English version of this website is now available

Factsheets are available on innovations in the cotton supply chains, sustainability indicators for cotton farming systems (related to the SEEP report), economic information, etc.

Enjoy your visit.

 

Articles related to genetics & breeding 03/18

List provived by
Ahmed Elkomy elkomy_a@yahoo.com

QTL mapping for some important drought tolerant traits in upland cotton
M. A. Saleem et al.
The Journal of Animal & Plant Sciences, 2015, 25(2): 502-509.
Corresponding author: asifsaleempbg@gmail.com


Drought stress is a major factor limiting crop production. Genetic improvement is possible in cotton and other crops against drought stress by molecular breeding. A drought tolerant (B-557) and a drought susceptible (FH-1000) cultivar were crossed to develop F2 population. The parents and the F2 population were studied under osmotic stress in hydroponic culture. A survey of 524 SSR and EST-SSR primers revealed a lot of DNA polymorphism between the drought resistant and drought susceptible cultivar.

Identification of drought-responsive genes in a drought tolerant cotton (Gossypium hirsutum L.) cultivar under reduced irrigation field conditions and development of candidate gene markers for drought tolerance
Laura Rodriguez-Uribe et al.
Mol Breeding, 2014
Corresponding author: jinzhang@nmsu.edu


Cotton productivity is affected by water deficit,  and little is known about the molecular basis of drought tolerance in cotton. In this study, microarray analysis was conducted to identify drought-responsive genes in the third topmost leaves of the field-grown drought- tolerant cotton (Gossypium hirsutum L.) cultivar Acala 1517-99 under drought stress conditions. Water stress was imposed by withholding irrigation for 9 days in the early squaring stage, which resulted in 10–15 % reduction in plant growth compared to the well-watered plants.

A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton
Joseph I           Said et al.
BMC Genomics 2013, 14 (776): 2-22.
Corresponding author: jinzhang@nmsu.edu


The  study  of  quantitative  trait  loci  (QTL)  in  cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and pest resistance, branch number, seed quality and yield and yield related traits, drought tolerance, and morphological traits.

Inducing Drought Tolerance in Upland Cotton (Gossypium hirsutum L.), Accomplishments and Future Prospects
Muhammad  Iqbal et al.
World Applied Sciences J., 2013, 21 (7): 1062-1069.
Corresponding author: Muhammad Iqbal, Department of Plant Breeding and Genetics, College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur- 63100, Pakistan


Cotton (Gossypium hirsutum L.) is dreadfully drought sensitive crop causing incentive reduction in yield. Although conventional breeding has been successful in the past in developing drought tolerant cotton cultivars by modifying the morphological and physiological traits, yet the approach is time consuming and labor intensive. Furthermore the polygenic nature of drought tolerance slows the progress.

QTL mapping for physiology, yield and plant architecture traits in cotton (Gossypium hirsutum L.) grown under well-watered versus water-stress conditions
Muhammad Saeed et al.
Electronic Journal of Biotechnology, 2011, vol.14 (3)
Corresponding author: cotton@njau.edu.cn


Increasing scarcity of irrigation water is a major threat to sustainable production of  cotton  (Gossypium hirsutum L.). Identifying genomic regions contributing to abiotic stress tolerance will help develop cotton cultivars suitable for water-limited regions through molecular marker-assisted breeding

Articles related to crop protection – 03/18

List provided by
Sandhya Kranthi: sandhya.kranthi@gmail.com

Endogenous Ethylene Concentration Is Not a Major Determinant of Fruit Abscission in Heat-Stressed Cotton (Gossypium hirsutumL.)
Najeb, Sarvar et al. 

Front. Plant Sci., 21 September 2017 https://doi.org/10.3389/fpls.2017.01615

We investigated the role of ethylene in the response of cotton to high temperature using cotton genotypes with genetically interrupted ethylene metabolism. In the first experiment, Sicot 71BRF and 5B (a lintless variant with compromised ethylene metabolism) were exposed to 45°C, either by instantaneous heat shock or by ramping temperatures by 3°C daily for 1 week. One day prior to the start of heat treatment, half the plants were sprayed with 0.8 mM of the ethylene synthesis inhibitor, aminoethoxyvinylglycine (AVG). In a subsequent experiment, Sicot 71BRF and a putatively heat-tolerant line, CIM 448, were exposed to 36 or 45°C for 1 week, and half the plants were sprayed with 20 μM of the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, (ACC). High temperature exposure of plants in both experiments was performed at the peak reproductive phase (65–68 days after sowing). Elevated temperature (heat shock or ramping to 45°C) significantly reduced production and retention of fruits in all cotton lines used in this study. At the termination of heat treatment, cotton plants exposed to 45°C had at least 50% fewer fruits than plants under optimum temperature in all three genotypes, while plants at 36°C remained unaffected. Heat-stressed plants continued producing new squares (fruiting buds) after termination of heat stress but these squares did not turn into cotton bolls due to pollen infertility. In vitro inhibition of pollen germination by high temperatures supported this observation. Leaf photosynthesis (Pn) of heat-stressed plants (45°C) measured at the end of heat treatments remained significantly inhibited, despite an increased leaf stomatal conductance (gs), suggesting that high temperature impairs Pn independently of stomatal behavior. Metabolic injury was supported by high relative cellular injury and low photosystem II yield of the heat-stressed plants, indicating that high temperature impaired photosynthetic electron transport. Both heat shock and ramping of heat significantly reduced ethylene release from cotton leaf tissues measured at the end of heat treatment but modulating ethylene production via AVG or ACC application had no significant effect on fruit production or retention in heat-stressed cotton plants. Instead, high temperature accelerated fruit abortion by impairing pollen development and/or restricting leaf photosynthesis.

The terpene synthase gene family in Gossypium hirsutum harbors a linalool synthase GhTPS12 implicated in direct defence responses against herbivores
Xin-Zheng Huang et al.
Plant Cell Environment 2017 DOI: 10.1111/pce.13088
Corresponding author: yjzhang@ippcaas.cn

The terpene synthase gene family in Gossypium hirsutum harbors a linalool synthase GhTPS12 implicated in direct defence responses against herbivores Abstract Herbivore‐induced terpenes have been reported to function as ecological signals in plant–insect interactions. Here, we showed that insect‐induced cotton volatile blends contained 16 terpenoid compounds with a relatively high level of linalool. The high diversity of terpene production is derived from a large terpene synthase (TPS) gene family. The TPS gene family of Gossypium hirsutum and Gossypium raimondii consist of 46 and 41 members, respectively. Twelve TPS genes (GhTPS4–15) could be isolated, and protein expression in Escherichia coli revealed catalytic activity for eight GhTPS. The upregulation of the majority of these eight genes additionally supports the function of these genes in herbivore‐induced volatile biosynthesis. Furthermore, transgenic Nicotiana tabacum plants overexpressing GhTPS12 were generated, which produced relatively large amounts of (3S)‐linalool. In choice tests, female adults of Helicoverpa armigera laid fewer eggs on transgenic plants compared with non‐transformed controls. Meanwhile, Myzus persicae preferred feeding on wild‐type leaves over leaves of transgenic plants. Our findings demonstrate that transcript accumulation of multiple TPS genes is mainly responsible for the production and diversity of herbivore‐induced volatile terpenes in cotton. Also, these genes might play roles in plant defence, in particular, direct defence responses against herbivores.

Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum.
Naqvi, R.Z. et al.
Scientific reports Vol7 doi:10.1038/s41598-017-15963-9

Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD

Hydrogen peroxide reduces heat-induced yield losses in cotton (Gossypium hirsutum ) by protecting cellular membrane damage.
Sarwar,M., Saleem, M.F., Najeeb,U., Shakeel,A., S.Ali. M.F.Bilal.,
OI: 10.1111/jac.12203. Journal of Agronomy and Crop Science
Corresponding author: najeeb.ullah@sydney.edu.au

We investigated the effect of various growth substances such as hydrogen peroxide, salicylic acid (SA), moringa leaf-extract (MLE) and ascorbic acid (ASA) on leaf physiology and seed cotton yield (SCY) of heat-stressed cotton. Cotton plants were exposed to elevated temperatures at three reproductive stages, either by staggering planting time in the field or by increasing growth cabinet temperatures (38/24°C and 45/30°C) in glasshouse. Elevated temperature at any reproductive phase significantly damaged cellular membrane and reduced SCY. Plants exposed to 38/24°C and 45/30°C in glasshouse produced 63% and 22% lower SCY, respectively, compared with plants under optimal temperature ((32/20°C). In response to high temperature, cotton plants up-regulated activities of anti-oxidative enzymes e.g. peroxidase and ascorbic acid. However, this defensive system could not protect cellular membrane of stressed plants from extreme temperature (38 and 45°C). In contrast, growth substances such as H2O2, ASA and MLE significantly increased anti-oxidative enzymes activity to an extent, which reduced heat-induced damage to cellular membrane. No significant effect of any regulator was observed on SCY under optimum temperatures; although H2O2, MLE and ASA significantly increased SCY of heat-stressed cotton. Hydrogen peroxide increased SCY of April and May thermal regimes crops by 16% (averaged across both sowing dates) under field, while it caused 14% and 20% increase in SCY of plants exposed to sub (38/24°C) and supra optimal (45/30°C) thermal regimes under glasshouse. We concluded that growth regulators, specifically, H2O2 can protect cotton crops from heat-induced cellular membrane damage by up-regulating antioxidant defense system.

Searching for resistance sources to Verticillium wilt of cotton in seedlings from Gossypium spp.
Mehmet Erhan Göre & Oktay Erdoğan & Nedim Altın.
plant pathol. (2017) 42:28–31 DOI 10.1007/s40858-016-0120-6

 Verticillium dahliae is a major wilt pathogen impacting cotton production in Turkey. Isolates of V. dahliae can be characterized as defoliating (D) or nondefoliating (ND) pathotypes based on symptom expression in cotton. Currently there are no fungicides identified that can manage this pathogen. Host resistance is the most economical and environmentally friendly means to manage this disease. Cotton genotypes, comprising the main cultivars and some breeding lines available in Turkey, were evaluated under controlled conditions for resistance to verticillium wilt. To establish adequate conditions for resistance expression, experiments examining isolate pathogenicity and the most appropriate inoculum concentration were carried out first. Based on the obtained data, 10 cultivars were then inoculated with D and ND pathotypes by the “pot immersion” method at 106 conidia/mL inoculum concentration and the plants were evaluated considering both internal and external disease symptoms. Plants were scored on a 0 to 4 scale for above-ground symptoms (0 = healthy; 4 = dead plant) ca. two weeks after inoculation. Significant differences in resistance level were observed among the genotypes (p < 0.05). The cultivar Maydos Yerlisi had the lowest level of wilt, with a mean rating of 1.0. The cultivar Nazilli NDT-15 had the strongest wilt, with a mean rating of 3.3. These results suggest that ‘Maydos Yerlisi’ can be used in cotton breeding programs to develop resistant varieties to V. dahliae.

Value of Neonicotinoid Insecticide Seed Treatments in Mid-South Cotton (Gossypium hirsutum[Malvales: Malvaceae]) Production Systems
H. North et al.
Journal of Economic Entomology, Volume 111, Issue 1, 9 February 2018, Pages 10–15, https://doi.org/10.1093/jee/tox324
Corresponding author: jnorth@entomology.msstate.edu

Neonicotinoid insecticides are currently one of two classes of chemicals available as a seed treatment for growers to manage early season insect pests of cotton, Gossypium hirsutum L. (Malvales: Malvaceae), and they are used on nearly 100% of cotton hectares in the midsouthern states. An analysis was performed on 100 seed-treatment trials from Arkansas, Louisiana, Mississippi, and Tennessee to determine the value of neonicotinoid seed treatments in cotton production systems. The analysis compared seed treated with neonicotinoid insecticides seed treatments plus a fungicide with seed only treated with fungicide. When analyzed by state, cotton yields were significantly greater when neonicotinoid seed treatments were used compared with fungicide-only treatments. Cotton treated with neonicotinoid seed treatments yielded 123, 142, 95, and 104 kg ha−1, higher than fungicide only treatments for Arkansas, Louisiana, Mississippi, and Tennessee, respectively. Across all states, neonicotinoid seed treatments provided an additional 115 kg lint ha−1comparedwith fungicide only treated seed. Average net returns from cotton with a neonicotinoid seed treatment were $1,801 per ha−1compared with $1,660 per ha−1 for cottonseed treated with fungicide only. Economic returns for cotton with neonicotinoid seed treatments were significantly greater than cottonseed treated with fungicide only in 8 out of 15 yr representing every state. These data show that neonicotinoid seed treatments provide significant yield and economic benefits in Mid-South cotton compared with fungicide only treated seed.

Enhanced plant growth promoting role of phycomolecules coated zinc oxide nanoparticles with P supplementation in cotton (Gossypium hirsutum L.)
P. Venkatachalam et al.
Plant Physiology and Biochemistry,Volume 110, 2017,Pages 118-127,https://doi.org/10.1016/j.plaphy.2016.09.004.
Corresponding author: pvenkat67@yahoo.com

This report focuses on application of zinc oxide nanoparticles (ZnONPs) carrying phycomolecule ligands as a novel plant growth promoter aimed at increasing the crop productivity. The present investigation examined the effect of ZnONPs on plant growth characteristics, and associated biochemical changes in cotton (Gossypium hirsutum L.) following growth in a range of concentrations (25–200 mg L−l ZnONPs) in combination with 100 mM P in a hydroponic system. Treated plants registered an increase in growth and total biomass by 130.6% and 131%, respectively, over control. Results demonstrated a significant increase in the level of chlorophyll a (141.6%), b (134.7%), carotenoids (138.6%), and total soluble protein contents (179.4%); at the same time, a significant reduction (68%) in the level of malondialdehyde (MDA) in leaves with respect to control. Interestingly, a significant increase in superoxide dismutase (SOD, 264.2%), and peroxidase (POX, 182.8%) enzyme activitiesfollowed by a decrease in the catalase (CAT) activity, in response to above treatments. These results suggest that bioengineered ZnONPs interact with meristematic cells triggering biochemical pathways conducive to an accumulation of biomass. Further investigations will map out the mode of action involved in growth promotion.

Large-scale identification of Gossypium hirsutum genes associated with Verticillium dahliae by comparative transcriptomic and reverse genetics analysis.
Zhang,W. et al.
PLoS ONE 12(8): e0181609 https://doi.org/10.1371/journal.pone.0181609

Verticillium wilt is a devastating disease of cotton, which is caused by the soil-borne fungus Verticillium dahliae (Vdahliae). Although previous studies have identified some genes or biological processes involved in the interaction between cotton and Vdahliae, its underlying molecular mechanism remains unclear, especially in Ghirsutum. In the present study, we obtained an overview of transcriptome characteristics of resistant upland cotton (Ghirsutum) after Vdahliae infection at 24 h post-inoculation (hpi) via a high-throughput RNA-sequencing technique. A total of 4,794 differentially expressed genes (DEGs) were identified, including 820 up-regulated genes and 3,974 down-regulated genes. The enrichment analysis showed that several important processes were induced upon Vdahliae infection, such as plant hormone signal transduction, plant-pathogen interaction, phenylpropanoid-related and ubiquitin-mediated signals. Moreover, we investigated some key regulatory gene families involved in the defense response, such as receptor-like protein kinases (RLKs), WRKY transcription factors and cytochrome P450 (CYPs), via virus-induced gene silencing (VIGS). GhSKIP35, a partner of SKP1 protein, was involved in ubiquitin-mediated signal. Over-expression of GhSKIP35 in Arabidopsis improved its tolerance to Verticillium wilt in transgenic plants. Collectively, global transcriptome analysis and functional gene characterization provided significant insights into the molecular mechanisms of GhirsutumVdahliae interaction and offered a number of candidate genes as potential sources for breeding wilt-tolerance in cotton

Flupyradifurone effectively manages whitefly Bemisia tabaci MED (Hemiptera: Aleyrodidae) and tomato yellow leaf curl virus in tomato
Emmanouil Roditakis et al.
Pest Management Science
Corresponding author: eroditakis@gmail.com

The cotton whitefly Bemisia tabaci (Gennadius) is among the most important pests of numerous crops and a vector of more than 100 plant viruses, causing significant crop losses worldwide. Managing this pest as well as inhibiting the transmission of major viruses such as tomato yellow leaf curl virus (TYLCV) are of utmost importance for sustainable yields. The efficacy against both whitefly and virus transmission of the novel systemic butenolide insecticide flupyradifurone was investigated in this study.
RESULTS: The inhibition of TYLCV transmission by flupyradifurone was compared to that by thiamethoxam, a neonicotinoid insecticide reported to inhibit virus transmission. The experiment was performed under high virus pressure conditions (10 viruliferous insects per plant for 48 h) using a fully characterized field strain of B. tabaci. The insecticides were foliarly applied at recommended label rates under greenhouse conditions. Flupyradifurone suppressed virus transmission by 85% while levels of suppression after thiamethoxam treatments were just 25% and significantly lower. In untreated control plots, 100% of plants were infected by TYLCV. The observed difference in the potential to suppress virus transmission is linked to a strong knockdown effect as well as prolonged feeding inhibition in flupyradifurone treatments.
CONCLUSION: Flupyradifurone is shown to be an extremely useful, fast-acting, new chemical tool in integrated crop management offering simultaneous control of whiteflies and strong suppression of viral infections via its rapid knockdown action and good residual activity.

Flavonoid Profile of the Cotton Plant, Gossypium hirsutum: A Review
Aaron Nix, Cate Paull * and Michelle Colgrave
Plants (Basel). 2017 Sep 25;6(4). pii: E43. doi: 10.3390/plants6040043
Corresponding author: aaron.nix@hotmail.com

 Cotton, Gossypium hirsutum L., is a plant fibre of significant economic importance, with seeds providing an additional source of protein in human and animal nutrition. Flavonoids play a vital role in maintaining plant health and function and much research has investigated the role of flavonoids in plant defence and plant vigour and the influence these have on cotton production. As part of ongoing research into host plant/invertebrate pest interactions, we investigated the flavonoid profile of cotton reported in published, peer-reviewed literature. Here we report 52 flavonoids representing seven classes and their reported distribution within the cotton plant. We briefly discuss the historical research of flavonoids in cotton production and propose research areas that warrant further investigation.

Genome wide identification of cotton (Gossypium hirsutum)-encoded microRNA targets against Cotton leaf curl Burewala virus
Shweta , Yusuf Akhter , Jawaid Ahmad Khan
Gene. 2018 Jan 5;638:60-65. doi: 10.1016/j.gene.2017.09.061.
Corresponding author: jkhan1@jmi.ac.in

Cotton leaf curl Burewala virus (CLCuBV, genus Begomovirus) causes devastating cotton leaf curl disease. Among various known virus controlling strategies, RNAi-mediated one has shown potential to protect host crop plants. Micro(mi) RNAs, are the endogenous small RNAs and play a key role in plant development and stress resistance. In the present study we have identified cotton (Gossypium hirsutum)-encoded miRNAs targeting the CLCuBV. Based on threshold free energy and maximum complementarity scores of host miRNA-viral mRNA target pairs, a number of potential miRNAs were annotated. Among them, ghr-miR168 was selected as the most potent candidate, capable of targeting several vital genes namely C1, C3, C4, V1 and V2 of CLCuBV genome. In addition, ghr-miR395a and ghr-miR395d were observed to target the overlapping transcripts of C1 and C4 genes. We have verified the efficacy of these miRNA targets against CLCuBV following suppression of RNAi-mediated virus control through translational inhibition or cleavage of viral mRNA

Diversity of alphasatellites associated with cotton leaf curl disease in Pakistan
Komal Siddiqui , Shahid Mansoor  , Rob W. Briddon , Imran Amin.
Virology ReportsVolume 6, December 2016, Pages 41-52.

 Background Cotton is a major cash crop of Pakistan and its production is mainly hindered by cotton leaf curl disease (CLCuD). This disease is caused by monopartite begomovirus associated with two satellites named as betasatellite and alphasatellite. Betasatellites are true satellites entirely dependent on helper begomoviruses and are symptom determinants which are essentially required for the typical symptoms of the disease. Alphasatellites are self-replicating circular ssDNA molecules which are associated with CLCuD complex. The role of alphasatellite is not fully understood.
Result Cotton samples showing typical CLCuD symptoms were collected from areas across central Punjab, Pakistan during year 2011–12. All samples contained alphasatellites. Mixed-infection of alphasatellites associated with CLCuD complex was documented. Few samples showed the presence of more than one species of alphasatellite. A total of 45 alphasatellites were cloned and sequenced. The size of these alphasatellite ranges from 1362 to 1378 bp. All alphasatellites showed three conserved features i.e. 1) A stem-loop structure with a nonanucleotide (TAGTATTAC) sequence (2) An ORF encoding a Rep protein of about 36.6 kDa, having up to 315 amino acids (3) An A-rich region of ~200 nt. Based on BLAST results we have found six distinct species of alphasatellites namely; Gossypium darwinii symptomless alphasatellite (GDarSLA), Guar leaf curl alphasatellite (GrLCuA), Okra leaf curl alpha satellite (OLCuA), Tomato leaf curl Pakistan alphasatellite (ToLCPKA), Cotton leaf curl Multan alphasatellite (CLCuMA), and Cotton leaf curl Burewala alphasatellite (CLCuBuA). This was also confirmed by phylogenetic analysis. By considering the species cut-off limit for alphasatellites (83%) the isolates fall into 5 species. But the percentage identity between some CLCuBuA and CLCuMA was 83.3, so they are proposed to be considered as two different species. Conclusion Our data shows that at least six species of alphasatellites are found associated with cotton leaf curl disease in Pakistan. Field samples are often associated with multiple species and one sample was found associated with three distinct alphasatellites in a single plant under field conditions. Infection of multiple alphasatellite and their probable role in CLCuD are discussed.

Overview of the South African Plant-Parasitic Nematode Survey (SAPPNS).
Marais M., Swart A., Buckley N.
(2017) In: Fourie H., Spaull V., Jones R., Daneel M., De Waele D. (eds) Nematology in South Africa: A View from the 21st Century.
Corresponding author: MaraisM@arc.agric.za

The foundation and growth of the South African Plant-Parasitic Nematode Survey is presented from its launch in 1987 to the present. Initially four objectives were identified, namely, (i) making an inventory of all the plant-parasitic nematodes found in South Africa, (ii) studying the biogeography of plant-parasitic nematodes, (iii) establishing an electronic database at the Plant Protection Research and (iv) drawing maps that represent the distribution of the nematodes pests. In 2006, the second phase of the project was initiated to digitise all the specimens deposited in the National Collection of Nematodes (NCN), a task that was completed in 2014. The wealth of data contained in the database has allowed fresh insights into the knowledge base of local and international nematologists and, at the same time, exposed huge gaps that still exist. The data show, for example, that eight of the nine Trichodorus spp. reported from South Africa are endemic to South Africa and that only one record exists where more than one species of Trichodorus occurs concomitantly at the same locality. The database also shows that there is a dearth of nematode data from thicket, grassland, savanna, Nama and succulent Karoo biomes.

Comparative host selection responses of specialist (Helicoverpa assulta) and generalist (Helicoverpa armigera) moths in complex plant environments
Wei-zheng Li et al.
https://doi.org/10.1371/journal.pone.0171948

We tested the behavioral responses of ovipositing females and natal larvae of two sibling species, generalist Helicoverpa armigera (Hübner) and a specialist Helicoverpa assulta(Guenée), to odor sources emitted from different combinations of six plant species (tobacco, Nicotiana tabacum; hot pepper, Capsicum annuum; tomato, Solanum esculentum; cotton, Gossypium hirsutum; peanut, Arachis hypogaea; maize, Zea mays). Under the conditions of plant materials versus corresponding controls, both stages of both species could find their corresponding host plants. However, Hassulta females and larvae exhibited a supersensitive and an insensitive response, respectively. Under the conditions of tobacco paired with each plant species, Hassulta females exhibited more specialized ovipositional response to tobacco than its sibling. When each plant species were combined with tobacco and tested against tobacco reference, peanut played an opposite role in the two species in their ovipositional responses to tobacco, and cotton can enhance the approaching response of Harmigera larvae when combined with tobacco. It seems that two attractive host plants also can act antagonistically with respect to host selection of the generalist via volatile exchange. Tomato should better be excluded from host list of Hassulta.

Protecting cotton crops under elevated CO2from waterlogging by managing ethylene
Ullah Najeeb, Daniel K. Y. Tan, Michael P. Bange and Brian J. Atwell
Functional Plant Biology 45(3) 340-349

Soil waterlogging and subsequent ethylene release from cotton (Gossypium hirsutum L.) tissues has been linked with abscission of developing cotton fruits. This glasshouse study investigates the effect of a 9-day waterlogging event and CO2 enrichment (eCO2, 700 parts per million (ppm)) on a fully linted cultivar ‘Empire’ and a lintless cotton mutant (5B). We hypothesised that cotton performance in extreme environments such as waterlogging can be improved through mitigating ethylene action. Plants were grown at 28:20°C day:night temperature, 50–70% relative humidity and a 14:10 light:dark photoperiod under natural light and were exposed to waterlogging and eCO2 at early reproductive growth. Ethylene synthesis was inhibited by spraying aminoethoxyvinylglycine (830 ppm) 1 day before waterlogging. Waterlogging significantly increased ethylene release from both cotton genotypes, although fruit production was significantly inhibited only in Empire. Aminoethoxyvinylglycine consistently reduced waterlogging-induced abscission of fruits, mainly in Empire. Limited damage to fruits in 5B, despite increased ethylene production during waterlogging, suggested that fruit abscission in 5B was inhibited by disrupting ethylene metabolism genetically. Elevated CO2 promoted fruit production in both genotypes and was more effective in 5B than in Empire plants. Hence 5B produced more fruits than Empire, providing additional sinks (existing and new fruit) that enhanced the response to CO2 enrichment.

Effect of dates of sowing on population of sucking insect pests in desi cotton (Gossypium arboreum L.)
Suman Devi and Pala Ram
Journal of Entomology and Zoology Studies 2018; 6(1): 1041-1044

The present study was conducted at Chaudhary Charan Singh Haryana University, Hisar, and experimental area of the Department of Entomology during the Kharif season of 2016 and 2017. The pooled data of both the years revealed that maximum population of leafhopper (Amrasca biguttula biguttula) nymphs (3.94 nymphs/leaf) was recorded in late sown while minimum population (2.91 nymphs/leaf) was recorded in early sown cotton. In case of thrips (Thrips tabaci Linderman), the population of thrips adults was highest (3.99 adults per leaf) in late sown crop while population was least (2.89 adults per leaf) in normal sown cotton. In case of whitefly (Bemisia tabaci Gennadius), the population of whitefly adults was highest (4.46 adults/leaf) in late sown while population of whitefly adults was least (2.88 adults/leaf) in early sown cotton.

New Earliness Index and Integration of Earliness Additive Genes in the New Genotype of Cotton (Gossypium hirsutum L.)
Gholamhossein Hosseini.
Int. J. Life. Sci. Scienti. Res., 3(3): 1016-1019 MAY 2017

Cotton (Gossypium hirsutum L.) is an important fiber crop in the world being used in the textile industry and over 90% of cotton grown in the world is upland cotton. An experimental design carried out for integration of earliness genes from sindose-80 to bulgare-557 during 2005 to 2016 in the Department of Botany, University of PuneIndia and Agricultural Research Center of Tehran-Iran. The first cross carried out between sindose-80 and bulgare-557 in 2005 and after crossing five years selection was done among segregated population till to F5. In 2011 the second cross carried out as a back cross between the new variety and sindose-80. Five years selection was also done after second cross. In 2016, the new earliness genotype compared with the five native and commercial cotton varieties in RCBD design. The criterion for earliness was a new earliness index of combined picking and day (CPD), which has been presented as a new earliness index in this paper along with EFD and FFT indexes. Mean comparison of traits such as three earliness indexes, boll per plant, micronaire and yield showed priority of the new earliness genotype. Comparison of the three earliness indexes indicated priority of CPD index, which is combined by both time and weight to the two conventional indexes such as EFD and FFT which are showing time and weight affects in the earliness response.

Salicylic acid-related cotton (Gossypium arboreum) ribosomal protein GaRPL18 contributes to resistance to Verticillium dahliae
Qian Gong et al.
BMC Plant Biology

Background
Verticillium dahliae is a phytopathogenic fungal pathogen that causes vascular wilt diseases responsible for considerable decreases in cotton yields. The complex mechanism underlying cotton resistance to Verticillium wilt remains uncharacterized. Identifying an endogenous resistance gene may be useful for controlling this disease.
Results
We cloned the ribosomal protein L18 (GaRPL18) gene, which mediates resistance to Verticillium wilt, from a wilt-resistant cotton species (Gossypium arboreum). We then characterized the function of this gene in cotton and Arabidopsis thaliana plants. GaRPL18 encodes a 60S ribosomal protein subunit important for intracellular protein biosynthesis. However, previous studies revealed that some ribosomal proteins are also inhibitory toward oncogenesis and congenital diseases in humans and play a role in plant disease defense. Here, we observed that V. dahliae infections induce GaRPL18expression. Furthermore, we determined that the GaRPL18 expression pattern is consistent with the disease resistance level of different cotton varieties. GaRPL18expression is upregulated by salicylic acid (SA) treatments, suggesting the involvement of GaRPL18 in the SA signal transduction pathway. Virus-induced gene silencing technology was used to determine whether the GaRPL18 expression level influences cotton disease resistance. Wilt-resistant cotton species in which GaRPL18 was silenced became more susceptible to V. dahliae than the control plants because of a significant decrease in the abundance of immune-related molecules. We also transformed A. thaliana ecotype Columbia (Col-0) plants with GaRPL18 according to the floral dip method. The plants over expressing GaRPL18 were more resistant to V. dahliae infections than the wild-type Col-0 plants. The enhanced resistance of transgenic A. thaliana plants to V. dahliae is likely mediated by the SA pathway.
Conclusion: Our findings provide new insights into the role of GaRPL18, indicating that it plays a crucial role in resistance to cotton “cancer”, also known as Verticillium wilt, mainly regulated by an SA-related signaling pathway mechanism.

Diversity analysis of cotton (Gossypium hirsutumL.) germplasm using the CottonSNP63K Array
Lori L. Hinze et.al (2017)
BMC Plant Biology

Background
Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.
Results
The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.
Conclusions
Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.

Study of Cotton Leaf Senescence Induced by Alternaria alternata Infection.
Wei Liu et al.
Plant Senescence pp 161-171
Part of the Methods in Molecular Biology book series (MIMB, volume 1744)
Corresponding author: fjqi@ippcaas.cn

Premature leaf senescence in cotton, which often happens during the mid to late growth period, has been occurring with an increasing frequency in many cotton-growing areas and causing serious reduction in yield and quality. One of the key factors causing cotton leaf senescence is the infection of Alternaria leaf spot pathogens (Alternaria species), which often happens when cotton plants encounter adverse environmental conditions, such as chilling stress and physiological impairment. Stressed cotton leaves are apt to be infected by Alternaria leaf spot pathogens (Alternaria alternata) because of the reduction in disease resistance, leading to the initiation of leaf senescence. Here we describe the induction of cotton leaf senescence by Alternaria alternata infection, including the evaluation of the disease index and measure of physiological impairment associated with cotton leaf senescence and analysis of possible molecular mechanism using microarray.

Sources of plant resistance to thrips: a potential core component in cotton
Junji Miyazaki, Warwick N. Stiller & Lewis J. Wilson
IPM DOI: 10.1111/eea.12501
SPECIAL ISSUE – INSECT-PLANT INTERACTIONS: HOST SELEC TION, HERBIVORY, AND PLAN T RESISTANCE
Corresponding author: lewis.wilson@csiro.au

Thrips (Thysanoptera: Thripidae) are important pests of seedling cotton and their damage can delay crop maturity and/or reduce yield. Plant resistance to thrips in cotton would reduce the need to treat crops with insecticides for their control. This would support integrated pest management strategies by reducing the risk of selecting insecticide resistance in concomitant pests and of disrupting the natural enemy complex. Traits that reduce thrips abundance in cotton are poorly understood, but dense leaf hairs and high gossypol content are implicated to negatively affect thrips. Furthermore, some diploid cottons are resistant against thrips. Thrips abundance and damage on a range of Gossypium (Malvaceae) genotypes including hairy leaf, smooth leaf (glabrous), okra leaf shape, and diploid species was evaluated over four crop seasons. Thrips were significantly less abundant and they caused less damage on diploid cotton genotypes from Gossypium arboreum L. (BM13H, Roseum A256), Gossypium thurberi Tod. (GOS5310), and Gossypium trilobum (Moc. & Sess. ex DC.) Skov. (GOS5332) than on the standard commercial Gossypium hirsutum L. cv. Sicot 71. There was no significant relationship between thrips abundance or damage and leaf hairiness, leaf hardness, or leaf shape, though conclusions about the value of these traits must be made cautiously as they are confounded across genotypes that differ in a range of traits simultaneously. The diploid cottons had a lower damage per thrips ratio, indicating that they are more tolerant of thrips feeding damage and thus could be valuable sources of host plant resistance to thrips. Introduction Thrips (Thysanoptera: Thripidae) are important pests on seedling cotton (Malvaceae) in Australia and most other regions where cotton is grown (Quisenberry & Rummel, 1979; Wilson & Bauer, 1993; Bournier, 1994; Arif et al., 2006; Cook et al., 2011; Zhang et al., 2014). Common species on cotton seedlings in Australia are tobacco thrips (Thrips tabaci Lindeman), western flower thrips [Frankliniella occidentalis(Pergande)], and tomato thrips (Frankliniella schultzei Trybom) (Wilson & Bauer, 1993; Leigh, 1995). Thrips feeding on the growing terminal tissues of seedlings results in damage proportional to the thrips density, and ranges from mild to severe leaf distortion, reduced leaf area, and, in severe cases, highly stunted leaves and death of the plant.

Genetics and Genomics of Cotton Leaf Curl Disease, Its Viral Causal Agents and Whitefly Vector: A Way Forward to Sustain Cotton Fiber Security
Mehboob-ur- Rahman et al.
Front Plant Sci. 2017 Jul 4;8:1157.

 

Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc., and practicing mixed type farming system have further exaggerated the situation by adding synergy to the evolution of new viral strains and vectors. Efforts to control this disease using host plant resistance remained successful using two gene based-resistance that was broken by the evolution of new resistance breaking strain called Burewala virus. Development of transgenic cotton using both pathogen and non-pathogenic derived approaches are in progress. In future, screening for new forms of host resistance, use of DNA markers for the rapid incorporation of resistance into adapted cultivars overlaid with transgenics and using genome editing by CRISPR/Cas system would be instrumental in adding multiple layers of defense to control the disease-thus cotton fiber production will be sustained.

Whitefly, Bemisia tabaci genetic groups Asia-I, Asia-II-1 and Asia-II-7 on the Indian subcontinent

N. C. Naveen et al.
Scientific Reports volume7, Article number: 40634 (2017)

The present study is a summary of the current level of the insecticide resistance to selected organophosphates, pyrethroids, and neonicotinoids in seven Indian field populations of Bemisia tabacigenetic groups Asia-I, Asia-II-1, and Asia-II-7. Susceptibility of these populations was varied with Asia-II-7 being the most susceptible, while Asia-I and Asia-II-1 populations were showing significant resistance to these insecticides. The variability of the LC50 values was 7x for imidacloprid and thiamethoxam, 5x for monocrotophos and 3x for cypermethrin among the Asia-I, while, they were 7x for cypermethrin, 6x for deltamethrin and 5x for imidacloprid within the Asia-II-1 populations. When compared with the most susceptible, PUSA population (Asia-II-7), a substantial increase in resistant ratios was observed in both the populations of Asia-I and Asia-II-1. Comparative analysis during 2010–13 revealed a decline in susceptibility in Asia-I and Asia-II-1 populations of B. tabaci to the tested organophosphate, pyrethroid, and neonicotinoid insecticides. Evidence of potential control failure was detected using probit analysis estimates for cypermethrin, deltamethrin, monocrotophos and imidacloprid. Our results update resistance status of B. tabaci in India. The implications of insecticide resistance management of B. tabaci on Indian subcontinent are discussed.