The current status of nitrogen fertiliser use efficiency and future research directions for the Australian cotton industry

Fifty years of sustained investment in research and development has left the Australian cotton industry well placed to manage nitrogen (N) fertiliser. The average production in the Australian cotton industry today is greater than two tonnes of lint per hectare due to improved plant genetics and crop management. However, this average yield is well below the yield that would be expected from the amount of N fertiliser used. It is clear from the recent studies that across all growing regions, conversion of fertiliser N into lint is not uniformly occurring at application rates greater than 200–240 kg·hm−2 of N. This indicates that factors other than N availability are limiting yield, and that the observed nitrogen fertiliser use efficiency (NFUE) values may be caused by subsoil constraints such as sodicity and compaction. There is a need to investigate the impact of subsoil constraints on yield and NFUE. Gains in NFUE will be made through improved N fertiliser application timing, better targeting the amount of fertiliser applied for the expected yield, and improved soil N management. There is also a need to improve the ability and confidence of growers to estimate the contribution of soil N mineralisation to the crop N budget. Many Australian studies including data that could theoretically be collated in a meta-analysis suggest relative NFUE values as a function of irrigation technique; however, with the extensive list of uncontrolled variables and few studies using non-furrow irrigation, this would be a poor substitute for a single field-based study directly measuring their efficacies. In irrigated cotton, a re-examination of optimal NFUE is due because of the availability of new varieties and the potential management and long-term soil resilience implications of the continued removal of mineralised soil N suggested by high NFUE values. NFUE critical limits still need to be derived for dryland systems.

The current status of nitrogen fertiliser use efficiency and future research directions for the Australian cotton industry
MACDONALD Ben C. T., LATIMER James O., SCHWENKE Graeme D., NACHIMUTHU Gunasekhar and BAIRD Jonathan C.
Journal of Cotton Research. 2018; 1:15.
https://doi.org/10.1186/s42397-018-0015-9

Designations for individual genomes and chromosomes in Gossypium

Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.

Designations for individual genomes and chromosomes in Gossypium
WANG Kunbo, WENDEL Jonathan F. and HUA Jinping
Journal of Cotton Research. 2018; 1:3.
https://doi.org/10.1186/s42397-018-0002-1

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development, and phytohormone and abiotic stress responses

[Background] RING-H2 finger E3 ligase (RH2FE3) genes encode cysteine-rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome-wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported.

[Methods] We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated Ka/Ks values of G. hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all-versus-all BLASTP searches. We predicted cis-regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue-specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction (qRT-PCR) analysis.

[Results] We investigated 140 G. hirsutum, 80 G. arboreum, and 89 G. raimondii putative RH2FE3 genes and their evolutionary mechanisms and compared them with orthologs in Arabidopsis and rice. A domain-based analysis of the G. hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G. hirsutum chromosomes, and 60 duplication events (4 tandem and 56 segmental duplications) and 98 orthologs were detected. cis-elements were detected in the promoter regions of G. hirsutum RH2FE3 genes. Microarray data and qRT-PCR analyses showed that G. hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the identified genes were up-regulated in response to phytohormones (brassinolide, gibberellic acid (GA), indole-3-acetic acid (IAA), and salicylic acid (SA)) and abiotic stresses (cold, heat, drought, and salt).

[Conclusions] The genome-wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis-element prediction, and expression profile analysis of G. hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome-wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G. hirsutum RH2FE3 genes.

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development, and phytohormone and abiotic stress responses
QANMBER Ghulam, YU Daoqian, LI Jie, WANG Lingling, MA Shuya, LU Lili, YANG Zuoren and LI Fuguang
Journal of Cotton Research. 2018; 1:1.
https://doi.org/10.1186/s42397-018-0004-z

Genome-wide analysis of Rf-PPR-like (RFL) genes and a new InDel marker development for Rf1 gene in cytoplasmic male sterile CMS-D2 Upland cotton

[Background] Cytoplasmic male sterility in flowering plants is a convenient way to use heterosis via hybrid breeding and may be restored by nuclear restorer-of-fertility (Rf) genes. In most cases, Rf genes encoded pentatricopeptide repeat (PPR) proteins and several Rf genes are present in clusters of similar Rf-PPR-like (RFL) genes. However, the Rf genes in cotton were not fully characterized until now.

[Results] In total, 35 RFL genes were identified in G. hirsutum, 16 in G. arboreum, and 24 in G. raimondii. Additionally, four RFL-rich regions were identified; the RFL-rich region in Gh_D05 is the probable location of Rf-PPR genes in cotton and will be studied further in the future. Furthermore, an insertion sequence was identified in the promoter sequence of Gh_D05G3392 gene in the restorer line, as compared with the CMS-D2 line and maintainer lines. An InDel-R marker was then developed and could be used to distinguish the restorer line carrying Rf1 from other genotypes without the Rf1 allele.

[Conclusion] In this study, genome-wide identification and analysis of RFL genes have identified the candidate Rf-PPR genes for CMS in Gossypium. The identification and analysis of RFL genes and sequence variation analysis will be useful for cloning Rf genes in the future and also for three-line hybrid breeding in cotton.

ZHANG Bingbing, ZHANG Xuexian, GUO Liping, QI Tingxiang, WANG Hailin, TANG Huini, QIAO Xiuqin, KASHIF Shahzad, XING Chaozhu and WU Jianyong
Journal of Cotton Research. 2018; 1:12.
https://doi.org/10.1186/s42397-018-0013-y

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

[Background] The SWEET (Sugars will eventually be exported transporters) gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, the comprehensive analysis of SWEET genes has not been reported in cotton.

[Results] In this study, we identified 22, 31, 55 and 60 SWEET genes from the sequenced genomes of Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification.

[Conclusion] SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEET genes and more candidates for specific genetic modification, which will be useful in future research.

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses
ZHAO Lanjie, YAO Jinbo, CHEN Wei, LI Yan, LÜ Youjun, GUO Yan, WANG Junyi, YUAN Li, LIU Ziyang and ZHANG Yongshan

Journal of Cotton Research. 2018; 1:7.
https://doi.org/10.1186/s42397-018-0007-9

Hypoxia tolerance studies for yield, fiber and physiological traits in cotton (Gossypium hirsutum L.)

[Background] Hypoxia tolerance studies in cotton are very rare in Pakistan. Unpredicted and excessive rainfalls result in severe losses to cotton crop in many regions of the country due to lack of hypoxia tolerance in current cotton varieties. The genotypes that can tolerate flooding are not reported earlier. The studies were conducted to explore hypoxia tolerance in local germplasm which will help to develop hypoxia tolerant cotton varieties.

[Method] An experiment with randomized complete blocks was designed to study the hypoxia tolerance in different cotton varieties. The genotypes were given two treatments i.e., water logged and non-water logged conditions.

[Results] The genotypes showed significant variability for yield, fiber and physiological traits. The hypoxia studies revealed that there is significant reduction for plant height in water sensitive genotype LRA-5166. The genotype MNH-786 showed better yield and MNH-556 showed superior ginning outturn percentage under water logged conditions. Staple length, strength and micronaire values also decreased under hypoxia. Similar pattern of negative effects were observed for Chlorophyll a, b contents and chl a/b ratio. Two hypoxia tolerant cultivars CIM-573 and MNH-564 had significantly higher chlorophyll a (1.664, 1.551) than other cultivars under both normal and waterlogged conditions. There was a significant decrease in total free amino acids in all genotypes/cultivars due to waterlogging. Free amino acid contents were significantly higher in two waterlogging sensitive cultivars, CEDIX and N-KRISHMA, than other cultivars under both non-waterlogged and waterlogged conditions. Waterlogging caused a significant reduction in shoot soluble proteins and increase in shoot proline. The genotype LRA-5166 was the highest in shoot soluble proteins content and showed significant decrease in shoot proline.

[Conclusions] With respect to yield MNH-786 showed better results and regarding ginning outturn percentage MNH-556 exhibited superior performance. The genotypes CIM-573 and MNH-564 showed higher chlorophyll a values. The above said genotypes may be exploited for further studies related to hypoxia tolerance.

Hypoxia tolerance studies for yield, fiber and physiological traits in cotton (Gossypium hirsutum L.)
HUSSAIN Altaf, FAROOQ Jehanzeb, AHMAD Saghir, MAHMOOD Abid, SADIQ M. Attiq, ZAFAR Ullah Zafar and ATHAR Habib-Ur-Rehman

Journal of Cotton Research. 2018; 1:8.
https://doi.org/10.1186/s42397-018-0008-8

Efficiency of cotton bollworm (Helicoverpa armigera Hübner) control of different Bt cotton varieties in North China

[Background] The cotton bollworm (Helicoverpa armigera) is one of cotton’s most destructive insect pests in terms of yield and quality. Since 1997, China has grown commercially available transgenic Bacillus thuringiensis (Bt) cotton. We aimed to investigate the variation in resistance of transgenic Bt cotton varieties to cotton bollworm in North China.

[Methods] Populations of cotton bollworm were monitored from 2008 to 2015 in environments where Bt cotton was planted adjacent to other non-Bt crops. The study included 197 Bt cotton varieties planted in 42 counties/locations in three provinces (Hebei, Shandong and Henan) of North China, which were evaluated through field investigations, bioassays, and enzyme-linked immunosorbent assays (ELISA).

[Results] The average number of cotton bollworms never exceeded the action threshold (10 larvae per 100 cotton plants), however, their number reached 19.55 per 100 cotton plants in 2011. The ratios of damaged plants to total Bt cotton stem-tips, buds, and bolls was low except in 2010, when the ratios reached 1.82%, 2.09%, and 10.63%, respectively. The results of bioassay showed that the corrected mortality were higher at the second generation cotton bollworm stage than the third and fourth germination stages. Totally, Bt protein content declined sharply at the seedling stage from 2008 to 2015.

[Conclusions] This study indicated that almost all Bt cotton varieties were capable to effectively control the populations of cotton bollworm in North China.

Efficiency of cotton bollworm (Helicoverpa armigera Hübner) control of different Bt cotton varieties in North China
LÜ Limin, LUO Junyu, ZHANG Shuai, YU Qianlin, MA Ligang, LIU Xiaofeng, WANG Chunyi, MA Xiaoyan, MA Yan and CUI Jinjie

Journal of Cotton Research. 2018; 1:4.
https://doi.org/10.1186/s42397-018-0003-0

Comparative transcriptome study provides insights into acquisition of embryogenic ability in upland cotton during somatic embryogenesis

[Background] The conversion from non-embryogenic callus (NEC) to embryogenic callus (EC) is the key bottleneck step in regeneration of upland cotton (Gossypium hirsutum), and hinders the transgenic breeding of upland cotton. To investigate molecular mechanisms underlying acquisition of embryogenic potential during this process, comparation analysis of transcriptome dynamics between two upland cotton cultivars with different somatic embryogenesis abilities was conducted.

[Results] Differentially expressed genes involved in the transformation from NEC to EC were detected in the two different cultivars. Principal component analysis based on DEGs showed that the NEC tissues of the two cultivars were highly heterogeneous, whereas the derived EC tissues were similar, which suggested the homogeneousness of EC between different lines. In the highly embryogenic cultivar CCRI 24, more of these genes were down-regulated, whereas, in the recalcitrant cultivar CCRI 12, more were up-regulated. Bioinformatics analysis on these DEGs showed that the vast majority of differentially expressed genes were enriched in metabolism and secondary metabolites biosynthesis pathways. Flavonoid biosynthesis and phenylpropanoid biosynthesis pathways were enriched in both cultivars, and the associated genes were down-regulated more in CCRI 24 than in CCRI 12. We deduced that vigorous secondary metabolism in CCRI 12 may hinder primary metabolism, resulting in tardiness of cell differentiation. Interestingly, genes involved in the plant hormone signal transduction pathway were enriched in the recalcitrant cultivar CCRI 12, but not in CCRI 24, suggesting more radical regulation of hormone signal transduction in the recalcitrant cultivar. Signal transduction rather than biosynthesis of plant hormones is more likely to be the determining factor triggering NEC to EC transition in recalcitrant cotton lines. Transcription factor encoding genes showed differential regulation between two cultivars.

[Conclusions] Our study provides valuable information about the molecular mechanism of conversion from NEC to EC in cotton and allows for identification of novel genes involved. By comparing transcriptome changes in transformation from NEC to EC between the two cultivars, we identified 46 transcripts that may contribute to initiating embryogenic shift.

Comparative transcriptome study provides insights into acquisition of embryogenic ability in upland cotton during somatic embryogenesis
SUN Ruibin, TIAN Ruiping, MA Dan, WANG Shaohui and LIU Chuanliang

Journal of Cotton Research. 2018; 1:9
https://doi.org/10.1186/s42397-018-0010-1

Genotypic variation in spatiotemporal distribution of canopy light interception in relation to yield formation in cotton

[Background] Within-canopy interception of photosynthetically active radiation (PAR) impacts yield and other agronomic traits in cotton (Gossypium hirsutum L.). Field experiments were conducted to investigate the influence of 6 cotton varieties (they belong to 3 different plant types) on yield, yield distribution, light interception (LI), LI distribution and the relationship between yield formation and LI in Anyang, Henan, in 2014 and 2015.

[Result] The results showed that cotton cultivars with long branches (loose-type) intercepted more LI than did cultivars with short branches (compact-type), due to increased LI in the middle and upper canopy. Although loose-type varieties had greater LI, they did not yield significantly higher than compact-type varieties, due to decreased harvest index. Therefore, improving the harvest index by adjusting the source-to-sink relationship may further increase cotton yield for loose-type cotton. In addition, there was a positive relationship between reproductive organ biomass accumulation and canopy-accumulated LI, indicating that enhancing LI is important for yield improvement for each cultivar. Furthermore, yield distribution within the canopy was significantly linearly related to vertical LI distribution.

[Conclusion] Therefore, optimizing canopy structure of different plant type and subsequently optimizing LI distribution within the cotton canopy can effectively enhance the yield.

Genotypic variation in spatiotemporal distribution of canopy light interception in relation to yield formation in cotton
XING Fangfang, HAN Yingchun, FENG Lu, ZHI Xiaoyu, WANG Guoping, YANG Beifang, FAN Zhengyi, LEI Yaping, DU Wenli, WANG Zhanbiao, XIONG Shiwu, LI Xiaofei and LI Yabing

Journal of Cotton Research, 2018; 1:13.
https://jcottonres.biomedcentral.com/articles/10.1186/s42397-018-0012-z

Saponin synthesis and cotton growth is antagonistically regulated by solar UV-B radiation

An article of Journal of Cotton Research has been published online.

[Background] Earlier we have reported that the exclusion of solar UV-B increased the growth and yield of cotton plants as compared with ambient UV-B. The UV-B radiation effects on the saponins and the impact of ambient and reduced UV-B on the accumulation of saponins has not been investigated yet. Thus a field experiment was conducted to study the influence of solar UV-B on the growth response and saponin synthesis in cotton (Gossypium hirsutum) var. Vikram plants by the exclusion of UV-B. The cotton plants were grown in specially designed iron chambers, wrapped with filters that excluded UV-B (<315 nm), or transmitted ambient UV-B. [Results] Exclusion of ambient UV-B enhanced the growth of cotton plants in terms of plant height and leaf area. Greater plant height in UV-B excluded plants was due to elongated internode and more number of nodes. Enhancement in growth was accompanied by a decrease in the accumulation of saponins, which was quantified by the spectrophotometric, TLC and HPLC methods. Solvent extraction of saponins from the internodes and leaves were used for the bioassay of Amaranthus hypocotyl growth and expansion of cucumber cotyledons. Extracts obtained from the UV-B excluded plants (leaves and internodes) promoted the growth to a larger extent as compared with the extracts obtained from ambient grown plants.

[Conclusions] The result indicates that solar UV-B may possibly suppress the plant growth by regulating the synthesis of natural growth inhibitor’s like saponin.

Saponin synthesis and cotton growth is antagonistically regulated by solar UV-B radiation
DEHARIYA Priti, KATARIA Sunita, GURUPRASAD Kadur Narayan, PANDEY Govind Prakash

Journal of Cotton Research, 2018, 1:14

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-018-0014-x