Identification and Functional Analysis of Betv1 in Three D Genome-containing Wild Cotton Varieties

Abstract:

[Objective] By analyzing the major birch pollen allergen Betv1 gene family in D genomes of cotton and comparing the expression patterns of three diploid D-genome cotton varieties with different Verticillium wilt resistance levels, we aimed to provide a theoretical basis for further studies on the role of Betv1 genes in cotton resistant to Verticillium wilt. [Method] The Betv1 genes were identified, and a bioinformatics analysis of the physicochemical properties of their encoded sequences in Gossypium raimondii (D5) was performed. The transcriptome sequencing and quantitative real time-PCR of G. raimondii (D5), Gossypium trilobum (D8) and Gossypium thurberi (D1) were used to verify the expression patterns of Bet v 1 genes under Verticillium dahlia infection stress. Betv1 genes were silenced by virus-induced gene silencing in G. hirsutum to identify their functions. [Result] The D genome of cotton contains 59 members, 58 of which have introns and are distributed on eight chromosomes, and most encode hydrophilic proteins that localize to the cytoplasm. The expression levels of Betv1 genes in three wild cotton species having D genomes after being inoculated with V. dahliae were consistent with their disease resistance levels. The genes were separated into three groups based on their expression levels. Genes of Group 3 responded to V. dahliae infection and were highly expressed in disease-resistant cotton species G. thurberi. This indicated that Group 3 genes may be involved in the immune response of Verticillium wilt. A gene with a high expression level was screened out of Group 3. A corresponding homologous gene was silenced in G. hirsutum by virus-induced gene silencing, and gene-silenced plants were more susceptible to V. dahliae, indicating that the gene plays a positive regulatory role in the progress of Verticillium wilt resistance in cotton. [Conclusion] The Betv1 genes act in response to V. dahliae infection and are critical in cotton resistance to Verticillium wilt. The information obtained provides a basis for further studies of the cotton Bet v 1 family genes and their functions.

Key words: wild cotton; Verticillium wilt; Betv1 gene; transcriptome; quantitative real time-PCR (qRT-PCR); virus-induced gene silencing (VIGS)

Cotton Science. 2019, 31(5):361-380.

https://doi.org/10.11963/1002-7807.dqmzy.20190723

Comparative transcriptional analysis provides insights of possible molecular mechanisms of wing polyphenism induced by postnatal crowding in Aphis gossypii

Background
Aphis gossypii is a worldwide sap-sucking pest with a variety of hosts and a  vector of more than 50 plant viruses. The strategy of wing polyphenism, mostly resulting from population density increasing, contributes to the evolutionary success of this pest. However, the related molecular basis remains unclear. Here, we identified the effects of postnatal crowding on wing morph determination in cotton aphid, and examined the transcriptomic differences between wingless and wing morphs.

Results
Effect of postnatal crowding on wing determination in A. gossypii was evaluated firstly. Under the density of 5 nymphs·cm− 2, no wing aphids appeared. Proportion of wing morphs rised with the increase of density in a certain extent, and peaked to 56.1% at the density of 20 nymphs·cm− 2, and reduced afterwards. Then, transcriptomes of wingless and wing morphs were assembled and annotated separately to identify potentially exclusively or differentially expressed transcripts between these two morphs, in which 3 126 and 3 392 unigenes annotated in Nr (Non-redundant protein sequence) database were found in wingless or wing morphs exclusively. Moreover, 3 187 up- and 1 880 down-regulated genes were identified in wing versus wingless aphid. Pathways analysis suggested the involvement of differentially expressed genes in multiple cellular signaling pathways involved in wing morphs determination, including lipid catabolic and metabolism, insulin, ecdysone and juvenile hormone biosynthesis. The expression levels of related genes were validated by the reverse transcription quantitative real time polymerase chain reaction (RT-qPCR) soon afterwards.

Conclusions
The present study identified the effects of postnatal crowding on wing morphs induction and demonstrated that the critical population density for wing morphs formation in A. gossypii was 20 nymphs·cm− 2. Comparative transcriptome analysis provides transcripts potentially expressed exclusively in wingless or wing morph, respectively. Differentially expressed genes between wingless and wing morphs were identified and several signaling pathways potentially involved in cotton aphid wing differentiation were obtained.

Authors:

JI Jichao, ZHANG Shuai, LUO Junyu, WANG Li, ZHU Xiangzhen, ZHANG Kaixin, ZHANG Lijuan & CUI Jinjie

Journal of Cotton Research. 2019,2:17

https://doi.org/10.1186/s42397-019-0036-z

Comparative studies on seed protein characteristics in eight lines of two Gossypium species

[Abstract]
Background: In order to achieve the targets aiming at the improvement of protein quality, knowledge regarding seed protein fractions and polypeptides constituting them in different crops is essential. Besides having high nutritional value as animal feed and human food, the protein isolates from cottonseed meal have also been proven promising as industrial raw materials for a number of applications. As far as Indian work on the characterization of cotton seed proteins is concerned, relatively meagre reports are available. Keeping in mind the importance of cotton seed proteins, lines belonging to Gossypium arboreum L. (Indian cotton) and G. hirsutum L. (American cotton) which are grown in all the major cotton growing states in India were selected for analysing their seed protein characteristics.

Results: Whereas G. arboreum (A-genome) lines revealed a lower range of seed protein content i.e. 19.5~24.3%, an upper range (21.8~29.5%) could be observed in lines of G. hirsutum (AD-genome). Globulins represented dominating fraction in both species followed by albumins, glutelins and prolamins. A significant positive correlation between albumins/globulins and seed protein content in G. arboreum /G. hirsutum, respectively, was observed. Intraspecific electrophoretic variation in seed protein extracts was observed in the region of molecular weight 22 kDa – 27 kDa in lines of both the species; however some lines with A-genome showed similarity in banding pattern with AD-genome. Four polypeptides with disulphide-linkages were also reported for the first time. Albumins were observed to reveal more variations in their electrophoretic pattern between the lines of two species followed by globulins.

Conclusion: On the basis of present and previous studies, screening the lines with low or high protein content will lead the selection of lines with superior polypeptide fraction important for nutritional and industrial purposes. On comparing the composition and behaviour of four 2-S linked polypeptides with other plant groups, these were suggested to be legumin-like in nature. The similarity in banding patterns between the lines of A-genome and AD-genome species marked towards the close evolutionary relationship between these two. Albumin fractions on the basis of our results could be taken for cultivar differentiation in cotton crop.

[Keywords]
Gossypium, SDS-PAGE, Seed proteins, Globulins

Original text: https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0024-3

[Authors] SINGH Arvinder, KAUR Amanjot

JCR-Physiology and Pathology Thematic Series Call For Paper

Coordinator:
Professor Hezhong DONG, Cotton Research Centre, Shandong Academy of Agricultural Sciences, China;
Professor Zhiguo ZHOU, Nanjing Agricultural University, China

Journal of Cotton Research is hosting a thematic series on cotton physiology and pathology. The research community is encouraged to share original findings, methodology, results, databases, and/or software and opinions.

Scopes that may be covered in the submissions may include, but are not limited to the following:

1. growth and organ development;
2. plant and shoot architecture;
3. water, fertilizer, light, etc. use efficiency;
4. intelligent agriculture;
5. rhizosphere and other plant-environment interactions;
6. main disease and resistance.

Submission Deadline: 30 September 2019

Submit Now

https://jcottonres.biomedcentral.com/cottonpap

Evaluation of genetic diversity in short duration cotton (Gossypium hirsutum L.)

[Background] Cotton (Gossypium hirsutum L.) is an important fiber crop in Bangladesh. Genetic diversity among the genotypes of a germplasm has a great importance for cotton breeding. An experiment was carried out at the experimental field of Cotton Research, Training and Seed Multiplication Farm, Sreepur, Gazipur during the cropping season of 2015–2016 with 100 genotypes to evaluate genetic diversity of cotton genotypes for short duration using field performance.

[Results] The genotypes under study were grouped into ten clusters through multivariate analysis using GENSTAT-5. Cluster III contained maximum number of genotypes (16) while cluster X contained the least number of genotypes (7). The inter cluster distances were larger than intra cluster distances in all cases suggesting wider genetic diversity among the genotypes of different clusters. The maximum and minimum inter cluster distances were observed between clusters II and V (10.78) and clusters VIII and IX (3.30), respectively. The results indicated diverse and close relationship among the genotypes of those clusters. Earliness index, single boll weight and days to boll opening showed the higher contribution to the genetic divergence among 19 characters.

[Conclusion] Based on the results of genetic diversity and earliness index, the genotypes from cluster II could be used as parent in hybridization program for the development of short duration cotton variety.

Evaluation of genetic diversity in short duration cotton (Gossypium hirsutum L.)

AKTER T., ISLAM A. K. M. A., RASUL M. G., KUNDU S., KHALEQUZZAMAN and AHMED J. U.
Journal of Cotton Research. 2019; 2:1.
https://doi.org/10.1186/s42397-018-0018-6

Irrigation’s effect and applied selection on the fiber quality of Ethyl MethaneSulfonate (EMS) treated upland cotton (Gossypium hirsutum L.)

[Background] Producing rainfed cotton (Gossypium hirsutum L.) with high fiber quality has been challenging in the Texas High Plains because of extended periods of insufficient rainfall during sensitive boll developmental stages. Genetic variation created by Ethyl MethaneSulfonate (EMS) mutagen has successfully improved fiber quality of cotton. However, little is known about the effect of water deficit environments on fiber quality. Three EMS treated populations were advanced from the first to the fourth generation (M1 to M4) as bulk harvested populations. In 2014, single-plant divergent selection was applied based on perceived morphological and agronomic differences seen during and at the end of the season.

[Results] Analyses from these selections in 2014–2016 showed significant (P < 0.05) improvement between and within populations for fiber traits (micronaire, length, strength, uniformity, and elongation) when compared with the original non-treated EMS source; some selections were found to have excellent fiber quality under diverse irrigation-regimes.

[Conclusions] Some of these selections are being considered for germplasm release and could be useful for improving the fiber quality of cotton under water limited conditions, thereby helping to ensure the long-term survival of the cotton industry on the Texas High Plains.

Irrigation’s effect and applied selection on the fiber quality of Ethyl MethaneSulfonate (EMS) treated upland cotton (Gossypium hirsutum L.)
WITT Travis W. , ULLOA Mauricio, PELLETIER Mathew G. , MENDU Venugopal and RITCHIE Glen L.
Journal of Cotton Research. 2018; 1:17.
https://jcottonres.biomedcentral.com/articles/10.1186/s42397-018-0016-8

JCR-Cotton High Speed Phenotyping Thematic Series Call For Paper

Journal of Cotton Research

Cotton High Speed Phenotyping
Thematic Series Call For Paper
Coordinator: Professor Eric F. Hequet, Texas Tech University, USA; Dr. Glen Ritchie, Texas Tech University, USA

Author’s allowance: The sponsor, Institute of Cotton Research, CAAS, grants to cover not only APC for the submission, but also the author’s allowance once published.

High speed phenotyping is critical to improve cotton research and production. It can be applied to large scale commercial fields, research fields, breeding lines, and even at the individual plant level. The main goals are to improve yield, fiber quality, stress and disease resistance, etc… Recently, advances in high speed phenotyping in cotton have been achieved. The Journal of Cotton Research is hosting a thematic series on this topic. The research community is encouraged to share original findings, methodology, results, databases, and/or software and opinions.

Scopes that may be covered in the submissions may include, but are not limited to the following:
1. Platform design: air-based and/or land-based;
2. Data capture and processing: sensors (RGB, IR, multispectral, sonic, etc.), integration of multiple sensors, information processing technologies;
3. Data analysis and Metadata: analysis of very large data sets, validation with ground truth, practical application examples (breeding programs, site specific irrigation scheduling, etc.).

Submission Deadline: April 30, 2019

https://jcottonres.biomedcentral.com/cottonhsp

Genetic diversity and population structure of Gossypium arboreum L. collected in China

[Background] Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars.

[Method] A set of 197 Gossypium arboreum accessions were genotyped using 80 genome-wide SSR markers to establish patterns of the genetic diversity and population structure. These accessions were collected from three major G. arboreum growing areas in China. A total of 255 alleles across 80 markers were identified in the genetic diversity analysis.

[Results] Three subgroups were found using the population structure analysis, corresponding to the Yangtze River Valley, North China, and Southwest China zones of G. arboreum growing areas in China. Average genetic distance and Polymorphic information content value of G. arboreum population were 0.34 and 0.47, respectively, indicating high genetic diversity in the G. arboreum germplasm pool. The Phylogenetic analysis results concurred with the subgroups identified by Structure analysis with a few exceptions. Variations among and within three groups were observed to be 13.61% and 86.39%, respectively.

[Conclusion] The information regarding genetic diversity and population structure from this study is useful for genetic and genomic analysis and systematic utilization of economically important traits in G. arboreum.

Genetic diversity and population structure of Gossypium arboreum L. collected in China
JIA Yinhua, PAN Zhaoe, HE Shoupu, GONG Wenfang, GENG Xiaoli, PANG Baoyin, WANG Liru and DU Xiongming
Journal of Cotton Research. 2018; 1:11.
https://doi.org/10.1186/s42397-018-0011-0

Map-based cloning of a recessive gene v1 for virescent leaf expression in cotton (Gossypium spp.)

[Background] Virescence, as a recognizable phenotype in the early development stage of cotton, is not only available for research on chloroplast development and photosynthesis but also for heterosis exploitation in cotton.

[Methods] In current study, for fine mapping of virescent-1 (v1) in cotton, three populations with a total of 5 678 individuals were constructed using T582 which has the virescent trait. Tobacco rattle virus, TRV1 and TRV2 (pYL156), were used as vectors for the virus-induced gene silencing (VIGS) assay.

[Results] The v1 gene was fine-mapped to a 20 kb interval on chromosome 20 of tetraploid cotton. We identified only one candidate gene with four single nucleotide polymorphisms between parents, among which the single nucleotide polymorphism at the position of 1 082 base pair caused the change of amino acid residue from Arg (3–79) to Lys (T582). The relative expression of the candidate gene in virescent plants was extensively lower than that in normal plants. Nullification of the gene by VIGS significantly turned the green leaf of normal cotton plants into yellow. We named this candidate gene as GhRVL.

[Conclusions] This study will facilitate the further research on virescent formation, and will be useful for breeding of hybrid cottons.

Map-based cloning of a recessive gene v1 for virescent leaf expression in cotton (Gossypium spp.)
ZHANG Youping, WANG Qiaolian, ZUO Dongyun, CHENG Hailiang, LIU Ke, ASHRAF Javaria, LI Simin, FENG Xiaoxu, YU John Z. and SONG Guoli
Journal of Cotton Research. 2018; 1:10.
https://doi.org/10.1186/s42397-018-0009-7

Identification and screening of nitrogen-efficient cotton genotypes under low and normal nitrogen environments at the seedling stage

[Background] Large quantities of nitrogen (N) fertilizer applied to cotton cropping systems support high yields but cause adverse environmental impacts such as N2O emission and water eutrophication. The development of cotton cultivars with higher N use efficiencies suitable for low-N conditions is therefore important for sustainable production. In this study, we evaluated 100 cotton genotypes in 2016 for N use efficiency and related traits at the seedling stage.

[Methods] Sand culture experiment was conducted with low N levels (0.01 g·kg−1) or normal N levels (0.1 g·kg−1). We investigated plant height, SPAD value (soil plant analysis development chlorophyll meter), dry weight, N accumulation, N utilization efficiency, and N uptake efficiency. Through descriptive statistics, principal component analysis and heatmap clustering analysis, we confirmed the evaluation index system of N-efficient genotypes and the classification of N-efficient genotypes.

[Results] Significant differences were observed among N levels and genotypes for all agronomic traits and N levels. Coefficients of variation varied greatly and ranged from 6.7~28.8 and 7.4~20.8 under low-N and normal-N treatment, respectively. All traits showed highly significant positive correlations with each other, except SPAD value. The principal components under both N levels were similar, showing that total dry weight, aboveground dry weight, total N accumulation, and N uptake efficiency were important components. We confirmed these four traits as suitable screening indexes for low N tolerance. Based on the results of heatmap clustering and scatter diagram analysis of N efficiency value, 10 genotypes were found low-N tolerant, in which five varieties were inefficient under both low and normal N conditions, while four varieties were found efficient under low-N conditions but inefficient under normal-N conditions. Only one variety was efficient under both low and normal-N conditions. Meanwhile, 20 genotypes were identified as low-N sensitive ones, in which 19 genotypes were inefficient under low-N conditions but efficient under normal-N conditions, one variety was inefficient under both low and normal-N conditions.

[Conclusion] We preliminarily identified Kashi as a low-N tolerant and N-efficient cotton genotype, and CCRI 64 as a low-N sensitive and N-inefficient cotton genotype. Further studies should be carried out to verify the yield and heritability effect of specific genotypes in the field.

Identification and screening of nitrogen-efficient cotton genotypes under low and normal nitrogen environments at the seedling stage
ZHANG Hengheng†, FU Xiaoqiong†, WANG Xiangru, GUI Huiping, DONG Qiang, PANG Nianchang, WANG Zhun, ZHANG Xiling and SONG Meizhen
†Contributed equally
Journal of Cotton Research. 2018; 1:6.
https://jcottonres.biomedcentral.com/articles/10.1186/s42397-018-0006-x