Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage

Combined genome and transcriptome analysis of elite fiber quality in Gossypium barbadense

Gossypium barbadense, which is one of several species of cotton, is well known for its superior fiber quality. However, the genetic basis of its high-quality fiber remains largely unexplored. Here, we resequenced 269 G. barbadense accessions. Phylogenetic structure analysis showed that the set of accessions was clustered into 3 groups: G1 and G2 mainly included modern cultivars from Xinjiang, China, and G3 was related to widely introduced accessions in different regions worldwide. A genome-wide association study of 5 fiber quality traits across multiple field environments identified a total of 512 qtls (main-effect QTLs) and 94 qtlEs (QTL-by-environment interactions) related to fiber quality, of which 292 qtls and 57 qtlEs colocated with previous studies. We extracted the genes located in these loci and performed expression comparison, local association analysis, and introgression segment identification. The results showed that high expression of hormone-related genes during fiber development, introgressions from Gossypium hirsutum, and the recombination of domesticated elite allelic variation were 3 major contributors to improve the fiber quality of G. barbadense. In total, 839 candidate genes with encoding region variations associated with elite fiber quality were mined. We confirmed that haplotype GB_D03G0092H traced to G. hirsutum introgression, with a 1-bp deletion leading to a frameshift mutation compared with GB_D03G0092B, significantly improved fiber quality. GB_D03G0092H is localized in the plasma membrane, while GB_D03G0092B is in both the nucleus and plasma membrane. Overexpression of GB_D03G0092H in Arabidopsis (Arabidopsis thaliana) significantly improved the elongation of longitudinal cells. Our study systematically reveals the genetic basis of the superior fiber quality of G. barbadense and provides elite segments and gene resources for breeding high-quality cotton cultivars.

Dissecting the major genetic components underlying cotton lint development

Numerous genetic loci and several functionally characterized genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fiberless seed trait of 'SL1-7-1' and found that MYB25-like_At and HD1_At were very lowly expressed in 'SL1-7-1' ovules during fiber initiation. We then dissected the genetic components involved in determination of lint% using segregating populations derived from crosses of fuzzless mutants and intermediate segregants with different lint%, which not only confirmed the HD1_At locus but identified the HD1_Dt locus as being the major genetic components contributing to fiber initiation and lint%. The segregating populations also allowed us to evaluate the relative contributions of MYB25-like_At, MYB25-like_Dt, HD1_At, and HD1_Dt to lint%. Haplotype analysis of an Upland cotton (Gossypium hirsutum) population with 723 accessions (including 81 fuzzless seed accessions) showed that lint% of the accessions with the LP allele (higher lint%) at MYB25-like_At, MYB25-like_Dt, or HD1_At was significantly higher than that with the lp allele (lower lint%). The lint% of the Upland cotton accessions with 3 or 4 LP alleles at MYB25-like and HD1 was significantly higher than that with 2 LP alleles. The results prompted us to propose a strategy for breeding high-yielding cotton varieties, i.e. pyramiding the LP alleles of MYB25-like and HD1 with new lint% LP alleles without negative impact on seed size and fiber quality.

Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense

INTRODUCTION

Sea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare.

OBJECTIVES

We aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton.

METHODS

Through genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3-79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton.

RESULTS

One reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian.

CONCLUSION

Our study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.

Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits

INTRODUCTION

The simultaneous improvement of fiber quality and yield for cotton is strongly limited by the narrow genetic backgrounds of Gossypium hirsutum (Gh) and the negative genetic correlations among traits. An effective way to overcome the bottlenecks is to introgress the favorable alleles of Gossypium barbadense (Gb) for fiber quality into Gh with high yield.

OBJECTIVES

This study was to identify superior loci for the improvement of fiber quality and yield.

METHODS

Two sets of chromosome segment substitution lines (CSSLs) were generated by crossing Hai1 (Gb, donor-parent) with cultivar CCRI36 (Gh) and CCRI45 (Gh) as genetic backgrounds, and cultivated in 6 and 8 environments, respectively. The kmer genotyping strategy was improved and applied to the population genetic analysis of 743 genomic sequencing data. A progeny segregating population was constructed to validate genetic effects of the candidate loci.

RESULTS

A total of 68,912 and 83,352 genome-wide introgressed kmers were identified in the CCRI36 and CCRI45 populations, respectively. Over 90 % introgressions were homologous exchanges and about 21 % were reverse insertions. In total, 291 major introgressed segments were identified with stable genetic effects, of which 66(22.98 %), 64(21.99 %), 35(12.03 %), 31(10.65 %) and 18(6.19 %) were beneficial for the improvement of fiber length (FL), strength (FS), micronaire, lint-percentage (LP) and boll-weight, respectively. Thirty-nine introgression segments were detected with stable favorable additive effects for simultaneous improvement of 2 or more traits in Gh genetic background, including 6 could increase FL/FS and LP. The pyramiding effects of 3 pleiotropic segments (A07:C45Clu-081, D06:C45Clu-218, D02:C45Clu-193) were further validated in the segregating population.

CONCLUSION

The combining of genome-wide introgressions and kmer genotyping strategy showed significant advantages in exploring genetic resources. Through the genome-wide comprehensive mining, a total of 11 clusters (segments) were discovered for the stable simultaneous improvement of FL/FS and LP, which should be paid more attention in the future.

GBSOT4 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Flavonoid

Sulfotransferases (SOTs) (EC 2.8.2.-) are sulfate regulatory proteins in a variety of organisms that have been previously shown to be involved in regulating a variety of physiological and biological processes, such as growth, development, adaptation to land, stomatal closure, drought tolerance, and response to pathogen infection. However, there is a lack of comprehensive identification and systematic analysis of SOT in cotton, especially in G. barbadense. In this study, we used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structure, expression patterns, evolutionary relationships, selection pressure and stress response of SOT gene family members in G. barbadense. In this study, a total of 241 SOT genes were identified in four cotton species, among which 74 SOT gene members were found in G. barbadense. According to the phylogenetic tree, 241 SOT protein sequences were divided into five distinct subfamilies. We also mapped the physical locations of these genes on chromosomes and visualized the structural information of SOT genes in G. barbadense. We also predicted the cis-acting elements of the SOT gene in G. barbadense, and we identified the repetitive types and collinearity analysis of SOT genes in four cotton species. We calculated the Ka/Ks ratio between homologous gene pairs to elucidate the selective pressure between SOT genes. Transcriptome data were used to explore the expression patterns of SOT genes, and then qRT-PCR was used to detect the expression patterns of GBSOT4, GBSOT17 and GBSOT33 under FOV stress. WGCNA (weighted gene co-expression network analysis) showed that GB_A01G0479 (GBSOT4) belonged to the MEblue module, which may regulate the resistance mechanism of G. barbadense to FOV through plant hormones, signal transduction and glutathione metabolism. In addition, we conducted a VIGS (virus-induced gene silencing) experiment on GBSOT4, and the results showed that after FOV inoculation, the plants with a silenced target gene had more serious leaf wilting, drying and cracking than the control group, and the disease index of the plants with the silenced target gene was significantly higher than that of the control group. This suggests that GBSOT4 may be involved in protecting the production of G. barbadense from FOV infection. Subsequent metabolomics analysis showed that some flavonoid metabolites, such as Eupatorin-5-methylether (3'-hydroxy-5,6,7,4'-tetramethoxyflavone, were accumulated in cotton plants in response to FOV infection.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton

BACKGROUND

Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown.

RESULTS

By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae.

CONCLUSIONS

We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

BACKGROUND

Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield.

RESULTS

Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation.

CONCLUSIONS

A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.

Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Structural variations (SVs) have long been described as being involved in the origin, adaption, and domestication of species. However, the underlying genetic and genomic mechanisms are poorly understood. Here, we report a high-quality genome assembly of Gossypium barbadense acc. Tanguis, a landrace that is closely related to formation of extra-long-staple (ELS) cultivated cotton. An SV-based pan-genome (Pan-SV) was then constructed using a total of 182 593 non-redundant SVs, including 2236 inversions, 97 398 insertions, and 82 959 deletions from 11 assembled genomes of allopolyploid cotton. The utility of this Pan-SV was then demonstrated through population structure analysis and genome-wide association studies (GWASs). Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an SV-based GWAS, certain SVs responsible for speciation, domestication, and improvement in tetraploid cottons were identified. Importantly, some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS. In particular, a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G. barbadense. Collectively, this study provides new insights into genome-wide, gene-scale SVs linked to important agronomic traits in a major crop species and highlights the importance of SVs during the speciation, domestication, and improvement of cultivated crop species.

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

Efficient imaging and computer vision detection of two cell shapes in young cotton fibers

PREMISE

The shape of young cotton (Gossypium) fibers varies within and between commercial cotton species, as revealed by previous detailed analyses of one cultivar of G. hirsutum and one of G. barbadense. Both narrow and wide fibers exist in G. hirsutum cv. Deltapine 90, which may impact the quality of our most abundant renewable textile material. More efficient cellular phenotyping methods are needed to empower future research efforts.

METHODS

We developed semi-automated imaging methods for young cotton fibers and a novel machine learning algorithm for the rapid detection of tapered (narrow) or hemisphere (wide) fibers in homogeneous or mixed populations.

RESULTS

The new methods were accurate for diverse accessions of G. hirsutum and G. barbadense and at least eight times more efficient than manual methods. Narrow fibers dominated in the three G. barbadense accessions analyzed, whereas the three G. hirsutum accessions showed a mixture of tapered and hemisphere fibers in varying proportions.

DISCUSSION

The use or adaptation of these improved methods will facilitate experiments with higher throughput to understand the biological factors controlling the variable shapes of young cotton fibers or other elongating single cells. This research also enables the exploration of links between early cell shape and mature cotton fiber quality in diverse field-grown cotton accessions.

Natural variation of GhSI7 increases seed index in cotton

qSI07.1, a major QTL for seed index in cotton, was fine-mapped to a 17.45-kb region, and the candidate gene GhSI7 was verified in transgenic plants. Improving production to meet human needs is a vital objective in cotton breeding. The yield-related trait seed index is a complex quantitative trait, but few candidate genes for seed index have been characterized. Here, a major QTL for seed index qSI07.1 was fine-mapped to a 17.45-kb region by linkage analysis and substitutional mapping. Only GhSI7, encoding the transcriptional regulator STERILE APETALA, was contained in the candidate region. Association test and genetic analysis indicated that an 845-bp-deletion in its intron was responsible for the seed index variation. Origin analysis revealed that this variation was unique in Gossypium hirsutum and originated from race accessions. Overexpression of GhSI7 (haplotype 2) significantly increased the seed index and organ size in cotton plants. Our findings provided a diagnostic marker for breeding and selecting cotton varieties with high seed index, and laid a foundation for further studies to understand the molecular mechanism of cotton seed morphogenesis.

Retrieving a disrupted gene encoding phospholipase A for fibre enhancement in allotetraploid cultivated cotton

After polyploidization originated from one interspecific hybridization event in Gossypium, Gossypium barbadense evolved to produce extra-long staple fibres than Gossypium hirsutum (Upland cotton), which produces a higher fibre yield. The genomic diversity between G. barbadense and G. hirsutum thus provides a genetic basis for fibre trait variation. Recently, rapid accumulation of gene disruption or deleterious mutation was reported in allotetraploid cotton genomes, with unknown impacts on fibre traits. Here, we identified gene disruptions in allotetraploid G. hirsutum (18.14%) and G. barbadense (17.38%) through comparison with their presumed diploid progenitors. Relative to conserved genes, these disrupted genes exhibited faster evolution rate, lower expression level and altered gene co-expression networks. Within a module regulating fibre elongation, a hub gene experienced gene disruption in G. hirsutum after polyploidization, with a 2-bp deletion in the coding region of GhNPLA1D introducing early termination of translation. This deletion was observed in all of the 34 G. hirsutum landraces and 36 G. hirsutum cultivars, but not in 96% of 57 G. barbadense accessions. Retrieving the disrupted gene GhNPLA1D using its homoeolog GhNPLA1A achieved longer fibre length in G. hirsutum. Further enzyme activity and lipids analysis confirmed that GhNPLA1A encodes a typical phospholipase A and promotes cotton fibre elongation via elevating intracellular levels of linolenic acid and 34:3 phosphatidylinositol. Our work opens a strategy for identifying disrupted genes and retrieving their functions in ways that can provide valuable resources for accelerating fibre trait enhancement in cotton breeding.

Gb_ANR-47 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Proanthocyanidins

Anthocyanidin reductase (ANR) is an important regulator of flavonoid metabolism, and proanthocyanidins, the secondary metabolites of flavonoids, play an important role in the response of plants to pathogenic stress. Therefore, in this study, the expression analysis of the ANR gene family of Gossypium barbadense after inoculation with Fusarium oxysporum f. sp. vasinfectum (FOV) was performed at different time points. It was found that Gb_ANR-47 showed significant differences in the disease-resistant cultivar 06-146 and the susceptible cultivar Xinhai 14, as well as in the highest root expression. It was found that the expression of Gb_ANR-47 in the resistant cultivar was significantly higher than that in the susceptible cultivar by MeJA and SA, and different amounts of methyl jasmonate (MeJA) and salicylic acid (SA) response elements were found in the promoter region of Gb_ANR-47. After silencing GbANR-47 in 06-146 material by VIGS technology, its resistance to FOV decreased significantly. The disease severity index (DSI) was significantly increased, and the anthocyanin content was significantly decreased in silenced plants, compared to controls. Our findings suggest that GbANR-47 is a positive regulator of FOV resistance in Gossypium barbadense. The research results provide an important theoretical basis for in-depth analysis of the molecular mechanism of GbANR-47 and improving the anti-FOV of Gossypium barbadense.

Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance

Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.

Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton

Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.

Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense

BACKGROUND

Calcium dependent protein kinases (CDPKs) are a class of important calcium signal sensing response proteins, which play an important regulatory role in response to abiotic stress. However, researchers have not been excavated CDPKs' role in drought in sea-island cotton(Gossypium barbadense L. 'H7124').

RESULTS

Eighty-four CDPK genes have been identified in G. barbadense. These GbCDPK genes are unevenly distributed on 26 chromosomes, and segmental duplication is the significant way for the extension of CDPK family. Also, members within the same subfamily share a similar gene structure and motif composition. There are a large number of cis-elements involved in plant growth and response to stresses in the promoter regions of GbCDPKs. Additionally, these GbCDPKs show differential expression patterns in cotton tissues. The transcription levels of most genes were markedly altered in cotton under heat, cold, salt and PEG treatments, while the expressions of some GbCDPKs were induced in cotton under drought stress. Among these drought-induced genes, we selected GbCDPK32, GbCDPK68, GbCDPK74, GbCDPK80 and GbCDPK83 for further functional characterization by virus-induced gene silencing (VIGS) method.

CONCLUSIONS

In conclusion, the principal findings of this prospective study are that CDPKs were associated with drought. These findings provide a solid foundation for the development of future molecular mechanism in sea-island cotton.

A Calmodulin-Like Gene (GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense

Sea Island cotton (Gossypium barbadense) is world-renowned for its superior natural fiber. Although fiber strength is one of the most important fiber quality traits, genes contributing to fiber strength are poorly understood. Production of sea island cotton also is inextricably linked to improving its relatively low yield, thus enhancing the importance of joint improvement of both fiber quality and yield. We used genomic variation to uncover the genetic evidence of trait improvement resulting from pedigree breeding of Sea Island cotton. This pedigree was aimed at improving fiber strength and yielded an elite cultivar, XH35. Using a combination of genome-wide association study (GWAS) and selection screens, we detected 82 putative fiber-strength-related genes. Expression analysis confirmed a calmodulin-like gene, GbCML7, which enhanced fiber strength in a specific haplotype. This gene is a major-effect gene, which interacts with a minor-effect gene, GbTUA3, facilitating the enhancement of fiber strength in a synergistic fashion. Moreover, GbCML7 participates in the cooperative improvement of fiber strength, fiber length, and fiber uniformity, though a slight compromise exists between the first two of these traits and the latter. Importantly, GbCML7 is shown to boost yield in some backgrounds by increasing multiple yield components to varying degrees, especially boll number. Our work provides valuable genomic evidence and a key genetic factor for the joint improvement of fiber quality and yield in Sea Island cotton.

CottonGVD: A Comprehensive Genomic Variation Database for Cultivated Cottons

Cultivated cottons are the most important economic crop, which produce natural fiber for the textile industry. In recent years, the genetic basis of several essential traits for cultivated cottons has been gradually elucidated by decoding their genomic variations. Although an abundance of resequencing data is available in public, there is still a lack of a comprehensive tool to exhibit the results of genomic variations and genome-wide association study (GWAS). To assist cotton researchers in utilizing these data efficiently and conveniently, we constructed the cotton genomic variation database (CottonGVD; http://120.78.174.209/ or http://db.cngb.org/cottonGVD). This database contains the published genomic information of three cultivated cotton species, the corresponding population variations (SNP and InDel markers), and the visualized results of GWAS for major traits. Various built-in genomic tools help users retrieve, browse, and query the variations conveniently. The database also provides interactive maps (e.g., Manhattan map, scatter plot, heatmap, and linkage disequilibrium block) to exhibit GWAS and expression GWAS results. Cotton researchers could easily focus on phenotype-associated loci visualization, and they are interested in and screen for candidate genes. Moreover, CottonGVD will continue to update by adding more data and functions.