Tetraploid Cotton Species Research Articles

Evolutionary comparison of lncRNAs in four cotton species and functional identification of LncR4682-PAS2-KCS19 module in fiber elongation.

Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.

Comparative analysis of SIMILAR to RCD ONE (SRO) family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development

BackgroundSRO (Similar to RCD1) genes family is largely recognized for their importance in the growth, development, and in responding to environmental stresses. However, genome-wide identification and functional characterization of SRO genes from cotton species have not been reported so far.ResultsA total of 36 SRO genes were identified from four cotton species. Phylogenetic analysis divided these genes into three groups with distinct structure. Syntenic and chromosomal distribution analysis indicated uneven distribution of GaSRO, GrSRO, GhSRO, and GbSRO genes on A2, D5 genomes, Gh-At, Gh-Dt, Gb-At, and Gb-Dt subgenomes, respectively. Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes. In promoter analysis, several elements responsive to the growth, development and hormones were found in GhSRO genes, implying gene induction during cotton growth and development. Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes. Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues. In addition, specific expression pattern of some GhSRO genes during ovule development depicted their involvement in these developmental processes.ConclusionThe data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses.

Cytokinin oxidase/dehydrogenase (CKX), responsible for irreversible cytokinin degradation, also controls plant growth and development and response to abiotic stress. While the CKX gene has been studied in other plants extensively, its function in cotton is still unknown. Therefore, a genome-wide study to identify the CKX gene family in the four cotton species was conducted using transcriptomics, quantitative real-time PCR (qRT-PCR) and bioinformatics. As a result, in G. hirsutum and G. barbadense (the tetraploid cotton species), 87 and 96 CKX genes respectively and 62 genes each in G. arboreum and G. raimondii, were identified. Based on the evolutionary studies, the cotton CKX gene family has been divided into five distinct subfamilies. It was observed that CKX genes in cotton have conserved sequence logos and gene family expansion was due to segmental duplication or whole genome duplication (WGD). Collinearity and multiple synteny studies showed an expansion of gene families during evolution and purifying selection pressure has been exerted. G. hirsutum CKX genes displayed multiple exons/introns, uneven chromosomal distribution, conserved protein motifs, and cis-elements related to growth and stress in their promoter regions. Cis-elements related to resistance, physiological metabolism and hormonal regulation were identified within the promoter regions of the CKX genes. Expression analysis under different stress conditions (cold, heat, drought and salt) revealed different expression patterns in the different tissues. Through virus-induced gene silencing (VIGS), the GhCKX34A gene was found to improve cold resistance by modulating antioxidant-related activity. Since GhCKX29A is highly expressed during fibre development, we hypothesize that the increased expression of GhCKX29A in fibres has significant effects on fibre elongation. Consequently, these results contribute to our understanding of the involvement of GhCKXs in both fibre development and response to abiotic stress.

Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton (Gossypium) Species.

Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A1-genome) and G. mustelinum Miers ex Watt (AD4-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C22H25NO6) treatment. The fertile F1C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F1C and F2C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8-92.2%, the fertility of seeds in hybrid bolls from 9.7-16.3%, and the pollen viability rates from 36.6-63.8%. Two transgressive plants with long fiber of 35.1-37.0 mm and one plant with extra-long fiber of 39.1-41.0 mm were identified in the F2C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.

Comparative analysis of genome sequences of the two cultivated tetraploid cottons, Gossypium hirsutum (L.) and G. barbadense (L.)

With innovations in sequencing technology and the progress of high-performance computing systems, it is now relatively straightforward to sequence and assemble complex genomes. Many genomes from multiple cotton species have been released in recent years, with the highly homozygous standard genetic lines of two cultivated allotetraploid cottons, i.e., Gossypium hirsutum TM-1 and G. barbadense 3–79, assembled multiple times by different research groups using diverse sequencing technologies. The assembly quality among these genomes is variable, even between multiple accessions or versions of the same species, which can generate both confusion in choosing the appropriate genome for genetic analysis and obstacles when comparing results among the different reference genomes. Accordingly, an assessment of the many cotton genome sequences is necessary to facilitate both choice of genome sequence and comparisons between different versions or species. Here we comprehensively assess and compare genome assembly accuracy, completeness, and contiguity for nine G. hirsutum assemblies and four G. barbadense assemblies using multiple analysis strategies with the same criteria. We identify centromeric regions and several large-scale inversions among genomes from the same accession, indicating structural errors introduced during sequence ordering and orientation in G. hirsutum and G. barbadense genome assembly. Gene relationships between annotations from multiple genomes are defined within and across species, and the results are available at the Cotton Paralogs Groups Search website (https://ihope.shinyapps.io/cottonParalogs/), a convenient resource for converting gene ids and comparing annotations between different genome versions. This study comprehensively assesses and compares assembly quality among multiple versions of the two cultivated tetraploid cotton species with different assembly strategies, illustrating the challenges of sequencing and assembling complex genomes and providing a resource for cotton genomics.

Genome-wide identification and characterization of polycomb repressive complex 2 core components in upland cotton (Gossypium hirsutum L.)

BackgroundThe evolutionarily conserved Polycomb Repressive Complex 2 (PRC2) plays a vital role in epigenetic gene repression by depositing tri-methylation on lysine residue K27 of histone H3 (H3K27me3) at the target loci, thus participating in diverse biological processes. However, few reports about PRC2 are available in plant species with large and complicated genomes, like cotton.ResultsHere, we performed a genome-wide identification and comprehensive analysis of cotton PRC2 core components, especially in upland cotton (Gossypium hirsutum). Firstly, a total of 8 and 16 PRC2 core components were identified in diploid and tetraploid cotton species, respectively. These components were classified into four groups, E(z), Su(z)12, ESC and p55, and the members in the same group displayed good collinearity, similar gene structure and domain organization. Next, we cloned G. hirsutum PRC2 (GhPRC2) core components, and found that most of GhPRC2 proteins were localized in the nucleus, and interacted with each other to form multi-subunit complexes. Moreover, we analyzed the expression profile of GhPRC2 genes. The transcriptome data and quantitative real-time PCR (qRT-PCR) assays indicated that GhPRC2 genes were ubiquitously but differentially expressed in various tissues, with high expression levels in reproductive organs like petals, stamens and pistils. And the expressions of several GhPRC2 genes, especially E(z) group genes, were responsive to various abiotic and biotic stresses, including drought, salinity, extreme temperature, and Verticillium dahliae (Vd) infection.ConclusionWe identified PRC2 core components in upland cotton, and systematically investigated their classifications, phylogenetic and synteny relationships, gene structures, domain organizations, subcellular localizations, protein interactions, tissue-specific and stresses-responsive expression patterns. Our results will provide insights into the evolution and composition of cotton PRC2, and lay the foundation for further investigation of their biological functions and regulatory mechanisms.

Genome wide identification and evolutionary analysis of vat like NBS-LRR genes potentially associated with resistance to aphids in cotton.

Nucleotide Binding Site - Leucine Rich Repeat (NBS-LRR) genes play a significant role in plant defense against biotic stresses and are an integral part of signal transduction pathways. Vat gene has been well reported for their role in resistance to Aphis gossypii and viruses transmitted by them. Despite their importance, Vat like NBS-LRR resistance genes have not yet been identified and studied in cotton species. This study report hundreds of orthologous Vat like NBS-LRR genes from the genomes of 18 cotton species through homology searches and the distribution of those identified genes were tend to be clustered on different chromosome. Especially, in a majority of the cases, Vat like genes were located on chromosome number 13 and they all shared two conserved NBS-LRR domains, one disease resistant domain and several repeats of LRR on the investigated cotton Vat like proteins. Gene ontology study on Vat like NBS-LRR genes revealed the molecular functions viz., ADP and protein binding. Phylogenetic analysis also revealed that Vat like sequences of two diploid species, viz., G. arboreum and G. anomalum, were closely related to the sequences of the tetraploids than all other diploids. The Vat like genes of G. aridum and G. schwendimanii were distantly related among diploids and tetraploids species. Various hormones and defense related cis-acting regulatory elements were identified from the 2kb upstream sequences of the Vat like genes implying their defensive response towards the biotic stresses. Interestingly, G. arboreum and G. trilobum were found to have more regulatory elements than larger genomes of tetraploid cotton species. Thus, the present study provides the evidence for the evolution of Vat like genes in defense mechanisms against aphids infestation in cotton genomes and allows further characterization of candidate genes for developing aphid and aphid transmitted viruses resistant crops through cotton breeding.

Genome-wide analysis of the SBT gene family involved in drought tolerance in cotton.

The subtilisin-like proteases (SBTs) are a large family of serine peptidases that are unique to plants. Previous studies have shown that SBTs are associated with developmental processes and environmental responses. However, comprehensive identification and systematic analysis of the SBT family have not been conducted in cotton. We used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structures, expression modes, evolutionary relationships, selection pressures and stress responses of SBT gene family members in upland cotton. In this study, we identified 120 and 112 SBTs in the tetraploid cotton species G. hirsutum and G. barbadense, while 67 and 69 SBTs were identified in the diploid species G. arboreum and G. raimondii, respectively; these SBTs were divided into five distinct subfamilies. We identified the SBT gene GhSBT27A, and explore its function through virus-induced gene silencing and transmission electron microscopy. These results suggested that the GhSBT27A gene was involved in the response to drought stress. These results lay a foundation for further study on the drought stress mechanism of cotton.

Genomewide Identification and Characterization of the Genes Involved in the Flowering of Cotton.

Flowering is a prerequisite for flowering plants to complete reproduction, and flowering time has an important effect on the high and stable yields of crops. However, there are limited reports on flowering-related genes at the genomic level in cotton. In this study, genomewide analysis of the evolutionary relationship of flowering-related genes in different cotton species shows that the numbers of flowering-related genes in the genomes of tetraploid cotton species Gossypium hirsutum and Gossypium barbadense were similar, and that these numbers were approximately twice as much as the number in diploid cotton species Gossypium arboretum. The classification of flowering-related genes shows that most of them belong to the photoperiod and circadian clock flowering pathway. The distribution of flowering-related genes on the chromosomes of the At and Dt subgenomes was similar, with no subgenomic preference detected. In addition, most of the flowering-related core genes in Arabidopsis thaliana had homologs in the cotton genome, but the copy numbers and expression patterns were disparate; moreover, flowering-related genes underwent purifying selection throughout the evolutionary and selection processes. Although the differentiation and reorganization of many key genes of the cotton flowering regulatory network occurred throughout the evolutionary and selection processes, most of them, especially those involved in the important flowering regulatory networks, have been relatively conserved and preferentially selected.

Increasing floral visitation and hybrid seed production mediated by beauty mark in Gossypium hirsutum.

SummaryHybrid crop varieties have been repeatedly demonstrated to produce significantly higher yields than their parental lines; however, the low efficiency and high cost of hybrid seed production has limited the broad exploitation of heterosis for cotton production. One option for increasing the yield of hybrid seed is to improve pollination efficiency by insect pollinators. Here, we report the molecular cloning and characterization of a semidominant gene, Beauty Mark (BM), which controls purple spot formation at the base of flower petals in the cultivated tetraploid cotton species Gossypium barbadense. BM encodes an R2R3 MYB113 transcription factor, and we demonstrate that GbBM directly targets the promoter of four flavonoid biosynthesis genes to positively regulate petal spot development. Introgression of a GbBM allele into G. hirsutum by marker‐assisted selection restored petal spot formation, which significantly increased the frequency of honeybee visits in G. hirsutum. Moreover, field tests confirmed that cotton seed yield was significantly improved in a three‐line hybrid production system that incorporated the GbBM allele. Our study thus provides a basis for the potentially broad application of this gene in improving the long‐standing problem of low seed production in elite cotton hybrid lines.

Genome-wide identification and analysis of Oleosin gene family in four cotton species and its involvement in oil accumulation and germination

BackgroundCotton is not only a major textile fiber crop but also a vital oilseed, industrial, and forage crop. Oleosins are the structural proteins of oil bodies, influencing their size and the oil content in seeds. In addition, the degradation of oleosins is involved in the mobilization of lipid and oil bodies during seed germination. However, comprehensive identification and the systematic analysis of the Oleosin gene (OLEOs) family have not been conducted in cotton.ResultsAn in-depth analysis has enabled us to identify 25 and 24 OLEOs in tetraploid cotton species G. hirsutum and G. barbadense, respectively, while 12 and 13 OLEOs were identified in diploid species G. arboreum and G. raimondii, respectively. The 74 OLEOs were further clustered into three lineages according to the phylogenetic tree. Synteny analysis revealed that most of the OLEOs were conserved and that WGD or segmental duplications might drive their expansion. The transmembrane helices in GhOLEO proteins were predicted, and three transmembrane models were summarized, in which two were newly proposed. A total of 24 candidate miRNAs targeting GhOLEOs were predicted. Three highly expressed oil-related OLEOs, GH_A07G0501 (SL), GH_D10G0941 (SH), and GH_D01G1686 (U), were cloned, and their subcellular localization and function were analyzed. Their overexpression in Arabidopsis increased seed oil content and decreased seed germination rates.ConclusionWe identified OLEO gene family in four cotton species and performed comparative analyses of their relationships, conserved structure, synteny, and gene duplication. The subcellular localization and function of three highly expressed oil-related OLEOs were detected. These results lay the foundation for further functional characterization of OLEOs and improving seed oil content.

THE NATURE OF INHERITANCE OF THE COLORED COTTON FIBER TRAIT

The article provides information on the biology of diploid and tetraploid cotton species, character and patterns of inheritance of fiber color. The fabric obtained from naturally colored cotton fibers has the properties of greater hygiene and hypoallergenic. Clothing made from such a fabric does not cause irritation on the skin, as the fabric perfectly passes air.

Differentiation in the genetic basis of stem trichome development between cultivated tetraploid cotton species

BackgroundCotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood.ResultsIn this study, Gossypium hirsutum (Gh) and G. barbadense (Gb) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F2 populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F1 generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties.ConclusionBased on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.

Effect of Chromosome Substitution from Alien Tetraploid Cotton Species in Upland Cotton on (+) and (-) Gossypol Enantiomer Levels in Cottonseed

Cottonseed contains high quality protein meal for feed and oil for human consumption, but gossypol in cottonseed has potential toxicity and detrimental effects that limit cottonseed use as food for humans and monogastric animals. Therefore, identifying germplasm containing lower gossypol content is critical. The objective of this research was to investigate the influence of specific chromosomes or chromosome segments from Gossypium barbadense, G. tomentosum, and G. mustelinum, respectively, on (+) and (−) gossypol levels when substituted into G. hirsutum. A total of 11 genotypes were used in this study: nine chromosome substitution lines (CS lines) were investigated for cottonseed gossypol level in field experiments in 2013 and 2014; TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as controls. Results showed significant variation in gossypol level and its fractions among CS lines. This variation is a result of chromosome substitution, although it was also affected by environment (location) as location x genotype was significant. Significant positive relationships between total gossypol, (+) gossypol, and (−) gossypol were found. This research demonstrated significant differences among the nine CS lines, and some CS lines had significantly lower gossypol level in cottonseed. These results provide an alternative breeding approach for possibly selecting low levels of gossypol and improving cottonseed nutritional qualities using CS lines.

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement.

Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.

Comparative Functional Studies on Two Diploid Cotton Genomes Reveals Functional Differences of Basic Helix-loop-helix Proteins in Arabidopsis Trichome Initiation

Background: The cultivated tetraploid cotton species (AD genomes) was originated from two ancestral diploid species (A and D genomes). While the ancestral A-genome species produce spinnable fibers, the D- genome species do not. Cotton fibers are unicellular trichomes originating from seed coat epidermal cells, and currently there is an immense interest in understanding the process of fiber initiation and development. Current knowledge demonstrates that there is a great of deal of resemblance in initiation mechanism between by Arabidopsis trichome and cotton fiber.
 Methodology: In this study, we performed comparative functional studies between A genome and D-genome species in cotton by using Arabidopsis trichome initiation as a model. Four cotton genes TTG3, MYB2, DEL61 and DEL65 were amplified from A-genome and D-genome species, and transformed into their homolog trichomeless mutants Arabidopsis ttg1, gl1, and gl3egl3, respectively.
 Results: Our data indicated that the transgenic plants expressing TTG3 and MYB2 genes from A-genome and D-genome species complement the ttg1 and gl1 mutants, respectively. We also discovered complete absences of two functional basic helix loop helix (bHLH) proteins (DEL65/DEL61) in D- diploid species and one (DEL65) that is functional in A-genome species, but not from D-genome species. This observation is consistent with the natural phenomenon of spinnable fiber production in A- genome species and absence in D-genome species.

Identification of a genome-specific repetitive element in the Gossypium D genome.

The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.

Genetic Basis of Fiber Improvement and Decreased Stress Tolerance in Cultivated Versus Semi-Domesticated Upland Cotton.

Crop domestication from wild ancestors has resulted in the wide adaptation coupled with improved yield and quality traits. However, the genetic basis of many domesticated characteristics remains to be explored. Upland cotton (Gossypium hirsutum) is the most important tetraploid cotton species, accounting for about 90% of world cotton commerce. Here, we reveal the effects of domestication on fiber and stress traits through comprehensive analyses of semi-domesticated races and cultivated cotton accessions. A total of 416 cotton accessions were genotyped, and a decrease in genetic diversity from races to landraces and modern cultivars was detected. Furthermore, 71 domestication selective sweeps (DSS) and 14 improvement selective sweeps (ISS) were identified, with the Dt sub-genome experiencing stronger selection than the At sub-genome during the both selection types. The more expressed genes and a delay in the expression peak of genes related to secondary cell wall (SCW) development in modern cultivars compared to semi-domesticated cotton races, may have contributed to long fibers in these plants. However, down-regulation of genes related to stress response was responsible for decreasing stress tolerance in modern cultivars. We further experimentally confirmed that silencing of PR1 and WRKY20, genes that showed higher expression in the semi-domesticated races, drastically compromised cotton resistance to V. dahliae. Our results reveal fiber improvement and decreased stress tolerance as a result of the domestication of modern upland cotton cultivars.

The Rise of Cotton Genomics.

Cotton is the most important fiber crop, but its polyploid genome is complex and difficult to improve. Recent advances in obtaining high-quality genome sequences of cultivated tetraploid and diploid cotton species may now overcome this hurdle, as well as provide new insights on important fiber quality and disease resistance genes.

Genomic Comparison of the P-ATPase Gene Family in Four Cotton Species and Their Expression Patterns in Gossypium hirsutum

Plant P-type H+-ATPase (P-ATPase) is a membrane protein existing in the plasma membrane that plays an important role in the transmembrane transport of plant cells. To understand the variety and quantity of P-ATPase proteins in different cotton species, we combined four databases from two diploid cotton species (Gossypium raimondii and G. arboreum) and two tetraploid cotton species (G. hirsutum and G. barbadense) to screen the P-ATPase gene family and resolved the evolutionary relationships between the former cotton species. We identified 53, 51, 99 and 98 P-ATPase genes from G. arboretum, G. raimondii, G. barbadense and G. hirsutum, respectively. The structural and phylogenetic analyses revealed that the gene structure was consistent between P-ATPase genes, with a close evolutionary relationship. The expression analysis of P-ATPase genes showed that many P-ATPase genes were highly expressed in various tissues and at different fiber developmental stages in G. hirsutum, suggesting that they have potential functions during growth and fiber development in cotton.