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Key message: Transcription factors (TFs) are the key regulators in plant development and stress adaptation. Understanding interactions of TFs in cotton crop is important for enhancing stress tolerance and yield enhancement. Among plant TFs, bZIPs plays a major role in seed germination, flower development, biotic and abiotic stress response. Most of the bZIP proteins from cotton remains uncharacterized and can be utilized for crop improvement. Bioinformatics analysis of bZIPs of cultivated cotton species G. hirsutum along with two sub-genome species G. arboreum and G. raimondii at one platform will certainly help the researchers in the selection of specific cotton bZIP genes according to the close alignment with Arabidopsis orthologs or sub-genome homolog for functional characterization. Cotton is an important commodity in the world economy. Transcription factors (TFs) are the key regulators in plant development and stress adaptation. Understanding interactions of TFs in cotton crop is important for enhancing stress tolerance and yield enhancement. Among plant TFs, bZIPs plays a major role in seed germination, flower development, biotic and abiotic stress response. Most of the bZIP proteins from cotton remains uncharacterized and can be utilized for crop improvement. In this study, we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species Gossypium hirsutum along with two sub-genome species of allotetraploid cotton, Gossypium arboreum and Gossypium raimondii. A total of 228 bZIP genes of G. hirsutum, 91 bZIP genes of G. arboreum and 86 bZIP genes of G. raimondii were identified from CottonGen database. Cotton bZIP genes were annotated in standard pattern according to their match with Arabidopsis bZIPs. Multiple genes with similar bZIP designations were observed in cotton, linked to the gene duplication. Cotton bZIPs are distributed across all 13 chromosomes with varied density. Phylogenetic characterization of all three cotton species bZIPs classified them into 12 subfamilies, namely A, B, C, D, E, F, G, H, I, J, K and S and further into eight subgroups according to their predicted functional similarities, viz., A1, A2, A3, C1, C2, S1, S2 and S3. Subfamilies A and S are having maximum number of bZIP genes, subfamilies B, H, J and K are single-member families. Cotton bZIP protein functions were predicted from identified motifs and orthologs from varied species. Basic region leucine zipper (BRLZ) domain analysis of G. raimondii bZIPs revealed the presence of conserved basic region motif N-X7-R/K in almost all subfamily members, variants are GrbZIP62 with N-X7-I motif and GrbZIP76 with K-X7-R motif. Leucine heptad repeats motif, are also present in variant numbers from two to nine with leucine or other hydrophobic amino acid at designated position among 12 subfamily members. STRING protein interaction network analysis of G. raimondii bZIPs observed strong interaction between A and D, B and K, and C and S subfamily members. [ABSTRACT FROM AUTHOR]

Summary: Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species. Significance Statement: There is little knowledge regarding the population‐scaled recombination rate variation in cotton. Genome‐wide fine‐scaled recombination maps were constructed and characterized the population‐scaled recombination rate in Gossypium hirsutum and G. arboreum in the present study; and GWAS revealed that agronomic trait QTL tended to be co‐located in high‐recombination regions, which revealed that recombination contributed to the domestication and genetic improvement of cotton. [ABSTRACT FROM AUTHOR]

Abiotic stress is an important limiting factor in crop growth and yield around the world. Owing to the continued genetic erosion of the upland cotton germplasm due to intense selection and inbreeding, attention has shifted towards wild cotton progenitors which offer unique traits that can be introgressed into the cultivated cotton to improve their genetic performance. The purpose of this study was to characterize the Pkinase gene family in a previously developed genetic map of the F2 population derived from a cross between two cotton species: Gossypium hirsutum (CCRI 12-4) and Gossypium darwinii (5-7). Based on phylogenetic analysis, Pkinase (PF00069) was found to be the dominant domain with 151 genes in three cotton species, categorized into 13 subfamilies. Structure analysis of G. hirsutum genes showed that a greater percentage of genes and their exons were highly conserved within the group. Syntenic analysis of gene blocks revealed 99 duplicated genes among G. hirsutum, Gossypium arboreum and Gossypium raimondii. Most of the genes were duplicated in segmental pattern. Expression pattern analysis showed that the Pkinase gene family possessed species-level variation in induction to salinity and G. darwinii had higher expression levels as compared to G. hirsutum. Based on RNA sequence analysis and preliminary RT-qPCR verification, we hypothesized that the Pkinase gene family, regulated by transcription factors (TFs) and miRNAs, might play key roles in salt stress tolerance. These findings inferred comprehensive information on possible structure and function of Pkinase gene family in cotton under salt stress.

Background: The most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. G. arboreum L. (A-genome) and G. raimondii Ulbr. (D-genome) are two of closely-related extant progenitors. Gene expression studies in allotetraploid cotton are complicated by the homoeologous loci of A- and D-genome origins. To develop genomic resources for gene expression and cotton breeding, we sequenced and assembled expressed sequence tags (ESTs) derived from G. arboreum and G. raimondii. Results: Roche/454 FLX sequencing technology was employed to sequence normalized cDNA libraries prepared from leaves, roots, bolls, ovules, and fibers in G. arboreum and G. raimondii, respectively. Sequencing reads from two independent libraries in each species were combined to assemble high-quality EST contigs. The combined sequencing reads included 1,699,776 from A-genome and 1,464,815 from D-genome, which were clustered into 89,588 contigs in the A-genome and 65,542 contigs in the D-genome. These contigs represented ~80% of EST collections in Cotton Gene Index 11 (CGI11, March 2011). Compared to the D-genome transcript database, 27,537 and 10,452 contigs were unique transcripts in A and D genomes, respectively. Further analysis using self-blastn reduced the unigene contig number by 52% in A-genome and 57% in D-genome, suggesting that 50% or more of contigs are paralogs or isoforms within each species. The majority of EST contigs (73-81%) were conserved between A- and D-genomes, whereas 27% and 19% contigs were specific to A- and D-genomes, respectively. Using these ESTs, we generated a total of 75,754 genome-specific single nucleotide polymorphism (SNP) (gSNPs or GNPs) or homoeologous-specific SNPs (hSNPs) of 10,885 contigs or genes between A and D genomes, indicating a possibility of separating allelic expression for those genes in allotetraploid cotton. Conclusions: Expressed genes are highly redundant within each diploid progenitor and between A and D progenitor species, suggesting that diploid progenitors in cotton are likely ancient tetraploids. This large set of A- and D-genome ESTs and GNPs will be valuable resources for genome annotation, gene expression, and crop improvement in allotetraploid cotton. [ABSTRACT FROM AUTHOR]

A tri-specific hybrid with delayed pigment gland morphogenesis was obtained by crossing the amphidiploid of (G. arboreum × G. bickii) F1 and an upland cotton germplasm with pigment gland genotype of Gl2Gl2gl3gl3. The tri-specific hybrid was a typical interspecific hybrid with high sterile, and the chromosome configuration at meiosis MI of PMC was 2n = 52 = 41.04 I + 4.54 II + 0.57III + 0.04. The crossover value of bivalent was 1.19. Two fertile plants with objective character were obtained in BCs population by continuously backcrossing with Gl2Gl2gl3gl3 as recurrent parent to the tri-specific hybrid, and a new upland cotton germplasm, named ABH-0318, with delayed pigment gland morphogenesis trait was developed through selfing and screening. The pigment gland trait of ABH-0318 was stable, and there were almost no pigment glands observed in the dormant seeds, although there were a few pigment glands confined to cotyledon edges, and the gossypol content in the dormant seeds was 0.017% only, being a typical low gossypol cotton type. However, a large quantity of pigment glands emerged in cotyledons and other main organs of plant after seed germination, and the gossypol contents in the upper parts of the plant were similar to that of ordinary glanded cotton types. Genetic analysis demonstrated that the delayed pigment gland morphogenesis trait of this germplasm was controlled by the interaction of the genes located in two pigment gland loci, Gl2 and Gl3. Among them, the gene located in locus of Gl2, derived from Gbickii, was dominance to up-land cotton pigment gland alleles, Gl2 and gl2, but was recessive epistatic to another glanded gene Gl3, which was named Gl2b temporarily. While the gene located in the locus of Gl3 was a recessive gene come from upland cotton. [ABSTRACT FROM AUTHOR]

Abiotic stress is an important limiting factor in crop growth and yield around the world. Owing to the continued genetic erosion of the upland cotton germplasm due to intense selection and inbreeding, attention has shifted towards wild cotton progenitors which offer unique traits that can be introgressed into the cultivated cotton to improve their genetic performance. The purpose of this study was to characterize the Pkinase gene family in a previously developed genetic map of the F2 population derived from a cross between two cotton species: Gossypium hirsutum (CCRI 12-4) and Gossypium darwinii (5-7). Based on phylogenetic analysis, Pkinase (PF00069) was found to be the dominant domain with 151 genes in three cotton species, categorized into 13 subfamilies. Structure analysis of G. hirsutum genes showed that a greater percentage of genes and their exons were highly conserved within the group. Syntenic analysis of gene blocks revealed 99 duplicated genes among G. hirsutum, Gossypium arboreum and Gossypium raimondii. Most of the genes were duplicated in segmental pattern. Expression pattern analysis showed that the Pkinase gene family possessed species-level variation in induction to salinity and G. darwinii had higher expression levels as compared to G. hirsutum. Based on RNA sequence analysis and preliminary RT-qPCR verification, we hypothesized that the Pkinase gene family, regulated by transcription factors (TFs) and miRNAs, might play key roles in salt stress tolerance. These findings inferred comprehensive information on possible structure and function of Pkinase gene family in cotton under salt stress. [ABSTRACT FROM AUTHOR]