Cotton is the most widely cultivated commercial crop producing natural fiber around the world.As a critical trait for fiber quality,fiber strength principally determined during the secondary wall thickening period.Bas...Cotton is the most widely cultivated commercial crop producing natural fiber around the world.As a critical trait for fiber quality,fiber strength principally determined during the secondary wall thickening period.Based on the developed BC5F3:5 CSSLs(chromosome segment substitution lines)from Gossypium hirsutum CCRI36×G.barbadense Hai 1,the superior MBI9915 was chosen to construct the secondary segregated population BC7F2 with its recurrent parent CCRI36,which was subsequently subjected to Bulk segregant RNA-sequencing(BSR-seq)for rapid identification of candidate genes related to fiber strength.A total of 4 fiber-transcriptome libraries were separately constructed and sequenced,including two parents(CCRI36 and MBI9915)and two extreme pools at 20 DPA(days post anathesis).Through multiple comparisons,536 DEGs(differentially expressed genes)were overlapped at 20 DPA.Allelic-polymorphism comparison in mRNA sequences revealed 831 highly probable SNPs between two extreme pools related to fiber strength.Linkage analysis was performed between two extreme pools with SNP-index method.Eighteen correlated regions with 1981 annotation genes were obtained between two pools at 20 DPA,of which 12 common DEGs were similarly identified both between two parents and two pools.One gene(Gh_A07G0837)in the candidate region related to fiber strength was differentially expressed in both parents and extreme pools and involved in fiber strength development through reactive oxygen species(ROS)activity.Co-expression analysis of Gh_A07G0837 showed that Gh_A07G0837 may cooperate with other genes to regulate fiber strength.The reliability of BSR-seq results was validated by the quantitative real-time PCR(qRT-PCR)experiments on 5 common DGEs 20 DPA.Co-expressed analysis results indicated that there were some genes expressed especially low in MBI9915,resulting in good fiber strength.Focusing on bulked segregant analysis on the extreme pools derived from superior CSSL population,this study indicates that BSR-seq can be efficiently applied on rapid identification of candidate genes related to fiber strength,which make contributions to our understanding of fiber quality formation in cotton.展开更多
Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acti...Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes,subsequently activating or repressing their transcription.In the present study,we systematically examined the functional diversification of the NAC transcription factor(NAC-TFs)family by analyzing their chromosomal location,structure,phylogeny,and expression pattern in Gossypium raimondii(Gr)and G.arboreum(Ga).The 145 and 141 NAC genes identified in the Gr and Ga genomes,respectively,were annotated and divided into 18 subfamilies,which showed distinct divergence in gene structure and expression patterns during fiber development.In addition,when the functional parameters were examined,clear divergence was observed within tandem clusters,which suggested that subfunctionalization had occurred among duplicate genes.The expression patterns of homologous gene pairs also changed,suggestive of the diversification of gene function during the evolution of diploid cotton.These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species.展开更多
基金This study was supported by the National Natural Science Foundation of China(31801404 and 31621005)Joint Funds of the National Natural Science Foundation(U1804103)+1 种基金Science and Technology development Project of Henan Province(192102110127 and 182102410041)the Project of Director(1610162020040904).
文摘Cotton is the most widely cultivated commercial crop producing natural fiber around the world.As a critical trait for fiber quality,fiber strength principally determined during the secondary wall thickening period.Based on the developed BC5F3:5 CSSLs(chromosome segment substitution lines)from Gossypium hirsutum CCRI36×G.barbadense Hai 1,the superior MBI9915 was chosen to construct the secondary segregated population BC7F2 with its recurrent parent CCRI36,which was subsequently subjected to Bulk segregant RNA-sequencing(BSR-seq)for rapid identification of candidate genes related to fiber strength.A total of 4 fiber-transcriptome libraries were separately constructed and sequenced,including two parents(CCRI36 and MBI9915)and two extreme pools at 20 DPA(days post anathesis).Through multiple comparisons,536 DEGs(differentially expressed genes)were overlapped at 20 DPA.Allelic-polymorphism comparison in mRNA sequences revealed 831 highly probable SNPs between two extreme pools related to fiber strength.Linkage analysis was performed between two extreme pools with SNP-index method.Eighteen correlated regions with 1981 annotation genes were obtained between two pools at 20 DPA,of which 12 common DEGs were similarly identified both between two parents and two pools.One gene(Gh_A07G0837)in the candidate region related to fiber strength was differentially expressed in both parents and extreme pools and involved in fiber strength development through reactive oxygen species(ROS)activity.Co-expression analysis of Gh_A07G0837 showed that Gh_A07G0837 may cooperate with other genes to regulate fiber strength.The reliability of BSR-seq results was validated by the quantitative real-time PCR(qRT-PCR)experiments on 5 common DGEs 20 DPA.Co-expressed analysis results indicated that there were some genes expressed especially low in MBI9915,resulting in good fiber strength.Focusing on bulked segregant analysis on the extreme pools derived from superior CSSL population,this study indicates that BSR-seq can be efficiently applied on rapid identification of candidate genes related to fiber strength,which make contributions to our understanding of fiber quality formation in cotton.
基金the National High Technology Research and Development Program of China (2013AA102601)the National Natural Science Foundation of China (31471538)
文摘Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes,subsequently activating or repressing their transcription.In the present study,we systematically examined the functional diversification of the NAC transcription factor(NAC-TFs)family by analyzing their chromosomal location,structure,phylogeny,and expression pattern in Gossypium raimondii(Gr)and G.arboreum(Ga).The 145 and 141 NAC genes identified in the Gr and Ga genomes,respectively,were annotated and divided into 18 subfamilies,which showed distinct divergence in gene structure and expression patterns during fiber development.In addition,when the functional parameters were examined,clear divergence was observed within tandem clusters,which suggested that subfunctionalization had occurred among duplicate genes.The expression patterns of homologous gene pairs also changed,suggestive of the diversification of gene function during the evolution of diploid cotton.These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species.
