Fine Mapping And Candidate Gene Identification Of QFL-12-2 In Chromosome Introgression Line Carrying Gossypium Barbadense Chromosomal Segments In Gossypium Hirsutum Background

Cotton(Gossypium hirsutum)is an important economic crop and the largest source of natural fiber for global textile industry.The demand for better fiber quality is kept increasing along with the rapid development of modern textile industries.The principal purposes of cotton breeding also shift from solely increasing yield to simultaneously improvement of both yield as well as fiber quality.Fiber length is an important index to evaluate cotton fiber quality,and increasing cotton fiber length is becoming an important target in cotton breeding programs.We evaluated the 332 introgression lines which were constructed by using Hail,a cultivar of G.barbadense,as the donor parent,CCRI45,an cultivar of G.hirsutum,as the recurrent parent.Based on the fiber quality and yield traits performance,one introgression line MBI7747 was selceted to construct F2 population with CCRI45.2292 SSR markers covering the whole genome of cotton evenly distributed on 26 chromosomes were used to test their polymorphism between MBI7747 and CCRI45,then the polymorphic markers were used to genotype the whole F2 population.A certain number of F2 plant were randomly selected to form a F2:3 population,which were planted in two ecological locations to evaluate their phenotypic performance and the same above mentioned polymorphic markers were used to verify their genotypes of F2:3 population.Based on these genotypic and phenotypic results,Icipapping was used to identify the QTLs relating to fiber quality and yield traits.Totally 23 QTLs of fiber yield and quality traits were identified in the three environments.a.There are 5 QTLs relating to fiber yield traits,including 4 for lint percentage,with phenotypic contribution rates of 6.95%-28.86%;1 for boll weight,with phenotypic contribution rate of 14.65%.b.A total of 18 QTLs relating to fiber quality traits were identified,including 6 for fiber length,with phenotypic contribution rates of 2.05%-20.99%;2 for fiber uniformity,with phenotypic contribution rates of 3.07%-13.58%;5 for fiber micronaire value,with phenotypic contribution rates of 1.98%-22.23%;3 for fiber elongation,with phenotypic contribution rates of 2.10%-7.66%;2 for fiber strength,with phenotypic contribution rates of 3.24%-7.73%.c.qFL-12-5,qFL-14-1,qFL-7-1 and qLP-14-1 were detected consistently in two environments.qFL-12-2 was detected consistently in three environments.Based on the above mentioned QTL mapping results,qFL-12-2 was fine mapped.For fine mapping,a comprehensive analysis of the QTL region was conducted and SSR markers were developed within this region based on the genomic sequencing database of G.hirsutum and G.ramondii.Finally 13 polymorphic SSR markers were identified.Then using the F2 plants those harbored the target fragment to construct the secondary large segregation population,using the aforementioned polymorphic SSR markers to genotype the secondary population and to finish the fine mapping of the QTL qFL-12-2.On the other hand,using the original mapping population and the aforementioned SSR markers to fine map qFL-12-2.Both mapping results indicated that FL-12-2 was mapped in a short genetic distance of 1.6 cM,while in a physical distance of 0.65 Mb between SSR markers of NJ106 and NJ189.According to the databases of upland cotton sequencing and gene annotation,this region harbored a total of 13 genes.At the same time,in order to better understanding the differences of gene expression profiles between the introgression lines and their recurrent parent during fiber developmental stages,the developing fiber cells of 3 introgression lines MBI7747,MBI7561,MBI7285 with different fiber length and fiber strength,and CCRI45 were sampled at 7DPA,10DPA,15DPA,20DPA,25DPA and 28DPA.The fiber samples were performed transcriptome sequencing and anslysis.Comparisons of gene expression profiles were conducted and totally1775 differential expressed genes(DEGs)during fiber elongation stages(7DPA,10DPA,15DPA,20DPA),and 2200 DEGs during fiber secondary cell wall thickening stages(15DPA,20DPA,25DPA and 28DPA)were identified based on Gfold analysis.Both of these DEGs were conducted GO and DEGG analysis.The results indicated that in the fiber elongation stage,DEGs were mainly enriched in cell wall synthesis,nucleosome formation and other metabolic process,in the secondary wall thickening stage,DEGs were mainly enriched in the Lignin metabolism,water transport and calcium dependent adhesion molecule of protein and other biological processes.Combining the results of fine mapping and those of tanscriptome sequencing,of the 13 genes harbored in the region of qFL-12-2 seven ones were differentially expressed.After verification by qPCR and analysis of biological information,GbALMT12 and GbNAC071 were identified as candidate genes,This lays a solid foundation for further gene cloning and molecular elucidation of fiber development mechanism.