Analysis Of Genetic Copposition Of Upland Cotton Cultivars In Xinjiang

The Xinjiang Uygur autonomous region is the largest cotton-growing area in China,where is the largest high-quality cotton producing area in China.However,the genetic relationship between foundation parents and modern cultivars,the artificial selection of genomic fragments carrying excellent agronomic traits,and the genetic variation that occurs during cultivar improvement are largely uncharacterized.We could study the artificial selection of the modern Upland cotton cultivars during their breeding process in Xinjiang and analyze the important candidate genes involved by using whole genome re-sequencing technology.On the other hand,IBD segments between modern cultivars and foundation parents were analyzed at the genome level and candidate genes related to yield and fiber quality were detected.Thus,it has important guiding significance for the breeding of cotton cultivars and the improvement of yield and fiber quality.In this study,we selected four landraces introduced from the former Soviet Union(C1470,611Б,KK1543,108Φ)and three major cultivars that have important effects on the improvement of cotton cultivars in China(DPL15,STV2B,UGDM)as seven foundation parents,then selected 69 typical Xinjiang modern cultivars,constructing a natural population.Firstly,we investigated nine agronomic traits improvement between foundation parents and modern cultivars,then re-sequenced all accessions to identify SNP variation.Based on the mountains of SNPs,we studied phylogenetic tree and the genetic diversity of the population,then identified the artificial selection regions in the process of improvement from foundation parents to modern cultivars.Finally,we analyzed the IBD segments between modern cultivars and their foundation parents in Xinjiang to study the inheritance regions and explore important candidate genes.The main results were summarized as follows:The cultivars of Upland cotton in Xinjiang have been continuously improved,and the lint yield and fiber quality have been significantly improved,especially,the lint percentage have been improved the most among nine traits from around 37%to more than 40%,indicating that the lint percentage is the priory goal in the cotton breeding process.We obtained more than 1.8Tb clean data and identified 2,395,681 SNPs via whole genome re-sequencing technology.Of them,45,511 were located within protein-coding genes,28,654 nonsynonymous,174 stop-loss and 605 stop-gain SNPs.Combined with the neighbor-joining tree,population structure and principal component analysis,these accessions could be divided into two groups.Group 1 contained 40 modern cultivars together with DPL15,STV2B,UGDM and 611Б,while Group 2 contained 29 modern cultivars together with the former Soviet Union cultivars:108Φ,C1470 and KK1543,suggesting that Xinjiang modern Upland cotton were not only related to the varieties of the former Soviet Union closely,but also have close relationship with the American and Uganda cultivars.The Fst values between the foundation parents and modern improved cultivars were 0.0271.The nucleotide diversity levels of the foundation parents(πparents=8.91 E-05)were a little higher than that of the modern varieties(πcultivars=8.04E-05).We detected 156 improvement-selective sweeps covering 23.86 Mb of the whole genome,and 318 candidate genes were identified in these sweeps,which maybe play important roles not only in fiber quality improvement and increase in lint yield,but also in stress-related responses.We then focused on 31 nonsynonymous genes and identified two candidate genes,GhAATF1 and Ghm TERF1,located in the selection sweep ranging from 3.8 to 4.0 Mb on chr.A13,involved in lint percentage and lint yield increases in Xinjiang.A total of 10,385 IBD segments were identified between foundation parents and modern cultivars,while 5,705 IBD segments were inherited from the former Soviet Union,3,639 were from America or Uganda in Africa,1.041 IBD regions came from two or more foundation parents.By calculating the average genetic constitutions of the modern cultivars in Xinjiang,the mean coverage percentages derived from C1470.1080.KK1543,DPL15,UGDM,STV2B,and 611Б were approximately 6.851%,6.847%,6.719%6.080%,5.969%,5.583%and 4.887%,respectively.Consequently,the foundation parents introduced from the former Soviet Union(total coverage percentage:25.31%)played more important roles than those introduced directly from America and Africa(total coverage percentage:17.63%)in modern Xinjiang cultivars,which is consistent with the breeding history in Xinjiang,where breeders introduced the former Soviet Union cotton varieties to improve cotton adaptation and yield in the 1960s.A total of 192 unique IBD regions involved in the artificial selection sweeps,including 93 genes contained nonsynonymous,stop gain or stop loss SNPs.Number of genes were involved in fiber development or tolerance response.Moreover,gene GhARF3 was found to be located in the Xinluzao 13 IBD segment from 2,403,609 to 2,951,829 on chr.A10 inherited from 108Φ,and in the Xinluzao 35 IBD region from 1,198,185 to 2,888,834 on chr.A10 inherited from 611Б,whose haplotypes were significantly associated with fiber length and fiber strength.These results could shed light on the genetic mechanism of artificial selection during cotton breeding and lay foundation for facilitating next-generation precision breeding of cotton and other crops.