Genomic Insights Into The Genetic Basis Of Upland Cotton Improvement In China Based On The MAGIC Population

Upland cotton(Gossypium hirsutum L.)is the most widely grown cotton species in the world,and the genetic analysis of its complex traits such as fiber yield and quality has been a hot spot for research.With the development of sequencing technology and cost reduction,many resequencing projects based on cotton natural populations have been reported.However,the inherent structure of natural populations makes it difficult to correctly detect variants for target traits and particularly uncover rare variants.These problems could be solved by constructing multi-parental populations.Combining the superiority of whole-genome sequencing technology,the multi-parental population could be an efficient tool to identify loci and candidate genes associated with complex traits,which is important for resolving the genetic structure of complex traits and accelerating the breeding process.In this study,16 founders that played important roles in Chinese cotton breeding were selected and a MAGIC population consisting of 920 recombinant inbred lines(RILs)was constructed.The population structure and genetic characteristics were compared between the MAGIC population and natural populations.Phenotypic identification and genome-wide association analysis were performed for 12 yield and quality-related traits of the MAGIC population,and the origin and distribution of elite alleles were traced by combining China’s cotton breeding history.The main results are as follows:1.Sixteen Chinese backbone cultivars were selected as founders and developed a MAGIC population consisting of 920 RILs.Sixteen founders and 920 RILs of the MAGIC population were sequenced,and 5.6 TB of resequencing data were obtained.A total of 4,774,181 high-quality genome-wide variants were identified by sequence mapping and variant identification.2.By comparing the MAGIC population and two natural populations,it is found that the genetic diversity of the MAGIC population is smaller than that of two natural populations,but it has a simpler population structure,a smaller LD,and could retain a higher proportion of high-quality variants in the variants filtering process.This suggests that the MAGIC population has an advantage over the natural population in identifying QTLs associated with quantitative traits.3.MAGIC RILs and 16 founders were planted,and 12 traits related to lint yield and fiber quality were evaluated in two years at 3 locations.The heritability of each trait and the correlations among the traits were calculated.Four fiber quality traits(fiber length,strength,elongation ratio and uniformity)were significantly and positively correlated(0.47～0.84),while the first three were negatively correlated(-0.45～0.09)with the micronaire value.Lint percentage was positively correlated with the micronaire value and lint index,but was negatively correlated with the seed index,fiber length and fiber strength.Boll weight was positively correlated with seed index,lint index,fiber length,strength and elongation ratio,and negatively correlated with boll number.The heritability ranged from 13.20%(number of fruiting branches)to 89.10%(lint index),with most traits having heritability greater than 70%,indicating that the MAGIC population was stable for the traits.4.Genome-wide association study(GWAS)was conducted based on multi-environment phenotypes and genome-wide variants,and a total of 54 significantly associated loci were identified,25 of which were pleiotropic loci.The pleiotropy of these loci was consistent with the correlation between phenotypes,which provides a genome-level explanation for the correlation between complex traits in cotton.5.The origin and distribution of elite alleles were traced by combining China’s cotton breeding history and public sequencing data.More than 90%of the elite alleles identified in this study could be traced in the early introduced upland cotton varieties from aboard,indicating that the foreign-introduced varieties constitute the genetic basis of Chinese cotton breeding,but also lead to a narrow genetic basis.According to the distribution pattern of elite alleles in Chinese cultivars,it was found that varieties from the Yangtze and Yellow River regions made better use of elite alleles from America and Uganda,while upland cotton from the northwest inland cotton regions made more use of elite alleles of Soviet and Chinese native origin,but less use of that from America and Uganda.This difference in the genetic composition may be related to the introduction history of different cotton regions in China,but it is also a potential growth point for the upland cotton cultivars in Xinjiang.6.Based on the results of association analysis,the candidate genes for flowering time and fiber quality were screened by combining variant annotation and protein function annotation within the candidate intervals,RNA-seq and other methods.GH_D03G1136 on chromosome D03 was identified as a candidate gene affecting flowering time,and a 2-bp deletion in the exon was identified as a causal variant leading to earlier flowering time;GH_A10G2501 on chromosome A10 was identified as a candidate gene affecting fiber quality,and 1-bp deletion in the exon region was identified as a causal variant improving fiber quality.In summary,a 16-parental upland cotton MAGIC population was constructed and conducted GWAS for 12 complex traits.Fifty-four identified loci provided a genomic explanation for the complex correlation of fiber yield and quality.Combined with large-scale resequencing data analysis,it reveals a narrow genetic basis of Chinese cotton cultivars.In addition,differences in the composition of elite alleles between varieties from the northwest inland region and the Yangtze and Yellow River regions were also found.Finally,one candidate gene related to flowering time and one related to fiber quality were identified.This study provided an important theoretical basis and valuable resources for the genetic improvement of upland cotton in China.