Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton

Authors: WANG, MAOJUN - Huazhong Agricultural University; QI, ZHENGYANG - Huazhong Agricultural University; Thyssen, Gregory; Naoumkina, Marina; Jenkins, Johnie; McCarty, Jack; XIAO, YINGJIE - Huazhong Agricultural University; LI, JIANYING - Huazhong Agricultural University; ZHANG, XIANLONG - Huazhong Agricultural University; Fang, David

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2021
Publication Date: 1/17/2022
Citation: Wang, M., Qi, Z., Thyssen, G.N., Naoumkina, M.A., Jenkins, J.N., McCarty, J.C., Xiao, Y., Li, J., Zhang, X., Fang, D.D. 2022. Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton. Communications Biology. 5:60. https://doi.org/10.1038/s42003-022-03022-7.
DOI: https://doi.org/10.1038/s42003-022-03022-7

Interpretive Summary: Cotton is the most important crop for production of natural and renewable fiber for textile industry. To accelerate the discovery of genes associated with fiber quality, we sequenced the genomes of a unique population called MAGIC and its 11 parents. This population consists of 550 individual progeny lines. We established a mosaic genome map through tracing the origin of DNA fragments that share identity-by-descent (IBD). We performed two complementary genome wide association study (GWAS) methods – single DNA marker-based GWAS (sGWAS) and IBD-based haplotype GWAS (hGWAS). We identified a total of 25 single marker based quantitative trait loci (sQTLs) and 14 hQTLs related to cotton fiber quality, of which 26 were novel QTLs. These QTLs jointly accounted for an average of 32.8% of the phenotypic variance (13~41% per trait). Two major QTLs detected by both GWAS methods were responsible for fiber strength and length. A encoding the MATE efflux family protein was identified as a novel candidate gene for fiber length. Beyond the additive QTLs, we detected prevalent interactions between QTLs (epistasis) that contributed to the genetics of fiber quality, pinpointing another regulatory layer for trait variance. These results provide targets for future molecular selections and genetic manipulations in cotton fiber improvement.

Technical Abstract: To accelerate the discovery of genomic variations and genes associated with fiber quality, we sequenced a multiple-parent advanced-generation inter-cross (MAGIC) population, consisting of 550 individuals created by inter-crossing 11 founders, and established a mosaic genome map through tracing the origin of haplotypes that share identity-by-descent (IBD). We performed two complementary GWAS methods – SNP-based GWAS (sGWAS) and IBD-based haplotype GWAS (hGWAS). A total of 25 sQTLs and 14 hQTLs related to cotton fiber quality were identified, of which 26 were novel QTLs. These QTLs jointly accounted for an average of 32.8% of the phenotypic variance (13~41% per trait). Two major QTLs detected by both GWAS methods were responsible for fiber strength and length. The gene Ghir_D11G020400 (GhZF14) encoding the MATE efflux family protein was identified as a novel candidate gene for fiber length. Beyond the additive QTLs, we detected prevalent epistatic interactions that contributed to the genetics of fiber quality, pinpointing another regulatory layer for trait variance. These results provide targets for future molecular selections and genetic manipulations in cotton fiber improvement.