Growth period QTL‐allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity group extension. (16th October 2021)

• Record Type: Journal Article
• Authors: Liu, Xueqin; Li, Chunyan; Cao, Jiqiu; Zhang, Xiaoyan; Wang, Can; He, Jianbo; Xing, Guangnan; Wang, Wubin; Zhao, Jinming; Gai, Junyi
• Is Part Of: Plant journal. Volume 108:Number 6(2021)
• Page Start: 1624
• Page End: 1643
• Publication Date: 2021-10-16
• Subjects: soybean (Glycine max (L.) Merr.) -- days to flowering (DTF) or to maturity (DTM) -- restricted two‐stage multi‐locus genome‐wide association study (RTM‐GWAS) -- QTL‐allele matrix -- geographic differentiation -- maturity group (MG) extension -- evolutionary motivation; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.15531
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: Soybean ( Glycine max (L.) Merr.) has been disseminated globally as a photoperiod/temperature‐sensitive crop with extremely diverse days to flowering (DTF) and days to maturity (DTM) values. A population with 371 global varieties covering 13 geographic regions and 13 maturity groups (MGs) was analyzed for its DTF and DTM QTL‐allele constitution using restricted two‐stage multi‐locus genome‐wide association study (RTM‐GWAS). Genotypes with 20 701 genome‐wide SNPLDBs (single‐nucleotide polymorphism linkage disequilibrium blocks) containing 55 404 haplotypes were observed, and 52 DTF QTLs and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (two to 13 per locus) were detected, explaining 84.8% and 74.4% of the phenotypic variance, respectively. The QTL‐allele matrix characterized with all QTL‐allele information of each variety in the global population was established and subsequently separated into geographic and MG set submatrices. Direct comparisons among them revealed that the genetic adaptation from the origin to geographic subpopulations was characterized by new allele/new locus emergence (mutation) but little allele exclusion (selection), while that from the primary MG set to emerged early and late MG sets was characterized by allele exclusion without allele emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on 28 respective loci, 10–12 loci each with three to six alleles being most active. Further recombination potential for faster maturation (12–21 days) or slower maturation (14–56 days) supported allele convergence (recombination) as a constant genetic factor in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into nine biological processes, indicating multi‐functional DTF/DTM genes are involved in a complex gene network. In summary, we identified QTL‐alleles relatively thoroughly using RTM‐GWAS for direct matrix comparisons and subsequent analysis. Significance Statement: In global cultivated soybeans, covering 13 geographic regions and 13 maturity groups (MGs), 52 days to flowering (DTF) and 59 days to maturity (DTM) QTLs (including 29 and 21 new ones) with 241 and 246 alleles (multiple alleles per locus) were detected, respectively, using restricted two‐stage multi‐locus genome‐wide association study. Through direct comparisons of DTF/DTM QTL‐allele matrices among geographic subpopulations and MG sets for relative importance of evolutionary factors, the former were characterized by new allele emergence while the latter were characterized by old allele exclusion, in addition to inheritance and recombination.