Identification and confirmation of novel genetic loci and domestication gene GmGA20ox1 regulating primary root length in soybean seedling stage

Soybean is one of the major oil and economic crops for human beings, and the adequate root length ensures proper growth, development, stress tolerance, and yield in soybean. However, only a limited number of quantitative trait loci (QTLs) and genes governing primary root length (PRL) are currently identified in soybean. In this study, extensive variation of the PRL was observed in 324 soybean accessions in the seedling stage, and the soybean lines belonging landrace or cultivar subpopulation showed higher PRL than that belonging wild subpopulation. Eight single nucleotide polymorphisms (SNPs) of three novel QTLs that significantly associated with PRL were detected by genome-wide association study (GWAS), and they are distributed on chromosome (Chr.) 2, 19, and 20, respectively. The candidate genes were searched in three QTLs candidate regions, and all 22 putative candidate genes detected are in QTL qPRL_1. Four tandem duplications of gibberellin 20 oxidase 1-like (GA20ox1) were detected in the linkage disequilibrium (LD) block in the qPRL_1 region, and only GmGA20ox1 (Glyma.02G136000) showed higher expression in root tissue. A notable disparity in the PRL trait was observed when the association panel was genotyped using the SNP of Chr02_14101363 (C/G), and only the landrace and cultivar subpopulation accessions possessed the CC allele. The variant Chr02_14101363 (C/G) was located within the coding sequence region of the GmGA20ox1 gene and resulted in a nonsynonymous mutation. Eleven haplotypes were generated by eight SNPs in GmGA20ox1 and its promoter region, and soybean accessions carrying the superior haplotype (Hap3) of GmGA20ox1 showed highest average PRL trait and higher expression of GmGA20ox1. The genetic diversity analysis of GmGA20ox1 indicated that it was most likely selected during soybean domestication and improvement process, leading to the highest proportion of Hap3 of GmGA20ox1 both in landrace and cultivar subpopulations. The qPRL_1 and GmGA20ox1 identified in this study provide valuable genetic resources for soybean root traits, and GmGA20ox1 could be applied for soybean molecular breeding to develop desirable root system architecture (RSA) in the future.