Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number

Developing crops with better root systems is a promising strategy to ensure productivity in both optimum and stress environments. Root system architectural traits in 397 soybean accessions were characterized and a high‐density single nucleotide polymorphisms (SNPs)‐based genome‐wide association study was performed to identify the underlying genes associated with root structure. SNPs associated with root architectural traits specific to landraces and elite germplasm pools were detected. Four loci were detected in landraces for lateral root number (LRN) and distribution of root thickness in diameter Class I with a major locus on chromosome 16. This major loci was detected in the coding region of unknown protein, and subsequent analyses demonstrated that root traits are affected with mutated haplotypes of the gene. In elite germplasm pool, 3 significant SNPs in alanine‐glyoxalate aminotransferase, Leucine‐Rich Repeat receptor/No apical meristem, and unknown functional genes were found to govern multiple traits including root surface area and volume. However, no major loci were detected for LRN in elite germplasm. Nucleotide diversity analysis found evidence of selective sweeps around the landraces LRN gene. Soybean accessions with minor and mutated allelic variants of LRN gene were found to perform better in both water‐limited and optimal field conditions. Comprehensive analysis of 397 soybean accessions revealed extreme phenotypic variation for root system between land‐races and elite cultivars. Genome wide association analysis identified candidate genes associated with different root architectural traits. High throughput genotypic data through integration of SoySNP50K and Whole Genome Sequence complements the SNP discovery for trait of interest. A rare synonymous minor allele in LRN gene was found to increase lateral root number through altering cortex cell size and hormone concentration. Soybean accessions with the different haplotype of LRN gene had higher yield under water‐stressed and optimum environments.