Identification of the genetic locus associated with the crinkled leaf phenotype in a soybean (Glycine max L.) mutant by BSA-Seq technology

Abstract

The leaf is the main photosynthetic organ of plants, and it plays a significant role in the yield of crop species. Identifying the causal mutations and candidate genes that underlie leaf phenotypic variation is an important breeding target in soybean grain yield improvement. An ethyl methyl sulfonate (EMS)-induced soybean mutant DWARFCRINKLEDLEAF1 (DCL1) with an aberrant crinkled leaf phenotype was identified in the background of the soybean cultivar Zhongpin 661 (Zp661). We constructed an F2 segregating population from a cross between Zp661 and DCL1 in order to investigate the genomic locus associated with the crinkled leaf trait. Using bulk segregant analysis (BSA) combined with the whole-genome resequencing method, the Euclidean distance (ED) correlation algorithm detected 12 candidate genomic regions with a total length of 20.32 Mb that were linked to the target trait. Following a comparative analysis of the sequence data for the wild-type and mutant pools, only one single nucleotide mutation (C:G>T:A) located on the first exon of Glyma.19G207100 was found to be associated with the trait. Candidate gene validation based on a CAPS marker derived from the detected single-nucleotide polymorphism (SNP) indicated a nucleotide polymorphism between the two parents. Therefore, our findings reveal that Glyma.19G207100, which is renamed as GLYCINE MAX DWARF CRINKLED LEAF 1 (GmDCL1), is a promising candidate gene involved in the morphogenesis of the crinkled leaf trait of the soybean mutant DCL1. This study provides a basis for the functional validation of this gene, with prospects for soybean breeding targeting grain yield enhancement.