Identification And Cloning Of Ouantitative Trait Locus Of Long-Juvenile In Soybean

Soybean[Glycine Max(L.)Merr.]is an important legume crop originating in temperate regions.Soybean is a facultative short-day(SD)plant,and cultivars that originate from temperate regions generally undergo a very short juvenile phase and early flowering when grown in low latitude regions,thereby resulting in extremely low grain yield.However,introduction of the long-juvenile(LJ)trait,which extends the vegetative phase and improves yield under SD environments,has largely overcome this constraint and has enabled the expansion of soybean production to tropical regions.In this research,we identified QTLs(Quantitive Trait Locus)related to LJ trait with Genome-wide association study(GWAS),QTL mapping and Map-based cloning.The main results are as follows:1.We identified LJ trait locus in soybean using GWAS based on whole-genome sequencing data of 338 soybean germplasm accessions and phenotype in two environments under SD condition.A total of 11 significantly SNPs related to LJ trait were detected in our study.Combining the data from two environments,2 consistent novel intervals were identified in chromosome 6 and chromosome 19.2.We provide a new strategy to rapidly identify consistent novel QTLs by using multiple genetic populations and Genotyping-by-Sequencing(GBS)approach.In this study,we developed six F2 populations and grew them under SD conditions.A total of seven QTLs related to the LJ trait were identified by integrating flowering time(R1)and high-density genetic maps.There were three consistent QTLs repeatedly detected in different populations and one of them has been previously reported,yet two are novel.We predicted candidate genes in two intervals by resequencing data and Gene Ontology(GO).3.Fine-mapping E6 locus to a genomic region of 239-kb on chromosome 4 using populations derived from the cross between Paranagoiana and Harosory,and found a candidate gene named ELF3.Sequencing,expression and complementation test revealed that E6 is the candidate gene ELF3.The e6 allele had a Tyl/copia-like retrotransposon inserted in the fourth exon that resulted in a premature stop codon in Paranagoiana.E6 is a loss-of-function allele of J.In Conclusion,we identified several loci related to LJ trait with Genome-wide association study(GWAS),QTL mapping.In addition,we cloned the E6 gene,and found that E6 is a loss-of-function allele of J.This research not only provides fundamental resources for fine-mapping candidate genes associated to the LJ trait,but also helps to drive improvements in soybean breeding for tropical regions.