Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Lidong Dong ,Chunbao Zhang ,Haiyang Li ,Lingshuang Wang ,Xiaohui Yuan ,Tong Su ,Fanjiang Kong ,Zhuoran Gan ,Yongli Li ,Sijia Lü ,James L Weller ,Zhihong Hou ,Yuhang Zhang ,Qun Cheng ,Chao Fang ,Kun Kou ,Kai Wang ,Yan Lin ,Lingping Kong ,Liyu Chen ,Baohui Liu

doi:10.1038/s41467-021-25800-3

Abstract

Soybean (Glycine max) serves as a major source of protein and edible oils worldwide. The genetic and genomic bases of the adaptation of soybean to tropical regions remain largely unclear. Here, we identify the novel locus Time of Flowering 16 (Tof16), which confers delay flowering and improve yield at low latitudes and determines that it harbors the soybean homolog of LATE ELONGATED HYPOCOTYL (LHY). Tof16 and the previously identified J locus genetically additively but independently control yield under short-day conditions. More than 80% accessions in low latitude harbor the mutations of tof16 and j, which suggests that loss of functions of Tof16 and J are the major genetic basis of soybean adaptation into tropics. We suggest that maturity and yield traits can be quantitatively improved by modulating the genetic complexity of various alleles of the LHY homologs, J and E1. Our findings uncover the adaptation trajectory of soybean from its temperate origin to the tropics.

Highlights

Soybean (Glycine max) serves as a major source of protein and edible oils worldwide
This genome-wide association studies (GWAS) peak is consistent with the SD flowering quantitative trait loci (QTL) on chromosome 16 that we previously identified using two F2 segregation populations, PI591429 × PI628930 and PI240664 × BR12116
Since we demonstrated that Time of Flowering 16 (Tof16)/LHY1a controls flowering time, maturity, and grain yield in soybean, we asked whether the other LATE ELONGATED HYPOCOTYL (LHY) family members control these soybean traits and whether these homologs could potentially be used for agricultural applications

Summary

Introduction

Soybean (Glycine max) serves as a major source of protein and edible oils worldwide. The genetic and genomic bases of the adaptation of soybean to tropical regions remain largely unclear. We identify the novel locus Time of Flowering 16 (Tof16), which confers delay flowering and improve yield at low latitudes and determines that it harbors the soybean homolog of LATE ELONGATED HYPOCOTYL (LHY). We identify a novel locus that controls flowering time and yield in soybean under SD conditions This locus, Tof[16], harbors a LATE ELONGATED HYPOCOTYL (LHY) gene, as reveals by whole-genome resequencing and genome-wide association studies (GWAS) and by positional cloning of quantitative trait loci (QTL). Our findings uncover the genetic and genomic basis for the adaptation of soybean to low-latitude regions and provide a new approach for precise breeding for improve soybean productivity in the tropics

Methods

Results

Conclusion