Dissecting the Genetic Basis of Local Adaptation in Soybean

Nonoy B Bandillo,George L Graef,Michael B Kantar,Robert M Stupar,Aaron J Lorenz,Justin E Anderson,James E Specht

doi:10.1038/s41598-017-17342-w

Abstract

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars. Our combined application of methods in environmental association mapping and detection of selection targets provide a better understanding of how geography and selection may have shaped genetic variation among soybean landraces. Moreover, we identified several important candidate genes related to drought and heat stress, and revealed important genomic regions possibly involved in the geographic divergence of soybean.

Highlights

Soybean (Glycine max) is the leading legume crop produced in the world[1], accounting for nearly half of the total world production of vegetable oils[2] and a large majority of the oilseed meal included in livestock feed[3]
We explore the genetic variation in a georeferenced collection of locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation in soybean
Our results provide a better understanding of how geography, environment, and selection may have shaped the distribution of genetic variation among soybean landraces, and begins to identify loci possibly associated with adaptation to diverse environmental conditions

Summary

Introduction

Soybean (Glycine max) is the leading legume crop produced in the world[1], accounting for nearly half of the total world production of vegetable oils[2] and a large majority of the oilseed meal included in livestock feed[3]. By the 20th century, it has been estimated that as many as 20,000–45,000 distinct landraces were grown by farmers in China alone[5] Several factors, such as the self-pollinating nature of soybean and its adaptation to specific latitudinal clines due to photoperiodism led to diverged pockets of landraces that are both morphologically and genetically diverse, even from within small areas in China[5,7]. Recent landscape genomics and EAA studies on some of the world’s most important crops such as sorghum[19], maize[20], and barley[21] provide insights into the genetic architecture and genes underlying local adaptation No such studies have been performed in soybean, but a recent study has been performed on soybean’s wild ancestor, Glycine soja. Our results provide a better understanding of how geography, environment, and selection may have shaped the distribution of genetic variation among soybean landraces, and begins to identify loci possibly associated with adaptation to diverse environmental conditions

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Conclusion