Genome-Wide Analysis of DREB Genes Identifies a Novel Salt Tolerance Gene in Wild Soybean (Glycine soja).

Zhihong Hou,Yongli Li,Baohui Liu,Qun Cheng,Fanjiang Kong,Lidong Dong,Yuhan Cheng,Dianfeng Zheng,Naijie Feng,Hao Du,Tai Li,Weiwei Li

doi:10.3389/fpls.2022.821647

Abstract

Salt stress is a major factor limiting the growth and yield of soybean (Glycine max). Wild soybeans (Glycine soja) contain high allelic diversity and beneficial alleles that can be re-introduced into domesticated soybeans to improve adaption to the environment. However, very few beneficial alleles have been identified from wild soybean. Here, we demonstrate that wild soybean is more salt tolerant than cultivated soybean and examine dehydration responsive element-binding (DREB) family transcription factor genes to look for advantageous alleles that might improve drought tolerance in cultivated soybean. Our genome-wide analysis identified 103 DREB genes from the Glycine max genome. By combined RNA-sequencing and population genetics of wild, landrace, and cultivated soybean accessions, we show that the natural variation in DREB3a and DREB3b is related to differences in salt tolerance in soybean accessions. Interestingly, DREB3b, but not DREB3a, appears to have undergone artificial selection. Soybean plants carrying the wild soybean DREB3b allele (DREB3b39Del) are more salt tolerant than those containing the reference genome allele (DREB3bRef). Together, our results suggest that the loss of the DREB3b39Del allele through domestication of cultivated soybean may be associated with a reduction in salt tolerance. Our findings provide crucial information for improving salt tolerance in soybean through molecular breeding.

Highlights

Our results show that DREB3b contributes to salt tolerance and may have undergone natural and artificial selection
Phenotype was evaluated in a growth chamber at 25◦C, revealing significantly reduced salt tolerance in landrace and cultivated soybean compared to wild accessions in two biological replicates (Figures 1D,E)
These results suggest that artificial selection may have had a strong effect on the genetic diversity in the cultivated soybeans

Summary

Introduction

High salt levels in soil cause stress that affects plant growth and salinization of farmland restricts global agricultural production (Flowers, 2004; Munns and Tester, 2008; Ondrasek et al, 2011). Soybean [Glycine max (L.) Merr.] is an economically important crop for oil and protein (Graham and Vance, 2003). It is classified as a moderately salt-sensitive crop; under salt stress, soybean yields may be reduced by up to 40% (Papiernik et al, 2005; Munns and Tester, 2008). Soybean cultivars show variation in their salt sensitivity: under saline conditions, salt-sensitive cultivars have a 37% decrease in yield compared with salt-tolerant cultivars (Parker et al, 1983). This natural variation in salt tolerance provides opportunities to increase soybean production under saline conditions (Guan et al, 2014; Qi et al, 2014). This lack of knowledge has greatly inhibited attempts to improve salt tolerance in crops

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Results

Conclusion