Abstract
Salt tolerance is an important trait that affects the growth and yield of plants growing in saline environments. The salt tolerance gene GmSALT3 was cloned from the Chinese soybean cultivar Tiefeng 8, and its variation evaluated in Chinese wild soybeans and landraces. However, the potential role of GmSALT3 in cultivation, and its genetic variation throughout the history of Chinese soybean breeding, remains unknown. Here we identified five haplotypes of GmSALT3 in 279 Chinese soybean landraces using a whole genome resequencing dataset. Additionally, we developed five PCR-based functional markers: three indels and two cleaved amplified polymorphic sequences (CAPS) markers. A total of 706 Chinese soybean cultivars (released 1956–2012), and 536 modern Chinese breeding lines, were genotyped with these markers. The Chinese landraces exhibited relatively high frequencies of the haplotypes H1, H4, and H5. H1 was the predominant haplotype in both the northern region (NR) and Huanghuai region (HHR), and H5 and H4 were the major haplotypes present within the southern region (SR). In the 706 cultivars, H1, H2, and H5 were the common haplotypes, while H3 and H4 were poorly represented. Historically, H1 gradually decreased in frequency in the NR but increased in the HHR; while the salt-sensitive haplotype, H2, increased in frequency in the NR during six decades of soybean breeding. In the 536 modern breeding lines, H2 has become the most common haplotype in the NR, while H1 has remained the highest frequency haplotype in the HHR, and H5 and H1 were highest in the SR. Frequency changes resulting in geographically favored haplotypes indicates that strong selection has occurred over six decades of soybean breeding. Our molecular markers could precisely identify salt tolerant (98.9%) and sensitive (100%) accessions and could accurately trace the salt tolerance gene in soybean pedigrees. Our study, therefore, not only identified effective molecular markers for use in soybean, but also demonstrated how these markers can distinguish GmSALT3 alleles in targeted breeding strategies for specific ecoregions.
Highlights
Salt stress is a major environmental factor affecting agricultural plant productivity, which in turn, can threaten food security (Zhu, 2016)
H2 was found in salt sensitive soybean cultivar 85-140, of which a 3.78-kb retro transposon insertion resulted in a truncated GmSALT3 protein
Gene cloning related to agronomic traits has facilitated the development allele-specific functional DNA markers, which in turn, have been used in soybean research to validate genotypephenotype relationships and facilitate breeding efforts (Shin and Lee, 2012; Tsubokura et al, 2013, 2014; Jia et al, 2014; Zhai et al, 2014; Liu et al, 2015)
Summary
Salt stress is a major environmental factor affecting agricultural plant productivity, which in turn, can threaten food security (Zhu, 2016). The major salt tolerance quantitative trait locus (QTL) was mapped repeatedly on chromosome 3 (Chr. 3) in different salt tolerant germplasms (Lee et al, 2004; Hamwieh and Xu, 2008; Hamwieh et al, 2011; Ha et al, 2013; Guan et al, 2014a). Zhang et al (2019) identified a cation diffusion facilitator, GmCDF1 (Glyma08g10200), related with salt tolerance at the germination stage, but no interaction between this candidate gene and Glyma03g32900.1 was observed. While these studies have bolstered genetic resources for breeding salt tolerant soybeans (Zeng et al, 2017; Do et al, 2018), much remains to be learned
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