Identification of GmSALT3 haplotypes and development of molecular markers based on their diversity associated with salt tolerance in soybean

Lee, Seokhyung; Kim, Jeong-Hwa; Sundaramoorthy, Jagadeesh; Park, Gyu Tae; Lee, Jeong‐Dong; Kim, Jeong Hoe; Chung, Gyuhwa; Seo, Hak Soo; Song, Jong Tae

doi:10.1007/s11032-018-0845-7

Cited by 14 publications

(21 citation statements)

References 31 publications

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“…Haplotypes Hst-7, Hss-11, Hss-12, and Hd-1 were shown in only one Chinese soybean accession in their report, indicating these are minor alleles in Chinese soybeans. The H3 and H4 haplotypes identified in the present study were not found in any of the three structural variations listed in Patil's report (Patil et al, 2016), or in the 40 haplotypes of Lee's study (Lee et al, 2018). This lack of concordance is not surprising considering the greater number of Chinese soybean accessions used in the present experiment.…”

Section: Genomic Diversity Of Gmsalt3 In Chinese Soybean Landracescontrasting

confidence: 71%

“…The 4 bp insertion in the promoter of GmSALT3 was observed in our 279 resequencing dataset, while the ∼150 bp insertion was not (Figure 1). Reduced gene expression of the salt sensitive haplotypes has been reported by several researchers (Guan et al, 2014b;Do et al, 2016;Lee et al, 2018). This common variation in the promoter region of salt sensitive haplotypes raises the possibility that these insertions might affect the expression of GmSALT3.…”

Section: Functional Markers Of Gmsalt3 and Their Potential Use In Soybean Breedingmentioning

confidence: 75%

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Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China

Guan

Liu

et al. 2021

Front. Plant Sci.

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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.

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Section: Genomic Diversity Of Gmsalt3 In Chinese Soybean Landracescontrasting

confidence: 71%

Section: Functional Markers Of Gmsalt3 and Their Potential Use In Soybean Breedingmentioning

confidence: 75%

Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China

Guan

Liu

et al. 2021

Front. Plant Sci.

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“…In the 40 GmSALT3 haplotypes observed by Lee et al ( 2018), Ha, HTn, Hd-2, and Hd-3, which correspond to H1, H2, H5-1, and H5-2 in present study, were the four majority haplotypes in cultivated soybean (Lee et al, 2018). Haplotypes Hst-7, Hss-11, Hss-12, and Hd-1 were shown in only one Chinese soybean accession in their report, indicating these are minor alleles in Chinese soybeans.…”

Section: Genomic Diversity Of Gmsalt3 In Chinese Soybean Landracessupporting

confidence: 63%

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“…For instance, microsatellite marker-based genetic diversity has been investigated in the wild soybean at CWLGC that originated from the southern islands of Korea. Five hundred and thirty wild soybean accessions originating from China, Japan, and Korea included in the CWLGC have also been utilized for the successful identification of GmSALT3 haplotypes and the development of molecular markers related to salt tolerance [103].…”

Section: In Situ Conservation Of G Soja At Cwlgcmentioning

confidence: 99%

Korean Wild Soybeans (Glycine soja Sieb & Zucc.): Geographic Distribution and Germplasm Conservation

et al. 2020

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Domesticated crops suffer from major genetic bottlenecks while wild relatives retain higher genomic diversity. Wild soybean (Glycine soja Sieb. & Zucc.) is the presumed ancestor of cultivated soybean (Glycine max [L.] Merr.), and is an important genetic resource for soybean improvement. Among the East Asian habitats of wild soybean (China, Japan, Korea, and Northeastern Russia), the Korean peninsula is of great importance based on archaeological records, domestication history, and higher diversity of wild soybeans in the region. The collection and conservation of these wild soybean germplasms should be put on high priority. Chung’s Wild Legume Germplasm Collection maintains more than 10,000 legume accessions with an intensive and prioritized wild soybean germplasm collection (>6000 accessions) guided by the international code of conduct for plant germplasm collection and transfer. The center holds a library of unique wild soybean germplasms collected from East Asian wild habitats including the Korean mainland and nearby islands. The collection has revealed interesting and useful morphological, biochemical, and genetic diversity. This resource could be utilized efficiently in ongoing soybean improvement programs across the globe.

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Identification of GmSALT3 haplotypes and development of molecular markers based on their diversity associated with salt tolerance in soybean

Cited by 14 publications

References 31 publications

Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China

Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China

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Korean Wild Soybeans (Glycine soja Sieb & Zucc.): Geographic Distribution and Germplasm Conservation

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