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

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...

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Autores principales:	Rongxia Guan, Lili Yu, Xiexiang Liu, Mingqiang Li, Ruzhen Chang, Matthew Gilliham, Lijuan Qiu
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	soybean salt tolerance GmSALT3 haplotype markers Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/2d292b6eedd64306a601831c9ddaf5db
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spelling	oai:doaj.org-article:2d292b6eedd64306a601831c9ddaf5db2021-11-16T06:53:58ZSelection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China1664-462X10.3389/fpls.2021.794241https://doaj.org/article/2d292b6eedd64306a601831c9ddaf5db2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.794241/fullhttps://doaj.org/toc/1664-462XSalt 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.Rongxia GuanLili YuXiexiang LiuMingqiang LiRuzhen ChangMatthew GillihamLijuan QiuFrontiers Media S.A.articlesoybeansalt toleranceGmSALT3haplotypemarkersPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	soybean salt tolerance GmSALT3 haplotype markers Plant culture SB1-1110
spellingShingle	soybean salt tolerance GmSALT3 haplotype markers Plant culture SB1-1110 Rongxia Guan Lili Yu Xiexiang Liu Mingqiang Li Ruzhen Chang Matthew Gilliham Lijuan Qiu Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China
description	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.
format	article
author	Rongxia Guan Lili Yu Xiexiang Liu Mingqiang Li Ruzhen Chang Matthew Gilliham Lijuan Qiu
author_facet	Rongxia Guan Lili Yu Xiexiang Liu Mingqiang Li Ruzhen Chang Matthew Gilliham Lijuan Qiu
author_sort	Rongxia Guan
title	Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China
title_short	Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China
title_full	Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China
title_fullStr	Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China
title_full_unstemmed	Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China
title_sort	selection of the salt tolerance gene gmsalt3 during six decades of soybean breeding in china
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/2d292b6eedd64306a601831c9ddaf5db
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Selection of the Salt Tolerance Gene GmSALT3 During Six Decades of Soybean Breeding in China

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