title: Salinity tolerance in soybean is modulated by natural variation in GmSALT3.
abstract: The identification of genes that improve the salt tolerance of crops is essential for the effective utilization of saline soils for agriculture. Here, we use fine mapping in a soybean (Glycine max (L.) Merr.) population derived from the commercial cultivars Tiefeng 8 and 85-140 to identify GmSALT3 (salt tolerance-associated gene on chromosome 3), a dominant gene associated with limiting the accumulation of sodium ions (Na+) in shoots and a substantial enhancement in salt tolerance in soybean. GmSALT3 encodes a protein from the cation/H+ exchanger family that we localized to the endoplasmic reticulum and which is preferentially expressed in the salt-tolerant parent Tiefeng 8 within root cells associated with phloem and xylem. We identified in the salt-sensitive parent, 85-140, a 3.78-kb copia retrotransposon insertion in exon 3 of Gmsalt3 that truncates the transcript. By sequencing 31 soybean landraces and 22 wild soybean (Glycine soja) a total of nine haplotypes including two salt-tolerant haplotypes and seven salt-sensitive haplotypes were identified. By analysing the distribution of haplotypes among 172 Chinese soybean landraces and 57 wild soybean we found that haplotype 1 (H1, found in Tiefeng 8) was strongly associated with salt tolerance and is likely to be the ancestral allele. Alleles H2-H6, H8 and H9, which do not confer salinity tolerance, were acquired more recently. H1, unlike other alleles, has a wide geographical range including saline areas, which indicates it is maintained when required but its potent stress tolerance can be lost during natural selection and domestication. GmSALT3 is a gene associated with salt tolerance with great potential for soybean improvement.
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, 100081, Beijing, China.
authors.forename: Rongxia
authors.initials: R
authors.lastname: Guan
authors.forename: Yue
authors.initials: Y
authors.lastname: Qu
authors.forename: Yong
authors.initials: Y
authors.lastname: Guo
authors.forename: Lili
authors.initials: L
authors.lastname: Yu
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.forename: Jinghan
authors.initials: J
authors.lastname: Jiang
authors.forename: Jiangang
authors.initials: J
authors.lastname: Chen
authors.forename: Yulong
authors.initials: Y
authors.lastname: Ren
authors.forename: Guangyu
authors.initials: G
authors.lastname: Liu
authors.forename: Lei
authors.initials: L
authors.lastname: Tian
authors.forename: Longguo
authors.initials: L
authors.lastname: Jin
authors.forename: Zhangxiong
authors.initials: Z
authors.lastname: Liu
authors.forename: Huilong
authors.initials: H
authors.lastname: Hong
authors.forename: Ruzhen
authors.initials: R
authors.lastname: Chang
authors.forename: Matthew
authors.initials: M
authors.lastname: Gilliham
authors.forename: Lijuan
authors.initials: L
authors.lastname: Qiu
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D018556:Crops, Agricultural; D007887:Fabaceae / Q000166:cytology / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D017930:Genes, Reporter; D014644:Genetic Variation; D005843:Geography; D006239:Haplotypes; D010802:Phylogeny; D030821:Plants, Genetically Modified; D054712:Salinity; D055049:Salt Tolerance; D017422:Sequence Analysis, DNA; D012965:Sodium Chloride / Q000494:pharmacology; D030262:Soybean Proteins / Q000235:genetics* / Q000378:metabolism; D013025:Glycine max / Q000187:drug effects / Q000235:genetics* / Q000502:physiology
chemical_list: D030262:Soybean Proteins; D012965:Sodium Chloride
keywords: CHX; CHX20; Glycine max (L.) Merr.; Glycine soja Sieb. et Zucc; geographical distribution; haplotype; natural variation; salt exclusion; salt tolerance