title: Association mapping of soybean seed germination under salt stress.
abstract: Soil salinity is a serious threat to agriculture sustainability worldwide. Seed germination is a critical phase that ensures the successful establishment and productivity of soybeans in saline soils. However, little information is available regarding soybean salt tolerance at the germination stage. The objective of this study was to identify the genetic mechanisms of soybean seed germination under salt stress. One natural population consisting of 191 soybean landraces was used in this study. Soybean seeds produced in four environments were used to evaluate the salt tolerance at their germination stage. Using 1142 single-nucleotide polymorphisms (SNPs), the molecular markers associated with salt tolerance were detected by genome-wide association analysis. Eight SNP-trait associations and 13 suggestive SNP-trait associations were identified using a mixed linear model and the TASSEL 4.0 software. Eight SNPs or suggestive SNPs were co-associated with two salt tolerance indices, namely (1) the ratio of the germination index under salt conditions to the germination index under no-salt conditions (ST-GI) and (2) the ratio of the germination rate under salt conditions to the germination rate under no-salt conditions (ST-GR). One SNP (BARC-021347-04042) was significantly associated with these two traits (ST-GI and ST-GR). In addition, nine possible candidate genes were located in or near the genetic region where the above markers were mapped. Of these, five genes, Glyma08g12400.1, Glyma08g09730.1, Glyma18g47140.1, Glyma09g00460.1, and Glyma09g00490.3, were verified in response to salt stress at the germination stage. The SNPs detected could facilitate a better understanding of the genetic basis of soybean salt tolerance at the germination stage, and the marker BARC-021347-04042 could contribute to future breeding for soybean salt tolerance by marker-assisted selection.
authors.affiliation: National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Guizhen
authors.initials: G
authors.lastname: Kan
authors.affiliation: National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Wenming
authors.initials: W
authors.lastname: Yang
authors.affiliation: National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Deyuan
authors.initials: D
authors.lastname: Ma
authors.affiliation: Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226541, China.
authors.forename: Derong
authors.initials: D
authors.lastname: Hao
authors.affiliation: National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Zhenbin
authors.initials: Z
authors.lastname: Hu
authors.affiliation: National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. dyyu@njau.edu.cn.
authors.forename: Deyue
authors.initials: D
authors.lastname: Yu
mesh_terms: D000222:Adaptation, Physiological; D018525:Germination; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000254:growth & development*; D012965:Sodium Chloride; D013025:Glycine max / Q000196:embryology* / Q000235:genetics / Q000502:physiology; D013312:Stress, Physiological
chemical_list: D012965:Sodium Chloride
keywords: Genome-wide association mapping; Germination; Salt tolerance; Single-nucleotide polymorphisms; Soybean