title: Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.
abstract: Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt tolerance. Tolerance was evaluated by assessing the main root length (RL), the fresh and dry weights of roots (FWR and DWR), the biomass of seedlings (BS) and the length of hypocotyls (LH) of healthy seedlings after treatments with control, 100 mM NaCl or 10 mM Na2CO3 solutions for approximately one week under greenhouse conditions. A total of 83 QTL-by-environment (QE) interactions for salt tolerance index were detected: 24 for LR, 12 for FWR, 11 for DWR, 15 for LH and 21 for BS, as well as one epistatic QTL for FWR. Furthermore, 86 QE interactions for alkaline tolerance index were found: 17 for LR, 16 for FWR, 17 for DWR, 18 for LH and 18 for BS. A total of 77 QE interactions for the original trait indicator were detected: 17 for LR, 14 for FWR, 4 for DWR, 21 for LH and 21 for BS, as well as 3 epistatic QTL for BS. Small-effect QTL were frequently observed. Several soybean genes with homology to Arabidopsis thaliana and soybean salt tolerance genes were found in close proximity to the above QTL. Using the novel alleles of the QTL detected above, some elite parental combinations were designed, although these QTL need to be further confirmed. The above results provide a valuable foundation for fine mapping, cloning and molecular breeding by design for soybean alkaline and salt tolerance.
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China ; Institute of Crop Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China.
authors.forename: Wen-Jie
authors.initials: WJ
authors.lastname: Zhang
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Niu
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Su-Hong
authors.initials: SH
authors.lastname: Bu
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Jian-Ying
authors.initials: JY
authors.lastname: Feng
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Sheng-Xian
authors.initials: SX
authors.lastname: Yang
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Medrine Mmayi
authors.initials: MM
authors.lastname: Odinga
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Shi-Ping
authors.initials: SP
authors.lastname: Wei
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Xiao-Feng
authors.initials: XF
authors.lastname: Liu
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Yuan-Ming
authors.initials: YM
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D004843:Epistasis, Genetic / Q000235:genetics*; D018525:Germination / Q000235:genetics*; D006863:Hydrogen-Ion Concentration; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics*; D013025:Glycine max / Q000235:genetics* / Q000502:physiology*