Genome-wide association among soybean accessions for the genetic basis of salinity-alkalinity tolerance during germination
Yongce Cao
A , Xincao Zhang A , Shihao Jia A , Benjamin Karikari B C , Mingjun Zhang D , Zhangyi Xia A , Tuanjie Zhao B E and Fuqin Liang D E
+ Author Affiliations
- Author Affiliations
A Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, Shaanxi 716000, China.
B Soybean Research Institute of Nanjing Agricultural University, Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, National Centre for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu 210095, China.
C Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, PO Box TL 1882, Tamale, Ghana.
D Institute of Yan’an Agricultural Science, Yan’an, Shaanxi 716000, China.
E Corresponding authors. Email: tjzhao@njau.edu.cn; yankslfq@126.com
Crop and Pasture Science 72(4) 255-267 https://doi.org/10.1071/CP20459
Submitted: 19 November 2020 Accepted: 2 March 2021 Published: 28 April 2021
Abstract
Salinity-alkalinity stress is one of the main factors limiting crop growth and production. However, few genetic sources that can be used to improve soybean salinity-alkalinity tolerance are available. The objective of this study was to determine the genetic mechanisms for salinity-alkalinity tolerance in soybean during germination by a genome-wide association study (GWAS) using 281 accessions with 58 112 single nucleotide polymorphisms (SNPs). Four salinity-alkalinity tolerance (ST) indices namely ST-GR (germination ratio), ST-RFW (root fresh weight), ST-DRW (root dry weight), and ST-RL (root length) were used to assess soybean salinity-alkalinity tolerance. A total of 8, 4, 6, and 4 quantitative trait loci (QTL) accounted for 3.83–8.01% phenotypic variation in ST-GR, ST-RL, ST-RFW, and ST-RDW, respectively. Two common QTL (qST.5.1 and qST.16.1) associated with at least three indices located on chromosome 5 (~38.4 Mb) and chromosome 16 (~29.8 Mb), were determined as important loci for controlling salinity-alkalinity tolerance in soybean. We also predicted candidate genes for the two QTL. The significant SNPs and common QTL as well as the salinity-alkalinity tolerant accessions will improve the efficiency of marker-assisted breeding and candidate gene discovery for soybean salinity-alkalinity tolerance.
Keywords: crop production, genome-wide association study, soybean, germination, seed yield, seed quality, salinity-alkalinity stress, single nucleotide polymorphism, quantitative trait locus, recombinant inbred line, genetic mechanism.
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