Integration of genome-wide association studies reveal loci associated with salt tolerance score of rice at the seedling stage

• Published in: Journal of applied genetics 2023-12, Vol.64 (4), p.603-614
• Main Authors: Phan, Nhung Thi Hong, Van Pham, Cuong, Tang, Hanh Thi, Van Nguyen, Loc, Nguyen, Long Viet, Bertin, Pierre
• Format: Article
• Language: English
• Subjects: Analysis; Animal Genetics and Genomics; Biomedical and Life Sciences; Cultivation; Gene frequency; Genes; Genetic improvement; Genome-wide association studies; Genomes; Genomics; Grain cultivation; Haplotypes; Human Genetics; Hydroponics; Life Sciences; Microbial Genetics and Genomics; New varieties; Panels; Phylogeny; Plant breeding; Plant Genetics and Genomics; Plant Genetics • Original Paper; Quantitative genetics; Quantitative trait loci; Rice; Salinity tolerance; Salt tolerance; Seedlings; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Sodium chloride
• ISSN: 1234-1983; 2190-3883
• DOI: 10.1007/s13353-023-00775-7

Salt threatens rice cultivation in many countries. Hence, breeding new varieties with high salt tolerance is important. A panel of 2,391 rice accessions from the 3 K Rice Genome Project was selected to evaluate salt tolerance via the standard evaluation score (SES) in hydroponics under 60 mM NaCl at the seedling stage. Three sub-population panels including 1,332, 628, and 386 accessions from the original 2,391 ones were constructed based on low relatedness revealed by a phylogenetic tree generated by Archaeopteryx Tree. A genome-wide association study (GWAS) was conducted on the entire and sub-population panels using SES data and a selection of 5, 10, 20, and 40% of SNPs selected from the original 1,011,601 SNPs by filtering minor allele frequency > 5% and missing rate