Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Abstract Background Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits. Results There were 27 accessions performed well (SES < 5.0) under moderate salinity stress (EC12), and 5 accessions were tolerant under both EC12 and EC18. A total of 26 QTLs were identified for 9 measured traits. Eleven of these QTLs were co-located with known salinity tolerance genes. QTL/gene clusters were observed on chromosome 1, 2, 3, 6, 8 and 9. Six candidate genes were identified for five promising QTLs. The alleles of major QTL Saltol and gene O S HKT1;5 (SKC1) for Na+/K+ ratio identified in indica rice accessions were different from those in the temperate japonica rice accessions used in this study. Conclusion Salinity tolerant temperate japonica rice accessions were identified in this study, these accessions are important resources for breeding programs. SNPs located in the promising QTLs and candidate genes could be used for future gene validation and marker assisted selection. This study provided useful information for future studies on genetics and breeding of salinity tolerance in temperate japonica rice

Marie-Claire / dir. Jean Prouvost

28 juillet 19391939/07/28 (A0,N126)-1939/07/28.Appartient à l’ensemble documentaire : UnivJeun

Additional file 1: of Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Figure S1. Selection of 203 temperate japonica from the 3000 sequenced rice accessions. Left is the archaeopteryx tree of 3000 sequenced rice accessions using 365,710 SNPs, and the right is the archaeopteryx tree of 176 temperate japonica accessions using 68,786 SNPs. (DOCX 133 kb

Additional file 7: of Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Table S4. List of salinity tolerant accessions at seedling stage based on SES12. (DOCX 16 kb

Additional file 8: of Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Figure S4. Manhattan plots of different traits related to salinity tolerance at seedling stage. The genotyping and phenotyping data along with kinship matrix were analyzed using mixed linear model (MLM). (DOCX 1043 kb