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

Abstract

BackgroundSalinity 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.ResultsThere 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 OSHKT1;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.ConclusionSalinity 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.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0590-7) contains supplementary material, which is available to authorized users.

Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective

“…In another study of very same 3 K RGP SNP set using 203 temperate japonica rice accessions with 9 salinity traits, 26 QTLs were analysed which revealed 6 candidate genes in 11 known QTLs having SNPs. This study also reconfirmed the well-known major Saltol QTL having OS HKT1; 5 (SKC1) gene controlling Na+/K+ ratio (Batayeva et al 2018).…”

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

“…Rice is salt sensitive and its threshold for salt stress is electrical conductivity (EC) 3 dS m −1 in soils (Negrão et al, 2011). Salt stress affects rice productivity worldwide especially in coastal and inland areas (Batayeva et al, 2018). For example, Dasgupta et al (2014) reported that before 2050, the productivity of rice will decline of 15.6% in nine subdistricts in coastal Bangladesh where soil salinity of EC is estimated will exceed 4 dS m −1 .…”

“…With the advent of rapid and extensive DNA markers, this genetic diversity can be explored using genome-wide association studies (GWAS) which can assay multiple alleles within a specie, and identify the location of genes affecting traits with high accuracy (Huang et al, 2010). GWAS has been applied to salt stress tolerance in rice in 12 studies mostly using hydroponics (Kumar et al, 2015;Shi et al, 2017;Yu et al, 2017;Campbell et al, 2017;Batayeva et al, 2018;Cui et al, 2018;Frouin et al, 2018;Patishtan et al, 2018;Lekklar et al, 2019;Liu et al, 2019;Rohila et al, 2019;An et al, 2020). None have used both hydroponics and soil (although one has used hydroponics and the field; Liu et al, 2019) and none have included enough aus cultivars to assess that subpopulation.…”

Genome-wide association study on agronomic traits of temperate japonica rice (Oryza sativa L.)

“…Among those groups, there are 203 temperate japonica accessions from more than 30 countries. We previously evaluated the salinity tolerance of these temperate japonica accessions, and identified 27 salinity tolerant accessions and 26 QTLs related to salinity tolerance traits (Batayeva et al 2018). Here we report the evaluation and genetic analysis of some important agronomic traits of these temperate japonica accessions.…”