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

文献类型： 外文期刊

作者： Batayeva, Dariga 1 ; Labaco, Benedick 2 ; Ye, Changrong 2 ; Li, Xiaolin 3 ; Usenbekov, Bakdaulet 4 ; Rysbekova, Aim 1 ;

作者机构： 1.Kazakh State Womens Teacher Training Univ, Alma Ata 050040, Kazakhstan

2.Int Rice Res Inst, Laguna 4031, Philippines

3.Yunnan Acad Agr Sci, Inst Food Crops, Kunming 650205, Yunnan, Peoples R China

4.Minist Educ & Sci, Inst Plant Biol & Biotechnol, Alma Ata 050010, Kazakhstan

关键词： Genome-wide association studies;Seedling stage;Salinity tolerance;Candidate gene;Temperate japonica

期刊名称：BMC GENETICS （ 影响因子：2.797； 五年影响因子：3.263 ）

ISSN： 1471-2156

年卷期： 2018 年 19 卷

页码：

收录情况： SCI

摘要： 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 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. 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.

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