Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Tae-Ho Ham, Yebin Kwon, Yoonjung Lee, Jisu Choi and Joohyun Lee
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Tae-Ho Ham: Department of Crop Science, Konkuk University, Seoul 05029, Korea
Yebin Kwon: Department of Crop Science, Konkuk University, Seoul 05029, Korea
Yoonjung Lee: Department of Crop Science, Konkuk University, Seoul 05029, Korea
Jisu Choi: Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50434, Korea
Joohyun Lee: Department of Crop Science, Konkuk University, Seoul 05029, Korea

Agriculture, 2021, vol. 11, issue 4, 1-13

Abstract: We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

Keywords: GWAS; cold tolerance; seedling; rice (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2021
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