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

Tae-Ho Ham,Jisu Choi,Yoonjung Lee,Joohyun Lee,Yebin Kwon

doi:10.3390/agriculture11040318

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.

Highlights

Seed germination and seedling establishment are important factors required for the successful rooting of plants in an irrigated field [1]
Cold tolerance research in rice has generally been focused on the seedling stage and reproductive developmental stages, which are highly sensitive to unfavorable temperature conditions
A total of 127 rice accessions belonging to five different groups were used to evaluate cold tolerance at the seedling stage

Summary

Introduction

Seed germination and seedling establishment are important factors required for the successful rooting of plants in an irrigated field [1]. A temperature of 25–35 ◦ C is considered optimal for the growth of rice (Oryza sativa L) seedlings; the temperature of irrigation water is frequently below 15 ◦ C in tropical and subtropical areas at high altitudes [2]. Cold stress restricts rice plant growth and development at all stages of the life cycle. At the early growth stage, cold stress leads to poor germination rate, weak seedlings with wilting, yellowing or withering leaves, delayed seedling emergence, retarded plant development, and yield loss [4,5]. Japonica) varieties are well-adapted to temperate and sub-temperate regions and to high-altitude areas in subtropical regions and exhibit greater cold tolerance than indica rice Cold temperature affects the growth and development of rice plants during their entire life cycle, starting from seed germination to the grain filling stage, eventually leading to yield loss. Cold tolerance research in rice has generally been focused on the seedling stage and reproductive developmental stages, which are highly sensitive to unfavorable temperature conditions

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Discussion

Conclusion