Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

Abstract

Key message A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Abstract Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China. We improved the method to assess cold tolerance at the bud burst stage in indica rice, and used severity of damage (SD) and seed survival rate (SR) as the cold-tolerant indices. Population structure analysis demonstrated that the Chinese indica panel was divided into three subgroups. In total, 47 significant single-nucleotide polymorphism (SNP) loci associated with SD and SR, were detected by association mapping based on mixed linear model. Because some loci overlapped between SD and SR, the loci contained 13 genome intervals and most of them have been reported previously. A major QTL for cold tolerance on chromosome 1 at the position of 31.6 Mb, explaining 13.2% of phenotypic variation, was selected for further analysis. Through LD decay, GO enrichment, RNA-seq data, and gene expression pattern analyses, we identified three genes (LOC_Os01g55510, LOC_Os01g55350 and LOC_Os01g55560) that were differentially expressed between cold-tolerant and cold-sensitive varieties, suggesting they may be candidate genes for cold tolerance. Together, our results provide a new method to assess cold tolerance in indica rice, and establish the foundation for isolating genes related to cold tolerance that could be used in rice breeding.

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

“…Further, two major M-QTLs, qLTG(I) 1 (16.08%) and qLTGS(I-II) 1 (16.57%), on chromosome 1 at the 41.0 to 42.4 Mb region were clearly associated with the germination and seedling tolerance QTLs qCTGERM1-8 and qCTS1-5 and the other QTLs qSW1-1 to qSW1-4 (seed weight per plant) and qSWTCT1-1 (seed weight per panicle) expressed in the same genomic region under cold stress at the reproductive stage (Cui et al 2013;Yang et al 2016;Shakiba et al 2017). Similarly, two other QTLs, qLTG(I) 5 (18.56%) and qLTGS(I) 5 (23.38%), on chromosome 5 at the 28.65 Mb region were concomitant with qSWTNCT5 (seed weight per panicle), qCTB5 (cold tolerance at booting stage), and seedling-stage QTLs qCTSR5-1 (cold tolerance seed survival rate) and qCTSD5-2 (cold tolerance severity of damage) (Andaya and Mackill 2003b;Ranawake et al 2014;Shakiba et al 2017;Zhang et al 2018b). Lastly, qLTG(I) 7 (20.12%) located on chromosome 7 at 3.85 Mb is a novel locus, which is co-localized with second germination stage QTL LTG(II) (8.25%).…”

“…Through genome-wide association studies (GWAS) approaches, 97 QTLs were identified for LTS tolerance at the germination stage (Pan et al 2015;Sales et al 2017;Schläppi et al 2017). In a similar way, 211 QTLs for seedling-stage tolerance and 72 QTLs for booting-stage tolerance were identified while using diverse rice genetic resources (Pan et al 2015;Lv et al 2016;Wang et al 2016a;Shakiba et al 2017;Xiao et al 2018;Zhang et al 2018b).…”

Genome-wide association study of rice rooting ability at the seedling stage

“…GWAS is an e cient way to analyze genetic variation for multiple traits in rice (Lu et al 2016;Zhang et al 2018). In GWAS, accuracy and precision are in uenced by population structure, kinship, and LD decay rate.…”

Genetic basis analysis for indica germinability under low temperature using a new RILs population genotyping by whole-genome resequencing

“…Indica varieties are widely grown in double-rice cropping regions in subtropical zones, and is frequently harmed by exposure to low temperatures at the germination stage. Due to the lower cold tolerance than japonica, the studies of modern indica cultivated rices for cold tolerance are limited [24]. In our study, two double-cropped indica rice varieties CHT025 and WFB were used to address the genetic basis of cold tolerance for the first time.…”

“…It is noticeable that most QTLs for cold tolerance detected by the populations deriving from crosses between indica and japonica cultivars, such as Nipponbare/9311 [19] and 02428/CH891 [6], because indica rice varieties are more sensitive to low temperatures, and suffer cold stress more frequently, than do varieties of the japonica subspecies [20][21][22]. Although japonica rice is generally more cold tolerant than indica rice, there might be favorable alleles for cold tolerance existing in indica that can be used to enhance cold tolerance [23,24]. However, less analyses were carried out to detect the QTLs associated with cold tolerance using indica/indica population, especially for the double-cropped indica varieties.…”