Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes

Yang, Zemao; Huang, Daiqing; Tang, Weiqi; Zheng, Yanyan; Liang, Kun; Cutler, Adrian J.; Wu, Weiren

doi:10.1371/journal.pone.0068433

Cited by 131 publications

(131 citation statements)

References 36 publications

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“…Here, we detected a major QTL for cold tolerance on chromosome 1 that was also detected in a bi-parental population in a previous report (Yang et al 2013). The LD decay analysis indicated that an approximately 579 kb region at the associated locus was a candidate region for further study (Fig.…”

Section: Identification Of Candidate Gene Controlling Cold Tolerancesupporting

confidence: 77%

“…Additionally, except for qCTSD12-1, all of the QTLs for SD have been reported previously. Specifically, qCTSR1-2 and qCTSR5-2 detected in our study were also identified in a bulked segregant analysis (BSA) using high-throughput sequencing of pooled extremes (Yang et al 2013). qCTSR5-1 and qCTSR10-1 were detected in a previous study by linkage mapping using bi-parents and their derived population under low-temperature stress (Jiang et al 2006).…”

Section: Gwas Analysis For Cold Tolerance At the Bud Burst Stagesupporting

confidence: 65%

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

Zhang

et al. 2018

Plant Cell Rep

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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.

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Section: Identification Of Candidate Gene Controlling Cold Tolerancesupporting

confidence: 77%

Section: Gwas Analysis For Cold Tolerance At the Bud Burst Stagesupporting

confidence: 65%

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

Zhang

et al. 2018

Plant Cell Rep

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“…The MYBS3 transcriptional network responds more slowly than the CBF pathway to low temperatures, regulating low-temperature tolerance genes such as those involved in the repression of the CBF pathway, which distinguishes it as an independent low-temperature responsive cascade 120 . In addition, several QTLs [121][122][123] have been identified that may be exploited to obtain low-temperature yield stability in rice.…”

Section: Solutions For Aluminium and Boron Toxicitymentioning

confidence: 99%

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

2015

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Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.

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“…In our study, two QTLs qRC10 - 1 and qRC10 - 2 were identified on the same chromosome in DX. A QTL for cold tolerance ( qCTSS-10 ) was also identified in seedlings by Yang et al [52]. qCTSS-10 for 7°C cold treatment was mapped by high-throughput sequencing in the F 3 mapping population from a cross between a cold-tolerant japonica rice variety (Nipponbare) and a cold-sensitive indica variety.…”

Section: Discussionmentioning

confidence: 99%

Fine Mapping of qRC10-2, a Quantitative Trait Locus for Cold Tolerance of Rice Roots at Seedling and Mature Stages

et al. 2014

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Cold stress causes various injuries to rice seedlings in low-temperature and high-altitude areas and is therefore an important factor affecting rice production in such areas. In this study, root conductivity (RC) was used as an indicator to map quantitative trait loci (QTLs) of cold tolerance in Oryza rufipogon Griff., Dongxiang wild rice (DX), at its two-leaf stage. The correlation coefficients between RC and the plant survival rate (PSR) at the seedling and maturity stages were –0.85 and –0.9 (P = 0.01), respectively, indicating that RC is a reliable index for evaluating cold tolerance of rice. A preliminary mapping group was constructed from 151 BC2F1 plants using DX as a cold-tolerant donor and the indica variety Nanjing 11 (NJ) as a recurrent parent. A total of 113 codominant simple-sequence repeat (SSR) markers were developed, with a parental polymorphism of 17.3%. Two cold-tolerant QTLs, named qRC10-1 and qRC10-2 were detected on chromosome 10 by composite interval mapping. qRC10-1 (LOD = 3.1, RM171-RM1108) was mapped at 148.3 cM, and qRC10-2 (LOD = 6.1, RM25570-RM304) was mapped at 163.3 cM, which accounted for 9.4% and 32.1% of phenotypic variances, respectively. To fine map the major locus qRC10-2, NJ was crossed with a BC4F2 plant (L188-3), which only carried the QTL qRC10-2, to construct a large BC5F2 fine-mapping population with 13,324 progenies. Forty-five molecular markers were designed to evenly cover qRC10-2, and 10 markers showed polymorphisms between DX and NJ. As a result, qRC10-2 was delimited to a 48.5-kb region between markers qc45 and qc48. In this region, Os10g0489500 and Os10g0490100 exhibited different expression patterns between DX and NJ. Our results provide a basis for identifying the gene(s) underlying qRC10-2, and the markers developed here may be used to improve low-temperature tolerance of rice seedling and maturity stages via marker-assisted selection (MAS).Key MessageWith root electrical conductivity used as a cold-tolerance index, the quantitative trait locus qRC10-2 was fine mapped to a 48.5-kb candidate region, and Os10g0489500 and Os10g0490100 were identified as differently expressed genes for qRC10-2.

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Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes

Cited by 131 publications

References 36 publications

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

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

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

Fine Mapping of qRC10-2, a Quantitative Trait Locus for Cold Tolerance of Rice Roots at Seedling and Mature Stages

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