Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice

Wang, Dan; Liu, Jinling; Li, Chengang; Kang, Houxiang; Wang, Yue; Tan, Xinqiu; Liu, Minghao; Deng, Yufei; Wang, Zhilong; Liu, Yong; Zhang, Deyong; Xiao, Yinghui; Wang, Guoliang

doi:10.1186/s12284-016-0133-2

Cited by 82 publications

(78 citation statements)

References 35 publications

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“…We found several peaks located within or near previously reported QTLs (Table 3; S4 Table) including 11 in ALL ( qCTB1 and COLD3 , L21, qCTS4-1 , qCTS4-2 , qCTS7 , qCTS7-2 , qCTF8 , qCTS8-3 , qCTS1-5 , qCTS7-2 , and qCTF12 ), eight in INDICA (L21, L46, L107, qCST10 , qCTF12 , qCTS11-5 , qCTS6-2 and qCTS4-3 ), eight in JAPONICA [L8, L48, qLTG-4 , qCTS4-1 , qCTS4-2 , qCTS6-1 , COLD4 and qCTS7(2) ], four in temperate japonica [ qCTS4-1 , qCTS4-2 , qCTS1-5 , and qCTS11(2)-2 ] and 10 in tropical japonica ( qCTS5 , qCTS10 , L51, qLTG-5-2 , qCTS5 , L72, qPSST-7 , qCTS7 , L79, L102, and qLTG-10 ). The QTLs, qCTS4-1 , qCTS4-2 , COLD4 , qCTB5 and qCTS7(-2) were identified in JAPONICA which is in agreement with our study [1, 6, 13, 32, 44–49]. Moreover, qCTS4-1 and qCTS4-2 are two major QTLs that were observed in ALL , JAPONICA and temperate japonica; another major QTL, CTB7-2 , was detected in both JAPONICA and ALL ; and finally a QTL, qCTF12 was observed in both INDICA and ALL .…”

Section: Discussionsupporting

confidence: 92%

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Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

Shakiba

Edwards

Jodari³

et al. 2017

PLoS ONE

123

109

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Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.

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Section: Discussionsupporting

confidence: 92%

“…Wang et al [32] evaluated 295 RDP1 accessions genotyped with 36,901 high quality SNPs for cold tolerance at the seeding stage. Subsequent, GWA mapping identified 67 QTL located on 11 chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

Shakiba

Edwards

Jodari³

et al. 2017

PLoS ONE

123

109

View full text Add to dashboard Cite

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“…Lv et al (2016) detected 132 QTL for nature chilling and cold-shock tolerance at the seedling stage by a GWAS analysis of 527 rice cultivars. Wang et al (2016) identified 67 QTLs for cold tolerance at the seedling stage, and 56 of these QTLs were located in regions that had not been reported to contain cold tolerance-related QTLs. Shakiba et al (2017) identified 42 QTLs associated with cold tolerance at the seedling stage, 20 of which did not co-localize with previously reported cold-tolerant QTLs.…”

Section: Introductionmentioning

confidence: 99%

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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“…The challenge of global warming means that crop plants, including rice, will be more exposed to extreme growing environments, e.g., low and high temperatures. Although the response by rice to cold stress has been described (Zhi-guo et al, 2014; Wang D. et al, 2016; Shakiba et al, 2017), we still need to identify more effective genes that can regulate this response.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

et al. 2017

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Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in ‘Dongjin,’ the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the ‘L-phenylalanine catabolic process,’ within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified ‘Major Metabolic’ processes and ‘Regulatory Gene Modules’ as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.

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Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice

Cited by 82 publications

References 35 publications

Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

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

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

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