Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, SD; Nayak, D. K.; Mahender, Anumalla; Meher, Jitendriya; Anandan, A.; Pandit, Elssa

doi:10.1371/journal.pone.0160027

Cited by 73 publications

(71 citation statements)

References 69 publications

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“…The effect of seedling stage cold prolongs the growth duration of the rice plant, subsequently delay in flowering period of boro and dry season rice that coincides with high temperature stress period resulting in drastic reduction in yield (Pradhan et al, 2016). Therefore, cold tolerance breeding for seedling stage is important in boro and dry season rice.…”

Section: Discussionmentioning

confidence: 99%

“…Screening and identification of highly tolerant donors for seedling stage cold tolerance from the germplasm pool is an important step for selection of donor parents in cold tolerance breeding program. Molecular markers, usually SSR or Simple Sequence Length Polymorphism (SSLP) are commonly being used for assessing rice genetic diversity (Panaud et al, 1996; Wu and Tanksley, 1996; Xiao et al, 1996; Olufowote et al, 1997; Thanh et al, 1999; Herrera et al, 2008; Pervaiz et al, 2010; Das et al, 2013; Babu et al, 2014; Anandan et al, 2016; Pradhan et al, 2016). Hence, genetic diversity available in parental lines should be assessed by using the trait linked SSRs and gene specific markers for seedling stage chilling stress tolerance before selection of parental lines.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

et al. 2017

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Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR) and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7–21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

et al. 2017

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“…To better understand the genetic mechanism of cold tolerance, more genes related to this trait should be identified. Although bi-parental mapping populations are a good method for gene cloning, limitation of genetic diversity and long time period with less resolution are the shortcoming for discovering more new genes (Pradhan et al 2016). The genome-wide association study (GWAS) method has proved to be very useful for dissecting complicated quantitative traits based on a linkage disequilibrium mapping approach (Huang et al 2010(Huang et al , 2012b(Huang et al , 2016.…”

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 present association study was conducted on 60 diverse genotypes panel and 85 SSR markers The present association study focused on identification QTLs associated with yield and related traits in relatively small population and with limited markers [75]. Therefore, our study analogous with previous reports with a small, focused group of genotypes and limited marker pairs combination [12,13,60,67,69,75–77].…”

Section: Discussionmentioning

confidence: 79%

“…The 60 genotypes were differentiated into four sub-populations at K=4, i.e., POP1, POP2, POP3, and POP4. Similar sample sizes were used by several researchers in association analysis in rice [69, 70] and alfalfa [71]. The UPGMA cluster analysis grouped 60 genotypes into two major groups at 54 % of genetic similarity.…”

Section: Discussionmentioning

confidence: 99%

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Donde

Mohapatra

Baksh

et al. 2020

Preprint

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16A panel of 60 genotypes consisting of New Plant Types (NPTs) along with indica, tropical and 17 temperate japonica genotypes were phenotypically evaluated for four seasons in irrigated situation 18 for grain yield per se and component traits. Twenty NPT genotypes were found to be promising with 19 an average grain yield of 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to 20 identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were 21 found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A 22 moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 23 8% within genotypes, 68% among the genotypes within the population and 24% among the 24 populations were observed (AMOVA). The association analysis using GLM and MLM models led to 25 the identification of 30 and 10 SSR markers were associated with 70 and 16 QTLs, respectively. 26 Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely, 27 tiller number (qTL-6. 29 total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight 30 qTGW-8.1 ), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, 31 qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se 11.1). This information could be useful for identification of highly potential parents for development 33 of transgressive segregants. Moreover, super rice genotypes could be developed through pyramiding 34 of these QTLS for important yield traits for prospective increment in yield potentiality and breaking 35 yield ceiling. 36 Introduction 39Rice (Oryza sativa L.) is a staple crop for more than 3.5 billion people in the globe. In current 40 scenario, rice productivity is increasing rate at 1% per year which is less than the 2.4% per year rate 41 required to double the global production by 2050 [1]. Considering a glimpse of the history, a 42 quantum jump in productivity was achieved due to the green revolution in mid-sixties, which 43 drastically enhanced the rice production of the world. However, a ceiling of productivity potentiality 44 is reported by and large in semi-dwarf inbred indica genotypes since release of , in spite of 45 substantial improvement in yield stability, per day productivity and grain quality [3]. A 46 breakthrough in productivity barrier is necessitated because of increasing competition for natural 47 resources viz., land, water and others given population explosion coupled with expanding 48 industrialization, urbanization and diversion of agricultural land [1,4,5]. This is still aggravated with 49 the abnormal change in weather and climate with significant influence on crop productivity and 50 quality [6,7]. 51Rice scientists are facing many challenges for doubling rice production by 2050. Irrigated 52 rice has a share of 75% of total rice production in the world, although it has a share of about 55% of 53 the total rice area [2]. Therefore, improveme...

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Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

Cited by 73 publications

References 69 publications

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

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

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

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