Genome Wide Association Mapping for Drought Recovery Trait in Rice (Oryza Sativa L.)

Al-Shugeairy, Zaniab; Price, Adam H.; Robinson, David

doi:10.11648/j.ijaas.20150101.12

Cited by 9 publications

(5 citation statements)

References 29 publications

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“…The 22 QTLs whose confidence interval overlapped with an association detected in this study are listed in Additional file 1: Table S8. In addition to the co-locations with QTLs deriving from mapping populations, we also observed overlaps between the associations from our study and the associations for drought-related traits detected using genome-wide association mapping (Courtois et al 2013; Muthukumar et al 2015; Al-Shugeairy et al 2015; Swamy et al 2017, Guo et al 2018). It found only 58 overlaps in a total of 1889 GWAS sites collected, in which there are 31 associations from the present study underlying the QTLs q1, q4, q5, q7, q9, q11, q13, and q14 (Additional file 1: Table S9).…”

Section: Resultssupporting

confidence: 62%

“…This concerns traits related to abscisic acid (ABA) content (Quarrie et al 1997), cell membrane stability (Tripathy et al 2000) or cell osmotic adjustment (Lilley et al 1996; Zhang et al 2001; Robin et al 2003). Other QTLs associated with yield and yield-related traits (Muthukumar et al 2015; Swamy et al 2017), and drought recovery (Al-Shugeairy et al 2015) have been reported. Most of these QTLs have been identified using bi-parental or multiparental populations, which have limited allelic diversity and poor resolution in QTL positioning (Korte and Farlow 2013; Swamy et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

Hoang

Dinh

Nguyen

et al. 2019

Rice

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BackgroundDrought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance.ResultsThe panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed.ConclusionsSome of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0258-6) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

Hoang

Dinh

Nguyen

et al. 2019

Rice

View full text Add to dashboard Cite

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“…In general, higher genetic diversity in the population means a shorter LD decay distance, and vice versa [35]. Considering the LD decay distance in rice, adjacent SNPs with spans less than 200 kb [36,37] were defined as one single QTL, and the SNP with the lowest p-value was taken as the lead SNP to reduce redundant association signals between different traits and identify candidate genes. The LD decay distance determines the minimum number of molecular markers required for association analysis (minimum number of molecular markers = genome size/LD decay distance) and its subsequent resolution.…”

Section: Population Structure Kinship and Ld Decaymentioning

confidence: 99%

Section: Population Structure Kinship and Ld Decaymentioning

confidence: 99%

Genome-Wide Association Study of Xian Rice Grain Shape and Weight in Different Environments

Wang

Zhang

Wang

et al. 2023

Plants

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Drought is one of the key environmental factors affecting the growth and yield potential of rice. Grain shape, on the other hand, is an important factor determining the appearance, quality, and yield of rice grains. Here, we re-sequenced 275 Xian accessions and then conducted a genome-wide association study (GWAS) on six agronomic traits with the 404,411 single nucleotide polymorphisms (SNPs) derived by the best linear unbiased prediction (BLUP) for each trait. Under two years of drought stress (DS) and normal water (NW) treatments, a total of 16 QTLs associated with rice grain shape and grain weight were detected on chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12. In addition, these QTLs were analyzed by haplotype analysis and functional annotation, and one clone (GSN1) and five new candidate genes were identified in the candidate interval. The findings provide important genetic information for the molecular improvement of grain shape and weight in rice.

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“…In recent years, rice researchers widely used the genome-wide association studies (GWASs) to investigate the complex traits of agronomic and commercial importance including yield parameters, flowering time ( Huang et al, 2010 ; Huang et al, 2012 ; Rashid et al, 2022 ), and abiotic stresses like drought ( Al-Shugeairy et al, 2015 ) and salinity ( Kumar et al, 2015 ). Nonetheless, a few GWAS studies were conducted for lodging resistance ( Hu et al, 2013 ; Meng et al, 2021 ) in crops.…”

Section: Introductionmentioning

confidence: 99%

Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa. L) by genome-wide association analyses

et al. 2022

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Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance–related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength–related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.

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Genome Wide Association Mapping for Drought Recovery Trait in Rice (Oryza Sativa L.)

Cited by 9 publications

References 29 publications

Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

Genome-Wide Association Study of Xian Rice Grain Shape and Weight in Different Environments

Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa. L) by genome-wide association analyses

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