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

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

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Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Genetica ◽

10.1007/s10709-016-9932-z ◽

2016 ◽

Vol 144 (6) ◽

pp. 651-664 ◽

Cited By ~ 14

Author(s):

Gabriel Feresin Pantalião ◽

Marcelo Narciso ◽

Cléber Guimarães ◽

Adriano Castro ◽

José Manoel Colombari ◽

...

Keyword(s):

Grain Yield ◽

Association Study ◽

Water Deficit ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Rapid identification of a new gene influencing low amylose content in rice landraces (Oryza sativa L.) using genome-wide association study with specific-locus amplified fragment sequencing

Genome ◽

10.1139/gen-2016-0104 ◽

2017 ◽

Vol 60 (6) ◽

pp. 465-472 ◽

Cited By ~ 5

Author(s):

Xinghai Yang ◽

Baoxuan Nong ◽

Xiuzhong Xia ◽

Zongqiong Zhang ◽

Yu Zeng ◽

...

Keyword(s):

Association Study ◽

Candidate Gene ◽

Genome Wide Association Study ◽

Amylose Content ◽

Genome Wide Association ◽

Eating Quality ◽

Rice Landraces ◽

Genome Wide ◽

New Gene ◽

Specific Locus

Starch is the major component of milled rice, and amylose content (AC) affects eating quality. In this study, a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) data was performed for AC on a core collection of 419 rice landraces. Using the compressed mixed linear method based on the Q+K model, we identified a new gene, LAC6 (Chr6: 5.65–6.04 Mb), associated with AC in the low amylose content panel. The LAC6 candidate gene was detected by qRT-PCR in rice panicles. Results indicate that LOC_Os06g11130 was up-regulated, and LOC_Os06g11340 was significantly down-regulated, making it most likely a key candidate gene of LAC6. In conclusion, the findings provide a certain theoretiacal basis of molecular biology for genetic improvement of AC in rice and rice quality variety breeding.

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opulation Structure Analysis and Genome-Wide Association Study of Rice Landraces from Qiandongnan, China, using Specific–Locus Amplified Fragment Sequencing

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1679 ◽

2021 ◽

Vol 25 (02) ◽

pp. 388-396

Author(s):

Yan Li

Keyword(s):

Association Study ◽

Complex Traits ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Rice Landraces ◽

Genome Wide ◽

Sequencing Method ◽

A Genome ◽

Specific Locus

Uncovering the genetic basis of rice landraces has important applications in breeding. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of the agronomic traits of 60 rice species in Southeast Guizhou. We obtained a total of 178,287,776 reads, 314,065 SLAFs, and 571,521 single nucleotide polymorphisms (SNPs). A neighbor-joining phylogenetic tree, admixture proportions, and principal component analyses revealed that the investigated landraces were divided into japonica (heterozygosity rate 0.062) and indica (heterozygosity rate 0.073) groups. The groupings were consistent with the local classifications of ―He‖ and ―Gu‖ based on the resistance to seed shattering, and the SNPs clustered in the qSH1 gene. The GWAS of eight agronomic traits revealed that the signal peaks at four locations were closely related to previously reported genes or gene regions. This study demonstrates that the SLAF sequencing method combined with a GWAS may be effective for investigating the evolution of rice and identifying genes regulating complex traits in rice landraces cultivated in relatively isolated regions. © 2021 Friends Science Publishers

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Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2021.02047 ◽

2020 ◽

Vol 47 (6) ◽

pp. 1114-1123

Author(s):

Can CHEN ◽

Bao-Xuan NONG ◽

Xiu-Zhong XIA ◽

Zong-Qiong ZHANG ◽

Yu ZENG ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Blast Resistance ◽

Genome Wide Association ◽

The Core ◽

Rice Landraces ◽

Genome Wide ◽

Core Germplasm

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Genome-Wide Association Study to Identify Candidate Loci for Biomass Formation Under Water Deficit in Perennial Ryegrass

Frontiers in Plant Science ◽

10.3389/fpls.2020.570204 ◽

2020 ◽

Vol 11 ◽

Author(s):

Kristina Jaškūnė ◽

Andrius Aleliūnas ◽

Gražina Statkevičiūtė ◽

Vilma Kemešytė ◽

Bruno Studer ◽

...

Keyword(s):

Association Study ◽

Water Deficit ◽

Perennial Ryegrass ◽

Water Deprivation ◽

Genome Wide Association Study ◽

Leaf Growth ◽

Genome Wide Association ◽

Biomass Formation ◽

Genome Wide ◽

A Genome

Global warming is predicted to impact many agricultural areas, which will suffer from reduced water availability. Due to precipitation changes, mild summer droughts are expected to become more frequent, even in temperate regions. For perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf growth is a crucial factor determining biomass accumulation and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under normal conditions, the genetic regulation of leaf growth under water deficit in perennial ryegrass is poorly understood. Herein, we evaluated the response to water deprivation in a diverse panel of perennial ryegrass genotypes, employing a high-precision phenotyping platform. The study revealed phenotypic variation for growth-related traits and significant (P < 0.05) differences in leaf growth under normal conditions within the subgroups of turf and forage type cultivars. The phenotypic data was combined with genotypic variants identified using genotyping-by-sequencing to conduct a genome-wide association study (GWAS). Using GWAS, we identified DNA polymorphisms significantly associated with leaf growth reduction under water deprivation. These polymorphisms were adjacent to genes predicted to encode for phytochrome B and a MYB41 transcription factor. The result obtained in the present study will increase our understanding on the complex molecular mechanisms involved in plant growth under water deficit. Moreover, the single nucleotide polymorphism (SNP) markers identified will serve as a valuable resource in future breeding programs to select for enhanced biomass formation under mild summer drought conditions.

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