Genome-wide association study of rice rooting ability at the seedling stage

Abstract BackgroundRice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.ResultsTo characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.ConclusionsThrough evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.

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Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage

10.21203/rs.3.rs-33742/v1 ◽

2020 ◽

Author(s):

Xin Xu ◽

Junhua Ye ◽

Yingying Yang ◽

Mengchen Zhang ◽

Qun Xu ◽

...

Keyword(s):

Association Study ◽

Root Length ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Root Number ◽

Expression Levels ◽

Rooting Ability ◽

Genome Wide ◽

Population Structure Analysis

Abstract Background Rice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.Results To characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Combined with the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 32 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasms with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.Conclusions The goal of our research was to improve understanding of the genetic basis of rice rooting ability and provide useful molecular markers and germplasms for rice root breeding.

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Genome-Wide Association Study of Natural Variation in Arabidopsis Exposed to Acid Mine Drainage Toxicity and Validation of Associated Genes with Reverse Genetics

Plants ◽

10.3390/plants10020191 ◽

2021 ◽

Vol 10 (2) ◽

pp. 191

Author(s):

Bandana Ghimire ◽

Thangasamy Saminathan ◽

Abiodun Bodunrin ◽

Venkata Lakshmi Abburi ◽

Arjun Ojha Kshetry ◽

...

Keyword(s):

Acid Mine Drainage ◽

Association Study ◽

Root Length ◽

Natural Variation ◽

Genome Wide Association Study ◽

Mine Drainage ◽

The United States ◽

Genome Wide Association ◽

Acid Mine ◽

Genome Wide

Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes—cumulative root length, average root diameter, root surface area, root volume, and primary root length—in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.

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Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

10.21203/rs.3.rs-311085/v1 ◽

2021 ◽

Author(s):

Caijing Li ◽

Jindong Liu ◽

Jianxin Bian ◽

Tao Jin ◽

Baoli Zou ◽

...

Keyword(s):

Low Temperature ◽

Association Study ◽

Cold Tolerance ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Bud Burst ◽

Rice Varieties ◽

Rice Landraces ◽

Genome Wide

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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A novel variant associated with HDL-C levels by modifying DAGLB expression levels: An annotation-based genome-wide association study

European Journal of Human Genetics ◽

10.1038/s41431-018-0108-4 ◽

2018 ◽

Vol 26 (6) ◽

pp. 838-847 ◽

Cited By ~ 4

Author(s):

Dan Zhou ◽

Dandan Zhang ◽

Xiaohui Sun ◽

Zhiqiang Li ◽

Yaqin Ni ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Expression Levels ◽

Genome Wide ◽

Novel Variant

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Common Susceptibility Loci for Male Breast Cancer

JNCI Journal of the National Cancer Institute ◽

10.1093/jnci/djaa101 ◽

2020 ◽

Author(s):

Sarah Maguire ◽

Eleni Perraki ◽

Katarzyna Tomczyk ◽

Michael E Jones ◽

Olivia Fletcher ◽

...

Keyword(s):

Breast Cancer ◽

Association Study ◽

Genetic Correlation ◽

Male Breast Cancer ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Susceptibility Loci ◽

Single Nucleotide ◽

Genome Wide

Abstract Background The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. Methods We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10–06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. Results The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10–08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor–positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10–30). Conclusions These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.

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Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet

Scientific Reports ◽

10.1038/s41598-020-76230-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mahesh Pujar ◽

S. Gangaprasad ◽

Mahalingam Govindaraj ◽

Sunil S. Gangurde ◽

A. Kanatti ◽

...

Keyword(s):

Association Study ◽

Protein Content ◽

Pearl Millet ◽

Genome Wide Association Study ◽

Breeding Strategy ◽

Genome Wide Association ◽

Late Embryogenesis Abundant Protein ◽

Pentatricopeptide Repeat ◽

Genome Wide ◽

Population Structure Analysis

Abstract Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

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