Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations

Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

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Genome Wide Association Study of Resistance to PstS2 and Warrior Races of Stripe (Yellow) Rust in Bread Wheat Landraces

10.1101/2020.02.09.940775 ◽

2020 ◽

Author(s):

Muhammad Massub Tehseen ◽

Fatma Aykut Tonk ◽

Muzaffer Tosun ◽

Ahmed Amri ◽

Carolina P. Sansaloni ◽

...

Keyword(s):

Association Study ◽

Resistance Genes ◽

Genome Wide Association Study ◽

Snp Markers ◽

Genome Wide Association ◽

Adult Plant ◽

Mapping Panel ◽

Genome Wide ◽

Genomic Regions ◽

Trait Associations

ABSTRACTStripe rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to wheat production worldwide. The breakdown in resistance of certain major genes and new emerging aggressive races of stripe rusts are causing serious concerns in all main wheat growing areas of the world. To search for new sources of resistance genes and associated QTL for effective utilization in future breeding programs an association mapping panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the association mapping panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers at 19 genomic regions with significant SNP-trait associations for both seedling and adult plant stage resistance, the threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study are far away from any previously reported Yr gene or QTL hence, tagging novel genomic regions. The In-silico analysis of the novel QTL regions identified candidate resistance genes encoding proteins putative to plants disease resistance and defense mechanism.

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Genome wide association study SNPs in the human genome diversity project samples: does selection affect unlinked SNPs with shared trait associations?

Genome Biology ◽

10.1186/gb-2010-11-s1-o3 ◽

2010 ◽

Vol 11 (Suppl 1) ◽

pp. O3

Author(s):

Amanda M Casto ◽

Marcus W Feldman

Keyword(s):

Association Study ◽

Human Genome ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Human Genome Diversity Project ◽

Genome Diversity ◽

Genome Wide ◽

Trait Associations

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Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain

Frontiers in Genetics ◽

10.3389/fgene.2020.00213 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 6

Author(s):

Haritha Bollinedi ◽

Ashutosh Kumar Yadav ◽

K. K. Vinod ◽

S. Gopala Krishnan ◽

Prolay Kumar Bhowmick ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Rice Grain ◽

Genome Wide ◽

Trait Associations

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Genomewide association study reveals transient loci underlying the genetic architecture of biomass accumulation under cold stress in Sorghum

10.1101/760025 ◽

2019 ◽

Author(s):

Nadia Shakoor ◽

Erica Agnew ◽

Greg Ziegler ◽

Scott Lee ◽

César Lizárraga ◽

...

Keyword(s):

Cold Stress ◽

Association Study ◽

Candidate Genes ◽

Genome Wide Association Study ◽

Biomass Accumulation ◽

Genome Wide Association ◽

Early Season ◽

Genome Wide ◽

A Genome ◽

Related Trait

ABSTRACTSorghum bicolor is a promising cellulosic feedstock crop for bioenergy because of its potential for high biomass yields. However, in its early growth phases, sorghum is sensitive to cold stress, preventing early planting in temperate environments. Cold temperature adaptability is vital for the successful cultivation of both bioenergy and grain sorghum at higher latitudes and elevations, and for early season planting or to extend the growing season. Identification of genes and alleles that enhance biomass accumulation of sorghum grown under early cold stress would enable the development of improved bioenergy sorghum through breeding or genetic engineering. We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP is a collection of densely genotyped and racially, geographically, and phenotypically diverse accessions. The plants were weighed, watered, and imaged daily to measure growth dynamics and water use efficiency (WUE). Daily, non-destructive imaging allowed for a temporal analysis of growth-related traits in response to cold stress. We performed a genome-wide association study (GWAS) to identify candidate genomic intervals and genes controlling response to early cold stress. GWAS identified transient quantitative trait loci (QTL) strongly associated with each growth-related trait, permitting an investigation into the genetic basis of cold stress response at different stages of development. The analysis identified a priori and novel candidate genes associated with growth-related traits and the temporal response to cold stress.SIGNIFICANCE STATEMENTGenome-wide association study of bioenergy sorghum accessions phenotyped under early season cold stress revealed transient QTLs for highly heritable biomass and growth-related traits that appeared as the temperature increased and plants developed. Sorghum accessions clustered into multiple groups for each heritable trait with distinct growth profiles. GWAS identified candidate genes associated with growth traits and cold stress responses. The top-performing accessions with the highest growth-related trait values over time and temperature shifts will be useful for further genetic analysis and breeding or engineering efforts directed at biomass yield enhancements.

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