scholarly journals A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Xue Ren ◽  
Guang-Li Yang ◽  
Wei-Feng Peng ◽  
Yong-Xin Zhao ◽  
Min Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Close Association ◽  
Significant Snps ◽  
Genomic Region ◽  
Ovis Aries ◽  
Genome Wide Association ◽  
Chromosome 2 ◽  
Genome Wide ◽  
A Genome

Abstract Horns are a cranial appendage found exclusively in Bovidae, and play important roles in accessing resources and mates. In sheep (Ovies aries), horns vary from polled to six-horned, and human have been selecting polled animals in farming and breeding. Here, we conducted a genome-wide association study on 24 two-horned versus 22 four-horned phenotypes in a native Chinese breed of Sishui Fur sheep. Together with linkage disequilibrium (LD) analyses and haplotype-based association tests, we identified a genomic region comprising 132.0–133.1 Mb on chromosome 2 that contained the top 10 SNPs (including 4 significant SNPs) and 5 most significant haplotypes associated with the polycerate phenotype. In humans and mice, this genomic region contains the HOXD gene cluster and adjacent functional genes EVX2 and KIAA1715, which have a close association with the formation of limbs and genital buds. Our results provide new insights into the genetic basis underlying variable numbers of horns and represent a new resource for use in sheep genetics and breeding.

scholarly journals Erratum: A genome-wide association study identifies a genomic region for the polycerate phenotype in sheep (Ovis aries)

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Xue Ren ◽  
Guang-Li Yang ◽  
Wei-Feng Peng ◽  
Yong-Xin Zhao ◽  
Min Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Ovis Aries ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

scholarly journals A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

2020 ◽  
Vol 10 (5) ◽  
pp. 1685-1696
Author(s):  
Lorenzo Stagnati ◽  
Vahid Rahjoo ◽  
Luis F. Samayoa ◽  
James B. Holland ◽  
Virginia M. G. Borrelli ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Germination Rate ◽  
Fusarium Verticillioides ◽  
Screening Method ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Seedling Length ◽  
A Genome

Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.

scholarly journals A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

2018 ◽  
Author(s):  
Veena Devi Ganeshan ◽  
Stephen O. Opiyo ◽  
Samuel K. Mutiga ◽  
Felix Rotich ◽  
David M. Thuranira ◽  
...  
Keyword(s):  
Association Study ◽  
Magnaporthe Oryzae ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Sub Saharan Africa ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Sub Saharan ◽  
Genomic Regions

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.

scholarly journals Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Heredity ◽  
2020 ◽  
Author(s):  
Yanhua Zhang ◽  
Yuzhe Wang ◽  
Yiyi Li ◽  
Junfeng Wu ◽  
Xinlei Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Carcass Traits ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Pathway Enrichment Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

scholarly journals Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengfu Zhou ◽  
Huiyue Guan ◽  
Congcong Liu ◽  
Ziwei Zhang ◽  
Shenghui Geng ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Regulatory Elements ◽  
Genome Wide Association ◽  
Genetic Loci ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Background Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat. Results Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000. Conclusions To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

A genome-wide association study reveals a genomic region associated with the carrot root shape

2019 ◽  
pp. 129-134
Author(s):  
A. Macko-Podgórni ◽  
K. Stelmach ◽  
K. Kwolek ◽  
D. Senalik ◽  
P.W. Simon ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Genome Wide Association ◽  
Carrot Root ◽  
Genome Wide ◽  
A Genome
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