scholarly journals Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep

2021 ◽  
Author(s):  
Hongchang Zhao ◽  
Shaohua Zhu ◽  
Tingting Guo ◽  
Mei Han ◽  
Bowen Chen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Whole Genome ◽  
Sheep Breeding ◽  
Merino Sheep ◽  
Significance Threshold ◽  
Genome Wide ◽  
A Genome ◽  
Fleece Weight

Abstract To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following 4 fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (p = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (p = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, while 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h 2) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.

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 and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rueben G. Das ◽  
Doreen Becker ◽  
Vidhya Jagannathan ◽  
Orly Goldstein ◽  
Evelyn Santana ◽  
...  
Keyword(s):  
Association Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Night Blindness ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Congenital Stationary Night Blindness ◽  
Genome Wide ◽  
A Genome

Abstract Congenital stationary night blindness (CSNB), in the complete form, is caused by dysfunctions in ON-bipolar cells (ON-BCs) which are secondary neurons of the retina. We describe the first disease causative variant associated with CSNB in the dog. A genome-wide association study using 12 cases and 11 controls from a research colony determined a 4.6 Mb locus on canine chromosome 32. Subsequent whole-genome sequencing identified a 1 bp deletion in LRIT3 segregating with CSNB. The canine mutant LRIT3 gives rise to a truncated protein with unaltered subcellular expression in vitro. Genetic variants in LRIT3 have been associated with CSNB in patients although there is limited evidence regarding its apparently critical function in the mGluR6 pathway in ON-BCs. We determine that in the canine CSNB retina, the mutant LRIT3 is correctly localized to the region correlating with the ON-BC dendritic tips, albeit with reduced immunolabelling. The LRIT3-CSNB canine model has direct translational potential enabling studies to help understand the CSNB pathogenesis as well as to develop new therapies targeting the secondary neurons of the retina.

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 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.

scholarly journals NUDT15 Genetic Variation Is the Strongest Predictive Marker of Tolerance to 6-Mercaptopurine in Japanese Childhood ALL Patients: A Genome-Wide Association Study

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1347-1347
Author(s):  
Yoichi Tanaka ◽  
Kevin Y Urayama ◽  
Makiko Mori ◽  
Daisuke Hasegawa ◽  
Yasushi Noguchi ◽  
...  
Keyword(s):  
Maintenance Therapy ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Predictive Marker ◽  
Age At Diagnosis ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Japanese Study ◽  
Genome Wide ◽  
A Genome

Introduction In Asians, NUDT15 genetic variants have been reported to be associated with low tolerance to 6-mercaptopurine (6-MP). However, variation in 6-MP tolerance is still observed among patients without the NUDT15 variants. Some patients required high doses of 6-MP to obtain treatment effect. We performed a genome-wide association study (GWAS) in Japanese to confirm reported associations as well as to identify additional genetic loci associated with variation of 6-MP tolerance in childhood acute lymphoblastic leukemia (ALL) patients. Methods We included ALL patients enrolled into a Tokyo Children's Cancer Study Group (TCCSG) trial who started maintenance therapy by normal protocol dose (30-50 mg/m2/day). Whole genome single nucleotide polymorphism (SNP) microarray genotyping was performed followed by whole genome SNP imputation (Japanese reference genome). Data for over six million SNPs were available for analysis. Association analysis was performed adjusting for age at diagnosis and considering average 6-MP dose during 168 days from maintenance therapy initiation as the outcome. Results A total of 224 patients were included in the analysis. The median age at diagnosis was 4.7 (range = 0.9-15.7) years old and boys comprised 56.3%. The average 6-MP dose during the 168 days of maintenance therapy was 41.1 (range = 13.3-78.5) mg/m2/day. Variants representing 10 genomic regions showed potential association (P &lt; 5 x 10-6) with average 6-MP dose, in which one locus was genome-wide significant (13q14.2, rs116855232). Variant rs116855232 is located in the previously identified NUDT15 gene and represents the strongest association with average 6-MP dose within our Japanese study (β = -11.45, P = 8.5 x 10-10). In contrast, the TPMT locus, which is predictive of 6-MP intolerance in populations of European ancestry, was not associated with 6-MP dose in Japanese. Among the suggestive loci requiring further follow-up is a locus residing in AFF3 (2q11.2, P = 2.1 x 10-6), a gene previously implicated in childhood leukemia. Conclusion We have validated that NUDT15 rs116855232 is a locus with strong association with 6-MP tolerable dose, and it currently represents the most meaningful clinically predictive marker in Japanese. These findings indicated that NUDT15 genotyping should be considered prior to initiation of 6-MP treatment. Prospects for the identification of additional loci of 6-MP tolerance are high after further validation of suggestive loci observed in this Japanese study. Figure Disclosures No relevant conflicts of interest to declare.

A chemical genetic roadmap to improved tomato flavor

Science ◽  
2017 ◽  
Vol 355 (6323) ◽  
pp. 391-394 ◽  
Author(s):  
Denise Tieman ◽  
Guangtao Zhu ◽  
Marcio F. R. Resende ◽  
Tao Lin ◽  
Cuong Nguyen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Sequencing ◽  
Molecular Breeding ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Chemical Genetic ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Modern commercial tomato varieties are substantially less flavorful than heirloom varieties. To understand and ultimately correct this deficiency, we quantified flavor-associated chemicals in 398 modern, heirloom, and wild accessions. A subset of these accessions was evaluated in consumer panels, identifying the chemicals that made the most important contributions to flavor and consumer liking. We found that modern commercial varieties contain significantly lower amounts of many of these important flavor chemicals than older varieties. Whole-genome sequencing and a genome-wide association study permitted identification of genetic loci that affect most of the target flavor chemicals, including sugars, acids, and volatiles. Together, these results provide an understanding of the flavor deficiencies in modern commercial varieties and the information necessary for the recovery of good flavor through molecular breeding.

scholarly journals Genome-wide Association Study for Number of Vertebrae in an F2 Large White × Minzhu Population of Pigs

2015 ◽  
Author(s):  
Longchao Zhang ◽  
Xin Liu ◽  
Jing Liang ◽  
Kebin Zhao ◽  
Hua Yan ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Mammalian Embryos ◽  
Strong Candidate

Porcine carcass that is approximately 800 mm long may be expected to have one additional vertebra. Therefore, the number of vertebrae in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 593 F2 Large White × Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study identified 39 significant single-nucleotide polymorphisms (SNPs) on the chromosomes SSC1 and SSC7. An 8.82-Mb region that contained all 21 significant SNPs on SSC1 harbored the gene NR6A1, previously reported to influence the number of vertebrae in pigs. The remaining 18 significant SNPs on SSC7 were concentrated in a 4.56-Mb region, which was within the quantitative trait loci interval for number of vertebrae. A haplotype sharing analysis refined the locus to a segment of ~637 Kb. The most significant SNP, SIRI0001067, was contained in this refined region on SSC7 and located in one of the introns of TGFB3. As TGFB3 influences the development of vertebrae in mammalian embryos, the gene may be another strong candidate for the number of vertebrae in pigs.

scholarly journals Choosing the optimal population for a genome‐wide association study: A simulation of whole‐genome sequences from rice

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Kosuke Hamazaki ◽  
Hiromi Kajiya‐Kanegae ◽  
Masanori Yamasaki ◽  
Kaworu Ebana ◽  
Shiori Yabe ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Wide ◽  
A Genome ◽  
Optimal Population
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