Identification of Marbling Gene Loci in Commercial Pigs in Canadian Herds

A genome-wide association study (GWAS) was performed on the intramuscular fat percentage in pork chops in commercially available swine in Canada. The Duroc, Iberian, Lacombe, Berkshire, and Pietrain breeds were crossed with Large White sows, and their F1 offspring were ranked according to the intramuscular fat percentage (IMF %) obtained in their longissimus dorsi (LD) muscle loin chops. The ideal IMF % is considered to be >3%, whereas the average is ~1.5% in North American pork. The genetics of the top 10% and bottom 10% from our sample population were analysed by using 80,000 single nucleotide polymorphism (SNP) microarrays in the GWAS. Our sample population had an average IMF % of 2.5 ± 0.7%, but some pork achieved >7% IMF. GWAS analysis revealed SNP markers which were associated with the highest marbled pork chops on chromosomes 5, 7, and 16. Using the Sus scrofa/ susScr 11.1 map, we determined that the nearest genes were sarcospan (SSPN), Rh-associated glycoprotein (RHAG), and EGF-like fibronectin and laminin G (EGFLAM), which can be linked with muscular dystrophy disorders. We tested a subpopulation of Duroc-sired animals and found a different set of markers close to glycine receptor beta (GRLB) and potassium channel 3 (KCNJ3) on chromosomes 8 and 15. Based on our results, we could achieve pork with a good IMF of >4% from animals commercially bred and raised to standard market weights of 110 kg. The choice of obtaining a good marbling line of pigs is not necessarily breed-specific, but it is line-specific.

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Haplotype Analysis Improved Evidence for Candidate Genes for Intramuscular Fat Percentage from a Genome Wide Association Study of Cattle

PLoS ONE ◽

10.1371/journal.pone.0029601 ◽

2011 ◽

Vol 6 (12) ◽

pp. e29601 ◽

Cited By ~ 32

Author(s):

William Barendse

Keyword(s):

Association Study ◽

Candidate Genes ◽

Haplotype Analysis ◽

Genome Wide Association Study ◽

Intramuscular Fat ◽

Genome Wide Association ◽

Fat Percentage ◽

Genome Wide ◽

A Genome

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SNP Alleles Associated With Low Bolting Tendency in Sugar Beet

Frontiers in Plant Science ◽

10.3389/fpls.2021.693285 ◽

2021 ◽

Vol 12 ◽

Author(s):

Samathmika Ravi ◽

Giovanni Campagna ◽

Maria Cristina Della Lucia ◽

Chiara Broccanello ◽

Giovanni Bertoldo ◽

...

Keyword(s):

Sugar Beet ◽

Genome Wide Association Study ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

Allelic Status ◽

The One ◽

Detection Technologies

The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet (Beta vulgaris L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study. An elaborate 3-year field trial comprising 13 sugar beet lines identified L14 as the one exhibiting the lowest bolting tendency along with an increased survival rate after autumnal sowing. For SNP discovery following phenotyping, contrasting phenotypes of 24 non-bolting and 15 bolting plants of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq). An association model was established with a set of 10,924 RAD-based single nucleotide polymorphism (SNP) markers. The allelic status of the most significantly associated SNPs ranked based on their differential allelic status between contrasting phenotypes (p < 0.01) was confirmed on three different validation datasets comprising diverse sugar beet lines and varieties adopting a range of SNP detection technologies. This study has led to the identification of SNP_36780842 and SNP_48607347 linked to low bolting tendency and can be used for marker-assisted breeding and selection in sugar beet.

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Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon

International Journal of Molecular Sciences ◽

10.3390/ijms20215392 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5392

Author(s):

Joshi ◽

Shinde ◽

Nimmakayala ◽

Abburi ◽

Alaparthi ◽

...

Keyword(s):

Genome Wide Association Study ◽

Genetic Regulation ◽

Acetolactate Synthase ◽

Snp Markers ◽

Protein Amino Acid ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

A Minor

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.

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Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽

10.1139/gen-2015-0031 ◽

2015 ◽

Vol 58 (12) ◽

pp. 549-557 ◽

Cited By ~ 5

Author(s):

Everestus C. Akanno ◽

Graham Plastow ◽

Carolyn Fitzsimmons ◽

Stephen P. Miller ◽

Vern Baron ◽

...

Keyword(s):

Beef Cattle ◽

Genome Wide Association Study ◽

Average Daily Gain ◽

Snp Markers ◽

Genome Wide Association ◽

Research Centre ◽

Genome Wide ◽

A Genome ◽

Starting Point ◽

And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

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Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Plant Disease ◽

10.1094/pdis-08-21-1611-re ◽

2021 ◽

Author(s):

Dennis Katuuramu ◽

Sandra Branham ◽

Amnon Levi ◽

Patrick Wechter

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Citrullus Lanatus ◽

Phenotypic Variability ◽

Germplasm Collection ◽

Snp Markers ◽

Genome Wide Association ◽

Pseudoperonospora Cubensis ◽

Genome Wide ◽

A Genome

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

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Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis

Blood ◽

10.1182/blood-2008-04-147884 ◽

2008 ◽

Vol 112 (7) ◽

pp. 2709-2712 ◽

Cited By ~ 161

Author(s):

Maria E. Sarasquete ◽

Ramon García-Sanz ◽

Luis Marín ◽

Miguel Alcoceba ◽

Maria C. Chillón ◽

...

Keyword(s):

Multiple Myeloma ◽

Cytochrome P450 ◽

Genome Wide Association Study ◽

Osteonecrosis Of The Jaw ◽

Bisphosphonate Therapy ◽

Polymorphism Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome

Abstract We have explored the potential role of genetics in the development of osteonecrosis of the jaw (ONJ) in multiple myeloma (MM) patients under bisphosphonate therapy. A genome-wide association study was performed using 500 568 single nucleotide polymorphisms (SNPs) in 2 series of homogeneously treated MM patients, one with ONJ (22 MM cases) and another without ONJ (65 matched MM controls). Four SNPs (rs1934951, rs1934980, rs1341162, and rs17110453) mapped within the cytochrome P450-2C gene (CYP2C8) showed a different distribution between cases and controls with statistically significant differences (P = 1.07 × 10−6, P = 4.231 × 10−6, P = 6.22 × 10−6, and P = 2.15 × 10−6, respectively). SNP rs1934951 was significantly associated with a higher risk of ONJ development even after Bonferroni correction (P corrected value = .02). Genotyping results displayed an overrepresentation of the T allele in cases compared with controls (48% vs 12%). Thus, individuals homozygous for the T allele had an increased likelihood of developing ONJ (odds ratio 12.75, 95% confidence interval 3.7-43.5).

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Haplotypes within tandemly duplicated candidate genes at BnaA9.MRP5 modulate phytate concentration in canola (Brassica napus L.)

10.22541/au.161165160.08519096/v1 ◽

2021 ◽

Author(s):

Haijiang Liu ◽

xiaojuan Li ◽

Qianwen Zhang ◽

pan yuan ◽

Lei Liu ◽

...

Keyword(s):

Candidate Genes ◽

Oilseed Rape ◽

Genome Wide Association Study ◽

Mineral Elements ◽

Nucleotide Polymorphisms ◽

Brassica Napus L ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

Phytate Content

Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape B. napus (oilseed rape). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 x 106 single nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low -phytate variety (LPA20) was significantly elevated compared with a high -phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favorable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.

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Three New Single Nucleotide Polymorphisms Identified by a Genome-Wide Association Study in Korean Patients with Vitiligo

Journal of Korean Medical Science ◽

10.3346/jkms.2013.28.5.775 ◽

2013 ◽

Vol 28 (5) ◽

pp. 775 ◽

Cited By ~ 11

Author(s):

Kyung Ah Cheong ◽

Nan-Hyung Kim ◽

Minsoo Noh ◽

Ai-Young Lee

Keyword(s):

Single Nucleotide Polymorphisms ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Korean Patients ◽

Genome Wide ◽

A Genome

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Lifestyle factors and genetic variants on two biological age measures: evidence from 94,443 Taiwan Biobank participants

The Journals of Gerontology Series A ◽

10.1093/gerona/glab251 ◽

2021 ◽

Author(s):

Wan-Yu Lin

Keyword(s):

Genetic Variants ◽

Genome Wide Association Study ◽

Lifestyle Factors ◽

Biological Age ◽

Biological Aging ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

The Uk

Abstract Background Biological age (BA) can be estimated by phenotypes and is useful for predicting lifespan and healthspan. Levine et al. proposed a PhenoAge and a BioAge to measure BA. Although there have been studies investigating the genetic predisposition to BA acceleration in Europeans, little has been known regarding this topic in Asians. Methods I here estimated PhenoAgeAccel (age-adjusted PhenoAge) and BioAgeAccel (age-adjusted BioAge) of 94,443 Taiwan Biobank (TWB) participants, wherein 25,460 TWB1 subjects formed a discovery cohort and 68,983 TWB2 individuals constructed a replication cohort. Lifestyle factors and genetic variants associated with PhenoAgeAccel and BioAgeAccel were investigated through regression analysis and a genome-wide association study (GWAS). Results A unit (kg/m 2) increase of BMI was associated with a 0.177-year PhenoAgeAccel (95% C.I. = 0.163~0.191, p = 6.0×) and 0.171-year BioAgeAccel (95% C.I. = 0.165~0.177, p = 0). Smokers on average had a 1.134-year PhenoAgeAccel (95% C.I. = 0.966~1.303, p = 1.3×) compared with non-smokers. Drinkers on average had a 0.640-year PhenoAgeAccel (95% C.I. = 0.433~0.847, p = 1.3×) and 0.193-year BioAgeAccel (95% C.I. = 0.107~0.279, p = 1.1×) relative to non-drinkers. A total of 11 and 4 single-nucleotide polymorphisms (SNPs) were associated with PhenoAgeAccel and BioAgeAccel (p<5× in both TWB1 and TWB2), respectively. Conclusions A PhenoAgeAccel-associated SNP (rs1260326 in GCKR) and two BioAgeAccel-associated SNPs (rs7412 in APOE; rs16998073 near FGF5) were consistent with the finding from the UK Biobank. The lifestyle analysis shows that prevention from obesity, cigarette smoking, and alcohol consumption is associated with a slower rate of biological aging.

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