scholarly journals Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Qunhao Niu ◽  
Tianliu Zhang ◽  
Ling Xu ◽  
Tianzhen Wang ◽  
Zezhao Wang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Snp Array ◽  
Whole Genome Sequence ◽  
A Genome ◽  
High Conservation ◽  
Multiple Species ◽  
Body Stature

Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 117
Author(s):  
Donglin Ruan ◽  
Zhanwei Zhuang ◽  
Rongrong Ding ◽  
Yibin Qiu ◽  
Shenping Zhou ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bone Growth ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Snp Array ◽  
Single Step ◽  
Economic Traits ◽  
Association Analyses ◽  
Genealogical Information

Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

scholarly journals Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

2018 ◽  
Vol 50 (7) ◽  
pp. 523-531 ◽  
Author(s):  
Bingxing An ◽  
Jiangwei Xia ◽  
Tianpeng Chang ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Genome Wide Association ◽  
Heart Weight ◽  
Spleen Weight ◽  
Internal Organs ◽  
Genome Wide ◽  
A Genome

Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.

scholarly journals Genome-Wide Association Study Reveals Candidate Genes Involved in Fruit Trait Variation in Persian Walnut (Juglans regia L.)

2021 ◽  
Vol 11 ◽  
Author(s):  
Anthony Bernard ◽  
Julie Crabier ◽  
Armel S. L. Donkpegan ◽  
Annarita Marrano ◽  
Fabrice Lheureux ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Fruit Quality ◽  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Elucidating the genetic determinants of fruit quality traits in walnut is essential to breed new cultivars meeting the producers and consumers’ needs. We conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of Juglans regia from the INRAE walnut germplasm collection, previously genotyped using the AxiomTMJ. regia 700K SNP array. We phenotyped the panel for 25 fruit traits related to morphometrics, shape, volume, weight, ease of cracking, and nutritional composition. We found more than 60 marker-trait associations (MTAs), including a highly significant SNP associated with nut face diameter, nut volume and kernel volume on chromosome 14, and 5 additional associations were detected for walnut weight. We proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to be involved in fruit development in other species. We also confirmed associations on chromosomes 5 and 11 with nut suture strength, recently reported by the University of California, Davis. Our results enhance knowledge of the genetic control of important agronomic traits related to fruit quality in walnut, and pave the way for the development of molecular markers for future assisted selection.

scholarly journals A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Xinghua Li ◽  
Changsheng Nie ◽  
Yuchen Liu ◽  
Yu Chen ◽  
Xueze Lv ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Carrier State ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Challenge Experiment ◽  
Salmonella Pullorum

Abstract Background Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which causes high mortality. Furthermore, an outbreak of SP infection can result in a considerable number of carriers that become potential transmitters, thus, threatening fellow chickens and offspring. In this study, we conducted a genome-wide association study (GWAS) to detect potential genomic loci and candidate genes associated with two disease-related traits: death and carrier state. Methods In total, 818 birds were phenotyped for death and carrier state traits through a SP challenge experiment, and genotyped by using a 600 K high-density single nucleotide polymorphism (SNP) array. A GWAS using a single-marker linear mixed model was performed with the GEMMA software. RNA-sequencing on spleen samples was carried out for further identification of candidate genes. Results We detected a region that was located between 33.48 and 34.03 Mb on chicken chromosome 4 and was significantly associated with death, with the most significant SNP (rs314483802) accounting for 11.73% of the phenotypic variation. Two candidate genes, FBXW7 and LRBA, were identified as the most promising genes involved in resistance to SP. The expression levels of FBXW7 and LRBA were significantly downregulated after SP infection, which suggests that they may have a role in controlling SP infections. Two other significant loci and related genes (TRAF3 and gga-mir-489) were associated with carrier state, which indicates a different polygenic determinism compared with that of death. In addition, genomic inbreeding coefficients showed no correlation with resistance to SP within each breed in our study. Conclusions The results of this GWAS with a carefully organized Salmonella challenge experiment represent an important milestone in understanding the genetics of infectious disease resistance, offer a theoretical basis for breeding SP-resistant chicken lines using marker-assisted selection, and provide new information for salmonellosis research in humans and other animals.

scholarly journals Exploring the genetic architecture of feed efficiency traits in chickens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jorge Augusto Petroli Marchesi ◽  
Rafael Keith Ono ◽  
Maurício Egídio Cantão ◽  
Adriana Mércia Guaratini Ibelli ◽  
Jane de Oliveira Peixoto ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Efficiency ◽  
Gene Networks ◽  
Genome Wide Association Study ◽  
Body Weight Gain ◽  
Snp Array ◽  
Experimental Population ◽  
Economic Traits ◽  
A Genome ◽  
Genomic Regions

AbstractChicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.

PSXI-7 Genomic analysis of heterosis in a composite beef cattle breed

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 244-244
Author(s):  
El Hamidi Hay ◽  
Andrew Roberts
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Weaning Weight ◽  
Genome Wide ◽  
A Genome

Abstract Crossbreeding is widely used in the beef cattle industry to exploit benefits of heterosis. This study evaluated the effects of heterozygosity on growth traits in an Angus x Hereford cross population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1,530 animals, comprised of pure Line 1 Hereford, Angus and Angus x Line 1 Hereford crosses, were evaluated. Phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Effects of genomic heterozygosity on growth traits were estimated. These effects were -0.76 kg (P &lt; 0.001), 4.67 kg (P &lt; 0.0001), 42.39 kg (P &lt; 0.02) on birth weight, weaning weight and yearling weight respectively. A genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.

scholarly journals Identification of potential genes for resistance to tomato spotted wilt and leaf spots in peanut (Arachis hypogaea L.) through GWAS analysis

2019 ◽  
Author(s):  
Hui Zhang ◽  
Ye Chu ◽  
Phat Dang ◽  
Yueyi Tang ◽  
Jing Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Leaf Spot ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
The United States ◽  
Economic Losses ◽  
Major Qtls ◽  
Tomato Spotted Wilt ◽  
A Genome ◽  
Genomic Regions

Abstract Background Tomato spotted wilt (TSW), early leaf spot (ELS), and late leaf spot (LLS) are three serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. However, the genes underlying resistance to those diseases in peanut have not been well studied. We conducted a genome-wide association study (GWAS) for the three peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the U.S. peanut mini core collection. Results A total of 87 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.2% to 24.1%, in which 41 QTLs are for resistance to TSW, 18 QTLs for ELS, and 28 QTLs for LLS. Among the 87 QTLs, there were six, four, and two major QTLs with PVE higher than 14.9% for resistance to TSW, ELS, and LLS, respectively. Of the 12 major QTLs, 10 were located on the B sub-genome and only 2 were on the A sub-genome, which suggested that the B sub-genome has more significantly resistance genomic regions than the A sub-genome. In addition, two genomic regions on linkage group B09 were found to provide significant resistance to both ELS and LLS. A total of 22 non-redundant candidate genes were identified significantly associated with diseases, which include 18 candidate genes for TSW, 3 candidate genes for both ELS and LLS, and 1 candidate gene for LLS, respectively. Conclusions Most candidate genes in the associated regions are known to be involved in immunity and defense response. The QTLs and candidate genes obtained from this study will be useful to breed peanut for resistances to the diseases.

scholarly journals Identification of loci associated with pathological outcomes in Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis using whole-genome sequence data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Canive ◽  
Gerard Badia-Bringué ◽  
Patricia Vázquez ◽  
Oscar González-Recio ◽  
Almudena Fernández ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Mycobacterium Avium ◽  
Genome Wide Association Study ◽  
Cholesterol Metabolism ◽  
Sequence Data ◽  
Plasma Cholesterol ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Histological Lesion ◽  
A Genome

AbstractBovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous enteritis that affects cattle worldwide. According to their severity and extension, PTB-associated histological lesions have been classified into the following groups; focal, multifocal, and diffuse. It is unknown whether these lesions represent sequential stages or divergent outcomes. In the current study, the associations between host genetic and pathology were explored by genotyping 813 Spanish Holstein cows with no visible lesions (N = 373) and with focal (N = 371), multifocal (N = 33), and diffuse (N = 33) lesions in gut tissues and regional lymph nodes. DNA from peripheral blood samples of these animals was genotyped with the bovine EuroG MD Bead Chip, and the corresponding genotypes were imputed to whole-genome sequencing (WGS) data using the 1000 Bull genomes reference population. A genome-wide association study (GWAS) was performed using the WGS data and the presence or absence of each type of histological lesion in a case–control approach. A total of 192 and 92 single nucleotide polymorphisms (SNPs) defining 13 and 9 distinct quantitative trait loci (QTLs) were highly-associated (P ≤ 5 × 10−7) with the multifocal (heritability = 0.075) and the diffuse (heritability = 0.189) lesions, respectively. No overlap was seen in the SNPs controlling these distinct pathological outcomes. The identified QTLs overlapped with some QTLs previously associated with PTB susceptibility, bovine tuberculosis susceptibility, clinical mastitis, somatic cell score, bovine respiratory disease susceptibility, tick resistance, IgG level, and length of productive life. Pathway analysis with candidate genes overlapping the identified QTLs revealed a significant enrichment of the keratinization pathway and cholesterol metabolism in the animals with multifocal and diffuse lesions, respectively. To test whether the enrichment of SNP variants in candidate genes involved in the cholesterol metabolism was associated with the diffuse lesions; the levels of total cholesterol were measured in plasma samples of cattle with focal, multifocal, or diffuse lesions or with no visible lesions. Our results showed reduced levels of plasma cholesterol in cattle with diffuse lesions. Taken together, our findings suggested that the variation in MAP-associated pathological outcomes might be, in part, genetically determined and indicative of distinct host responses.

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