scholarly journals Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2259
Author(s):  
Ismail Mohamed Abdalla ◽  
Xubin Lu ◽  
Mudasir Nazar ◽  
Abdelaziz Adam Idriss Arbab ◽  
Tianle Xu ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Candidate Genes ◽  
Association Studies ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Holstein Cattle ◽  
Genome Wide Association Studies ◽  
Chinese Holstein ◽  
Genome Wide ◽  
Chinese Holstein Cattle

Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4 and CADPS. Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (p ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle.

Genome-Wide Association Studies for Immunoglobulin Concentrations in Colostrum and Serum in Chinese Holstein

2020 ◽  
Author(s):  
Shan Lin ◽  
Cuncun Ke ◽  
Lin Liu ◽  
Yahui Gao ◽  
Lingna Xu ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Association Studies ◽  
Early Death ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Economic Losses ◽  
Genome Wide Association Studies ◽  
Chinese Holstein ◽  
Genome Wide ◽  
Nf Kappab

Abstract BackgroundThe early death and health problems of calves caused substantial economic losses in dairy industry. As the immune system has not been fully developed in the neonates, transport of passive immune substance such as immunoglobulins (Ig) from mothers to newborn calves is essential in protecting neonates from infections in their early life. Therefore, concentrations of immunoglobulins in the colostrum and serum of dairy cows are critical traits when estimating potential disease resistance of its offspring. ResultsColostrum, blood and hair follicle samples were collected from the 620 Chinese Holstein cows within 24 hours after calving. The concentration of total IgG, IgG1, IgG2, IgA and IgM in both colostrum and serum were detected via ELISA methods. With GCTA software, genome-wide association studies (GWASs) were performed with 88,934 SNPs genotyped by using Illumina 50K (54,609 SNPs) and GeneSeek 150K (140,668 SNPs) chips in which 50K chip were imputed to 150K SNPs with BEAGLE. As a result, 20, 1 and 4 significant SNPs were detected associated with the concentrations of IgG2, IgA and IgM at genome-wide level (P < 3.16E–6); 11, 11, 35, 11 and 10 significant SNPs were identified associated with total IgG, IgG1, IgG2, IgA and IgM at suggestive level (P < 6.32E–5). Such SNPs were located in or proximate to (±1 Mb) 1,083 genes, which were functionally implicated in biological processes and pathways, such as immune response, negative regulation of immunoglobulin secretion, Fc-epsilon receptor and NF-kappaB signaling pathways. By combining the biological functions and the known QTL data for immune traits in bovine, 21 promising candidate functional genes were identified for immunoglobulins concentrations in colostrum and serum in dairy cattle, they were ABR, TIMM22, CRK, MYO1C, RILP, SERPINF2, AKT1, BCL11B, HHIPL1, DYNC1H1, HSP90AA1, TRAF3, KLC1, IL6, PYCARD, ITGAM, TGFB1I1, GUSB, CRCP, RABGEF1 and SBDS.ConclusionsIn this study, we identified 21 candidate genes related to concentrations of immunoglobulins in colostrum and serum in dairy cattle by performing GWASs. Our findings provide a groundwork for unraveling the key genes and causal mutations affecting immunoglobulins levels in colostrum and important information for genetic improvement of such traits in dairy cattle.

Genome-Wide Association Studies for Immunoglobulins in Colostrum and Serum in Chinese Holstein

2020 ◽  
Author(s):  
Shan Lin ◽  
Cuncun Ke ◽  
Lin Liu ◽  
Yahui Gao ◽  
Lingna Xu ◽  
...  
Keyword(s):  
Immune Response ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Functional Enrichment ◽  
Genome Wide Association ◽  
Holstein Cows ◽  
Genome Wide Association Studies ◽  
Chinese Holstein ◽  
Genome Wide ◽  
A Genome

Abstract BackgroundImmunoglobulins (Igs) are important components of the innate immune system, and fight pathogens as a part of the first defense line. Newborn dairy calves get maternal antibodies from colostrum. Therefore, contents of immunoglobulins in colostrum and serum of cows are essential traits when estimating potential natural disease resistance of calves. In this study, a genome-wide association study (GWAS) was performed to identify candidate genes that are responsible for the observed genetic variation of immunoglobulins contents in colostrum and blood in Holstein cows.ResultsColostrum, blood and hair follicle samples were collected from the 620 Chinese Holstein cows within 24 hours after calving. The concentration of IgG, IgG1, IgG2, IgA and IgM in both colostrum and serum were detected via ELISA methods, respectively. Using GCTA software, GWASs were performed with 88,934 SNPs genotyped by using Illumina 50K (54,609 SNPs) and GeneSeek 150K (140,668 SNPs) chips in which 50K chip were imputed to 150K SNPs with BEAGLE 3.0.4 software. As a result, 20 and 5 SNPs were detected genome-wide significantly associated with contents of the IgG and IgM in colostrum and serum (P<3.16E–6). In addition, 57, 11 and 10 SNPs were suggestive significantly associated with IgG, IgA and IgM traits (P<6.32E–5). Next, a total of 1,083 functional genes were identified that included or adjacent to these significant SNPs with a distance less than 1 Mb. Functional enrichment analysis showed that these genes were involved in immune related pathways, such as immune response, Fc gamma R-mediated phagocytosis, negative regulation of immunoglobulin secretion, humoral immune response, Fc-epsilon receptor and NF-kappaB signaling pathways. By integrating analysis of the functional enrichment and the known QTL data, we identified 21 candidate genes associated with contents of immunoglobulins in colostrum and serum, including ABR, TIMM22, CRK, MYO1C, RILP, SERPINF2, AKT1, BCL11B, HHIPL1, DYNC1H1, HSP90AA1, TRAF3, KLC1, IL6, PYCARD, ITGAM, TGFB1I1, GUSB, CRCP, RABGEF1 and SBDS.ConclusionsIn this study, we identified 21 candidate genes associated with immunoglobulins level in colostrum and serum in dairy cattle. This founding demonstrated the possibility of increasing immunity through selective breeding and provided an important information for molecular breeding of dairy cattle.

scholarly journals Genome-Wide Association Studies Reveal Susceptibility Loci for Noninfectious Claw Lesions in Holstein Dairy Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Ellen Lai ◽  
Alexa L. Danner ◽  
Thomas R. Famula ◽  
Anita M. Oberbauer
Keyword(s):  
Dairy Cattle ◽  
Candidate Genes ◽  
Linear Mixed Model ◽  
Association Studies ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Susceptibility Loci ◽  
Genome Wide ◽  
Claw Lesions

Sole ulcers (SUs) and white line disease (WLD) are two common noninfectious claw lesions (NICL) that arise due to a compromised horn production and are frequent causes of lameness in dairy cattle, imposing welfare and profitability concerns. Low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify the susceptibility loci for SU, WLD, SU and/or WLD, and any type of noninfectious claw lesion, genome-wide association studies (GWAS) were performed using generalized linear mixed model (GLMM) regression, chunk-based association testing (CBAT), and a random forest (RF) approach. Cows from five commercial dairies in California were classified as controls having no lameness records and ≥6 years old (n = 102) or cases having SU (n = 152), WLD (n = 117), SU and/or WLD (SU + WLD, n = 198), or any type of noninfectious claw lesion (n = 217). The top single nucleotide polymorphisms (SNPs) were defined as those passing the Bonferroni-corrected suggestive and significance thresholds in the GLMM analysis or those that a validated RF model considered important. Effects of the top SNPs were quantified using Bayesian estimation. Linkage disequilibrium (LD) blocks defined by the top SNPs were explored for candidate genes and previously identified, functionally relevant quantitative trait loci. The GLMM and CBAT approaches revealed the same regions of association on BTA8 for SU and BTA13 common to WLD, SU + WLD, and NICL. These SNPs had effects significantly different from zero, and the LD blocks they defined explained a significant amount of phenotypic variance for each dataset (6.1–8.1%, p &lt; 0.05), indicating the small but notable contribution of these regions to susceptibility. These regions contained candidate genes involved in wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. The LD block defined by the most significant SNP on BTA8 for SU included a SNP previously associated with SU. The RF models were overfitted, indicating that the SNP effects were very small, thereby preventing meaningful interpretation of SNPs and any downstream analyses. These findings suggested that variants associated with various physiological systems may contribute to susceptibility for NICL, demonstrating the complexity of genetic predisposition.

scholarly journals Genome-Wide Association Study Candidate Genes on Mammary System-Related Teat-Shape Conformation Traits in Chinese Holstein Cattle

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2020
Author(s):  
Mudasir Nazar ◽  
Xubin Lu ◽  
Ismail Mohamed Abdalla ◽  
Numan Ullah ◽  
Yongliang Fan ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Holstein Cattle ◽  
Dairy Production ◽  
Chinese Holstein ◽  
Genome Wide ◽  
Chinese Holstein Cattle

In the dairy industry, mammary system traits are economically important for dairy animals, and it is important to explain their fundamental genetic architecture in Holstein cattle. Good and stable mammary system-related teat traits are essential for producer profitability in animal fitness and in the safety of dairy production. In this study, we conducted a genome-wide association study on three traits—anterior teat position (ATP), posterior teat position (PTP), and front teat length (FTL)—in which the FarmCPU method was used for association analyses. Phenotypic data were collected from 1000 Chinese Holstein cattle, and the GeneSeek Genomic Profiler Bovine 100K single-nucleotide polymorphisms (SNP) chip was used for cattle genotyping data. After the quality control process, 984 individual cattle and 84,406 SNPs remained for GWAS work analysis. Nine SNPs were detected significantly associated with mammary-system-related teat traits after a Bonferroni correction (p < 5.92 × 10−7), and genes within a region of 200 kb upstream or downstream of these SNPs were performed bioinformatics analysis. A total of 36 gene ontology (GO) terms and 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to metabolic processes, immune response, and cellular and amino acid catabolic processes. Eleven genes including MMS22L, E2F8, CSRP3, CDH11, PEX26, HAL, TAMM41, HIVEP3, SBF2, MYO16 and STXBP6 were selected as candidate genes that might play roles in the teat traits of cows. These results identify SNPs and candidate genes that give helpful biological information for the genetic architecture of these teat traits, thus contributing to the dairy production, health, and genetic selection of Chinese Holstein cattle.

scholarly journals Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 806
Author(s):  
Yang Li ◽  
Lei Pu ◽  
Liangyu Shi ◽  
Hongding Gao ◽  
Pengfei Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Significant Snps ◽  
Genomic Region ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Teat Number ◽  
The Right

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs.

scholarly journals Genome-wide association studies for immunoglobulin concentrations in colostrum and serum in Chinese Holstein

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Shan Lin ◽  
Cuncun Ke ◽  
Lin Liu ◽  
Yahui Gao ◽  
Lingna Xu ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Cell Activation ◽  
Association Studies ◽  
Early Death ◽  
Genome Wide Association ◽  
Economic Losses ◽  
Common Disease ◽  
Genome Wide Association Studies ◽  
Chinese Holstein ◽  
Genome Wide

Abstract Background The early death and health problems of calves caused substantial economic losses in the dairy industry. As the immune system of neonates has not been fully developed, the absorption of maternal immunoglobulin (Ig) from colostrum is essential in protecting newborn calves against common disease organisms in their early life. The overwhelming majority of Ig in bovine whey is transported from the serum. Therefore, Ig concentration in the colostrum and serum of dairy cows are critical traits when estimating the potential disease resistance of its offspring. Results Colostrum, blood, and hair follicle samples were collected from 588 Chinese Holstein cows within 24 h after calving. The concentration of total IgG, IgG1, IgG2, IgA and IgM in both colostrum and serum were detected via ELISA methods. With GCTA software, genome-wide association studies (GWASs) were performed with 91,620 SNPs genotyped by GeneSeek 150 K (140,668 SNPs) chips. As a result, 1, 5, 1 and 29 significant SNPs were detected associated with the concentrations of colostrum IgG1, IgG2, IgA IgM, and serum IgG2 at the genome-wide level (P < 3.08E–6); 11, 2, 13, 2, 12, 8, 2, 27, 1 and 4 SNPs were found significantly associated with total IgG, IgG1, IgG2, IgA and IgM in colostrum and serum at the suggestive level (P < 6.15E–5). Such SNPs located in or proximate to (±1 Mb) 423 genes, which were functionally implicated in biological processes and pathways, such as immune response, B cell activation, inflammatory response and NF-kappaB signaling pathways. By combining the biological functions and the known QTL data for immune traits in bovine, 14 promising candidate functional genes were identified for immunoglobulin concentrations in colostrum and serum in dairy cattle, they were FGFR4, FGFR2, NCF1, IKBKG, SORBS3, IGHV1S18, KIT, PTGS2, BAX, GRB2, TAOK1, ICAM1, TGFB1 and RAC3. Conclusions In this study, we identified 14 candidate genes related to concentrations of immunoglobulins in colostrum and serum in dairy cattle by performing GWASs. Our findings provide a groundwork for unraveling the key genes and causal mutations affecting immunoglobulin concentrations in colostrum and important information for genetic improvement of such traits in dairy cattle.

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