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 Genome-Wide Association Study and Pathway Analysis for Female Fertility Traits in Iranian Holstein Cattle

2020 ◽  
Vol 20 (3) ◽  
pp. 825-851
Author(s):  
Ali Mohammadi ◽  
Sadegh Alijani ◽  
Seyed Abbas Rafat ◽  
Rostam Abdollahi-Arpanahi
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Female Fertility ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Holstein Cattle ◽  
Potential Candidate ◽  
Genome Wide ◽  
Fertility Traits

AbstractFemale fertility is an important trait that contributes to cow’s profitability and it can be improved by genomic information. The objective of this study was to detect genomic regions and variants affecting fertility traits in Iranian Holstein cattle. A data set comprised of female fertility records and 3,452,730 pedigree information from Iranian Holstein cattle were used to predict the breeding values, which were then employed to estimate the de-regressed proofs (DRP) of genotyped animals. A total of 878 animals with DRP records and 54k SNP markers were utilized in the genome-wide association study (GWAS). The GWAS was performed using a linear regression model with SNP genotype as a linear covariate. The results showed that an SNP on BTA19, ARS-BFGL-NGS-33473, was the most significant SNP associated with days from calving to first service. In total, [69] significant SNPs were located within 27 candidate genes. Novel potential candidate genes include OSTN, DPP6, EphA5, CADPS2, Rfc1, ADGRB3, Myo3a, C10H14orf93, KIAA1217, RBPJL, SLC18A2, GARNL3, NCALD, ASPH, ASIC2, OR3A1, CHRNB4, CACNA2D2, DLGAP1, GRIN2A and ME3. These genes are involved in different pathways relevant to female fertility and other characteristics in mammals. Gene set enrichment analysis showed that thirteen GO terms had significant overrepresentation of genes statistically associated with female fertility traits. The results of network analysis identified CCNB1 gene as a hub gene in the progesterone-mediated oocyte maturation pathway, significantly associated with age at first calving. The candidate genes identified in this study can be utilized in genomic tests to improve reproductive performance in Holstein cattle.

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.

scholarly journals Genome-Wide Association Study Identifies Candidate Genes Related to the Linoleic Acid Content in Soybean Seeds

2021 ◽  
Vol 23 (1) ◽  
pp. 454
Author(s):  
Qin Di ◽  
Angela Piersanti ◽  
Qi Zhang ◽  
Cristina Miceli ◽  
Hui Li ◽  
...  
Keyword(s):  
Linoleic Acid ◽  
Association Study ◽  
Candidate Genes ◽  
Acid Content ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Soybean Seeds ◽  
Potential Candidate ◽  
Genome Wide

Soybean (Glycine max (L.) Merrill) oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). The high content of linoleic acid (LA) contributes to the oil having poor oxidative stability. Therefore, soybean seed with a lower LA content is desirable. To investigate the genetic architecture of LA, we performed a genome-wide association study (GWAS) using 510 soybean cultivars collected from China. The phenotypic identification results showed that the content of LA varied from 36.22% to 72.18%. The GWAS analysis showed that there were 37 genes related to oleic acid content, with a contribution rate of 7%. The candidate gene Glyma.04G116500.1 (GmWRI14) on chromosome 4 was detected in three consecutive years. The GmWRI14 showed a negative correlation with the LA content and the correlation coefficient was −0.912. To test whether GmWRI14 can lead to a lower LA content in soybean, we introduced GmWRI14 into the soybean genome. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) showed that the overexpression of GmWRI14 leads to a lower LA content in soybean seeds. Meanwhile, RNA-seq verified that GmWRI14-overexpressed soybean lines showed a lower accumulation of GmFAD2-1A and GmFAD2-1B than control lines. Our results indicate that the down-regulation of the FAD2 gene triggered by the transcription factor GmWRI14 is the underlying mechanism reducing the LA level of seed. Our results provide novel insights into the genetic architecture of LA and pinpoint potential candidate genes for further in-depth studies.

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