Single-Nucleotide Polymorphism Variations Associated With Specific Genes Putatively Identified Enhanced Genetic Predisposition for 305-Day Milk Yield in the Girolando Crossbreed

Cruz, Alex Silva da; Silva, Danilo Conrado; Minasi, Lysa Bernardes; Teixeira, Larissa Kamídia de Farias; Rodrigues, Flávia Melo; Silva, Cláudio Carlos da; Carmo, Adriana Santana do; Silva, Marcos Vinícius Gualberto Barbosa da; Utsunomiya, Yuri Tani; Garcia, José Fernando; Cruz, Aparecido Divino da

doi:10.3389/fgene.2020.573344

Cited by 13 publications

(12 citation statements)

References 34 publications

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“…This SNP is located near to KHDRBS3 gene, which is a member of the signal transduction and the activator of RNA (STAR) family proteins. It has been reported that this gene is associated with the 305-day milk yield trait in two cattle breeds: Girolando crossbreed cattle [ 40 ] and primiparous Holstein cows [ 41 ]. Gene network interactions analysis, derived from GWAS-based results, revealed this gene is related to meat quality and growth traits of Brazilian Nelore beef cattle [ 42 ], as well as carcass weight trait in Hanwoo cattle [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

Abdalla

Jiang

Nazar

et al. 2023

Animals

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Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10−7) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.

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Section: Discussionmentioning

confidence: 99%

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

Abdalla

Jiang

Nazar

et al. 2023

Animals

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“…For the NSB trait, a number of candidate genes located within 20 kb of the genome-wide significant and suggestive significant SNPs were identified in both lines. Among them, the NUB1 gene has been reported to be associated with milk production traits in cows and sheep [ 55 , 56 ]. The TGFBR3 gene was also reported to be associated with oocyte maturation in pigs [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Wang

Shi

et al. 2022

IJMS

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Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.

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“…Since GWASs are ideal for discovering genes that encode complex traits and their mechanisms [ 5 ], they have been widely conducted in recent years to identify relationships between genomic variants and economically significant traits in dairy cattle populations. As a result, a large number of candidate genes and quantitative genomic areas were detected to be associated with economically important traits, including milk-related traits, fertility, growth, and meat and carcass quality [ 3 , 4 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]. GWASs conducted in various cattle breeds utilized different SNP chip platforms and were focused on the identification of potential candidate genes and genomic regions responsible for milk production traits including milk yield (MY), fat yield (FY), and protein yield (PY).…”

Section: Introductionmentioning

confidence: 99%

“…The most frequently reported candidate genes (DGAT1, GHR, MAPK15) and SNPs associated with milk production traits are located on chromosome 14 [ 4 ]. Other genes of interest harbored on chromosomes 14 and 20 are GNA14, PTBP2, and U6 which were closely associated with a higher MY [ 6 , 12 , 18 ], respectively. ITPR2 [ 19 ], ABCC9 [ 20 , 21 ], CPSF1 [ 21 ], PDE4 [ 13 ], and METTL15 [ 19 ] genes were reported to influence the expression of FY, while the genes associated with PY were PDHA2 [ 19 ], CTBP2 [ 19 ], MAPK9 [ 22 ], HPS3 [ 23 ], ARFGEF [ 24 ], SLCO1A2 [ 21 ], and MFSD1 [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle

Ristanic,

Zorc,

Glavinic

et al. 2024

Animals

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To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.

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Single-Nucleotide Polymorphism Variations Associated With Specific Genes Putatively Identified Enhanced Genetic Predisposition for 305-Day Milk Yield in the Girolando Crossbreed

Cited by 13 publications

References 34 publications

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle

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