Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle

Kim, Sang–Wook; Lim, Bee-Oh; Cho, Joohyeon; Lee, Seokhyun; Dang, Chang Gwon; Jeon, Jung-Hwan; Kim, Junmo; Lee, J.

doi:10.3390/ani11051392

Cited by 14 publications

(7 citation statements)

References 84 publications

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“…The study by Ning et al ( 40 ) used two models and a 70k SNP chip based on the Chinese Holsteins population and identified the DGAT1 gene to be related to milk ( 40 ). Kim et al ( 41 ) also obtained DGAT1 affecting MY and FY in the Korean cattle population ( 41 ). Cole et al ( 42 ) identified the PHKA2 gene to be highly significant for four body size traits (stature, strength, body depth, rump width) ( 42 ).…”

Section: Discussionmentioning

confidence: 93%

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Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows

et al. 2022

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Milk production and body conformation traits are critical economic traits for dairy cows. To understand the basic genetic structure for those traits, a genome wide association study was performed on milk yield, milk fat yield, milk fat percentage, milk protein yield, milk protein percentage, somatic cell score, body form composite index, daily capacity composite index, feed, and leg conformation traits, based on the Illumina Bovine HD100k BeadChip. A total of 57, 12 and 26 SNPs were found to be related to the milk production, somatic cell score and body conformation traits in the Holstein cattle. Genes with pleiotropic effect were also found in this study. Seven significant SNPs were associated with multi-traits and were located on the PLEC, PLEKHA5, TONSL, PTGER4, and LCORL genes. In addition, some important candidate genes, like GPAT3, CEBPB, AGO2, SLC37A1, and FNDC3B, were found to participate in fat metabolism or mammary gland development. These results can be used as candidate genes for milk production, somatic cell score, and body conformation traits of Holstein cows, and are helpful for further gene function analysis to improve milk production and quality.

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Section: Discussionmentioning

confidence: 93%

“…It is common in nature. For example, the DGAT1 gene is related to milk yield ( 40 ) and fat yield ( 26 , 41 ). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size ( 10 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows

et al. 2022

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“…Network analysis has been promoted as one of the most effective methods for decoding the key regulatory elements in biological systems and their intricate molecular machinery 38 , 39 . Here, the purpose of network analysis was to identify an association of DGAT1 with other proteins in a holistic view based on the information available in the STRING database.…”

Section: Discussionmentioning

confidence: 99%

Unraveling structural and conformational dynamics of DGAT1 missense nsSNPs in dairy cattle

Pathak

Lim

Park

et al. 2022

Sci Rep

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Cattle are domestic animals that have been nourishing humans for thousands of years. Milk from cattle represents a key source of high-quality protein, fat, and other nutrients. The nutritional value of milk and dairy products is closely associated with the fat content, providing up to 30% of the total fat consumed in the human diet. The fat content in cattle milk represents a major concern for the scientific community due to its association with human health. The relationship between milk fat content and diacylglycerol o-acyltransferase 1 gene (DGAT1) is well described in literature. Several studies demonstrated the difference in fat contents and other milk production traits in a wide range of cattle breeds, to be associated with missense non-synonymous single nucleotide polymorphisms (nsSNPs) of the DGAT1 gene. As a result, an nsSNPs analysis is crucial for unraveling the DGAT1 structural and conformational dynamics linked to milk fat content. DGAT1-nsSNPs are yet to be studied in terms of their structural and functional impact. Therefore, state-of-the-art computational and structural genomic methods were used to analyze five selected variants (W128R, W214R, C215G, P245R, and W459G), along with the wild type DGAT1. Significant structural and conformational changes in the variants were observed. We illustrate how single amino acid substitutions affect DGAT1 function, how this contributes to our understanding of the molecular basis of variations in DGAT1, and ultimately its impact in improving fat quality in milk.

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“…Several QTL and genes have been identi ed with associated to SCS (Mullen et al 2011; Marete et al 2018;Zeb et al 2020; Kim et al 2021). The genes work together and their interactions car out a biological functions and a group of genes that share common biological functions are considered as gene module (Gong et al 2007).…”

Section: Introductionmentioning

confidence: 99%

“…There is relationship between complement and coagulation(Donat et al 2019). SNP located on VWF has signi cant association with SCS(Kim et al 2021). TNFSF11, identi ed one of the hub gene in our study, is gene that its products expressed in T cells to stimulate dendritic cells and there is association between SNP of this gene with SCS(Marete et al 2018).…”

mentioning

confidence: 99%

Identification of hub genes associated with somatic cell score in dairy cow

Ghiasi

Khaldari

2022

Preprint

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Somatic cell count (SCC) is used as an indicator of udder health. The log transformation of SCC is called somatic cell score (SCS). Several QTL and genes have been identified with associated to SCS. The aim of this study was to identify most important genes associated to SCS. In this study we collected 168 genes reported significantly associated with SCS. Pathway analysis and network analysis used to identifying hub genes. Pathway analysis of these genes identified 73 GO terms associated to SCS. These top GO terms involved in molecular function, biological process and cellular component and the identified pathways directly or indirectly are related to immune system. The gene network was constructed and from this network the 17 hub genes (CD4, CXCL8, TLR4, STAT1, TLR2, CXCL9, CCR2, IGF1, LEP, SPP1, GH1, GHR, VWF, TNFSF11, IL10RA, NOD2 and PDGFRB) associated to SCS were identified. The subnetwork analysis resulted in 10 clusters that all identified hub genes (except VWF gene) are included in cluster 1. Most of hub genes and pathways identified in our study were mainly involved in inflammatory responses and cytokine response. Therefore the identified hub genes may be considered as main gene in genomic selection for SCS.

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Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle

Cited by 14 publications

References 84 publications

Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows

Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows

Unraveling structural and conformational dynamics of DGAT1 missense nsSNPs in dairy cattle

Identification of hub genes associated with somatic cell score in dairy cow

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