ArticlePloS one2016
Whole-Genome Resequencing of Holstein Bulls for Indel Discovery and Identification of Genes Associated with Milk Composition Traits in Dairy Cattle.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
- Genetic and Functional Dissection of the NFKB2 Gene: Implications for Milk Fatty Acid Biosynthesis in Dairy Cattle.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Genome-wide insights into selection signatures for transcription factor binding sites in cattle ROH regions.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Identification and Validation of Genus/Species-Specific Short InDels in Dairy Ruminants.BMC veterinary research · 2025Article
- Differential A1/A2 β-casein (Frontiers in veterinary science · 2025Article
- Genome-Wide Association Study of Insertions and Deletions Identified Novel Loci Associated with Milk Production Traits in Dairy Cattle.Animals : an open access journal from MDPI · 2024Article
- InDel mutations within the bovineAnimal biotechnology · 2024Article
- Genomic Insights and Conservation Priorities for Kongshan Cattle: A Whole-Genome Resequencing Approach.Animals : an open access journal from MDPI · 2024Article
- Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle.International journal of molecular sciences · 2024Article
- Transcriptomic analysis of yakAnimal biotechnology · 2023Article
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- The ins and outs of mammary gland calcium and zinc transport: A brief review.JDS communications · 2023Review
- Whole-genome sequencing identifies potential candidate genes for egg production traits in laying ducks (Anas platyrhynchos).Scientific reports · 2023Article
- Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population.Archives animal breeding · 2023Article
- Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese.Frontiers in veterinary science · 2022Article
- Genetic polymorphisms ofFrontiers in genetics · 2022Article
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- Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds.Genetics, selection, evolution : GSE · 2020Article
- Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken.BMC genomics · 2020Article
- Current Evidences and Future Perspectives for AMPK in the Regulation of Milk Production and Mammary Gland Biology.Frontiers in cell and developmental biology · 2020Review
- Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities.PloS one · 2020Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of whole-genome resequencing to obtain more information on genetic variation could produce a range of benefits for the dairy cattle industry, especially with regard to increasing milk production and improving milk composition. In this study, we sequenced the genomes of eight Holstein bulls from four half- or full-sib families, with high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage at an average effective depth of 10×, using Illumina sequencing. Over 0.9 million nonredundant short insertions and deletions (indels) [1-49 base pairs (bp)] were obtained. Among them, 3,625 indels that were polymorphic between the high and low groups of bulls were revealed and subjected to further analysis. The vast majority (76.67%) of these indels were novel. Follow-up validation assays confirmed that most (70%) of the randomly selected indels represented true variations. The indels that were polymorphic between the two groups were annotated based on the cattle genome sequence assembly (UMD3.1.69); as a result, nearly 1,137 of them were found to be located within 767 annotated genes, only 5 (0.138%) of which were located in exons. Then, by integrated analysis of the 767 genes with known quantitative trait loci (QTL); significant single-nucleotide polymorphisms (SNPs) previously identified by genome-wide association studies (GWASs) to be associated with bovine milk protein and fat traits; and the well-known pathways involved in protein, fat synthesis, and metabolism, we identified a total of 11 promising candidate genes potentially affecting milk composition traits. These were FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH. Our findings provide a basis for further study and reveal key genes for milk composition traits in dairy cattle.
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