Genetic variation analysis of Guanling cattle based on whole-genome resequencing
1
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Objective: The objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed.Methods: In this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high- multiplex polymerase chain reaction technology was employed to detect high-quality single nucleotide polymorphism (SNP) sites of other 55 Guanling cattle.Results: Our study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (<i>LEPR</i>, <i>AKAP9</i>, <i>SIX4</i>, <i>SPIDR</i>, <i>PRG4</i>, <i>FASN</i>) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy–Weinberg equilibrium.Conclusion: These findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle.
Abstract
Objective: The objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed. Methods: In this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high- multiplex polymerase chain reaction technology was employed to detect high-quality single nucleotide polymorphism (SNP) sites of other 55 Guanling cattle. Results: Our study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (LEPR, AKAP9, SIX4, SPIDR, PRG4, FASN) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy– Weinberg equilibrium. Conclusion: These findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle.
참고문헌 (34)
- Editorial Committee for Livestock, Poultry Variety Catalogue, Variety Atlas in Guizhou Province, "Guanling cattle (in Chinese)", Guizhou J Anim Husb Vet Med, pp.115~118 (1983)
- Liu R, "Analysis on the genetic diversity of mitochondrial DNA D-loop region complete sequence of Guanling cattle in Guizhou province(in Chinese)", J Mt Agric, 1, pp.33~36 (2005)
- The International HapMap Consortium, "The international HapMap project", Nature, 426, pp.789~796 (2003)[DOI]
- Eck SH, "Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery", Genome Biol, 10, pp.R82~ (2009)[DOI]
- Stothard P, "Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery", BMC Genomics, 12, pp.559~ (2011)[DOI]
- Chen S, "fastp : an ultra-fast all-in-one FASTQ preprocessor", Bioinformatics, 34, pp.i884~i890 (2018)[DOI]
- Li H, "Fast and accurate short read alignment with Burrows-Wheeler transform", Bioinformatics, 25, pp.1754~1760 (2009)[DOI]
- Van der Auwera GA, "From fastQ data to high-confidence variant calls : the genome analysis toolkit best practices pipeline", Curr Protoc Bioinformatics, 43, pp.11.0.1-33~ (2013)[DOI]
- Igoshin AV, "Genomewide association study for body weight in cattle populations from Siberia", Anim Genet, 50, pp.250~253 (2019)[DOI]
- Raza SHA, "Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle", Arch Biochem Biophys, 694, pp.108543~ (2020)[DOI]
- Abd El-Hack ME, "The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed", Mol Biol Rep, 45, pp.1445~1456 (2018)[DOI]
- Sun T, "Whole genome sequencing of simmental cattle for SNP and CNV discovery", BMC Genomics, 24, pp.179~ (2023)[DOI]
- The 1000 Genomes Project Consortium, "An integrated map of genetic variation from 1, 092 human genomes", Nature, 491, pp.56~65 (2012)[DOI]
- Albers CA, "Dindel : accurate indel calls from short-read data", Genome Res, 21, pp.961~973 (2011)[DOI]
- Choi JW, "Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing", PLoS ONE, 9, pp.e101127~ (2014)[DOI]
- Kawahara-Miki R, "Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi", BMC Genomics, 12, pp.103~ (2011)[DOI]
- Choi JW, "Whole genome resequencing of Heugu(Korean black cattle)for the genomewide SNP discovery", Korean J Food Sci Anim Resour, 33, pp.715~722 (2013)[DOI]
- Fujimoto A, "Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing", Nat Genet, 42, pp.931~936 (2010)[DOI]
- Makova KD, "Strong male-driven evolution of DNA sequences in humans and apes", Nature, 416, pp.624~626 (2002)[DOI]
- Chelikani PK, "Short communication : tissue distribution of leptin and leptin receptor mRNA in the bovine", J Dairy Sci, 86, pp.2369~2372 (2003)[DOI]
- Raza SHA, "Detection of polymorphisms in the bovine leptin receptor gene affects fat deposition in two Chinese beef cattle breeds", Gene, 758, pp.144957~ (2020)[DOI]
- Meng X, "Longissimus dorsi muscle transcriptomic analysis of simmental and Chinese native cattle differing in meat quality", Front Vet Sci, 7, pp.601064~ (2020)[DOI]
- Grifone R, "Six1 and Six4homeoproteins are required for Pax3 and Mrf expression during myogenesis in the mouse embryo", Development, 132, pp.2235~2249 (2005)[DOI]
- Wang G, "Novel polymorphisms of SIX4gene and their association with body measurement traits in Qinchuan cattle", Gene, 539, pp.107~110 (2014)[DOI]
- Huang T, "SPIDR is required for homologous recombination during mammalian meiosis", Nucleic Acids Res, 51, pp.3855~3868 (2023)[DOI]
- Zhang W, "Detection of candidate genes for growth and carcass traits using genome-wide association strategy in Chinese Simmental beef cattle", Anim Prod Sci, 58, pp.224~233 (2018)[DOI]
- Schmidt TA, "Disulfide-bonded multimers of proteoglycan 4(PRG4)are present in normal synovial fluids", Biochim Biophys Acta Gen Subj, 1790, pp.375~384 (2009)[DOI]
- Abubacker S, "Effect of disulfide bonding and multimerization on proteoglycan 4's cartilage boundary lubricating ability and adsorption", Connect Tissue Res, 57, pp.113~123 (2016)[DOI]
- Wakil SJ, "Fatty acid synthesis and its regulation", Annu Rev Biochem, 52, pp.537~579 (1983)[DOI]
- Oztabak K, "FASN gene polymorphism in indigenous cattle breeds of turkey", Folia Biol(Krakow), 62, pp.29~35 (2014)[DOI]
- Roy R, "Association of polymorphisms in the bovine FASN gene with milk-fat content", Anim Genet, 37, pp.215~218 (2006)[DOI]
- Chu M, "Association between singlenucleotide polymorphisms of fatty acid synthase gene and meat quality traits in Datong Yak(Bos grunniens)", Genet Mol Res, 14, pp.2617~2625 (2015)[DOI]
- Ji S, "Differential expression of PPARγ, FASN, and ACADM genes in various adipose tissues and Longissimus dorsi muscle from Yanbian Yellow cattle and Yan Yellow cattle", Asian-Australas J Anim Sci, 27, pp.10~18 (2014)[DOI]
- Hayakawa K, "The g. 841G>C SNP of FASN gene is associated with fatty acid composition in beef cattle", Anim Sci J, 86, pp.737~746 (2015)[DOI]
