Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data
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Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits.Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (<i>pi</i>, <i>F</i><sub>st</sub>, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions.Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (<i>pi</i>, <i>F</i><sub>st</sub>, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (<i>PLAG1</i>), dedicator of cytokinesis 3 (<i>DOCK3</i>), ephrin A2 (<i>EFNA2</i>), DAZ associated protein 1 (<i>DAZAP1</i>), Ral GTPase activating protein catalytic subunit alpha 1 (<i>RALGAPA1</i>), mediator complex subunit 13 (<i>MED13</i>), and decaprenyl diphosphate synthase subunit 2 (<i>PDSS2</i>), most of which were enriched in pathways related to muscle growth and differentiation and immunity.Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.
Abstract
Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.
참고문헌 (45)
- Qanbari S, "Classic selective sweeps revealed by massive sequencing in cattle", PLoS Genet, 10, pp.e1004148~ (2014)[DOI]
- Iqbal N, "Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan", PLoS One, 14, pp.e0215065~ (2019)[DOI]
- Zhang W, "Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle", BMC Genet, 19, pp.114~ (2018)[DOI]
- The Bovine Hapmap Consortium, "Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds", Science, 324, pp.528~532 (2009)[DOI]
- Cho IC, "A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs", PLoS Genet, 15, pp.e1008279~ (2019)[DOI]
- Matukumalli LK, "Development and characterization of a high density SNP genotyping assay for cattle", PLoS One, 4, pp.e5350~ (2009)[DOI]
- Zhang L, "Genome-wide association study of body weight traits in inner mongolia cashmere goats", Front Vet Sci, 8, pp.752746~ (2021)[DOI]
- Li Z, "Genome-wide genetic structure and differentially selected regions among Landrace, Erhualian, and Meishan pigs using specific-locus amplified fragment sequencing", Sci Rep, 7, pp.10063~ (2017)[DOI]
- Liu Z, "Genome-wide re-sequencing reveals population structure and genetic diversity of Bohai Black cattle", Anim Genet, 53, pp.133~136 (2022)[DOI]
- Liu Z, "Detection of selection signatures in South African Mutton Merino sheep using whole-genome sequencing data", Anim Genet, 53, pp.224~229 (2022)[DOI]
- Mao Y, "Genetic structure and differentiation of three Chinese indigenous cattle populations", Biochem Genet, 45, pp.195~209 (2007)[DOI]
- Ge F LH, "Analysis of growth and slaughter performances and meat quality of Luxi cattle", Shandong Agric Sci, 54, pp.112~120 (2022)
- Groeneveld LF, "Genetic diversity in farm animals--a review", Anim Genet, 41(Suppl 1), pp.6~31 (2010)[DOI]
- Li H, "Fast and accurate short read alignment with Burrows-Wheeler transform", Bioinformatics, 25, pp.1754~1760 (2009)[DOI]
- McKenna A, "The Genome Analysis Toolkit : a MapReduce framework for analyzing next-generation DNA sequencing data", Genome Res, 20, pp.1297~1303 (2010)[DOI]
- Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
- Addo S, "Runs of Homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds", PLoS One, 14, pp.e0225847~ (2019)[DOI]
- Yang J, "GCTA : a tool for genome-wide complex trait analysis", Am J Hum Genet, 88, pp.76~82 (2011)[DOI]
- Alexander DH, "Fast model-based estimation of ancestry in unrelated individuals", Genome Res, 19, pp.1655~1664 (2009)[DOI]
- Kumar S, "MEGA7 : molecular evolutionary genetics analysis version 7. 0 for bigger datasets", Mol Biol Evol, 33, pp.1870~1874 (2016)[DOI]
- Yan CL, "Population genomics reveals that natural variation in PRDM16 contributes to cold tolerance in domestic cattle", Zool Res, 43, pp.275~284 (2022)[DOI]
- Browning SR, "Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering", Am J Hum Genet, 81, pp.1084~1097 (2007)[DOI]
- Bu D, "KOBAS-i : intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis", Nucleic Acids Res, 49, pp.W317~W325 (2021)[DOI]
- Hu ZL, "Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB", Nucleic Acids Res, 47, pp.D701~D710 (2019)[DOI]
- Chen N, "Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia", Nat Commun, 9, pp.2337~ (2018)[DOI]
- "DOCK3regulates normal skeletal muscle regeneration and glucose metabolism"[URL]
- Sun T, "Selection signatures of Fuzhong Buffalo based on whole-genome sequences", BMC Genomics, 21, pp.674~ (2020)[DOI]
- Smith RWP, "DAZAP1, an RNA-binding protein required for development and spermatogenesis, can regulate mRNA translation", RNA, 17, pp.1282~1295 (2011)[DOI]
- Song Y, "Genome-wide association study reveals the PLAG1 gene for knuckle, biceps and shank weight in simmental beef cattle", PLoS One, 11, pp.e0168316~ (2016)[DOI]
- Li Y, "Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities", PLoS One, 15, pp.e0235218~ (2020)[DOI]
- Zhang T, "Determination of microbiological characteristics in the digestive tract of different ruminant species", Microbiologyopen, 8, pp.e00769~ (2019)[DOI]
- Saito R, "Genetic population structure of wild boars(Sus scrofa)in fukushima prefecture", Animals(Basel), 12, pp.491~ (2022)[DOI]
- Han Y, "Identification of selection signatures and loci associated with important economic traits in Yunan Black and Huainan pigs", Genes(Basel), 14, pp.655~ (2023)[DOI]
- Ma X, "Assessing Genomic diversity and selective pressures in bohai black cattle using wholegenome sequencing data", Animals(Basel), 12, pp.665~ (2022)[DOI]
- Lu X, "The relationship between myofiber characteristics and meat quality of Chinese Qinchuan and Luxi cattle", Anim Biosci, 34, pp.743~750 (2021)[DOI]
- Xia X, "Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using wholegenome sequencing data", BMC Genomics, 22, pp.43~ (2021)[DOI]
- Zheng T, "Research advances in and prospects of ornamental plant genomics", Hortic Res, 8, pp.65~ (2021)[DOI]
- Zwane AA, "Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa", Front Genet, 10, pp.273~ (2019)[DOI]
- Qiao R, "Population genetic structure analysis and identification of backfat thickness loci of Chinese synthetic Yunan pigs", Front Genet, 13, pp.1039838~ (2022)[DOI]
- Amoasii L, "A MED13-dependent skeletal muscle gene program controls systemic glucose homeostasis and hepatic metabolism", Genes Dev, 30, pp.434~446 (2016)[DOI]
- Rehman MS, "Comparative genomic characterization of relaxin peptide family in cattle and buffalo", Biomed Res Int, 2022, pp.1581714~ (2022)[DOI]
- Saatchi M, "Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds", BMC Genomics, 15, pp.442~ (2014)[DOI]
- Bongiorni S, "Identification of a short region on chromosome 6 affecting direct calving ease in Piedmontese cattle breed", PLoS One, 7, pp.e50137~ (2012)[DOI]
- Boyko AR, "Genomic analysis establishes correlation between growth and laryngeal neuropathy in Thoroughbreds", BMC Genomics, 15, pp.259~ (2014)[DOI]
- Nagaraj M, "GOLM1 depletion modifies cellular sphingolipid metabolism and adversely affects cell growth", J Lipid Res, 63, pp.100259~ (2022)[DOI]
