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Research Article

Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes

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References

  • https://nbagr.icar.gov.in/en/home/.
  • Bonhomme M, Chevalet C, Servin B, et al. Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics. 2010;186(1):241–262.
  • Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L. Natural selection has driven population differentiation in modern humans. Nat Genet. 2008;40(3):340–345.
  • Coyne JA, Orr HA. Speciation. Sunderland, MA: Sinauer Associates Incorporated; 2004.
  • Fisher RA. The Genetical Theory of Natural Selection. Oxford: The Clarendon Press; 1930.
  • Vohra V, Chhotaray S, Gowane G, et al. Genome-wide association studies in Indian Buffalo revealed genomic regions for lactation and fertility. Front Genet. 2021;12:696109.
  • Surya T, Vineeth MR, Sivalingam J, et al. Genomewide identification and annotation of SNPs in Bubalus bubalis. Genomics. 2019;111(6):1695–1698.
  • Tyagi SK, Mehrotra A, Singh A, et al. Comparative signatures of selection analyses identify loci under positive selection in the Murrah Buffalo of India. Front Genet. 2021;12:673697.
  • Singh R, Rajesh C, Mishra SK, et al. Comparative expression profiling of heat-stress tolerance associated HSP60 and GLUT-1 genes in Indian buffaloes. Indian J Dairy Sci. 2018;71(2):183–186.
  • Vohra V, Kumar M, Chopra A, Niranjan SK, Mishra AK, Kataria RS. Polymorphism in exon-40 of FASN gene in lesser-known buffalo breeds of India. J Anim Rese. 2015;5(2):325–328.
  • Vohra V, Singh M, Mukherjee K, Kataria RS. Identification and characterization of Chhattisgarhi buffalo population in India. Indian J Anim Sci. 2017;87(2):182–185.
  • Vohra V, Niranjan SK, Mishra AK, Kataria RS. Monograph on buffalo genetic resources of India-Gojri. National Bureau of Animal Genetic Resources, Karnal. 2015;(88):1-37.
  • Patro BN, Mishra PK, Rao PK. Chilika buffaloes in Orissa: a unique germplasm. Anim Genet Resour Inf. 2003;33:73–79.
  • Nanda DK, Singh R, Tomar SK, et al. Indian Chilika curd–A potential dairy product for Geographical Indication registration. Indian J Tradit Knowl. 2013;12(4):707–713.
  • Hellenthal G, Busby GB, Band G, et al. A genetic atlas of human admixture history. Science. 2014;343(6172):747–751.
  • Luikart G, England PR, Tallmon D, Jordan S, Taberlet P. The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet. 2003;4(12):981–994.
  • Charlesworth B. Elements of Evolutionary Genetics. Englewood, CO: Roberts Publishers; 2010.
  • Novembre J, Stephens M. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 2008;40(5):646–649.
  • Tennessen JA, Madeoy J, Akey JM. Signatures of positive selection apparent in a small sample of human exomes. Genome Res. 2010;20(10):1327–1334.
  • Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, Xu X. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 2010;329(5987):75–78.
  • Teer JK, Mullikin JC. Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet. 2010;19(R2):R145–R151.
  • Mathieson I, McVean G. Differential confounding of rare and common variants in spatially structured populations. Nat Genet. 2012;44(3):243–246.
  • Nelson SC, Crouch JM, Bamshad MJ, Tabor HK, Yu JH. Use of metaphors about exome and whole genome sequencing. Am J Med Genet A. 2016;170A(5):1127–1133.
  • Song S, Yao N, Yang M, et al. Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). BMC Genomics. 2016;17(1):122.
  • Maroti Z, Boldogkői Z, Tombácz D, Snyder M, Kalmár T. Evaluation of whole exome sequencing as an alternative to BeadChip and whole genome sequencing in human population genetic analysis. BMC Genomics. 2018;19(1):778.
  • Lin M, Whitmire S, Chen J, Farrel A, Shi X, Guo J. Effects of short indels on protein structure and function in human genomes. Sci Rep. 2017;7(1):9313.
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
  • Li H, Handsaker B, Wysoker A, et al. 1000 genome project data processing subgroup. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079.
  • Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014;30(17):2503–2505.
  • McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–1303.
  • DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491–498.
  • Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575.
  • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–959.
  • Wickham H. Ggplot2: Elegant Graphics for Data Analysis. 2nd ed. New York: Springer; 2009.
  • Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979;76(10):5269–5273.
  • Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123(3):585–595.
  • Schmidt D, Pool J. The effect of population history on the distribution of the Tajima’s D statistic. Population English Edition. 2002:1–8.
  • Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38(6):1358–1370.
  • Wright S. The genetical structure of populations. Ann Eugen. 1951;15(4):323–354.
  • Fariello MI, Boitard S, Naya H, SanCristobal M, Servin B. Detecting signatures of selection through haplotype differentiation among hierarchically structured populations. Genetics. 2013;193(3):929–941.
  • Danecek P, Auton A, Abecasis G, et al. 1000 genomes project analysis group. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–2158.
  • Mi H, Huang X, Muruganujan A, et al. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 2017;45(D1):D183–D189.
  • Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43(Database issue):D447–D452.
  • Borghese A. Buffalo production and research. REU Technical Series 2005;67:1–315.
  • Friel J, Bombarely A, Fornell CD, Luque F, Fernández-Ocaña AM. Comparative analysis of genotyping by sequencing and whole-genome sequencing methods in diversity studies of Olea europaea L. Plants. 2021;10(11):2514.
  • Gibbon A, Saunders CJ, Collins M, Gamieldien J, September AV. Defining the molecular signatures of Achilles tendinopathy and anterior cruciate ligament ruptures: A whole-exome sequencing approach. PLoS One. 2018;13(10):e0205860.
  • Shen Y, Ha W, Zeng W, Queen D, Liu L. Exome sequencing identifes novel mutation signatures of UV radiation and trichostatin A in primary human keratinocytes. Sci Rep. 2020;10(1):4943.
  • Otto SP. Detecting the form of selection from DNA sequence data. Trends Genet. 2000;16(12):526–529.
  • Przeworski M, Hudson RR, Di Rienzo A. Adjusting the focus on human variation. Trends Genet. 2000;16(7):296–302.
  • Vitalis R, Dawson K, Boursot P. Interpretation of variation across marker loci as evidence of selection. Genetics. 2001;158(4):1811–1823.
  • Nielsen R. Statistical tests of selective neutrality in the age of genomics. Heredity (Edinb). 2001;86(Pt 6):641–647.
  • Groeneveld LF, Lenstra JA, Eding H, Globaldiv Consortium, et al. Genetic diversity in farm animals–a review. Anim Genet. 2010;41 Suppl 1(s1):6–31.
  • Bruford MW, Ginja C, Hoffmann I, et al. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet. 2015;6:314.
  • Singh R, Mishra SK, Gurao A, et al. Current status and unique attributes of Indian Chilika bufalo for adaptation to brackish water ecology. Trop Anim Health Prod. 2021;53(6):544.
  • Vohra V, Singh NP, Chhotaray S, Raina VS, Chopra A, Kataria RS. Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India. PeerJ. 2021;9:e11846.
  • Barton NH, Keightley PD. Understanding quantitative genetic variation. Nat Rev Genet. 2002;3(1):11–21.
  • Ng PC, Levy S, Huang J, et al. Genetic variation in an individual human exome. PLoS Genet. 2008;4(8):e1000160.
  • Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet. 2010;19(R2):R131–R136.
  • Cheng Z, Ventura M, She X, et al. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature. 2005;437(7055):88–93.
  • Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 2006;38(1):82–85.
  • Wu K, Yang M, Liu H, Tao Y, Mei J, Zhao Y. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers. BMC Genet. 2014;15(1):35.
  • Zhou G, Zhang Q, Tan C, Zhang XQ, Li C. Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map. BMC Genomics. 2015;16(1):804.
  • Nazareno AG, Bemmels JB, Dick CW, Lohmann LG. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Mol Ecol Resour. 2017;17(6):1136–1147.
  • Willing EM, Dreyer C, Van Oosterhout C. Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. 2012.
  • Qu WM, Liang N, Wu ZK, Zhao YG, Chu D. Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly. Ecol Evol. 2020;10(1):38–49.
  • Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006;2(12):e190.
  • Singh R, Lava Kumar S, Mishra SK, et al. Mitochondrial sequence‐based evolutionary analysis of riverine-swamp hybrid bufaloes of India indicates novel maternal diferentiation and domestication patterns. Anim Genet. 2020;51(3):476–482.
  • Santos WB, Schettini GP, Maiorano AM, et al. Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping. BMC Genomics. 2021;22(1):737.
  • Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res. 2010;20(3):393–402.
  • Narum SR, Hess JE. Comparison of FST outlier tests for SNP loci under selection. Mol Ecol Resour. 2011;11 Suppl 1(s1):184–194.
  • Hoban S, Kelley JL, Lotterhos KE, et al. Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions. Am Nat. 2016;188(4):379–397.
  • Du C, Deng T, Zhou Y, et al. Systematic analyses for candidate genes of milk production traits in water buffalo (Bubalus Bubalis). Anim Genet. 2019;50(3):207–216.
  • Farhadian M, Rafat SA, Panahi B, Mayack C. Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process. Sci Rep. 2021;11(1):2367.
  • Pedrosa VB, Schenkel FS, Chen SY, et al. Genomewide association ana lyses of lactation persistency and milk production traits in Holstein cattle based on imputed whole-genome sequence data. Genes (Basel). 2021;12(11):1830.
  • Grudzien‐Nogalska E, Kiledjian M. New insights into decapping enzymes and selective mRNA decay. Wiley Interdiscip Rev: RNA. 2017;8(1):e1379.
  • Clancey E, Kiser JN, Moraes JGN, Dalton JC, Spencer TE, Neibergs HL. Genome-wide association analysis and gene set enrichment analysis with SNP data identify genes associated with 305-day milk yield in Holstein dairy cows. Anim Genet. 2019;50(3):254–258.
  • Li C, Cai W, Zhou C, et al. RNA-Seq reveals 10 novel promising candidate genes affecting milk protein concentration in the Chinese Holstein population. Sci Rep. 2016;6(1):26813.
  • Bionaz M, Loor JJ. Gene networks driving bovine milk fat synthesis during the lactation cycle. BMC Genomics. 2008;9(1):366.
  • Ibeagha-Awemu EM, Akwanji KA, Beaudoin F, Zhao X. Associations between variants of FADS genes and omega-3 and omega-6 milk fatty acids of Canadian Holstein cows. BMC Genet. 2014;15(1):25.
  • Gossett RE, Frolov AA, Roths JB, Behnke WD, Kier AB, Schroeder F. Acyl‐CoA binding proteins: Multiplicity and function. Lipids. 1996;31(9):895–918.
  • Nuttinck F, Gall L, Ruffini S, et al. PTGS2-related PGE2 affects oocyte MAPK phosphorylation and meiosis progression in cattle: late effects on early embryonic development. Biol Reprod. 2011;84(6):1248–1257.
  • Capitan A, Michot P, Baur A, et al. Genetic tools to improve reproduction traits in dairy cattle. Reprod Fertil Dev. 2014;27(1):14–21.
  • Lango Allen H, Estrada K, Lettre G, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010;467(7317):832–838.
  • Berndt SI, Gustafsson S, Mägi R, et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet. 2013;45(5):501–512.
  • Afonso J, Shim WJ, Boden M, et al. Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochem Biophys Rep. 2023;33:101420.
  • Xu J, Li J-T, Jiang Y, et al. Genomic basis of adaptive evolution: the survival of Amur Ide (Leuciscu s waleckii) in an extremely alkaline environment. Mol Biol Evol. 2017;34(1):145–159.
  • Bhat SA, Ahmad SM, Ibeagha-Awemu EM, et al. Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle. PLoS One. 2019;14(2):e0211773.
  • Sahoo S, Maji UJ, Mohanty S. Incidence and preliminary characterization of Lactic acid bacteria as potential probiotic strains from an artisanal milk product, Chilika curd of Odisha. IJDS. 2020;73(2):123–130.
  • Endres L, Begley U, Clark R, et al. Alkbh8 regulates selenocysteine-protein expression to protect against reactive oxygen species damage. PLoS One. 2015;10(7):e0131335.
  • Liu M, Sun J, Cui J, et al. INS-gene mutations: from genetics and beta cell biology to clinical disease. Mol Aspects Med. 2015;42:3–18.
  • Huang Y-Z, Zhan Z-Y, Sun Y-J, et al. Intragenic DNA methylation status down-regulates bovine IGF2 gene expression in different developmental stages. Gene. 2014;534(2):356–361.
  • Humphrey MB, Herrera-Sosa H, Gonzalez G, Lee R, Bryan J. Cloning of cDNAs encoding human caldesmons. Gene. 1992;112(2):197–204.
  • Mudadu MA, Porto-Neto LR, Mokry FB, et al. Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle. BMC Genomics. 2016;17(1):492.
  • Stachowiak MK, Hong JS, Viveros OH. Coordinate and differential regulation of phenylethanolamine N-methyltransferase, tyrosine hydroxylase and proenkephalin mRNAs by neural and hormonal mechanisms in cultured bovine adrenal medullary cells. Brain Res. 1990;510(2):277–288.
  • Xiang R, MacLeod IM, Bolormaa S, Goddard ME. Genome-wide comparative analyses of correlated and uncorrelated phenotypes identify major pleiotropic variants in dairy cattle. Sci Rep. 2017;7(1):9248.
  • Penna I, Vassallo I, Nizzari M, et al. A novel snRNA-like transcript affects amyloidogenesis and cell cycle progression through perturbation of Fe65L1 (APBB2) alternative splicing. Biochim Biophys Acta. 2013;1833(6):1511–1526.
  • Goetz DH, Holmes MA, Borregaard N, Bluhm ME, Raymond KN, Strong RK. The neutrophil lipocalin NGAL is a bacteriostatic agent that interferes with siderophore-mediated iron acquisition. Mol Cell. 2002;10(5):1033–1043.
  • Shashidharamurthy R, Machiah D, Aitken JD, et al. Differential role of lipocalin 2 during immune complex–mediated acute and chronic inflammation in mice. Arthritis Rheum. 2013;65(4):1064–1073.
  • Mauki DH, Tijjani A, Ma C, et al. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics. BMC Genomics. 2022;23(1):306.