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Research Articles

Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes

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References

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. In: Orlando L, ed. PLoS One. 2012;7(5):1.
  • Karlsson EK, Baranowska I, Wade CM, et al. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet. 2007;39(11):1321–12.
  • Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6(2):95–108.
  • Wang H, Misztal I, Aguilar I, Legarra A, Muir WM. Genome-wide association mapping including phenotypes from relatives without genotypes. Genet Res (Camb). 2012;94(2):73–83.
  • Misztal I, Legarra A, Aguilar I. Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J Dairy Sci. 2009;92(9):4648–4655.
  • VanRaden PM, Van Tassell CP, Wiggans GR, et al. Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci. 2009;92(1):16–24.
  • Boligon AA, Mercadante MEZ, Forni S, Lôbo RB, Albuquerque LG. Covariance functions for body weight from birth to maturity in Nellore cows1. J Anim Sci. 2010;88(3):849–859.
  • Frizzas OG, Grossi DA, Buzanskas ME, et al. Heritability estimates and genetic correlations for body weight and scrotal circumference adjusted to 12 and 18 months of age for male Nellore cattle. Animal. 2009;3(3):347–351.
  • Diskin MG, Kenny DA. Managing the reproductive performance of beef cows. Theriogenology. 2016;86(1):379–387.
  • Aguilar I, Misztal I, Johnson DL, Legarra A, Tsuruta S, Lawlor TJ. Hot topic: a unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score1. J Dairy Sci. 2010;93(2):743–752.
  • Browning BL, Browning SR. Genotype imputation with millions of reference samples. Am J Hum Genet. 2016;98(1):116–126.
  • Misztal I. Reliable computing in estimation of variance components. J Anim Breed Genet. 2008;125(6):363–370.
  • Christensen OF, Lund MS. Genomic prediction when some animals are not genotyped. Genet Sel Evol. 2010;42(1):2.
  • Garcia-Baccino CA, Legarra A, Christensen OF, et al. Metafounders are related to Fst fixation indices and reduce bias in single-step genomic evaluations. Genet Sel Evol. 2017;49(1):34.
  • Medeiros de Oliveira Silva R, Bonvino Stafuzza N, de Oliveira Fragomeni B, et al. Genome-wide association study for carcass traits in an experimental Nelore cattle population. PLoS One. 2017;12(1):e0169860.
  • Stafuzza NB, Costa e Silva EVd, Silva Rm de O, et al. Genome-wide association study for age at puberty in young Nelore bulls. J Anim Breed Genet. 2020;137(2):234–244.
  • Tien NQ, Tripathi VN. Genetic parameters of body weight at different ages and first lactation traits in Murrah buffalo heifers. Indian Vet J. 1990;67(9):821–825.
  • Gupta JP, Sachdeva GK, Gandhi RS, Chakaravarty AK. Developing multiple-trait prediction models using growth and production traits in Murrah buffalo. Buffalo Bulletin. Published online 2015. 9.
  • Thiruvenkadan AK, Panneerselvam S, Rajendran R. Non-genetic and genetic factors influencing growth performance in Murrah Buffalos. S Afr J Anim Sci. 2009;39(sup-1):102–106.
  • Basu SB, Rao M.K. Growth pattern in Murrah buffalo calves [India]. Indian Vet J. Published online 1979.
  • Khan MS. Response to selection for milk yield and lactation length in buffaloes. Asian Australas J Anim Sci. 1997;10(6):567–570.
  • Jakhar V, Vinayak AK, Singh KP. Genetic evaluation of performance attributes in Murrah buffaloes. Haryana Vet. 2016;55(1):66–69.
  • Godara A, Singh D, Dhaka SS. Genetic parameters among lactational performance traits in Murrah buffaloes. IJAR. 2015;49(5):579–584.
  • Sahoo S, Singh A, Gupta AK, Chakravarty AK, Singh M, Ambhore G. Estimates of genetic parameters of weekly test day milk yields and first lactation 305 day milk yield in Murrah buffaloes. Vet World. 2014;7(12):1094–1098.
  • Valsalan J, Chakravarty AK, Patil CS, et al. Enhancing milk and fertility performances using selection index developed for Indian Murrah buffaloes. Trop Anim Health Prod. 2014;46(6):967–974.
  • Rodrigues AE, Marques JRF, Araújo CV, Camargo Júnior RNC, Dias LNS. Estimation of genetic parameters of dairy buffaloes productive characteristics Eastern Amazon. Arq Bras Med Vet Zootec. 2010;62(3):712–717.
  • Mendes Malhado CH, Mendes Malhado AC, Amorim Ramos A, Souza Carneiro PL, Siewerdt F[, Pala A, UNESP. Genetic parameters by Bayesian inference for dual purpose Jaffarabadi buffaloes. Arch Anim Breed. 2012;55(6):567–576. Published online October 10,
  • Thiruvenkadan AK, Panneerselvam S, Ramanujam R, Murali N. Analysis on the productive and reproductive traits of Murrah buffalo cows maintained in the coastal region of India. Appl Anim Husb Rural Dev. 2010;3:1–5.
  • de Araujo Neto FR, Santos Dj de A, Fernandes Júnior GA, et al. Genome-wide association studies for growth traits in buffaloes using the single step genomic BLUP. J Appl Genet. 2020;61(1):113–115.
  • Barros CDC, Aspilcueta-Borquis RR, Fraga AB, Tonhati H. Genetic parameter estimates for production and reproduction traits in dairy buffaloes. Rev Caatinga. 2016;29(1):216–221.
  • Patil CS, Chakravarty AK, Kumar V, Sharma RK, Kumar P. Average performace of various first lactation 305 day and test day milk yield in Murrah buffaloes. Indian J Anim Res (India). 2012;46(3):310–312.
  • de Camargo G, Aspilcueta-Borquis R, Fortes M, et al. Prospecting major genes in dairy buffaloes. BMC Genomics. 2015;16(1):872.
  • Blattner C, Jennebach S, Herzog F, et al. Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev. 2011;25(19):2093–2105.
  • Alawi K, Keeble J. The paradoxical role of the transient receptor potential vanilloid 1 receptor in inflammation. Pharmacol Ther. 2010;125(2):181–195.
  • Baggio LL, Drucker DJ. Glucagon-like peptide-1 and glucagon-like peptide-2. Best Pract Res Clin Endocrinol Metab. 2004;18(4):531–554.
  • Wu J, Wang J, Yue B, et al. Research on association between variants and haplotypes of TRPV1 and TRPA1 genes with growth traits in three cattle breeds. Anim Biotechnol. 2019;30(3):202–211.
  • Gasser CL, Behlke EJ, Grum DE, Day ML. Effect of timing of feeding a high-concentrate diet on growth and attainment of puberty in early-weaned heifers1. J Anim Sci. 2006;84(11):3118–3122.
  • Bustin M. Chromatin unfolding and activation by HMGN**The nomenclature of the HMG protein superfamily has been recently revised (see Ref. 12 and http://www.informatics.jax.org/mgihome/nomen/genefamilies/hmgfamily.shtml). chromosomal proteins. Trends Biochem Sci. 2001;26(7):431–437.
  • Holahan MR. A shift from a pivotal to supporting role for the growth-associated protein (GAP-43) in the coordination of axonal structural and functional plasticity. Front Cell Neurosci. 2017;11:266.
  • Li Y, Gao Y, Kim YS, Iqbal A, Kim JJ. A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo. Asian-Australas J Anim Sci. 2017;30(1):8–19.
  • Zhang F, Wang Y, Mukiibi R, et al. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits. BMC Genomics. 2020;21(1):36.
  • Duan X, An B, Du L, et al. Genome-wide association analysis of growth curve parameters in Chinese Simmental beef cattle. Animals (Basel). 2021;11(1):192.
  • Taga H, Chilliard Y, Meunier B, et al. Cellular and molecular large-scale features of fetal adipose tissue: is bovine perirenal adipose tissue Brown1685. J Cell Physiol. 2012;227(4):1688–1700.
  • 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):235.
  • Lemos MVA, Chiaia HLJ, Berton MP, et al. Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure. BMC Genomics. 2016;17(1):213.
  • Cook SD, Rueger DC. Osteogenic protein-1: biology and applications. Clin Orthop Relat Res (1976-2007). 1996;324:29–38.
  • Zhang H, Liu A, Wang Y, et al. Genetic parameters and genome-wide association studies of eight longevity traits representing either full or partial lifespan in Chinese Holsteins. Front Genet. 2021;12:634986. 10.3389/fgene.2021.634986
  • Yoon W, Hwang SH, Lee SH, Chung J. Drosophila ADCK1 is critical for maintaining mitochondrial structures and functions in the muscle. PLoS Genet. 2019;15(5):e1008184.
  • Olivieri BF, Mercadante MEZ, Cyrillo JN, dos SG, et al. Genomic regions associated with feed efficiency indicator traits in an experimental Nellore cattle population. PLoS One. 2016;11(10):e0164390.
  • Kumar A, Kaur M, Ahlawat S, et al. Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India. Genomics. 2021;113(4):1639–1646.
  • Edea Z, Jeoung YH, Shin SS, et al. Genome–wide association study of carcass weight in commercial Hanwoo cattle. Asian-Australas J Anim Sci. 2018;31(3):327–334.
  • Shan L, Sun J, Zhang C, et al. The polymorphisms of bovine PCSK1 gene and their associations with growth traits. Genes Genom. 2011;33(1):57–63.
  • 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.
  • Mishra DC, Sikka P, Yadav S, et al. Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo. Genomics. 2020;112(5):3571–3578.
  • Abo-Ismail MK, Brito LF, Miller SP, et al. Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle. Genet Sel Evol. 2017;49(1):82.
  • Weng Z, Su H, Saatchi M, et al. Genome-wide association study of growth and body composition traits in Brangus beef cattle. Livest Sci. 2016;183:4–11.
  • Niu Q, Zhang T, Xu L, et al. Identification of candidate variants associated with bone weight using whole genome sequence in beef cattle. Front Genet. 2021;12:750746.
  • Jiang J, Ma L, Prakapenka D, VanRaden PM, Cole JB, Da Y. A large-scale genome-wide association study in U.S. Holstein cattle. Front Genet. 2019;10:412. 10.3389/fgene.2019.00412
  • Mészáros G, Eaglen S, Waldmann P, Sölkner J. A genome wide association study for longevity in cattle. Open J Genet. 2014;04(01):46–55.
  • Kim S, Lim B, Cho J, et al. Genome-wide identification of candidate genes for milk production traits in Korean Holstein cattle. Animals (Basel). 2021;11(5):1392.
  • Sahana G, Guldbrandtsen B, Thomsen B, et al. Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle1. J Dairy Sci. 2014;97(11):7258–7275.
  • 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.
  • Pedrosa VB, Schenkel FS, Chen SY, et al. Genomewide association analyses of lactation persistency and milk production traits in Holstein cattle based on imputed whole-genome sequence data. Genes (Basel). 2021;12(11):1830.
  • Finucane KA, McFadden TB, Bond JP, Kennelly JJ, Zhao FQ. Onset of lactation in the bovine mammary gland: gene expression profiling indicates a strong inhibition of gene expression in cell proliferation. Funct Integr Genomics. 2008;8(3):251–264.
  • Lin Y, Duan X, Lv H, et al. The effects of L-type amino acid transporter 1 on milk protein synthesis in mammary glands of dairy cows. J Dairy Sci. 2018;101(2):1687–1696.
  • Zhou J, Jiang M, Shi Y, Song S, Hou X, Lin Y. Prolactin regulates LAT1 expression via STAT5 (signal transducer and activator of transcription 5) signaling in mammary epithelial cells of dairy cows. J Dairy Sci. 2020;103(7):6627–6634.
  • Alshawi A, Essa A, Al-Bayatti S, Hanotte O. Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi cattle. Front Genet. 2019;10:609. 10.3389/fgene.2019.00609
  • Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-wide scanning for signatures of selection revealed the putative genomic regions and candidate genes controlling milk composition and coat color traits in Sahiwal cattle. Front Genet. 2021;12:699422.
  • Kusama K, Bai R, Matsuno Y, et al. Characterization of serum metabolome and proteome profiles identifies SNX5 specific for pregnancy failure in Holstein heifers. Life (Basel). 2022;12(2):309.
  • Irano N, Camargo G, Costa R, et al. Genome-wide association study for indicator traits of sexual precocity in Nellore cattle. PLoS One. 2016;11(8):e0159502.
  • Kiser JN, Keuter EM, Seabury CM, et al. Validation of 46 loci associated with female fertility traits in cattle. BMC Genomics. 2019;20(1):576.
  • Wu P, Wang K, Yang Q, et al. Identifying SNPs and candidate genes for three litter traits using single-step GWAS across six parities in Landrace and Large White pigs. Physiol Genomics. 2018;50(12):1026–1035.
  • Forde N, Duffy GB, McGettigan PA, et al. Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau. Physiol Genomics. 2012;44(16):799–810.
  • Low WY, Tearle R, Liu R, et al. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nat Commun. 2020;11(1):2071.
  • Mota LFM, Lopes FB, Fernandes Júnior GA, et al. Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers. Sci Rep. 2020;10(1):6481.
  • Chen Z, Brito LF, Luo H, et al. Genetic and genomic analyses of service sire effect on female reproductive traits in Holstein cattle. Front Genet. 2021;12:713575. 10.3389/fgene.2021.713575
  • Kiyonaka S, Kato K, Nishida M, et al. Selective and direct inhibition of TRPC3 channels underlies biological activities of a pyrazole compound. Proc Natl Acad Sci U S A. 2009;106(13):5400–5405.
  • Ghavideldarestani M, Atkin SL, Leese HJ, Sturmey RG. Expression and function of transient receptor potential channels in the female bovine reproductive tract. Theriogenology. 2016;86(2):551–561.
  • Berisha B, Sinowatz F, Schams D. Expression and localization of fibroblast growth factor (FGF) family members during the final growth of bovine ovarian follicles. Mol Reprod Dev. 2004;67(2):162–171.
  • Michael DD, Alvarez IM, Ocón OM, et al. Fibroblast growth factor-2 is expressed by the bovine uterus and stimulates interferon-tau production in bovine trophectoderm. Endocrinology. 2006;147(7):3571–3579.
  • Ocón-Grove OM, Cooke FNT, Alvarez IM, Johnson SE, Ott TL, Ealy AD. Ovine endometrial expression of fibroblast growth factor (FGF) 2 and conceptus expression of FGF receptors during early pregnancy. Domest Anim Endocrinol. 2008;34(2):135–145.
  • Zhou C, Li C, Cai W, et al. Genome-wide association study for milk protein composition traits in a Chinese Holstein population using a single-step approach. Front Genet. 2019;10:72. 10.3389/fgene.2019.00072
  • Chen SY, Schenkel FS, Melo ALP, et al. Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. BMC Genomics. 2022;23(1):331.