516
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Genome-wide association study for the level of prolificacy in Cameroon’s native goat

, , , , , , , & show all
Article: 2291472 | Received 02 Nov 2022, Accepted 01 Dec 2023, Published online: 24 Jan 2024

References

  • https://www.ebi.ac.uk/QuickGO/term/GO:0042392 Accessed on 30 June 2020.
  • http://www.pantherdb.org/about.jsp Accessed on 30 June 2020.
  • http://www.ncbi.nlm.nih.gov/ genome/gdv Accessed on 30 June 2020.
  • http://www.ensembl.org/index.html 30 June 2020.
  • http://www.genecards Accessed on 30 June 2020.
  • http://www.malacards.org Accessed on 30 June 2020.
  • http://www.proteinatlas.org Accessed on 30 June 2020.
  • http://www.informatics.jax.org Accessed on 30 June 2020.
  • http://www.geneontology.org Accessed on 30 June 2020.
  • Alawieh A, Sabra Z, Nokkari A, El-Assaad A, Mondello S, Zaraket F, Fadlallah B, Kobeissy FH. 2014. Bioinformatics approach to understanding interacting pathways in neuropsychiatric disorders. In: Trent R, editor. Clinical bioinformatics, methods in molecular biology. New York (NY): Springer; p. 157–172. Doi:10.1007/978-1-4939-0847-9_9.
  • Alexandre G, Arquet R, Fleury J, Troupé W, Boval M, Archimède H, Mahieu M, Mandonnet N. 2012. Systèmes d’élevage caprins en zone tropicale : analyse des fonctions et des performances. INRA Prod Anim. 25:305. Doi:10.20870/productions-animales.2012.25.3.3218.
  • Allen HL, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S, et al. 2010. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 467:832–838. Doi:10.1038/nature09410.
  • Al-Mamun HA, A Clark S, Kwan P, Gondro C. 2015. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol. 47:90. Doi:10.1186/s12711-015-0169-6.
  • ASEB. 2010. Rapport de l’analyse situationnelle et estimation des besoins dans le domaine de santé et environnement au Cameroun. MINEP, MNSANTE, OMS. 183.
  • Barillet F, Mariat D, Amigues Y, Faugeras R, Caillat H, Moazami-Goudarzi K, Rupp R, Babilliot JM, Lacroux C, Lugan S, et al. 2009. Identification of seven haplotypes of the caprine PrP gene at codons 127, 142, 154, 211, 222 and 240 in French Alpine and Saanen breeds and their association with classical scrapie. J Gen Virol. 90(3):769–776. Doi:10.1099/vir.0.006114-0.
  • Barrett JH, Taylor JC, Iles MM. 2014. Statistical perspectives for genome-wide association studies (GWAS). In: Trent R, editor. Clinical bioinformatics, methods in molecular biology. New York (NY): Springer; p. 47–61. Doi:10.1007/978-1-4939-0847-9_4.
  • Bejarano D, Martínez R, Manrique C, Parra LM, Rocha JF, Gómez Y, Abuabara Y, Gallego J. 2018. Linkage disequilibrium levels and allele frequency distribution in Blanco Orejinegro and Romosinuano Creole cattle using medium density SNP chip data. Genet Mol Biol. 41:426–433. Doi:10.1590/1678-4685-gmb-2016-0310.
  • Berihulay H, Islam R, Jiang L, Ma Y. 2019. Genome-wide linkage disequilibrium and the extent of effective population sizes in six Chinese goat populations using a 50 K single nucleotide polymorphism panel. Animals (Basel). 9:350. Doi:10.3390/ani9060350.
  • Brodie A, Azaria JR, Ofran Y. 2016. How far from the SNP may the causative genes be? Nucleic Acids Res. 44:6046–6054. Doi:10.1093/nar/gkw500.
  • Bush W, Moore J. 2012. Chapter 11: genome-wide association studies. PloS Comput Biol. 8(12):11. Doi:10.1371/journal.pcbi.1002822.
  • Chan Y, Salem RM, Hsu Y-HH, McMahon G, Pers TH, Vedantam S, Esko T, Guo MH, Lim ET, Franke L, et al. 2015. Genome-wide analysis of body proportion classifies height-associated variants by mechanism of action and implicates genes important for skeletal development. Am J Hum Genet. 96:695–708. Doi:10.1016/j.ajhg.2015.02.018.
  • Costa RB, Camargo GM, Diaz ID, Irano N, Dias MM, Carvalheiro R, Boligon AA, Baldi F, Oliveira HN, Tonhati H, Albuquerque LG. 2015. Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference. Genet Sel Evol. 47:67. Doi:10.1186/s12711-015-0146-0.
  • De R, Bush WS, Moore JH. 2014. Bioinformatics challenges in genome-wide association studies (GWAS). In: Trent R, editor. Clinical bioinformatics, methods in molecular biology. New York (NY): Springer; p. 63–81. Doi:10.1007/978-1-4939-0847-9_5.
  • Dhanda JS, Taylor DG, Murray PJ, Pegg RB, Shand PJ. 2003. Goat meat production: present status and future possibilities. Asian-Australas J Anim Sci. 16:1842–1852. Doi:10.5713/ajas.2003.1842.
  • Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, Tosser-Klopp G, Wang J, Yang S, Liang J, et al. 2013. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol. 31:135–141. Doi:10.1038/nbt.2478.
  • FAO. 2016. Annuaire Statistique de la FAO. FAO, Rome.
  • Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, et al. 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 324:528–532. Doi:10.1126/science.1167936.
  • Guðmundsdóttir ÓÓ. 2015. Genome-wide association study of muscle traits in Icelandic sheep [MSc]. Agricultural University of Iceland, Hvanneyri. 63.
  • Hong EP, Park JW. 2012. Sample size and statistical power calculation in genetic association studies. Genomics Inform. 10:117–122. Doi:10.5808/GI.2012.10.2.117.
  • Huson, H.J., Sonstegard, T.S., Silverstein, J., Woodward-Greene, M.J., Masiga, C., Muchadeyi, F., Rees, J., Sayre, B., Elbetagy, A., Rothschild, M., et al. 2014. Genetic and phenotypic characterization of African goat populations to prioritize conservation and production efforts for small-holder farmers in sub-Saharan Africa. American Society of Animal Science. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. 3
  • Khaitovich P, Kelso J, Franz H, Visagie J, Giger T, Joerchel S, Petzold E, Green RE, Lachmann M, Pääbo S. 2006. Functionality of intergenic transcription: an evolutionary comparison. PLOS Genet. 2:e171. 1590–1598. Doi:10.1371/journal.pgen.0020171.
  • Kouam SJ, Meutchieye F, Kenfack WP, Manjeli Y. 2015. Prolificacy and its relationship with body measurements in Cameroon native goats. Bull Anim Health Prod Afr. 63:235–241. Doi:10.4314/bahpa.v63i4.
  • Manjeli Y, Téguia A, Njwe RM, Tchoumboué J, Ayong EE. 1994. Enquête sur l’élevage caprin dans les hauts plateaux de l’ouest Cameroun. Presented at the Small Ruminant Research Network Workshop, Yaoundé, Cameroun. p. 99–103.
  • Marees AT, Kluiver Hd, Stringer S, Vorspan F, Curis E, Marie-Claire C, Derks EM. 2018. A tutorial on conducting genome-wide association studies: quality control and statistical analysis. Int J Methods Psychiatr Res. 27:e1608. 10. Doi:10.1002/mpr.1608.
  • Meutchieye F, Emma-Ngono PJ, Agaba M, Djikeng A, Manjeli Y. 2014. Genetic diversity of Cameroon indigenous goat populations using microsatellites. Livest Res Rural Dev. 26:7. ISSN 0121-3784.
  • Miao X, Luo Q, Zhao H, Qin X. 2016. Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity. Sci Rep. 6:9. Doi:10.1038/s41598-016-0002-7.
  • Mizugishi K, Li C, Olivera A, Bielawski J, Bielawska A, Deng C-X, Proia RL. 2007. Maternal disturbance in activated sphingolipid metabolism causes pregnancy loss in mice. J Clin Invest. 117:2993–3006. Doi:10.1172/JCI30674.
  • Muriuki C, Bush SJ, Salavati M, McCulloch MEB, Lisowski ZM, Agaba M, Djikeng A, Hume DA, Clark EL. 2019. A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats. Front Genet. 10:1080. 1–16. Doi:10.3389/fgene.2019.01080.
  • Murray C, Huerta-Sanchez E, Casey F, Bradley DG. 2010. Cattle demographic history modelled from autosomal sequence variation. Philos Trans R Soc B Biol Sci. 365:2531–2539. Doi:10.1098/rstb.2010.0103.
  • Njiki EW. 2011. Caractéristiques socio-économiques et techniques de l’élevage des petits ruminants dans les Départements de la Valée du Ntem et de la Mvilla (Sud-Cameroun) (Mémoire de fin d’étude). Université de Dschang, Dschang.
  • Onzima RB, Upadhyay MR, Doekes HP, Brito LF, Bosse M, Kanis E, Groenen MAM, Crooijmans RPMA. 2018. Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds. In: Frontier in Genetics, Sec. Livestock Genomics. Auckland. p. 1–13. Doi:10.3389/fgene.2018.00318.
  • Pailhoux E, Vigier B, Chaffaux S, Servel N, Taourit S, Furet J-P, Fellous M, Grosclaude F, Cribiu EP, Cotinot C, Vaiman D. 2001. A 11.7-kb deletion triggers intersexuality and polledness in goats. Nat Genet. 29:453–458. Doi:10.1038/ng769.
  • Paim TdP, Faria DA, Hay EH, McManus C, Lanari MR, Esquivel LC, Cascante MI, Alfaro EJ, Mendez A, Faco O, et al. 2019. New world goat populations are a genetically diverse reservoir for future use. Sci Rep. 9. Doi:10.1038/s41598-019-38812-3.
  • Pausch H, Flisikowski K, Jung S, Emmerling R, Edel C, Götz K-U, Fries R. 2011. Genome-wide association study identifies two major loci affecting calving ease and growth-related traits in cattle. Genetics. 187:289–297. Doi:10.1534/genetics.110.124057.
  • PNGE. 2009. Révision/Opérationnalisation du Plan National de la Gestion de l’Environnement (PNGE) vers un Programme Environnement (PE). Diagnostic de la situation de l’environnement au Cameroun, Diagnostic de la situation de l’environnement au Cameroun. p. 109.
  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 81:559–575. Doi:10.1086/519795.
  • Quan Q, Zheng Q, Ling Y, Fang F, Chu M, Zhang X, Liu Y, Li W. 2019. Comparative analysis of differentially expressed genes between the ovaries from pregnant and nonpregnant goats using RNA-Seq. J Biol Res-Thessaloniki. 26(3):12. Doi:10.1186/s40709-019-0095-9.
  • R Development Core Team. 2016. R: a language and environment for statistical computing, R foundation for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Doi:10.1007/978-3-540-74686-7.
  • Ricordeau G. 1992. Les objectifs et les critères de sélection. Synthèse des estimations de la variabilité génétique et des liaisons entre caractères dans les différentes espèces. Prod Anim. 5:107–116.
  • Rupp R, Mucha S, Larroque H, Mcewan J, Coningtont J. 2016. Genomic application in sheep and goat breeding. Anim Front. 6:39. Doi:10.2527/af.2016-0006.
  • Spencer CCA, Su Z, Donnelly P, Marchini J. 2009. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PloS Genet. 5(5):13.
  • Tarekegn GM, Wouobeng P, Jaures KS, Mrode R, Edea Z, Liu B, Zhang W, Mwai OA, Dessie T, Tesfaye K, et al. 2019. Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from East African, North African, and Asian conspecifics. PloS ONE. 14(4e):0214843. Doi:10.1371/journal.pone.0214843.
  • Tchouamo IR, Tchoumboué J, Thibault L. 2005. Caractéristiques socio-économiques et techniques de l’élevage de petits ruminants dans la province de l’ouest du Cameroun. Tropicultura. 23(4):201–211.
  • Tchoumboué J. 1997. Elevage des caprins en zone soudano-guinéenne d’altitude de Cameroun, Visite d’étude sur les systèmes d’élevage dans les zones humides et subhumides d’Afrique., CTA Publications. CTA, Wageningen. p. 148–153.
  • Teguia A, Manjeli Y, Tchoumboué J. 1997. L’incidence du calendrier agricole sur l’élevage des petits ruminants dans une zone densement peuplée: cas des Hauts-Plateaux de l’Ouest Cameroun. Tropicultura. 15:56–60.
  • Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, Donnadieu-Tonon C, Eggen A, Heuven HCM, Jamli S, et al. 2014. Design and characterization of a 52 K SNP chip for goats. PLoS ONE. 9(1):8. E86227. Doi:10.1371/journal.pone.0086227.
  • Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, Li Y, Yuan C, Geng R, Lan X, et al. 2016. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits. Sci Rep. 6:38932. Doi:10.1038/srep38932.
  • White SN, Mousel MR, Herrmann-Hoesing LM, Reynolds JO, Leymaster KA, Neibergs HL, Lewis GS, Knowles DP. 2012. Genome-wide association identifies multiple genomic regions associated with susceptibility to and control of ovine lentivirus. PLoS ONE. 7:10. Doi:10.1371/journal.pone.0047829.
  • Wijayanti D, Bai Y, Hanif Q, Chen H, Zhu H, Qu L, Guo Z, Lan X. 2022b. Goat CLSTN2 gene: tissue expression profile, genetic variation, and its associations with litter size. Anim Biotechnol. 18:1–10. Doi:10.1080/10495398.2022.2144342.
  • Wijayanti D, Zhang S, Bai Y, Pan C, Chen H, Qu L, Guo Z, Lan X. 2022c. Investigation on mRNA expression and genetic variation within goat SMAD2 gene and its association with litter size. Anim Biotechnol. 34(7):2674–2683. Doi:10.1080/10495398.2022.2077214.
  • Wijayanti D, Zhang S, Yang Y, Bai Y, Akhatayeva Z, Pan C, Zhu H, Qu L, Lan X. 2022a. Goat SMAD family member 1 (SMAD1): mRNA expression, genetic variants, and their associations with litter size. Theriogenology. 193:11–19. Doi:10.1016/j.theriogenology.2022.09.001.
  • Wouobeng P, Simo JK, Meutchieye F, Yacouba M, Agaba M. 2018. Polymorphism of prolificacy genes (BMP15, BMPR 1B and GDF9), in the Native Goat (Capra hircus) of Cameroon. Proceedings of the World Congress on Genetics Applied to Livestock Production. p. 761.
  • Zhang L, Liu J, Zhao F, Ren H, Xu L, Lu J, Zhang S, Zhang X, Wei C, Lu G, et al. 2013. Genome-wide association studies for growth and meat production traits in sheep. PLoS ONE. 8(6):12. E66569. DOI:10.1371/journal.pone.0066569.g002.