Genome-wide association study of growth performance and immune response to Newcastle disease virus of indigenous chicken in Rwanda

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cg.authorship.typesCGIAR and developing country instituteen_US
cg.contributor.affiliationUniversity of Rwandaen_US
cg.contributor.affiliationEgerton Universityen_US
cg.contributor.affiliationRwanda Agricultural and Animal Resources Development Boarden_US
cg.contributor.affiliationInternational Livestock Research Instituteen_US
cg.contributor.donorAfrica Biosciences Challenge Funden_US
cg.contributor.donorDepartment of Foreign Affairs and Trade, Australiaen_US
cg.contributor.donorSyngenta Foundation for Sustainable Agricultureen_US
cg.contributor.donorBill & Melinda Gates Foundationen_US
cg.contributor.donorDepartment for International Development, United Kingdomen_US
cg.contributor.donorSwedish International Development Cooperation Agencyen_US
cg.coverage.countryRwandaen_US
cg.coverage.iso3166-alpha2RWen_US
cg.coverage.regionAfricaen_US
cg.coverage.regionEastern Africaen_US
cg.creator.identifierNasser K. Yao: 0000-0002-1183-708Xen_US
cg.howPublishedFormally Publisheden_US
cg.identifier.doihttps://doi.org/10.3389/fgene.2021.723980en_US
cg.isijournalISI Journalen_US
cg.issn1664-8021en_US
cg.journalFrontiers in Geneticsen_US
cg.reviewStatusPeer Reviewen_US
cg.subject.ilriDISEASE CONTROLen_US
cg.subject.ilriGENETICSen_US
cg.subject.ilriINDIGENOUS BREEDSen_US
cg.subject.ilriPOULTRYen_US
cg.volume12en_US
dc.contributor.authorHabimana, R.en_US
dc.contributor.authorNgeno, K.en_US
dc.contributor.authorOkeno, T.O.en_US
dc.contributor.authorHirwa, C.D.en_US
dc.contributor.authorKeambou, T.C.en_US
dc.contributor.authorYao, Nasseren_US
dc.date.accessioned2021-11-10T08:18:31Zen_US
dc.date.available2021-11-10T08:18:31Zen_US
dc.identifier.urihttps://hdl.handle.net/10568/115937en_US
dc.titleGenome-wide association study of growth performance and immune response to Newcastle disease virus of indigenous chicken in Rwandaen_US
dcterms.abstractA chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E−5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E−5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E−5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.en_US
dcterms.accessRightsOpen Accessen_US
dcterms.audienceScientistsen_US
dcterms.available2021-08-16en_US
dcterms.bibliographicCitationHabimana, R., Ngeno, K., Okeno, T.O., Hirwa, C.D., Keambou, T.C. and Yao, N.K. 2021. Genome-wide association study of growth performance and immune response to Newcastle disease virus of indigenous chicken in Rwanda. Frontiers in Geneticsen_US
dcterms.issued2021-08-16en_US
dcterms.languageenen_US
dcterms.licenseCC-BY-4.0en_US
dcterms.publisherFrontiers Mediaen_US
dcterms.subjectanimal healthen_US
dcterms.subjectanimal diseasesen_US
dcterms.subjectchickensen_US
dcterms.subjectindigenous breedsen_US
dcterms.subjectnewcastle diseaseen_US
dcterms.subjectgeneticsen_US
dcterms.typeJournal Articleen_US

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