Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda

Richard Habimana; Kiplangat Ngeno; Tobias Otieno Okeno; Claire D' Andre Hirwa; Christian Keambou Tiambo; Nasser Kouadio Yao

doi:10.3389/fgene.2021.723980

Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda

Front Genet. 2021 Aug 16:12:723980. doi: 10.3389/fgene.2021.723980. eCollection 2021.

Authors

Richard Habimana^{1

2}, Kiplangat Ngeno², Tobias Otieno Okeno², Claire D' Andre Hirwa³, Christian Keambou Tiambo⁴, Nasser Kouadio Yao⁵

Affiliations

¹ College of Agriculture, Animal Science and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.
² Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya.
³ Rwanda Agricultural and Animal Resources Development Board, Kigali, Rwanda.
⁴ Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya.
⁵ Biosciences Eastern and Central Africa - International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya.

Abstract

A 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.

Keywords: genome-wide association studies; growth performance; indigenous chicken; putative gene; quantitative trait loci; single nucleotide polymorphism.