Habimana Richard, Ngeno Kiplangat, Okeno Tobias Otieno, Hirwa Claire D' Andre, Keambou Tiambo Christian, Yao Nasser Kouadio
College of Agriculture, Animal Science and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.
Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya.
Front Genet. 2021 Aug 16;12:723980. doi: 10.3389/fgene.2021.723980. eCollection 2021.
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 ( ≤ 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 ( ≤ 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 ( ≤ 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.
鸡的基因组有几个含有数量性状基因座（QTL）的区域。然而，特别是在非洲鸡种群中，需要对QTL效应进行复制和验证。本研究利用全基因组关联研究（GWAS），在卢旺达本地鸡（IC）中鉴定出与体重（BW）和新城疫（ND）抗体反应（AbR）相关的单核苷酸多态性（SNP）和推定基因。分别使用5%和10%的染色体错误检测率对多重检验进行校正，以确定显著阈值和提示性阈值。分别使用BioMart数据挖掘工具和变异效应预测工具对SNP和候选基因进行注释。在8号、11号和19号染色体上共鉴定出4个与BW显著相关（≤7.6E-5）的显著SNP（rs74098018、rs13792572、rs314702374和rs14123335）。在这些SNP附近，鉴定出4个基因，如前B细胞白血病同源盒1（PBX1）、GPATCH1、MPHOSPH6和MRM1。另外4个均位于1号染色体上的显著SNP（rs314787954、rs13623466、rs13910430和rs737507850）与鸡对ND的抗体反应强烈相关（≤7.6E-5）。与这4个SNP最接近的基因是细胞分裂周期16（CDC16）、含锌指BED型1（ZBED1）、黏液病毒（流感病毒）抗性1（MX1）和生长因子受体结合蛋白2（GRB2）相关衔接蛋白2（GRAP2）。此外，还报道了其他与BW和鸡对ND的抗体反应有提示性相关（≤1.5E-5）的SNP和基因。这项工作为发现调控BW和鸡对ND性状抗体反应的重要QTL的致病基因提供了一个有用的切入点。研究结果提供了有前景的基因和基于SNP的标记，可用于基于基因和/或标记辅助育种选择来改善IC种群的生长性能和对ND的抗性。
