Abstract
Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek’s Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity [body weight and body condition score (BCS)]. Combined data from the two chicken ecotypes, Horro (n = 384) and Jarso (n = 376), were jointly analyzed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22–0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection.
Highlights
IntroductionVillage poultry are important in low- and middle-income countries around the world (Hassan et al, 2004; Khobondo et al, 2015) and, are the focus of many development programs (Dana et al, 2010, 2011; Dinka et al, 2010; Ngeno, 2011; Magothe et al, 2012; Khobondo et al, 2015)
A moderately low heritability was estimated for PM antibody responses, and cestodes and Eimeria parasitism, while a low heritability was estimated for SG antibody responses and body condition score (BCS)
The pathways and networks constructed from the gene products located in the candidate regions for each of the studied traits are presented in Figure 2 and Supplementary Figure S2, respectively
Summary
Village poultry are important in low- and middle-income countries around the world (Hassan et al, 2004; Khobondo et al, 2015) and, are the focus of many development programs (Dana et al, 2010, 2011; Dinka et al, 2010; Ngeno, 2011; Magothe et al, 2012; Khobondo et al, 2015). In Ethiopia, previous poultry development programs concentrated on ways to increase the productivity of chickens by introducing commercial (exotic) breeds that perform highly under (semi) intensive management conditions Whilst this has been a relatively successful approach in peri-urban areas (FAO, 2008), it has not translated well into rural areas and smallholder farmers. In addition to focusing on increasing productivity, a focus toward raising the efficiency of the production system has been considered beneficial (Bettridge et al, 2018) This is especially true for rural smallholders who may be able to make significant gains in income and nutrition, but of necessity can afford little in the way of economic or opportunity costs that some of the previous chicken development programs in Ethiopia have required
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