AUTHOR=Banos Georgios , Lindsay Victoria , Desta Takele T. , Bettridge Judy , Sanchez-Molano Enrique , Vallejo-Trujillo Adriana , Matika Oswald , Dessie Tadelle , Wigley Paul , Christley Robert M. , Kaiser Peter , Hanotte Olivier , Psifidi Androniki 

TITLE=Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.543890

DOI=10.3389/fgene.2020.543890

ISSN=1664-8021

ABSTRACT=<p>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 <italic>Eimeria</italic> and cestode parasitism, and productivity [body weight and body condition score (BCS)]. Combined data from the two chicken ecotypes, Horro (<italic>n</italic> = 384) and Jarso (<italic>n</italic> = 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 (<italic>TOLLIP, ANGPTL5, BCL9, THEMIS2</italic>), MDV (<italic>GRM7</italic>), SG (<italic>MAP3K21</italic>), <italic>Eimeria</italic> (<italic>TOM1L1</italic>) and cestodes (<italic>TNFAIP1, ATG9A, NOS2</italic>) 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.</p>