Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions

Abstract

Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal’s immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of São Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix Axiom®600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments.

Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

“…The most representative gene on chromosome 7, with regards to production traits, is FTCD, which plays a main role in feed intake, in accordance with the quantitative trait loci identified [40]. Inside the last region identified on chromosome 8, the TRMT1L (tRNA Methyltransferase 1-Like) gene is noteworthy as it seems to be involved in chicken adaptation and survival in stressful conditions [41].…”

Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds

“…The hapFLK statistic that accounted for the haplotype information and hierarchical structure [36, 37] was used to identify selection footprints on the contrast model (river vs. swamp). HapFLK analyses revealed that a total of 12 genomic regions was identifed ( Fig 4 ).…”

Genetic Basis of Response of Ghanaian Local Chickens to Infection With a Lentogenic Newcastle Disease Virus

“…In Africa, local chickens are raised in free range scavenging and backyard systems ( Goromela et al, 2006 ). As a result, African local chicken ecotypes are adapted to extreme climatic conditions with low inputs of feed and veterinary services, as evidenced by the presence of selection signatures across the genomes of local chickens ( Fleming et al, 2016 , 2017 ; Walugembe et al, 2019a ). Although local chickens are well adapted to their environment and some unvaccinated local chickens have been reported to have anti-NDV antibodies ( Boakye et al, 2016 ), velogenic ND outbreaks often lead to loss of entire chicken flocks ( Guèye, 2002 ; Copland et al, 2018 ) due to lack of or ineffective vaccination.…”