Population genomics identifies patterns of genetic diversity and selection in chicken

Abstract

Background There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. Results Here, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources. Conclusions The work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic traits. Electronic supplementary material The online version of this article (10.1186/s12864-019-5622-4) contains supplementary material, which is available to authorized users.

Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

“…They possess their own genetic structure in subgroups. In admixture result, game breeds and red jungle clustered as one group until K = 16, suggesting domestic breeds and wild populations have mutual introgression (Li et al, 2019;Wang et al, 2020). It is consistent with our NJ tree results that all breeds from the same population clustered, except that game breeds.…”

“…On chromosome 11, more than 33% of the Silkies chickens, 24% of the Tibet chickens and 14% of Hongshan chickens had a ROH in the region from 1.91 to 4.00 Mb, from 2.31 to 5.66 Mb, and from 2.30 to 3.91 Mb, which contained NECAB2, SLC38A8, and NFATC3 genes, and several potential candidate genes for silky feathers. On chromosome 3, we showed that up to 40% of Beijing You chickens had a ROH between 69.38 and 70.93 Mb, retaining the gene ASCC3 which is also a candidate gene for silky feathers (Li et al, 2019). Besides, on chromosome 2, chromosome 3, and chromosome 13, we identified several potential candidate genes associated with egg production, eggshell quality and growth traits, such as GDF9, OPN, CDH9, CDH10, and KIF18A (Pines et al, 1995;Hincke et al, 2010;An et al, 2012;Lin et al, 2014;Wang et al, 2020).…”

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

“…Genes for aesthetic physical phenotypes including height, stature, coat and plumage colour are commonly encountered in genomic regions under selection in domestic animal populations since they are easily identifiable [42][43][44][45] . Conformation characteristics are among the most discernible traits in horses and are the principal observable traits on which Thoroughbreds are selected.…”

Whole genome phylogeny of Gallus: introgression and data-type effects

“…Due to its economic and agricultural importance, the wild progenitor of the Domestic Chicken, Gallus gallus (Red Junglefowl), was the first avian species whose genome was completely sequenced (ICGSC 2004). Since then, genomes of many of the hundreds of different breeds of Gallus gallus have been sequenced (e.g., Imsland et al 2012;Yi et al 2014;Wang et al 2015;Lawal et al 2018;Li et al 2019;Yang et al 2019), resulting in a large number of available chicken genomes.…”