Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Abstract

Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide singlenucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r 2 X0.3) in both traditional and village chickens at pairwise marker distances of B10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling B75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.

Haplo-block structure of Southern African village chicken populations inferred using genome-wide SNP data

“…Multiple short haploblocks imply that many recombination events occurred that broke up the historical ancestral blocks into smaller segments. These results were expected from outbred populations with high genetic diversity that has not been subjected to artificial selection pressures for specific production traits (Wragg et al, 2012). The average median block length (Table 1) observed in this study was 8.8 kb, and is comparable to that reported in chickens (Megens et al, 2009), wild dogs (Zhao et al, 2003;Lindblad-Toh et al, 2005), pigs (Amaral et al, 2008), and humans (Gabriel et al, 2002;Wall and Pritchard 2003).…”

“…This could have been caused by the sampling structure, in that one ecotype of chickens was obtained from Malawi whereas three ecotypes country were used for South Africa and Zimbabwe. The number of haplo-blocks in Malawi was similar to that observed by Wragg et al (2012) in traditional and village chicken populations. The number of haplo-blocks in populations from South Africa and Zimbabwe was similar to that observed by Qanbari et al (2010) in commercial lines (broilers and layers).…”

“…As a result, studies such as those by Megens et al (2009), Qanbari et al (2010, and Wragg et al (2012) are available and can be used for comparisons. The haplo-block structure of village chicken populations from Southern Africa should permit understanding of their genomics and provide baseline information for future investigations on haplotype variation in association with phenotypic traits of interest.…”

“…The first draft of the chicken genome was published in 2004 (International Chicken Genome Consortium, 2004) from which over 2.8 million SNPs have been discovered. The Illumina chicken iSelect 60K SNP chip has been useful for studying LD as well as haplo-blocks partitioning in commercial (Qanbari et al, 2010) and traditional free-range chickens (Wragg et al, 2012).…”

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

“…In addition, free-range scavenging village chickens (Dessie et al, 2011;Leroy et al 2012;Desta et al, 2013) also offer large potential to understand the genetic control of phenotypic diversity. Since village chickens possess a richness of accumulated recombination and a number of adaptive characteristics for extreme environments such as high temperature, they provide a useful genetic resource for high-resolution genetic mapping (Wragg et al, 2012;Megens and Groenen, 2012).…”