Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

Abstract

Breed utilization, genetic improvement, and industry consolidation are predicted to have major impacts on the genetic composition of commercial chickens. Consequently, the question arises as to whether sufficient genetic diversity remains within industry stocks to address future needs. With the chicken genome sequence and more than 2.8 million single-nucleotide polymorphisms (SNPs), it is now possible to address biodiversity using a previously unattainable metric: missing alleles. To achieve this assessment, 2551 informative SNPs were genotyped on 2580 individuals, including 1440 commercial birds. The proportion of alleles lacking in commercial populations was assessed by (1) estimating the global SNP allele frequency distribution from a hypothetical ancestral population as a reference, then determining the portion of the distribution lost, and then (2) determining the relationship between allele loss and the inbreeding coefficient. The results indicate that 50% or more of the genetic diversity in ancestral breeds is absent in commercial pure lines. The missing genetic diversity resulted from the limited number of incorporated breeds. As such, hypothetically combining stocks within a company could recover only preexisting within-breed variability, but not more rare ancestral alleles. We establish that SNP weights act as sentinels of biodiversity and provide an objective assessment of the strains that are most valuable for preserving genetic diversity. This is the first experimental analysis investigating the extant genetic diversity of virtually an entire agricultural commodity. The methods presented are the first to characterize biodiversity in terms of allelic diversity and to objectively link rate of allele loss with the inbreeding coefficient.alleles ͉ biodiversity ͉ poultry

Is Continued Genetic Improvement of Livestock Sustainable?

“…Modern commercial poultry stocks have lost about half the molecular variation of their native Jungle Fowl source, but most of this loss occurred before the current populations, including fanciers' strains, were bred (Muir et al 2008). Estimates of heterozygosity within two broiler and two layer commercial strains averaged 60 and 40% of that in a Red Jungle Fowl population (4.1 3 10 23 ) (Rubin et al 2010).…”

A locus-wide approach to assessing variation in the avian MHC: the B-locus of the wild turkey

“…A significant loss of species-wide minor alleles in commercial populations has been well documented in the chicken (Muir et al, 2008). Contraction of MHC haplotypes in commercial lines relative to wild birds has also been observed in a previous study of turkeys .…”

“…Sequencing the MHC locus of the chicken, quail and turkey (MHC-B) identified the classical MHC class I and II genes within an B50 kb distance (Shiina et al, 2004(Shiina et al, , 2007Chaves et al, 2009b). Commercial selection has clearly reduced allelic diversity in chicken lines (Muir et al, 2008). A sampling of genetic variation within commercial turkeys shows that some MHC haplotypes occur at high frequency within breeder lines (Chaves et al, 2010).…”

Genomics and Genome Sequencing: Benefits for Finfish Aquaculture

“…Moreover, new genotyping technologies enable the simultaneous analysis of a great number of these markers, which allows the construction of high density genetic maps (Goddard & Hayes, 2009). These techniques are now being widely used in species of agricultural importance and have led to the development of numerous dense SNP arrays, which are tools that are used to screen entire genomes for the genotypes of known SNPs (Matukumalli et al, 2009;Muir et al, 2008;Ramos et al, 2009). …”