家鸡基因组学研究中的又一篇经典PNAS paper

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

William M. Muira, Gane Ka-Shu Wongb,c, Yong Zhangc, Jun Wangc, Martien A. M. Groenend,
Richard P. M. A. Crooijmansd, Hendrik-Jan Megensd, Huanmin Zhange, Ron Okimotof, Addie Vereijkeng,
Annemieke Jungeriusg, Gerard A. A. Albersg, Cindy Taylor Lawleyh, Mary E. Delanyi, Sean MacEacherne,
and Hans H. Chenge,1

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.