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

Authors: MUIR, WILLIAM - PURDUE UNIVERSITY; WONG, GANE KA-SHU - UNIVERSITY OF ALBERTA; ZHANG, YONG - CHINESE ACAD. OF SCIENCES; WANG, JUN - CHINESE ACAD. OF SCIENCES; GROENEN, MARTIEN A M - WAGENINGEN UNIVERSITY; CROOIJMANS, RICHARD P M A - WAGENINGEN UNIVERSITY; MEGENS, HENDRIK-JAN - WAGENINGEN UNIVERSITY; Zhang, Huanmin; OKIMOTO, RON - COBB-VANTRESS, INC.; VEREIJKEN, ADDIE - HENDRIX GENETICS; JUNGERIUS, ANNEMIEKE - HENDRIX GENETICS; ALBERS, GERARD A A - HENDRIX GENETICS; TAYLOR LAWLEY, CINDY - ILLUMINA, INC.-SAN DIEGO; DELANY, MARY - UNIVERSITY OF CALIFORNIA; Maceachern, Sean; Cheng, Hans

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/23/2008
Publication Date: 11/11/2008
Citation: Muir, W.M., Wong, G., Zhang, Y., Wang, J., Groenen, M., Crooijmans, R., Megens, H., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G., Taylor Lawley, C., Delany, M.E., Maceachern, S.A., Cheng, H.H. 2008. Genome-Wide Assessment of Worldwide Chicken SNP Genetic Diversity Indicates Significant Absence of Rare Alleles in Commercial Breeds. Proceedings of the National Academy of Sciences. 105(45):17312-17317.

Interpretive Summary: The poultry breeding industry is based on the assumption that within populations under selection, genetic diversity exists for agriculturally important traits. Thus, by identifying superior individuals and using them as parents for the next generation, they raise the overall performance of the group. Recently, with the chicken genome sequence and the accompanying identification of million of sequence variants known as single nucleotide polymorphisms (SNPs), it was possible to quantify the amount of biodiversity present in current commercial populations compared to all chickens. We find that 50% or more of the genetic diversity has been lost, which is most likely the results of using only a limited number of chicken breeds to form the commercial stock. This information suggests that the industry might not have the genetic diversity to combat new and emerging diseases where the resistance is attributed to rare alleles, which might only be found in non-commercial breeds. Furthermore, our paper describes a number of new methods for analyzing genetic diversity, especially as it relates to inbreeding.

Technical 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 2.8+ million single nucleotide polymorphisms (SNPs), it is now possible to address biodiversity using a previously unattainable metric “loss of alleles.” To achieve this goal, 2551 informative SNPs were genotyped on 2580 individuals including 1440 commercial birds. The proportion of alleles lost was assessed by (1) estimating the global SNP allele frequency distribution from a hypothetical ancestral population (HAP) as a reference, then determining the portion of the distribution lost, and (2) determining the relationship between loss of alleles and the inbreeding coefficient. Results indicate 50% or more of the genetic diversity has been lost in every commercial pure line due to the limited number of incorporated breeds. And at most, only ~10% can be recovered by hypothetically combining all commercial stocks as significant diversity remains lost with low levels (<20%) of inbreeding. We establish that SNP weights act as sentinels of biodiversity and provide an objective assessment of which strains are most valuable for their contribution towards preservation of genetic diversity. This is the first experimental analysis investigating extant genetic diversity of virtually an entire agricultural commodity. And methods presented are the first to characterize loss of biodiversity in terms of lost alleles and to objectively link rate of allele loss with the inbreeding coefficient.