Giuseppe
Emeritus
Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds ? PNAS
Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds
1. William M. Muira, 2. Gane Ka-Shu Wongb,c, 3. Yong Zhangc, 4. Jun Wangc, 5. Martien A. M. Groenend, 6. Richard P. M. A. Crooijmansd, 7. Hendrik-Jan Megensd, 8. Huanmin Zhange, 9. Ron Okimotof, 10. Addie Vereijkeng, 11. Annemieke Jungeriusg, 12. Gerard A. A. Albersg, 13. Cindy Taylor Lawleyh, 14. Mary E. Delanyi, 15. Sean MacEacherne, and 16. Hans H. Chenge,1
Author Affiliations
1. aDepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907;
2. bUniversity of Alberta, Department of Biological Sciences and Department of Medicine, Edmonton, Alberta T6G 2E9, Canada;
3. cBeijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China;
4. dAnimal Breeding and Genomics Centre, Wageningen University, 6709 PG Wageningen, The Netherlands;
5. eUnited States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823;
6. fCobb-Vantress, Inc., Siloam Springs, AR 72761;
7. gHendrix Genetics, 5831 CK Boxmeer, The Netherlands;
8. hIllumina, Inc., San Diego, CA 92121; and
9. iDepartment of Animal Science, University of California Davis, Davis, CA 95616.
1. Edited by James E. Womack, Texas A&M University, College Station, TX, and approved September 23, 2008 (received for review July 8, 2008)
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
Footnotes
* 1To whom correspondence should be addressed at: USDA, ARS, Avian Disease and Oncology Laboratory, 3606 E. Mount Hope Rd. East Lansing, MI 48823. E-mail: hans.cheng@ars.usda.gov
* Author contributions: W.M.M., G.K.-S.W., M.G., and H.H.C. designed research; W.M.M., M.G., R.P.C., H.-J.M., A.V., A.J., C.T.L., and H.H.C. performed research; W.M.M., M.G., R.P.C., H.-J.M., H.Z., R.O., A.V., A.J., G.A.A., C.T.L., and H.H.C. contributed new reagents/analytic tools; W.M.M., G.K.-S.W., Y.Z., J.W., M.G., H.-J.M., M.E.D., S.M., and H.H.C. analyzed data; and W.M.M., G.K.-S.W., M.G., H.-J.M., H.Z., R.O., A.J., G.A.A., M.E.D., S.M., and H.H.C. wrote the paper.
* The authors declare no conflict of interest.
* This article is a PNAS Direct Submission.
* This article contains supporting information online at www.pnas.org/cgi/content/full/0806569105/DCSupplemental.
* ? 2008 by The National Academy of Sciences of the USA
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<cite cite="http://www.pnas.org/content/105/45/17312.short?rss=1">Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds ? PNAS</cite>1. William M. Muira, 2. Gane Ka-Shu Wongb,c, 3. Yong Zhangc, 4. Jun Wangc, 5. Martien A. M. Groenend, 6. Richard P. M. A. Crooijmansd, 7. Hendrik-Jan Megensd, 8. Huanmin Zhange, 9. Ron Okimotof, 10. Addie Vereijkeng, 11. Annemieke Jungeriusg, 12. Gerard A. A. Albersg, 13. Cindy Taylor Lawleyh, 14. Mary E. Delanyi, 15. Sean MacEacherne, and 16. Hans H. Chenge,1
Author Affiliations
1. aDepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907;
2. bUniversity of Alberta, Department of Biological Sciences and Department of Medicine, Edmonton, Alberta T6G 2E9, Canada;
3. cBeijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China;
4. dAnimal Breeding and Genomics Centre, Wageningen University, 6709 PG Wageningen, The Netherlands;
5. eUnited States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823;
6. fCobb-Vantress, Inc., Siloam Springs, AR 72761;
7. gHendrix Genetics, 5831 CK Boxmeer, The Netherlands;
8. hIllumina, Inc., San Diego, CA 92121; and
9. iDepartment of Animal Science, University of California Davis, Davis, CA 95616.
1. Edited by James E. Womack, Texas A&M University, College Station, TX, and approved September 23, 2008 (received for review July 8, 2008)
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
Footnotes
* 1To whom correspondence should be addressed at: USDA, ARS, Avian Disease and Oncology Laboratory, 3606 E. Mount Hope Rd. East Lansing, MI 48823. E-mail: hans.cheng@ars.usda.gov
* Author contributions: W.M.M., G.K.-S.W., M.G., and H.H.C. designed research; W.M.M., M.G., R.P.C., H.-J.M., A.V., A.J., C.T.L., and H.H.C. performed research; W.M.M., M.G., R.P.C., H.-J.M., H.Z., R.O., A.V., A.J., G.A.A., C.T.L., and H.H.C. contributed new reagents/analytic tools; W.M.M., G.K.-S.W., Y.Z., J.W., M.G., H.-J.M., M.E.D., S.M., and H.H.C. analyzed data; and W.M.M., G.K.-S.W., M.G., H.-J.M., H.Z., R.O., A.J., G.A.A., M.E.D., S.M., and H.H.C. wrote the paper.
* The authors declare no conflict of interest.
* This article is a PNAS Direct Submission.
* This article contains supporting information online at www.pnas.org/cgi/content/full/0806569105/DCSupplemental.
* ? 2008 by The National Academy of Sciences of the USA
-