Skip to main content Accessibility help
×
×
Home

An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations

  • JIAHAN LI (a1), QIN LI (a1), WEI HOU (a2), KUN HAN (a3), YAO LI (a1), SONG WU (a1), YANCHUN LI (a3) and RONGLING WU (a1) (a3) (a4)...

Summary

A linkage–linkage disequilibrium map that describes the pattern and extent of linkage dis-equilibrium (LD) decay with genomic distance has now emerged as a viable tool to unravel the genetic structure of population differentiation and fine-map genes for complex traits. The prerequisite for constructing such a map is the simultaneous estimation of the linkage and LD between different loci. Here, we develop a computational algorithm for simultaneously estimating the recombination fraction and LD in a natural outcrossing population with multilocus marker data, which are often estimated separately in most molecular genetic studies. The algorithm is founded on a commonly used progeny test with open-pollinated offspring sampled from a natural population. The information about LD is reflected in the co-segregation of alleles at different loci among parents in the population. Open mating of parents will reveal the genetic linkage of alleles during meiosis. The algorithm was constructed within the polynomial-based mixture framework and implemented with the Expectation–Maximization (EM) algorithm. The by-product of the derivation of this algorithm is the estimation of outcrossing rate, a parameter useful to explore the genetic diversity of the population. We performed computer simulation to investigate the influences of different sampling strategies and different values of parameters on parameter estimation. By providing a number of testable hypotheses about population genetic parameters, this algorithmic model will open a broad gateway to understand the genetic structure and dynamics of an outcrossing population under natural selection.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations
      Available formats
      ×

      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations
      Available formats
      ×

      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations
      Available formats
      ×

Copyright

Corresponding author

Corresponding author. Department of Statistics, University of Florida, Gainesville, FL 32611, USA. Tel: (352)392-3806. Fax. (352)392-8555. e-mail: rwu@stat.ufl.edu
*These authors contributed equally to this work.

References

Hide All
Ardlie, K. G., Kruglyak, L. & Seielstad, M. (2002). Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics 3, 299309.
Butcher, P. A. & Southerton, S. (2007). Marker-assisted selection in forestry species. In Marker-assisted Selection: Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish (ed. Guimaraes, E., Ruane, J., Scherf, B., Sonnino, A. and Dargie, J.), pp. 283–305, chapter 15. Rome: FAO.
Charlesworth, D. (2003). The effects of inbreeding on the genetic diversity of populations. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 358, 10511070.
Dawson, E., Abecasis, G. R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D. M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S., Carter, D., Papaspyridonos, M., Livingstone, S., Ganske, R., Lohmmussaar, E., Zernant, J., Tonisson, N., Remm, M., Magi, R., Puurand, T., Vilo, J., Kurg, A., Rice, K., Deloukas, P., Mott, R., Metspalu, A., Bentley, D. R., Cardon, L. R. & Dunham, I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature 418, 544548.
Farnir, F., Coppieters, W., Arranz, J.-J., Berzi, P., Cambisano, N., Grisart, B., Karim, L., Marcq, F., Moreau, L., Mni, M., Nezer, C., Simon, P., Vanmanshoven, P., Wagenaar, D. & Georges, M. (2000). Extensive genome-wide linkage disequilibrium in cattle. Genome Research 10, 220227.
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S. N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E. S., Daly, M. J. & Altshuler, D. (2002). The structure of haplotype blocks in the human genome. Science 296, 22252229.
Georges, M. (2007). Mapping, fine mapping, and molecular dissection of quantitative trait loci in domestic animals. Annual Review of Genomics and Human Genetics 8, 131162.
Hedrick, P. W. (1987). Gametic disequilibrium measures: proceed with caution. Genetics 117, 331341.
Hill, W. G. (1974). Estimation of linkage disequilibrium in randomly mating populations. Heredity 33, 229239.
Ingvarsson, P. K. (2002). A metapopulation perspective of genetic diversity and differentiation in partially self-fertilizing plants. Evolution 56, 23682373.
Ingvarsson, P. K. (2005). Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169, 945953.
Kremer, A., Caron, H., Cavers, S., Colpaert, N., Gheysen, G., Gribe, R., Lemes, M., Lowe, A. J., Margis, R., Navarro, C. & Salgueiro, F. (2005). Monitoring genetic diversity in tropical trees with multilocus dominant markers. Heredity 95, 274280.
Kuang, H., Richardson, T. E., Carson, S. D. & Bongarten, B. C. (1998). An allele responsible for seedling death in Pinus radiata D. Don. Theoretical and Applied Genetics 96, 640644.
Lewontin, R. C. (1964). The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 4967.
Li, Y. C., Li, Y., Wu, S., Han, K., Wang, Z. J., Hou, W., Zeng, Y. R. & Wu, R. L. (2007). Estimation of linkage disequilibria in diploid populations with multilocus dominant markers. Genetics 176, 18791892.
Liu, T., Todhunter, R. J., Lu, Q., Schoettinger, L., Li, H. Y., Littell, R. C., Bliss, S., Acland, G., Lust, G. & Wu, R. L. (2006). Extent and distribution of zygotic linkage disequilibrium in canine. Genetics 174, 439453.
McRae, A. F., MceWan, J. C., Dodds, K. G., Wilson, T., Crawford, A. M. & Slate, J. (2002). Linkage disequilibrium in domestic sheep. Genetics 160, 11131122.
Miller, A. J. & Schaal, B. A. (2006). Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae). Molecular Ecology 15, 14671480.
Nordborg, M. (2000). Linkage disequilibrium, gene trees and selfing: ancestral recombination graph with partial self-fertilization. Genetics 154, 923929.
Rafalski, A. & Morgante, M. (2004). Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends in Genetics 20, 103111.
Reich, D. E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P. C., Richter, D. J., Lavery, T., Kouyoumjian, R., Farhadian, S. F., Ward, R. & Lander, E. S. (2001). Linkage disequilibrium in the human genome. Nature 411, 199204.
Remington, D. L., Thornsberry, J. M., Matsuoka, Y., Wilson, L. M., Whitt, S. R., Doebley, J., Kresovich, S., Goodman, M. M. & Buckler, E. S. IV (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences of the USA 98, 1147911484.
Silbiger, R. N., Christ, S. A., Leonard, A. C., Garg, M., Lattier, D. L., Dawes, S., Dimsoski, P., McCormick, F., Wessendarp, T., Gordon, D. A., Roth, A. C., Smith, M. K. & Toth, G. P. (1998). Preliminary studies on the population genetics of the central stoneroller (Campostoma anomalum) from the Great Miami River Basin, Ohio. Environmental Monitoring and Assessment 51, 481495.
Tishkoff, S. A. & Williams, S. M. (2002). Genetic analysis of African populations: human evolution and complex disease. Nature Reviews Genetics 3, 611621.
Tishkoff, S. A., Dietzsch, E., Speed, W., Pakstis, A. J., Kidd, J. R., Cheung, K., Bonne-Tamir, B., Santachiara-Benerecetti, A. S., Moral, P., Krings, M., Pääbo, S., Watson, E., Risch, N., Jenkins, T. & Kidd, K. K. (1996). Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271, 13801387.
Tishkoff, S. A., Varkonyi, R., Cahinhinan, N., Abbes, S., Argyropoulos, G., Destro-Bisol, G., Drousiotou, A., Dangerfield, B., Lefranc, G., Loiselet, J., Piro, A., Stoneking, M., Tagarelli, A., Tagarelli, G., Touma, E. H., Williams, S. M. & Clark, A. G. (2001). Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293, 455462.
Weir, B. S. (1996). Genetic Data Analysis. Sunderland, MA: Sinauer.
Wu, R. L. & Zeng, Z.-B. (2001). Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157, 899909.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Genetics Research
  • ISSN: 0016-6723
  • EISSN: 1469-5073
  • URL: /core/journals/genetics-research
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed