Assessing Conservation Status of Crop Genetic Diversity:  Oxalis tuberosa  as a Test Case for New Methodologies for Clonal...
GSPC Target 9: 70% of the genetic diversity of crops including their wild relatives…  oca  –  Oxalis tuberosa
 
K. S. Zimmerer 2003 Soc. & Nat. Res. 16: 583-601 Seed Network (“seed flow”) studies via surveys of farmers &/or market ven...
Cusco Puno Cochabamba La Paz “ Ancient trade routes” hypothesis based on CIRNMA’s  market surveys image source: USGS DEM a...
Bryan Epperson Oca collection localities in 2005 & 2006 Instituto Nacional de Innovación Agraria, Perú International Potat...
Map of Quechua and Aymara languages from Heggarty and Beresford-Jones 2009 in British Academy Review Do areas of greater o...
random sampling from field (chacra)
sampling from storage
Areas of high or low genotypic diversity
 
 
Implicacions of restricted  distribucions of clones for  conservacion…
Somatic mutations lead to chimeric tubers, and then to clone-mates of differing pigmentation? Combine AFLP with morphologi...
~30 tubers from each of 40 localities grown out by INIA for characterization of morphological and molecular data
oca samples genotyped by AFLP from 30 collection localities GIS data plotted in R
AFLP genotypes of 954 oca individuals with 3 primer combinations 214  clones distinguished using AFLP and morphological da...
Moran’s I expectations for IBD N e  = Wright's neighborhood size
Moran’s I: average of 66 polymorphic AFLP alleles
Moran’s I: 66 individual polymorphic AFLP alleles
Moran’s I for oca AFLP alleles 1-10 (Km.)
Join Count based on sharing clone #116
Distributions of clones of oca in Peru graphed in R package ggplot2  62 clones with ≥ 5 reps in total sampling
Distributions of clones of oca in Peru graphed in R package ggplot2  62 clones with ≥ 5 reps in total sampling 27 private ...
Distributions of clones of oca in Peru graphed in R package ggplot2  62 clones with ≥ 5 reps in total sampling Central Que...
Distributions of clones of oca in Peru graphed in R package ggplot2  62 clones with ≥ 5 reps in total sampling Southern Qu...
Distributions of clones of oca in Peru graphed in R package ggplot2  62 clones with ≥ 5 reps in total sampling 46 reps 30 ...
Distributions of clones of oca in Peru graphed in R package ggplot2  62 clones with ≥ 5 reps in total sampling
Many clones are restricted to east or west side of Andes GIS data plotted in R
Aymara Southern Quechua Central Quechua GIS data plotted in R
Map of Quechua and Aymara languages from Heggarty and Beresford-Jones 2009 in British Academy Review Wombling analysis  fi...
Wombling analysis  found strongest boundary elements at edges between Quechua languages Map of Quechua and Aymara language...
Continuing analyses... Moran’s Eigenvector Maps (MEM) (Legendre & Fortin 2010) Redundancy Analysis (RDA) ) Akaike Informat...
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Assessing Conservation Status of Crop Genetic Diversity: Oxalis tuberosa as a Test Case for New Methodologies for Clonally Propagated Crops

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Emshwiller, et al., Presentation at International Botanical Congress in Melbourne, Australia, 28 July 2011

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Assessing Conservation Status of Crop Genetic Diversity: Oxalis tuberosa as a Test Case for New Methodologies for Clonally Propagated Crops

  1. 1. Assessing Conservation Status of Crop Genetic Diversity: Oxalis tuberosa as a Test Case for New Methodologies for Clonally Propagated Crops E Emshwiller, B K Epperson, T Theim, D Tay, T Medina, R C Girón, V Nina, J E Ángeles, P Catacora, J Tineo, W Cruz, K Vivanco, I Perez [email_address] 28 July 2011
  2. 2. GSPC Target 9: 70% of the genetic diversity of crops including their wild relatives… oca – Oxalis tuberosa
  3. 4. K. S. Zimmerer 2003 Soc. & Nat. Res. 16: 583-601 Seed Network (“seed flow”) studies via surveys of farmers &/or market vendors
  4. 5. Cusco Puno Cochabamba La Paz “ Ancient trade routes” hypothesis based on CIRNMA’s market surveys image source: USGS DEM and the Cornell Andes Project
  5. 6. Bryan Epperson Oca collection localities in 2005 & 2006 Instituto Nacional de Innovación Agraria, Perú International Potato Center, Perú Field Museum Chicago, USA UW-Madison, USA MSU, USA National Science Foundation, USA
  6. 7. Map of Quechua and Aymara languages from Heggarty and Beresford-Jones 2009 in British Academy Review Do areas of greater or lesser exchange of oca correlate with language variation?
  7. 8. random sampling from field (chacra)
  8. 9. sampling from storage
  9. 10. Areas of high or low genotypic diversity
  10. 13. Implicacions of restricted distribucions of clones for conservacion…
  11. 14. Somatic mutations lead to chimeric tubers, and then to clone-mates of differing pigmentation? Combine AFLP with morphological data to distinguish clones.
  12. 15. ~30 tubers from each of 40 localities grown out by INIA for characterization of morphological and molecular data
  13. 16. oca samples genotyped by AFLP from 30 collection localities GIS data plotted in R
  14. 17. AFLP genotypes of 954 oca individuals with 3 primer combinations 214 clones distinguished using AFLP and morphological data ~3/4 (161) of clones were found in only one locality For spatial statistics we -excluded clones with < 5 reps in the whole sample (leaving 62 ) -excluded AFLP alleles present in <5% or >95% of sample spatial autocorrelation analyses (Moran's I and join-count) with PASSaGE 2 GIS and spatial analysis with R ( http://www.R-project.org ) packages including: rgdal, lattice, sp, maptools, maps, spatstat, raster, car, ggplot2 None of AFLP alleles
  15. 18. Moran’s I expectations for IBD N e = Wright's neighborhood size
  16. 19. Moran’s I: average of 66 polymorphic AFLP alleles
  17. 20. Moran’s I: 66 individual polymorphic AFLP alleles
  18. 21. Moran’s I for oca AFLP alleles 1-10 (Km.)
  19. 22. Join Count based on sharing clone #116
  20. 23. Distributions of clones of oca in Peru graphed in R package ggplot2 62 clones with ≥ 5 reps in total sampling
  21. 24. Distributions of clones of oca in Peru graphed in R package ggplot2 62 clones with ≥ 5 reps in total sampling 27 private clones (found in only 1 locality in sampling)
  22. 25. Distributions of clones of oca in Peru graphed in R package ggplot2 62 clones with ≥ 5 reps in total sampling Central Quechua
  23. 26. Distributions of clones of oca in Peru graphed in R package ggplot2 62 clones with ≥ 5 reps in total sampling Southern Quechua
  24. 27. Distributions of clones of oca in Peru graphed in R package ggplot2 62 clones with ≥ 5 reps in total sampling 46 reps 30 reps localities where Aymara is spoken
  25. 28. Distributions of clones of oca in Peru graphed in R package ggplot2 62 clones with ≥ 5 reps in total sampling
  26. 29. Many clones are restricted to east or west side of Andes GIS data plotted in R
  27. 30. Aymara Southern Quechua Central Quechua GIS data plotted in R
  28. 31. Map of Quechua and Aymara languages from Heggarty and Beresford-Jones 2009 in British Academy Review Wombling analysis finds area of abrupt (steep) change in allele frequencies.
  29. 32. Wombling analysis found strongest boundary elements at edges between Quechua languages Map of Quechua and Aymara languages from Heggarty and Beresford-Jones 2009 in British Academy Review Wombling analysis finds area of abrupt (steep) change in allele frequencies.
  30. 33. Continuing analyses... Moran’s Eigenvector Maps (MEM) (Legendre & Fortin 2010) Redundancy Analysis (RDA) ) Akaike Information Criterion (AIC) <ul><li>IBR: modeling gene flow as circuit theory (McRae et al 2008, Ecology) , with “resistance” varying by </li></ul><ul><li>road condition (good vs. poor) </li></ul><ul><li>elevation changes along road </li></ul><ul><li>C) suitability of habitat for oca </li></ul><ul><li>D) language variation </li></ul>GIS data plotted in R
  31. 34. Thank you!

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