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Journal of Heredity Advance Access published online on March 14, 2008
Journal of Heredity, doi:10.1093/jhered/esn016
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Nucleotide Diversity and Linkage Disequilibrium in Wild Avocado (Persea americana Mill.)

Haofeng Chen, Peter L. Morrell, Marlene de la Cruz, and Michael T. Clegg

From the Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 (Chen, Morrell, and Clegg); and the School of Biological Sciences, University of California, Irvine, CA 92697 (de la Cruz)

Address correspondence to Michael T. Clegg at the address above, or e-mail: mclegg{at}uci.edu.

Resequencing studies provide the ultimate resolution of genetic diversity because they identify all mutations in a gene that are present within the sampled individuals. We report a resequencing study of Persea americana, a subtropical tree species native to Meso- and Central America and the progenitor of cultivated avocado. The sample includes 21 wild accessions from Mexico, Costa Rica, Ecuador, and the Dominican Republic. Estimated levels of nucleotide polymorphism and linkage disequilibrium (LD) are obtained from fully resolved haplotype data from 4 nuclear loci that span 5960 nucleotide sites. Results show that, although avocado is a subtropical tree crop and a predominantly outcrossing plant, the overall level of genetic variation is not exceptionally high (nucleotide diversity at silent sites, {pi}sil = 0.0102) compared with available estimates from temperate plant species. Intralocus LD decays rapidly to half the initial value within about 1 kb. Estimates of recombination rate (based on the sequence data) show that the rate is not exceptionally high when compared with annual plants such as wild barley or maize. Interlocus LD is significant owing to substantial population structure induced by mixing of the 3 botanical races of avocado.

Corresponding Editor: James Hamrick

Received June 28, 2007
Accepted January 25, 2008


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[Abstract] [Full Text] [PDF]


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