Adaptive Differences Associated with Neutral and Non-neutral Markers in the Core Collection for North American Plums (Prunus spp.)

Wednesday, July 24, 2013: 11:30 AM
Desert Salon 1-2 (Desert Springs J.W Marriott Resort )
Dario J. Chavez , Horticultural Sciences Department, University of Florida, Gainesville, FL
Thomas G. Beckman, Ph.D. , USDA–ARS, Byron, GA
W.R. Okie , USDA–ARS, Warner Robins, GA
José Chaparro , University of Florida, Gainesville, FL
North America is a center of diversity for Prunus L. species. The University of Florida Stone Fruit Breeding and Genetics Program in collaboration with the National Germplasm Repository and USDA–ARS (Project No. 5306-21000-018-00D) collected and identified ~400 genotypes of approx. 30 taxa native to the United States. A core collection of 13 species was used to compare the utility of selectively neutral sequences and sequences believed to be under selection pressure in the elucidation of phylogenetic relationships of North American plums. The core collection represented the major clades within subgenus Prunus section Prunocerasus. The American clade was represented by P. americana Marsh., P. hortulana L.H. Bailey, and P. mexicana S. Watson; the Chickasaw clade included P. angustifolia Marsh., P. munsoniana W. Wight & Hedrick, and P. umbellata Elliot; and the Beach clade was represented by P. geniculata Harper and P. maritima Marsh. Outgroups included: P. pumila L. (subgenus Cerasus section Microcerasus), P. persica (L.) Batsch cv. Okinawa, AP05-18ws (UF peach haploid), 02-01c (UF peach haploid) (subgenus Amygdalyus section Amygdalus), and P. fasciculata (Torr.) A. Gray (subgenus Emplectocladus). A total of 41 simple sequence repeat (SSR) markers distributed across the peach genome (~15–25 cM), 7 chloroplast genome regions, nuclear ribosomal repeat ITS, and 55 candidate genes believed to be associated with flowering and plant architecture were used. A Neighbor Joining (NJ) analysis of the SSR markers yielded different species relationships than the results obtained using chloroplast DNA (cpDNA) regions, internal transcribed spacer region (ITS), and nuclear genes Maximum Parsimony (MP) and Maximum Likelihood (ML) analyses. Phylogenetic analyses using cpDNA regions, ITS and nuclear genes yielded some of the previously known species relationships. A total of 27,278 bp of sequence per species was used. The observed polymorphism rates were 3.67%, 10.82%, and 7.27% for the cpDNA sequences, ITS, and nuclear genes, respectively. Sequence variation in exon and intron regions of nuclear genes was 4% and 11%, respectively. Several highly informative regions were identified that will be used for larger phylogenetic analysis within Prunus.
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