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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #334343
Title: Identifying the North American plum species phylogenetic signal using nuclear, mitochondrial, and chloroplast DNA markers

Author
item CHAVEZ, D. - University Of Georgia
item Beckman, Thomas
item CHAPARRO, J. - University Of Florida

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2016
Publication Date: 12/24/2016
Citation: Chavez, D.J., Beckman, T.G., Chaparro, J.X. 2016. Identifying the North American plum species phylogenetic signal using nuclear, mitochondrial, and chloroplast DNA markers. Journal of the American Society for Horticultural Science. 141(6):623-644.

Interpretive Summary: dentification of the various Prunus species has been classically performed using morphological characteristics. However, molecular approaches offer the possibility of a more definitive objective approach. Three sources of genetic material for this purpose exist, i.e. nuclear, mitochondrial and chloroplast. Each offer their own advantages particularly when studying possible species hybrids. In this study both approaches were used and compared for use in spectating a number of important North American plum species. The results suggested that nuclear DNA provided the most useful variation for determining species relations/groups within the North American group of species studied.

Technical Abstract: Premise of the study: Prunus L. phylogeny has extensively studied using cpDNA sequences. CpDNA has a slow rate of evolution which is beneficial to determine species relationships at a deeper level. However, a limitation of the chloroplast based phylogenies is its transfer by interspecific hybridization creating difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been widely reported. The main goal of this project was to measure and to identify nuclear regions that could provide an improved phylogenetic signal at the species level for Prunus. Methods: A total of 11 species across Prunus and within section Prunocerasus, were used. In addition, two peach (P. persica (L.) Batsch) haploids were used to test the reliability of the molecular markers developed in this project and to verify the amplification of single copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and three with isozymes, were tested. In addition, 41 SSR markers, seven cpDNA regions, and the ITS region, were used for species comparisons. Key results: Multiple regions were identified that provided the greatest number of characters, variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Nuclear genes had the highest amount of PICs (Potentially Informative Characters), followed by ITS, and cpDNA. Among these regions, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 were identified to be used in phylogenetic studies with a higher number of taxa. Conclusions: The use of PICs as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. However, PIC values need to be accompanied by a complementary phylogenetic analysis using the genomic region and the species of interest. This will allow selecting the region which can be used in phylogenetic studies with a higher number of taxa.