Proceedings of the XLVII Italian Society of Agricultural Genetics - SIGA Annual Congress

Verona, Italy - 24/27 September, 2003

ISBN 88-900622-4-X

Poster Abstract - 3.11

SEQUENCE DIVERSITY AND SNP MARKER DEVELOPMENT IN ALEPPO PINE (PINUS HALEPENSIS MILL)

G. G. VENDRAMIN*, M. ANZIDEI*, F. BAGNOLI**, C. PLOMION***, F. SEBASTIANI****, M. L. RACCHI**

*) IGV, CNR, Via Atto Vannucci 13, 50134 Firenze

**) DiBA, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze

***) UMR BIOGECO, INRA, Pierroton, France

****) DISTAF, Università degli Studi di Firenze, Via San Bonaventura 13, 50145 Firenze

molecular markers, SNPs, population genetics, phylogenesis

Direct analysis of genetic variation at sequence level (Single Nucleotide Polymorphisms, SNPs) offers several advantages over other types of DNA marker systems. In particular, this approach allows gathering phylogenetic information through sequence variation analysis and drawing inferences on allele and population history that cannot be obtained with any of the other marker systems available. Information about the frequency and distribution of SNPs in forest tree species is still lacking. The objective of this work consists in a preliminary analysis of SNP distribution in Aleppo pine (Pinus halepensis) and in a first analysis of their usefulness in its population genetic analysis. Based on isozymes, nuclear and chloroplast microsatellite data it appears to carry high levels of variability, most of which (>85%) resides within populations.

DNA extracted from seed endosperms that are haploid tissues were amplified and then sequenced. In this first phase attention was put on the CAD gene, which is involved in the lignin biosynthesis. Five populations sampled in different parts of the natural range of the species were analysed. Six endosperms for each population were used. The sequences were aligned using specific software, the single point mutations were identified, their frequencies estimated and the haplotypes were determined.

Based on preliminary data from about 1500 bp, the frequency of nucleotide changes appears to be high, with an average of one SNP every 150 bases overall. This frequency, which is much higher than that those observed in humans, appears to be similar that those observed in maize, Norway spruce and Maritime pine, which are commonly considered species with extremely high levels of variability. The estimated value of nucleotide variation appeared low. On the other hand the genetic differentiation among populations resulted higher than that estimated using neutral markers, suggesting that this gene is under selection.