Determination of pollen contamination in a clonal seed orchard of pinus brutia ten. in Antalya with chloroplast SSR (cpSSR) markers

Turkish red pine (Pinus brutia TEN.), because of its ecological and economic value, is one of the most important native forest tree species in Turkey. Seed orchards are established in order to obtain genetically high quality seeds and seedlings for reforestation and afforestation purposes. Pollen contamination is a serious problem in Pinus brutia seed orchards. Microsatellites, also known as simple sequence repeats (SSRs), are one of the most effective and useful ways of estimate pollen contamination level. So far, pollen contamination level has been estimated in only one seed orchard (P. brutia seed orchard in Asar-Antalya) in Turkey. The aim of this study is to estimate pollen contamination level in a 16 year-old P. brutia clonal seed orchard, located in Çığlık, Antalya, with the help of chloroplast microsatellite markers (cpSSRs). Microsatellite analysis was performed on both maternal and embryo tissues of seeds collected from Turkish red pine seed orchard and megagametophyte tissues of seeds or needles collected from close natural P. brutia population. Six cpSSR loci (Pt1254, Pt30204, Pt41093, Pt87268, Pt15169 and Pt71936) were analyzed.Six chloroplast SSR loci were analyzed. All, except Pt41093, were found to be polymorphic. A total of 23 alleles were determined for the analyzed six loci. The chloroplast microsatellite alleles were combined in 36 different haplotypes. According to haplotypes, that will be composed of the combination of alleles found at each cpSSR locus, genetic identity of each of the 30 clones in P. brutia seed orchard were determined. Twelve different haplotypes were observed in clones of the seed orchard. Studied ramets of randomly selected five clones in the seed orchard were not belong to the clones that they are supposed to be. Thirty-six different haplotypes were observed in embryos that are produced by the seed orchard clones, they were whereas 19 in natural Turkish red pine population.Eighty-seven embryos among the 300 analyzed had no compatible male parent within the seed orchard and their real male parents were considered to be located outside the seed orchard. Observed contamination (b) from external pollen sources was estimated as 0.29. This is minimum estimation of pollen contamination. Microsatellite-based paternity analysis revealed that the contamination rate (m) is 0.393 (39.3%). This level of pollen contamination is expected to reduce predicted genetic gain in the seed orchard crop by 20%.