Genetic Similarity and Pollen Dispersal Analysis on Pati Kopyor Coconut Population Based on SSR and SNAP Marker Analysis

Abstract

Pollination of female flower of kopyor coconut by male pollen of normal coconut could result in reduced kopyor fruit yield. Therefore, investigating pattern of pollen dispersal in a mix population of kopyor and normal coconut provenances would be beneficial. Moreover, evaluating genetic similarity among the studied population and their progenies would also beneficial for predicting the quality of produced seed nuts. The objectives of this experiment were : (1) to evaluated genetic similarity of the kopyor coconut parents population and their progenies, (2) to evaluate pattern of pollen dispersal among mix population of kopyor and normal fruit producing coconut in Pati, Central Java, (3) evaluated relevancy of pollen dispersal among mix population with their kopyor fruit yield. There were 95 adult palms evaluated as male parent candidate and 84 seeds harvested from 15 selected female parents as progeny population. The female parents were selected based on their high productivity from field evaluation. All population was used for genetic structure and similarity analysis and also pollen dispersal. Every adult palms were numbered using a marker and noted for the coordinate position using GPS. This research consisted of two stages, the first analyzed of genetic similarity among individual of adult plants and their progenies, and the second analyzed the pollen dispersal using molecular markers SSR and SNAP. The analyses of the genetic similarities were initiated with primer screening. Among 36 SSR loci tested, 32 loci resulted in a (+) product when they were used to amplify coconut DNA and only CnCir_B12, CnCir_86, CnCir_87 and CnCir_56 resulted in polymorphic SSR markers. Moreover, SNAP locus corresponding to position 14 of SNP of coconut sucrose synthase gene were also used. These loci were used to genotype candidate parents and progenies population. Results of the experiment indicated the average of allele per locus and average of PIC were 4.5 and 0.46, respectively. Cluster analysis using DICE coefficient based on molecular data resulted in an estimate of intra population of adult palms similarity and intra population of progenies were at least 18% and 43%, respectively. Intra population of progenies were more closely related than intra population of adult palms. Results of STRUCTURE analysis grouped most of the individuals into either Tall, Dwarf or Hybrid types, as they were suspected based on the morphology of the palms. However, a number of individuals grouped as Tall, and some as Dwarf based on their morphology, were actually identified as Hybrids based on alleles constitutions of the evaluated markers. The objectives of the second experiment were to evaluate pollen dispersal among coconut provenances using SSR and SNAP markers and its effects on kopyor fruit yield. Four SSR markers and one SNAP marker were used to genotype 95 provenances and 84 progenies harvested from 15 female parents. Parent-offspring relationships were determined based on genotype data using CERVUS software. The distances between male and female parents trees were calculated based on the GPS data after male parents identification. Results of the experiment indicated self-pollinations occurred in a number o sampled female parents since the distance of pollen dispersal was 0 m. Meanwhile, the furthest distance of pollen dispersal was 61.8 m. On the other hand the majority of pollination occurs at a distance of 0-10 m (33.3%). In term of pollen dispersal, the position of donor pollen relative to the recipient one was random. This indicated that the coconut pollen dispersal in the regions was not transferred by wind but probably was by insect pollinators help. Outcrossing rate in Tall, Dwarf and Hybrid type of coconuts were calculated as 100%, 72.7% and 82.1%, respectively. Therefore, levels of self-pollination in Tall, Dwarf and Hybrid coconut were 0%, 27.3% and 17.9%. There was a normal coconut in the region donating its pollen to kopyor female parents at the level of 8.3%. The existence of normal coconut palms around the kopyor coconut one might possibly reduce the kopyor fruit yield.