Genetic variation and relationships between Azerbaijani and Turkish olive genetic resources.

Olive (Olea europaea L.) is one of the most economically important crop from east to the west around the world. The aim of this research was to investigate the genetic relationship among 41 olive genotypes, including 11 well-known Turkish cultivars and 30 Azerbaijani olive genotypes using simple sequence repeat (SSR) markers. In this study, 19 SSR markers were amplified 115 polymorphic SSR alleles. The number of polymorphic alleles ranged from 3 to 10 with an average of 6.05. The observed heterozygosity (Ho) varied from 0.05 to 0.93 with an average of 0.63 and expected heterozygosity (He) differed from 0.26 to 0.86 with an average of 0.72. The polymorphism information content (PIC) ranged from 0.23 to 0.85 with a mean of 0.68. A UPGMA cluster analysis grouped olive genotypes into two distinct clusters and both clusters were divided into two subgroups. Similarly, STRUCTURE analysis assigned olive genotypes into two different gene pools (K = 2) and four gene pools were identified representing the two subgroups by STRUCTURE analysis for K = 4. The genetic similarity of olive genotypes ranged from 0.36 to 0.95. These results revealed that there was a high genetic variation among 30 Azerbaijani olive genotypes. 'Ayvalik 1'and 'Ayvalik 2' from Azerbaijani olive genotypes were different from Turkish local olive cultivar, "Ayvalik" indicating homonymy. This research also highlighted that Azerbaijani olive genotypes were totally distinct from Turkish olive cultivars demonstrating that these olive genotypes might have been imported to Azerbaijan from different countries other than Turkey. The outcomes of this study indicated that these diverse olive genotypes could be useful for development of new olive varieties in Azerbaijan and future breeding programs between two countries could be enhanced by means of these results.

Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive.

Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.

SNP Discovery by GBS in Olive and the Construction of a High-Density Genetic Linkage Map.

Genetic linkage maps are valuable tools for genetic, genomic, and crop breeding studies. Several genetic linkage maps were constructed for the olive (Olea europaea L.) genome, mainly using amplified fragment length polymorphisms (AFLPs) and simple sequence repeat (SSR) markers. However, AFLPs and SSR markers were not enough to develop a high-density olive linkage map. Genotyping-by-sequencing (GBS), a recently developed single-nucleotide polymorphism (SNP) identification methodology based on next-generation sequencing (NGS) technologies, has been demonstrated to be useful for the identification of a high number of SNP markers and the construction of high-density genetic linkage maps. In the present study, we identified a total of 10,941 SNPs from a cross between the olive cultivars 'Gemlik' and 'Edincik Su' using GBS and de novo SNP discovery implemented in the computer program "Stacks." A high-density genetic linkage map for the olive genome was constructed using 121 cross-pollinated full-sib F1 progeny and 5643 markers (21 SSRs, 203 AFLPs, and 5736 SNPs). This linkage map was composed of 25 linkage groups, covering 3049 cM of the olive genome, and the mean distance between the flanking markers was 0.53 cM. To the best of our knowledge, this map is the most saturated genetic linkage map in olive to date. We demonstrated that GBS is a valuable tool for the identification of thousands of SNPs for the construction of a saturated genetic linkage map in olive. The high-density genetic map developed in this study is a useful tool for locating quantitative trait loci and other economically important traits in the olive genome.

Screening and comparing tocopherols in the rapeseed (Brassica napus L.) and olive (Olea europaea L.) varieties using high-performance liquid chromatography.

Rapeseed and virgin olive oils are a good source of tocopherols. Tocopherols are the most important compounds having antioxidant activity in both crops. Little is known about the tocopherol contents of rapeseed and olive oil grown in Turkey. The aims of this research were to investigate some new rapeseed varieties and olive genotypes grown in northwest Turkey and to compare the tocopherol fractions and contents of both crops. For rapeseed, the data were collected in two growing seasons (2004-2005, 2005-2006) from a field experiment with 19 new rapeseed varieties. For olives, virgin olive oils produced from 21 different varieties were examined in the 2004-2005 and 2005-2006 growing seasons. The separation and identification of tocopherols and the analysis of their contents were successfully achieved using the high-performance liquid chromatographic method. According to the obtained results, gamma-tocopherol (44.200-118.900 mg/kg) was the major fraction of total tocopherol, followed by alpha-tocopherol (19.300-68.500 mg/kg) and delta-tocopherol (0.00-2.600 mg/kg) for rapeseeds. Regarding olive varieties, the alpha-tocopherol content changed between 52.000 and 194.750 mg/kg, followed by gamma-tocopherol ranging from 0.00 to 39.750 mg/kg. The total tocopherol content ranged between 83.900 and 173.800 mg/kg for rapeseed and between 52.100 and 213.075 mg/kg for olives. This study revealed that an important variability exists for tocopherol content and composition in rapeseed and olive varieties.

Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.).

Linkage mapping and genetic diversity studies with DNA markers in plant species assume that comigrating bands are identical, or at least that they have homologous sequences. To test this assumption in a plant with a large genome, sequence identities of 7 polymorphic amplified fragment length polymorphism (AFLP) markers of garlic, previously used to estimate similarity in genetic diversity studies, were characterized. Among 37 diverse garlic clones, 87 bands from these 7 polymorphisms were excised, amplicons were cloned, and 2 to 6 colonies were sequenced from each band, to yield a total of 191 DNA amplicons. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band; only 4 bands contained amplicons with little homology to the same-sized amplicons of other garlic clones. Of these 83 bands, 64 (73.6%) contained only highly homologous amplicons (>90% sequence identity), whereas 19 (21.8%) contained both homologous and nonhomologous amplicons, with sequence identities less than 60%. Of the 37 nonhomologous amplicons identified, 25 (67.5%) differed in length from other amplicons in the band. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones, making them useful for developing simple PCR-based markers in genetic mapping and diversity assessment.