Molecular identification of Date palm (Phoenix dactylifera L.) “Deglet noor” pollinator through analysis of genetic diversity of Algerian male and female ecotypes using SSRs markers

Date palm (Phoenix dactylifera L.) “pollinator or dokkar” influences fruit's quality and quickness of maturity "metaxenia". This study characterizes the genetic diversity and the relationships between different Algerian ecotypes of dokkars. In addition, we report on the use of microsatellites to identify pollinators that are genetically the closest to “Deglet Noor” and “Ghars” cultivars. A total of 25 microsatellites were used on 50 accessions from Algeria, showed high genetic variability. The number of amplified alleles was 135 and ranged from 2 (PDCAT3) to 12 (DP 159), with an average of 5.44. The average of observed heterozygosity ranged between 0.026 (DP169) and 1.00 (PDCAT10, DP171, DP160, DP159, MPdCIR32 and MPdCIR10), with a mean of 0.688 indicating high diversity of date palm accessions. The average of expected heterozygosity was 0.436 and varied between 0.098 (PDCAT3) and 0.6 (PDCAT2). Almost Fis values were negative for markers except for DP 169. Unweighted Pair Group Method with Arithmetic Averages (UPGMA) clustering highlighted close genetic relationships between male and female genotypes for “Deglet Noor” accessions and showed case of homonymy and presence of clones. Principal Coordinate Analysis (PCoA) showed pattern that evidences the genetic diversity existing among pollinators that allowed distinguishing them easily. The combination of two SSR allowed to unambiguously distinguish six dokkars. Overall, UPGMA and PCoA showed that accessions of same type were clustered according to their origin (Oasis). Among the 28 private alleles scored in this study, nine were scored for Deglet Noor". Bayesian analysis showed a conserved genetic structure mainly for "Deglet Noor". Our results suggest that specific SSR marker (MPDCIR35) that characterize both male and female individuals of "Deglet Noor", could be used as potential marker to select, at early stage of seedling, the closest pollinator to the female individual of this important commercial cultivar. In addition, MPdCIR25 represents potential marker to identify male individuals of "Ghars"

Verifying synonymies between grape cultivars from France and Northwestern Italy using molecular markers

Thirty-one grape cultivars from France and Northwestern Italy, presumed to be synonymous, were analyzed using RAPD (Random Amplified Polymorphic DNA) and SSR (Simple Sequence Repeats or microsatellite) markers to verify 25 synonym hypotheses. RAPD analyses were performed with 8 selected decamer primers and the profiles of 7 microsatellite loci were used in order to confirm RAPD results, if required. Sixteen synonymies were confirmed, including the French cv. Verdesse with the Italian cv. Bian ver, the French cv. Persan with the Italian cv. Biquet, the French cv. Chatus with the Italian cv. Neiret, the French cv. Gouais blanc with the Italian cvs Preveiral and Liseiret. Most of the investigated cultivars belong to the Vitis vinifera germplasm of both sides of the Western Alps and the occurrence of synonyms indicates the existence of a common pool of grapes grown under different names in this part of Europe.

Development of high-density genetic linkage maps and identification of loci for chestnut gall wasp resistance in Castanea spp

Castanea sativais an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilusYasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar 'Bouche de Betizac' (C. sativaxC. crenata) and studied by developing genetic linkage maps using a population derived from a cross between 'Bouche de Betizac' and the susceptible cultivar 'Madonna' (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of 'Bouche de Betizac' consisted of 1459 loci and spanned 809.6 cM; the map of 'Madonna' consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the 'Bouche de Betizac' map, explaining up to 67-69% of the phenotypic variance of the resistance trait (Rdk1). TheRdk1quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute toC. sativabreeding programs and to the study ofRdk1genes

Mining and validating grape (Vitis L.) ESTs to develop EST-SSR markers for genotyping and mapping

Grape expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping. An integrated pipeline including several computational tools for SSR identification and functional annotation was developed to identify 6,447 EST-SSR sequences from a total collection of 215,609 grape ESTs retrieved from NCBI. The 6,447 EST-SSRs were further reduced to 1,701 non-redundant sequences via clustering analysis, and 1,037 of them were successfully designed with primer pairs flanking the SSR motifs. From them, 150 pairs of primers were randomly selected for PCR amplification, polymorphism and heterozygosity analysis in V. vinifera cvs. Riesling and Cabernet Sauvignon, and V. rotundifolia (muscadine grape) cvs. Summit and Noble, and 145 pairs of these primers yielded PCR products. Pairwise comparisons of loci between the parents Riesling and Cabernet Sauvignon showed that 72 were homozygous in both cultivars, while 70 loci were heterozygous in at least one cultivar of the two. Muscadine parents Noble and Summit had 90 homozygous SSR loci in both parents and contained 50 heterozygous loci in at least one of the two. These EST-SSR functional markers are a useful addition for grape genotyping and genome mapping

Genetic characterization of date palm (Phoenix dactylifera L.) germplasm cultivated in Algeria

Algeria is one of the leading date producers in the world, where approximately 2.2 millions of inhabitants are economically dependent upon them. Furthermore, dates production area covers more than 20% of the total surface used for Arboriculture. World date palm germplasm accounts for thousands of cultivars. Moreover, in recent investigations on Algerian date palm inventory, more than 940 cultivars have been reported. This high genetic variability is mainly due to the dioecious behavior of reproduction along with traditional farming system practiced particularly, in the Southwestern Algeria. In the last decade, we have developed hundreds of SSR loci for the identification of date cultivars in order to constitute the national database, with which aim to provide useful SSR markers for various applications particularly in the field of molecular breeding. The present research reports the characterization of the most important 40 cultivars grown in Algeria, assessed by microsatellite markers. The results indicate that these markers present a very effective tool for evaluating genetic diversity in date palm. They will certainly allow a better management of the genetic resources and eventually extent the present collection with new selective material for future breeding program. Cross-transferability in different species and genera were also evaluated

Characterization and genetic relationships of wild species and old garden roses based on microsatellite analysis.

Six polymorphic sequence-tagged microsatellite sites (STMSs) were used to characterize 65 accessions of old garden roses [OGRs (Rosa L. spp.)] from seven botanical sections and 13 horticultural groups. Aims of the study were to define the genetic profiles of accessions and to provide information useful for the classification and pedigree reconstruction of OGRs. In roses, a precise botanical classification is difficult due to repeated hybridization carried out in breeding; OGRs are classified in horticultural groups on the basis of their original parentage or of their morphological traits. A total of 82 alleles were detected at six loci. The number of alleles per locus ranged from six to 21, with an average of 13.7 alleles per locus. A dendrogram was constructed by cluster analysis, displaying the relative genetic similarities between species' accessions, hybrids, and cultivars. Cluster analysis grouped the genotypes into seven major clusters that were substantially consistent with their classification into botanical sections and horticultural groups. Several hypotheses of apportionment of accessions to horticultural groups were evaluated on the basis of the relative position in the dendrogram of the analyzed individuals. Results demonstrated that DNA analyses can contribute to drawing the botanic classification of rose accessions, improving the genetic knowledge on the background of modern rose, and providing the basis for breeding programs