Chloroplast microsatellites markers to assess genetic diversity in wild and cultivated grapevines of Iran

Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species

Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.

Hairy root culture optimization and resveratrol production from Vitis vinifera subsp. sylvesteris

Resveratrol is a polyphenolic compound produced in very low levels in grapes. To achieve high yield of resveratrol in wild grape, three Agrobacterium rhizogenes strains, Ar318, ArA4 and LBA9402, were used to induce hairy roots following infection of internodes, nodes or petioles of in vitro grown Vitis vinifera subsp. sylvesteris accessions W2 and W16, and cultivar Rasha. The effects of inoculation time, age of explants, bacterial concentration and co-cultivation times were examined on the efficiency of the production of hairy roots. Strains Ar318, ArA4 and LBA9402 all induced hairy roots in the tested genotypes, but the efficiency of ArA4 strain was higher than the other strains. The highest hairy root production was with using internodes as explants. The transformation of hairy roots lines was confirmed by PCR detection of rolB gene. Half Murashige and Skoog (MS) medium was better for biomass production compared with MS medium. HPLC analysis of resveratrol production in the hairy root cultures showed that all the genotypes produced higher amounts of resveratrol than control roots. The highest amount of resveratrol was produced from W16 internode cultures, which was 31-fold higher than that of control root. Furthermore, TLC analysis showed that treatments of hairy roots with sodium acetate and jasmonate elevated resveratrol levels both in hairy root tissue and excreted into the half MS medium. These results demonstrate that endogenous and exogenous factors can affect resveratrol production in hairy root culture of grape, and this strategy could be used to increase low resveratrol production in grapes.

Chloroplast based genetic diversity among Chinese grapes genotypes

Chloroplast simple sequence repeat (cpSSR) markers previously reported were used to analyze chloroplast diversity of Chinese grapes. Nine cpSSR primer pairs from the chloroplast genomes of citrus and tobacco (Nicotiana tabacum L.) were found useful for analyzing the grapes chloroplast genome (cpDNA). Selected cpSSR primer pairs showed polymorphism among 64 varieties, with polymorphism information content (PIC) values ranging from 0.522 to 0.659, with an average of 0.590. Results depicted that a total number of 43 alleles were detected on nine loci with an average of 4.77 alleles per locus with highest number of six alleles for marker ARCP2 and CCMP10. Gene diversity explained by these cpSSR makers ranged from 4 to 68% with an average of 63.66% per marker. The genetic relationship suggested by UPGMA based dendrogram divided the genotypes into three main clusters and four subgroups, results showed that 2B is the biggest group. Overall Hong Ma Ge and Da LI Mei Gui Xiung 98% similar, while 64-1-19 was the most diverse as compared to rest of genotypes.

Genetic diversity of wild and cultivated grapevine accessions from southeast Turkey

Wild grapevine genetic diversity in southeast Turkey has not been documented to date. In the present work, in order to clarify the relationships between wild and cultivated grape accessions from southeastern Turkey, 22 nuclear and three chloroplast microsatellite loci were used on 21 wild grapevine Vitis vinifera L. ssp. sylvestris (Gmelin) and 13 cultivated grapevine Vitis vinifera ssp. sativa accessions. The number of alleles per SSR locus ranged from 4 (VVIn16) to 20 (VVIv67) and the mean allele number per locus was 10.09. Expected locus heterozygosity ranged from 0.586 (locus VVIb01) to 0.898 (locus (VVIv67)). The three cpSSR molecular markers presented variation in size both in cultivars and in wild Turkish accessions. Two size variants were detected for cpSSR3 (106 and 107 bp) for cpSSR5 (104 and 105 bp), and for cpSSR10 (115 and 116 bp). The six alleles in wild grapevines fell into three haplotypes B, C and D. A genetic structure according to accessions taxonomic status (wild or cultivated) was revealed by UPGMA analysis. This highlighted a clear separation between domesticated and wild accessions in Turkish germplasm. The results pointed out the need to further collect and characterize this wild and cultivated grapevine germplasm.

Chloroplast genome diversity in Portuguese grapevine (Vitis vinifera L.) cultivars

Grapevine chloroplast (cp) DNA diversity was analysed for the first time through amplification and digestion of fragments of the large single copy (LSC) region by polymerase chain reaction-restriction fragment length polymorphism methodology and also by amplification of three microsatellite loci, previously described as polymorphic in grapevine. Thirty-eight grapevine cultivars collected mainly in the North of Portugal, including some neglected cultivars, four international cultivars (Chasselas, Muscat of Alexandria, Muscat of Hamburg and Pinot) and Vitis riparia and Vitis rupestris, were used in this study with the main goal of finding out their cpDNA diversity and compare the obtained results with previously published data on cultivars from other regions to ascertain their possible origin. Two different alleles were found in each of the three cpSSR loci. Allele variants of the three loci combined in a total of three different haplotypes (A, B and D). The most frequent haplotype, A, was previously reported as the most frequent in Iberian Peninsula and Occidental Europe. Haplotype B was unique to Rabigato, Muscat of Alexandria, V. riparia and V. rupestris. This haplotype was previously proposed to be an ancestral haplotype. Twenty-seven fragments of the LSC region of Vitis vinifera cpDNA were amplified and then digested with HinfI and TaqI restriction enzymes. Polymorphisms were found in the trnT-psbC (TC) and orf184-petA (OA) fragments. In the TC fragment, the polymorphism corresponds to a point mutation in a restriction site of TaqI and is only present in all cultivars with cpSSR haplotype D. In the OA fragment, a short deletion exclusive to the Rabigato cultivar was found. In this case, one sequence tagged site-based marker was developed and will be very useful in future phylogenetic and fingerprinting studies in a broader number of cultivars and in wild grapevine populations. Inference about the progenitors of the Touriga Franca cultivar is done. The present work supports and completes its origin as a descendent of the female and male parents, Marufo and Touriga Nacional.

Gene pool variation and phylogenetic relationships of an indigenous northeast Italian grapevine collection revealed by nuclear and chloroplast SSRs

A germplasm safeguard programme was set up with 19 grapevine varieties considered as indigenous to northeastern Italy. To better estimate how genetic structure can be used to obtain a conservation perspective of local varieties, genetic variability was examined at 30 nuclear and 3 chloroplast polymorphic microsatellite loci in the native varieties plus 7 European cultivars taken as reference. The genetic profiles of all the cultivars were searched for possible parentage relationships and several suspected cases of the same variety having different names were investigated. The alleles shared at the loci suggest a parent-offspring relationship between Merlot and Cabernet Franc, 'Gruaja' and 'Negrara Veronese', and Marzemina Nera and Marzemina Bianca. Alleles at the 30 nuclear loci are consistent with Raboso Veronese being the progeny of Marzemina Bianca and Raboso Piave. Chloroplast-specific haplotypes were singled out for the first time in this indigenous germplasm and should be considered typical of the region. It is hypothesized that there are many specific haplotypes for the local varieties due to a past contribution of wild grapevine to the cultivated gene pool. The majority of investigated cultivars were demonstrated to constitute an independent source of genetic variation, and therefore a possible valuable resource of genetic traits for breeders.