Polymorphism of chloroplast microsatellite DNA loci in Russian potato cultivars

The cpSSR method was for the first time used to analyze the plastome in 29 Russian potato Solanum tuberosum cultivars. The informativeness coefficient H and the alleles of the NTCP6, NTCP8, and NTCP9 loci were determined. In total, 14 allelic variants of the microsatellite cpDNA loci were identified. The NTCP8 and NTCP9 cpSSR displayed the greatest allele polymorphism in the cultivars examined. A cultivar-specific haplotype of the chloroplast genome was observed for 20 out of 29 cultivars.     

Polymorphism of chloroplast microsatellite DNA loci in Russian potato cultivars

The cpSSR method was for the first time used to analyze the plastome in 29 Russian potato Solanum tuberosum cultivars. The informativeness coefficient H and the allele variability of the NTCP6, NTCP8, and NTCP9 loci were determined. In total, 14 allelic variants of the microsatellite cpDNA loci were identified. The NTCP8 and NTCP9 cpSSR displayed the highest allele polymorphism in the cultivars examined. A cultivar-specific haplotypes of the chloroplast genome were observed for 20 out of 29 cultivars.     

Dormant Buds and Adventitious Root Formation by Vitis and Other Woody Plants

Viticulture has historically depended upon clonal propagation of winegrape, tablegrape, and rootstock cultivars. Dependence on clonal propagation is perpetuated by consumer preference, legal regulations, a reproductive biology that is incompatible with sustaining genetic lines, and the fact that grapevine breeding is a slow process. Adventitious root formation is a key component to successful clonal propagation. In spite of this fact, grapevine has not been a centerpiece for adventitious root research. Dormant woody canes represent complex assemblages of tissues and organs. Factors that further contribute to such complexity include levels of endogenous plant growth regulators, the extent and duration of dormancy, carbohydrate storage, transport, the presence or absence of dormant buds or emergent shoots, and preconditioning treatments. For the above reasons, the mechanisms driving adventitious root formation by grapevine and other woody cuttings are poorly understood. We present results indicating that the dormant bud on cane cuttings from a non-recalcitrant to root Vitis vinifera cultivar, cv. Cabernet Sauvignon, slows or inhibits adventitious root emergence. In contrast to Cabernet Sauvignon, removal of the dormant bud from cane cuttings of a recalcitrant to root hybrid rootstock (V. berlandieri × V. riparia cv. 420A) and an intermediate to root hybrid rootstock (V. riparia × V. rupestris cv. 101-14) had no influence on adventitious root emergence. Reciprocal transplanting of nodes containing dormant buds among all three cultivars did not affect rooting behavior. Our results indicate that the commonly held belief that bud removal diminishes adventitious root emergence is not true.     

Dormant Buds and Adventitious Root Formation by <Emphasis Type="Italic">Vitis</Emphasis> and Other Woody Plants

Viticulture has historically depended upon clonal propagation of winegrape, tablegrape, and rootstock cultivars. Dependence on clonal propagation is perpetuated by consumer preference, legal regulations, a reproductive biology that is incompatible with sustaining genetic lines, and the fact that grapevine breeding is a slow process. Adventitious root formation is a key component to successful clonal propagation. In spite of this fact, grapevine has not been a centerpiece for adventitious root research. Dormant woody canes represent complex assemblages of tissues and organs. Factors that further contribute to such complexity include levels of endogenous plant growth regulators, the extent and duration of dormancy, carbohydrate storage, transport, the presence or absence of dormant buds or emergent shoots, and preconditioning treatments. For the above reasons, the mechanisms driving adventitious root formation by grapevine and other woody cuttings are poorly understood. We present results indicating that the dormant bud on cane cuttings from a non-recalcitrant to root Vitis vinifera cultivar, cv. Cabernet Sauvignon, slows or inhibits adventitious root emergence. In contrast to Cabernet Sauvignon, removal of the dormant bud from cane cuttings of a recalcitrant to root hybrid rootstock (V. berlandieri × V. riparia cv. 420A) and an intermediate to root hybrid rootstock (V. riparia × V. rupestris cv. 101-14) had no influence on adventitious root emergence. Reciprocal transplanting of nodes containing dormant buds among all three cultivars did not affect rooting behavior. Our results indicate that the commonly held belief that bud removal diminishes adventitious root emergence is not true.     

QTL analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in Vitis

In the recent past, genetic analyses of grapevine focused mainly on the identification of resistance loci for major diseases such as powdery and downy mildew. Currently, breeding programs make intensive use of these results by applying molecular markers linked to the resistance traits. However, modern genetics also allows to address additional agronomic traits that have considerable impact on the selection of grapevine cultivars. In this study, we have used linkage mapping for the identification and characterization of flowering time and ripening traits in a mapping population from a cross of V3125 (‘Schiava Grossa’ × ‘Riesling’) and the interspecific rootstock cultivar ‘Börner’ (Vitis riparia × Vitis cinerea). Comparison of the flowering time QTL mapping with data derived from a second independent segregating population identified several common QTLs. Especially a large region on linkage group 1 proved to be of special interest given the genetic divergence of the parents of the two populations. The proximity of the QTL region contains two CONSTANS-like genes. In accordance with data from other plants such as Arabidopsis thaliana and Oryza sativa, we hypothesize that these genes are major contributors to control the time of flowering in Vitis.     

An extreme cytoplasmic bottleneck in the modern European cultivated potato (Solanum tuberosum) is not reflected in decreased levels of nuclear diversity

We have used the polymorphic chloroplast (cp) and nuclear simple sequence repeats (SSRs) to analyse levels of cytoplasmic and nuclear diversity in the gene pool of the European cultivated potato (Solanum tuberosum ssp. tuberosum). Primers designed from the complete chloroplast sequence of tobacco (Nicotiana tabacum) were used to amplify polymorphic products in a range of potato cultivars. Combining the data from seven polymorphic cpSSR loci gave 26 haplotypes, one of which (haplotype A) accounted for 151 out of the 178 individuals studied and corresponded to the T-type cytoplasm previously identified in cultivated potatoes using chloroplast restriction fragment length polymorphism analysis. Phylogenetic and diversity analyses of the relationships between cpSSR haplotypes confirmed much higher levels of cytoplasmic diversity outwith the T-type group. Diversity levels at eight nuclear SSR loci, however, were not significantly different between cytoplasmic groups, suggesting a severe maternal bottleneck in the evolution of the modern cultivated potato. These results highlight the importance in quantifying levels of cytoplasmic as well as nuclear diversity and confirm the need for a change in breeding practices to increase levels of non-T-type cytoplasm in the cultivated gene pool, thus helping reduce problems associated with pollen sterility. This may be facilitated by germplasm analysis using cpSSRs, which will allow efficient selection of diverse cytoplasm donors.     

Characterization of genome-wide long terminal repeat retrotransposons provide insights into trait evolution of four grapevine species

Grapevine is one of the most economically important crops in the world. Although long terminal repeat (LTR) retrotransposons are thought to have played an important role in plants, its distribution in grapevine is not clear. Here, we identified genome-wide intact LTR retrotransposons in a total of six high-quality grapevine genomes from Vitis vinifera L., Vitis sylvestris C.C. Gmel., Vitis riparia Michx. and Vitis amurensis Rupr. with an average of 2938 per genome. Among them, the Copia superfamily (particularly for Ale) is a major component of the LTR retrotransposon in grapevine. Insertion time and copy number analysis revealed that the expansion of 70% LTR retrotransposons concentrating on approximately 2.5 Ma was able to drive genome size variation. Phylogenetic tree and syntenic analyses showed that most LTR retrotransposons in these genomes formed and evolved after species divergence. Furthermore, the function and expression of genes inserted by LTR retrotransposons in V. vinifera (Pinot noir) and V. riparia were explored. The length and expression of genes related to starch metabolism and quinone synthesis pathway in Pinot noir and environmental adaptation pathway in V. riparia were significantly affected by LTR retrotransposon insertion. The results improve the understanding of LTR retrotransposons in grapevine genomes and provide insights for its potential contribution to grapevine trait evolution.     

Effect of UV-C on peroxidase isoenzymes in axillary bud cultures ofVitis species differing in fungal resistance toPlasmopara viticola

The effect of shortwave (250 nm) UV radiation (UV-C) on the level of peroxidase activity and peroxidase isoenzyme patterns in leaves of resistant ([Vitis vinifera x Viris riparia] x Vitis rupestris andVitis rupestris) and susceptible (Vitis vinifera) grapevine species toPlasmopara viticola (downy mildew) was studied. The results show that although UV-C did not produce significant changes in peroxidase activity in susceptible species, and only minor changes in resistant species, treatment with UV-light induces an acidic isoperoxidase (isoperoxidase A₁), capable of oxidising 4-hydroxystilbenes in resistant species. It was named HSPrx 2. Since peroxidase is apparently the enzyme responsible for ε-viniferin synthesis from resveratrol in grapevines, a close relationship between this peroxidase isoenzyme and ε-viniferin synthesis which occurs in grapevine leaves after UV-C treatment must be expected.     

Use of in vitro method to evaluate some grapevine varieties for tolerance and susceptibility to sodium bicarbonate-induced chlorosis

Nodal shoot segments of four grapevine genotypes well known for their Fe-chlorosis characteristic [Vitis vinifera × Vitis berlandieri Fercal, resistant; V. berlandieri × Vitis rupestris 1103 P, mid-resistant; Solonis (Vitis riparia × V. rupestris × Vitis candicans) × Othello (Vitis labrusca × V. riparia × V. vinifera) 1613 C, susceptible; V. vinifera L. cv. Perlette, resistant] were cultured in vitro. The effects of three levels of iron sodium ethylene-diaminotetraacetate (FeNaEDTA; 9, 18, 36 mg l⁻¹) and three mixtures of iron and 840 mg l⁻¹ NaHCO₃ (sodium bicarbonate) in the Murashige and Skoog (MS) medium supplemented 4.9 μM indole-3-butyric acid (IBA) were compared. We assayed the chlorosis rating of leaves, total chlorophyll of leaves, dry shoot weights of the plantlets, and active and total Fe content of the leaves. The most suitable concentration in determining the reaction of genotypes to iron chlorosis was 9 mg l⁻¹ FeNaEDTA. Bicarbonate addition had negative effects on the iron intake and development of plants. While all genotypes were affected by non-ferrous conditions, Fercal and Perlette were found to be the most resistant genotypes and 1613 C rootstock as the most susceptible. The chlorosis rating of the tested genotypes ranked according to their known degree of tolerance and susceptibility to lime-induced chlorosis. The results of this study showed that the in vitro technique could successfully be used in viticulture to get results in shorter times in the studies, aiming at breeding new rootstocks and varieties suitable to calcareous soil conditions and determining the reactions of existing genotypes to Fe chlorosis.     

Variation in recombination rates across Vitis species

Recombination rate data are presented for three populations of grape based on framework genetic linkage maps developed with simple-sequence repeat markers. These linkage maps were constructed from different Vitis species and represent three genetic backgrounds. The first population is pure Vitis vinifera, derived from a cross of the European cultivars Riesling and Cabernet Sauvignon. The second is an interspecific cross between two commercially used rootstock cultivars of different North American Vitis species parentage, Ramsey (Vitis champinii) and Riparia Gloire (Vitis riparia). The third population, D8909-15 (Vitis rupestris × (Vitis arizonica/Vitis girdiana form)) × F8909-17 (V. rupestris × (V. arizonica/Vitis candicans form)), is an F1 from two half-sibs. Genome-wide and chromosome-wide recombination rates varied across the three populations and among the six Vitis parents. Global recombination rates in the parents of the third F1 population, with a complex Vitis background, were significantly reduced. In the first and third populations, the recombination rate was significantly greater in the male parent. Specific genome locations with frequent heterogeneity in recombination were identified, suggesting that recombination rates are not equal across the Vitis genome. The identification of regions with suppressed or high recombination will aid grape breeders and geneticists who rely on recombination events to introgress disease resistance genes from the genomes of wild Vitis species, develop fine-scale genetic maps, and clone disease resistance genes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular characterization and evolutionary pattern of the 9- cis -epoxycarotenoid dioxygenase NCED1 gene in grapevine

This study provides the first analysis of the level and patterns of nucleotide polymorphism of the NCED1 gene in grapevine (Vitis vinifera L.). A total of 123 sequences of the gene were analyzed to give a sample of 50 wild accessions and 73 cultivars. A high single nucleotide polymorphism and haplotype diversity was revealed in the cultivars studied, especially Tunisian germplasms which present an important and diverse reservoir of genetic diversity for grape breeding and conservation. The haplotype distribution highlights two origins of the cultivars studied: one may be related to primary grapevine gene pool domestication while the second seems to be more recent. Thus, besides domestication, gene introgression has also played a role in shaping the current varietal landscape of grape cultivars. Higher nucleotide and haplotype polymorphism was recorded for cultivars. This was accompanied by a higher recombination rate in cultivated grapevines for this gene, a recent selective sweep in wild samples and a balancing selection in cultivars. The conservation of genetic diversity of the endangered wild germplasm is important to ensure that the wild population can be used in future breeding programs of the domesticated cultivars. The high number of alleles discovered can be used as a valuable source for association studies between allele frequencies and phenotypic variations in this gene. In addition to natural selection, molecular evidence shows that genetic variation in this locus appears to be shaped by a combination of mutation and recombination events.     

Study of the relationship between the cultivars of Vitis vinifera and the white-fruited and hermaphrodite Chinese wild grapes

Chinese wild grapes are almost exclusively dioecious and black-fruited, with rare reports of white and hermaphrodite types in V. davidii. To reveal the molecular mechanisms of these phenotypic variations, specific primers were designed to detect the genotypes of mybA-related genes in Vitis species, including the Chinese wild Vitis species, V. riparia, V. rupestris, cultivars of Vitis vinifera and its hybrids. We report here that three mybA-related genes, VvmybA1a, VvmybA2 and VvmybA3, were only detected in cultivars of V. vinifera and its hybrids, but not in V. riparia, V. rupestris or Chinese wild Vitis species, indicating that these genes could be used to test the genetic relationship to V. vinifera. On the other hand, the genes were not detected in the dioecious varieties of V. davidii, but were in the hermaphrodites. In particular, the white-fruited varieties were homozygous for VvmybA1a and showed a low expression of mybA-related genes and UFGT during the entire maturation period. Simple sequence repeat analysis showed that the hermaphrodite varieties of V. davidii, including the white-fruited varieties, were more closely related to V. vinifera cv. Pinot Noir and V. labruscana cv. Kyoho. These results suggested that the white-fruited and hermaphrodite varieties of V. davidii could be the result of its crossing with V. vinifera. It provides a new approach to identify truly Chinese wild varieties and to search for possible hybridization events.     

Design of grapevine (Vitis vinifera L.) cultivar-specific SCAR primers for PCR fingerprinting

Among 34 grapevine cultivars (Vitis vinifera L.), eight putative genotype-specific RAPD markers, from ’Albariño’, ’Caíño blanco’, ’Chardonnay’, ’Folle blanche’, ’Grenache blanc’, ’Malvasía Sitges’, ’Torrontés’ and ’Treixadura’ respectively, were selected to transform into SCAR markers. Of these, seven markers were cloned and then five which showed a positive specific hybridization signal were sequenced. For these five markers, 30 sequence-specific primers ranging from 14 to 29 bases were designed to amplify genomic DNA from 64 grapevine cultivars under more-stringent PCR conditions. Only, two primer pairs, OpA11₁₁₇₅p17R/ p17F and OpD10₈₀₀p14R/p14F, still produced a specific SCAR marker, the ’Folle blanche’ ScA11₁₁₇₅ and the ’Malvasía Sitges’ ScD10₈₀₀ respectively. Moreover, the ScA11₁₁₇₅ marker was amplified only in ’Folle blanche’ among the 64 cultivars tested with a large annealing temperature range using either two different Taq DNA polymerases or two separate thermocyclers. In addition, we discuss the initial polymorphism originated by the RAPD technique and suggest a new design of SCAR primers to obtain reliable cultivar-specific SCAR markers from single PCR-based bands for identification purposes.     

Genetic relationship between Chinese wild Vitis species and American and European Cultivars based on ISSR markers

Inter-simple sequence repeat (ISSR) markers were employed to detect the genetic diversity among 70 grape accessions including 52 clones of 17 Chinese wild grape species, seven interspecific hybrids, 10 Vitis vinifera L. cultivars, and one strain of Vitis riparia L. A total of 119 polymorphic bands with an average of 11.9 per primer were observed. The unweighted pair-group method (UPGMA) analysis indicated that the 70 clones or accessions had a similarity range from 0.08 to 0.93, indicating that abundant diversities exist among these accessions. Based on cluster analysis and principal coordinate analysis, all accessions could be divided into two major groups, the Chinese wild grape group, and the American and European cultivar group. The largest distance was found among V. riparia MichX, Vitis piasezkii, V. vinifera L. interspecific hybrid (Vitis binifera × V. labrusca) and the wild grapes native to China.     

Cytological characteristic of two strains of grapevine (Vitis riparia × Vitis labrusca) callus culture

The structure of the cells was studied in two strains of grapevine calli (Vitis riparia ×V. labrusca). These callus cultures contained only highly vacuolised cells. The pattern of division in these slightly cytosolic cells was described. In both callus strains caryological instability has been found.     

Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.)

Ziziphus is an important genus within the family Rhamnaceae. This genus includes several important fruit tree species that are widely planted in China and India, such as the Chinese jujube (Ziziphus jujuba Mill.), the wild jujube (Z. acidojujuba), and the Indian jujube (Z. mauritiana). However, information about their domestication based on the chlorotype diversity of Chinese jujube population is lacking. In this study, chloroplast microsatellite (cpSSR) markers were developed and used to investigate the genetic relationships between and domestication of jujube cultivars and wild jujube populations. Primer sets flanking each of the 46 cpSSR loci in non-coding regions of the chloroplast genome sequence of Z. jujuba Mill. cv. ‘Junzao’ were designed. In total, 10 markers showed polymorphisms from 15 samples (9 jujube cultivars and 6 wild jujube individuals), of which 8 loci were due to variations in the number of mononucleotide (A/T) repeats and 2 were due to indels. Six cpSSR markers were used in further analyses of 81 additional samples (63 jujube cultivars, 17 wild jujube samples, and 1 Indian jujube). Using these cpSSR markers, the number of alleles per locus ranged from two to four. In general, the Shannon Index (I) for each cpSSR ranged from 0.159 to 0.1747, and the diversity indices (h) and uh were 0.061 to 0.435 and 0.062 to 0.439, respectively. Seven chlorotypes were found; the Indian jujube showed distinct chlorotypes, and both the Chinese and wild jujube had four chlorotypes and shared two chlorotypes. A dominant chlorotype (G) accounted for 53 of 72 jujube cultivars and 13 of 23 wild jujube individuals. All chlorotypes were highly localized along the Yellow River, from the mid- to the lower reaches, suggesting a wide origin of jujube. These cpSSR markers can be applied to population and evolution studies of Chinese jujube and wild jujube.     

Resistance to crown gall disease in transgenic grapevine rootstocks containing truncated <Emphasis Type="Italic">virE2</Emphasis> of <Emphasis Type="Italic">Agrobacterium</Emphasis>

A truncated form of the Ti-plasmid virE2 gene from Agrobacterium tumefaciens strains C58 and A6, and A. vitis strain CG450 was transferred and expressed in somatic embryos of grapevine rootstocks 110 Richter (Vitis rupestris × V. berlandieri), 3309 Couderc (V. rupestris × V. riparia) and Teleki 5C (V. berlandieri × V. riparia) via Agrobacterium-mediated transformation to confer resistance to crown gall disease. Transformation was confirmed in 98% of the 322 lines by enzyme-linked immunosorbent assay for the neomycin phosphotransferase II protein and 97% of 295 lines by polymerase chain reaction for the truncated virE2 transgene. Southern blot analysis revealed the insertion of truncated virE2 at one to three loci in a subset of seven transgenic 110 Richter lines. In vitro resistance screening assays based on inoculations of shoot internode sections showed reduced tumorigenicity and very small galls in 23 of 154 transgenic lines. Non-transformed controls had a 100% tumorigenicity rate with very large galls. Disease resistance assay at the whole plant level in the greenhouse revealed seven transgenic lines (3 lines of 110 Richter, 2 lines of 3309 Couderc and 2 lines of Teleki 5C) were resistant to A. tumefaciens strain C58 and A. vitis strains TM4 and CG450 with a substantially reduced percentage of inoculation sites showing gall as compared to controls. No association was found between the level of resistance to crown gall disease and the source Agrobacterium strain of virE2. Taken together, our data showed that resistance to crown gall disease can be achieved by expressing a truncated form of virE2 in grapevines.     

Effect of <Emphasis Type="Italic">Medicago sativa</Emphasis> ferritin gene on stress tolerance in transgenic grapevine

The effect of Medicago sativa (alfalfa) ferritin gene (MsFer) on abiotic stress tolerance was tested using transgenic Vitis berlandieri × Vitis rupestris cv. ‘Richter 110’ grapevine rootstock lines. Leaf discs from transgenic plants maintained higher photosynthetic activity after NaCl, tert-butyl-hydroperoxide (t-BHP) or paraquat treatment than control ones. These results indicate that the increased production of ferritin significantly improved abiotic stress tolerance in transgenic grapevine plants.     

Chloroplast microsatellite polymorphisms in Vitis species.

The use of consensus chloroplast microsatellites primers for dicotyledonous chloroplast genomes revealed the existence of intra and interspecific length variation within the genus Vitis. Three chloroplast microsatellite loci were found to be polymorphic in samples of Vitis vinifera, Vitis berlandieri, Vitis riparia, and Vitis rupestris out of a total of 10 consensus primer pairs tested. These polymorphisms were always due to a variable number of mononucleotide residues within A and (or) T stretches in the amplified regions. Chloroplast microsatellite polymorphisms were used to demonstrate the maternal inheritance of chloroplast in V. vinifera and to characterise the chloroplast haplotypes present in wine grape cultivars of this species grown in Spain and Greece. The different distribution of haplotype frequencies in the two ends of the Mediterranean growth area suggests the existence of independent domestication events for grapevine.