Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines.

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software structure, we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.

Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms.

The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a 'wine culture', have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species' distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

A genetic analysis of seed and berry weight in grapevine.

Fruit size and seedlessness are highly relevant traits in many fruit crop species, and both are primary targets of breeding programs for table grapes. In this work we performed a quantitative genetic analysis of size and seedlessness in an F1 segregating population derived from the cross between a classical seeded (Vitis vinifera L. 'Dominga') and a newly bred seedless ('Autumn Seedless') cultivar. Fruit size was scored as berry weight (BW), and for seedlessness we considered both seed fresh weight (SFW) and the number of seeds and seed traces (SN) per berry. Quantitative trait loci (QTL) analysis of BW detected 3 QTLs affecting this trait and accounting for up to 67% of the total phenotypic variance. QTL analysis for seedlessness detected 3 QTLs affecting SN (explaining up to 35% of total variance) and 6 affecting SFW (explaining up to 90% of total variance). Among them, a major effect QTL explained almost half of the phenotypic variation for SFW. Comparative analysis of QTLs for these traits reduced the number of grapevine genomic regions involved, one of them being a major effect QTL for seedlessness. Association analyses showed that microsatellite locus VMC7F2, closely linked to this QTL, is a useful marker for selection of seedlessnes.

DNA methylation increases throughout Arabidopsis development.

We used amplified fragment length polymorphisms (AFLP) to analyze the stability of DNA methylation throughout Arabidopsis development. AFLP can detect genome-wide changes in cytosine methylation produced by DNA demethylation agents, such as 5-azacytidine, or specific mutations at the DDM1 locus. In both cases, cytosine demethylation is associated with a general increase in the presence of amplified fragments. Using this approach, we followed DNA methylation at methylation sensitive restriction sites throughout Arabidopsis development. The results show a progressive DNA methylation trend from cotyledons to vegetative organs to reproductive organs.

Genetic relationship among cultivated and wild grapevine accessions from Tunisia.

We have used nuclear and chloroplast molecular markers to genotype cultivated and wild accessions of Vitis vinifera L. from Tunisia and assess their genetic relationships. Fifty-five distinct genotypes were identified among 80 cultivated accessions, including 18 genotypic groups containing between 2 and 5 accessions per group. They could represent a total of 60 distinct cultivars owing to berry colour variation found within identical genotype groups. Most of the 55 genotypes represent unique table grape genotypes except for one of them that was found identical to the genotype of table grape cultivar Rosseti. Hybridization among cultivars as well as self pollinations seems to have played an important role in their origin since several groups of closely related cultivars were observed. Furthermore, a parentage analysis showed a high probability for a parent hybrid relationship within two groups of three cultivars. No strong genetic similarities were found between cultivated and wild samples indicating that the cultivated accessions do not derive from local Vitis vinifera L. populations but could have been introduced from other regions in historic times.

Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers.

AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/ HpaII and EcoRI/ MspI patterns in different ecotypes revealed that 35-43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation.

Genetic structure of natural populations of the grass endophyte Epichloë festucae in semiarid grasslands.

Plants of red fescue (Festuca rubra), a commercially important turf grass, are infected by the fungal endophyte Epichloë festucae in semiarid natural grasslands, known as dehesas, in western Spain. We used amplified fragment length polymorphism (AFLP) markers to analyse the genetic polymorphism existing in two natural populations of Epichloë festucae. Linkage disequilibrium and the presence of clonal lineages indicated that nonrecombinant asexual reproduction predominates in both populations. However, most genetic variation detected was found to occur within populations, with only a moderate amount of genetic differentiation between populations (F(ST): 0.197). Overall, the study suggests that dehesa grasslands are useful reservoirs of Epichloë festucae endophytes, and provides information on population structure which is relevant to design sampling strategies.

A Brassica oleracea gene expressed in a variety-specific manner may encode a novel plant transmembrane receptor.

The species Brassica oleracea includes several agricultural varieties characterized by the proliferation of different types of meristems. Using a combination of subtractive hybridization and PCR (polymerase chain reaction) techniques we have identified several genes which are expressed in the reproductive meristems of the cauliflower curd (B. oleracea var. botrytis) but not in the vegetative meristems of Brussels sprouts (B. oleracea var. gemmifera) axillary buds. One of the cloned genes, termed CCE1 (CAULIFLOWER CURD EXPRESSION 1) shows specific expression in the botrytis variety. Preferential expression takes place in this variety in the meristems of the curd and in the stem throughout the vegetative and reproductive stages of plant growth. CCE1 transcripts are not detected in any of the organs of other B. oleracea varieties analyzed. Based on the nucleotide sequence of a cDNA encompassing the complete coding region, we predict that this gene encodes a transmembrane protein, with three transmembrane domains. The deduced amino acid sequence includes motifs conserved in G-protein-coupled receptors (GPCRs) from yeast and animal species. Our results suggest that the cloned gene encodes a protein belonging to a new, so far unidentified, family of transmembrane receptors in plants. The expression pattern of the gene suggests that the receptor may be involved in the control of meristem development/arrest that takes place in cauliflower.

early bolting in short days: an Arabidopsis mutation that causes early flowering and partially suppresses the floral phenotype of leafy.

The time of flowering in Arabidopsis is controlled by multiple endogenous and environmental signals. Some of these signals promote the onset of flowering, whereas others repress it. We describe here the isolation and characterization of two allelic mutations that cause early flowering and define a new locus, EARLY BOLTING IN SHORT DAYS (EBS). Acceleration of flowering time in the ebs mutants is especially conspicuous under short-day photoperiods and results from a reduction of the adult vegetative phase of the plants. In addition to the early flowering phenotype, ebs mutants show a reduction in seed dormancy, plant size, and fertility. Double mutant analysis with gibberellin-deficient mutants indicates that both the early-flowering and the precocious-germination phenotypes require gibberellin biosynthesis. Analysis of the genetic interactions among ebs and several mutations causing late flowering shows that the ft mutant phenotype is epistatic over the early flowering of ebs mutants, suggesting that the precocious flowering of ebs requires the FT gene product. Finally, the ebs mutation causes an increase in the level of expression of the floral homeotic genes APETALA3 (AP3), PISTILLATA (PI), and AGAMOUS (AG) and partially rescues the mutant floral phenotype of leafy-6 (lfy-6) mutants. These results suggest that EBS participates as a negative regulator in developmental processes such as germination, flowering induction, and flower organ specification.

Constitutive expression of Arabidopsis LEAFY or APETALA1 genes in citrus reduces their generation time.

Citrus trees have a long juvenile phase that delays their reproductive development by between 6 and 20 years, depending on the species. With the aim of accelerating their flowering time, we transformed juvenile citrus seedlings to constitutively express the Arabidopsis LEAFY (LFY) or APETALA1 (AP1) genes, which promote flower initiation in Arabidopsis. Both types of transgenic citrus produced fertile flowers and fruits as early as the first year, notably through a mechanism involving an appreciable shortening of their juvenile phase. Furthermore, expression of AP1 was as efficient as LFY in the initiation of flowers, and did not produce any severe developmental abnormality. Both types of transgenic trees flowered in consecutive years, and their flowering response was under environmental control. In addition, zygotic and nucellar derived transgenic seedlings had a very short juvenile phase and flowered in their first spring, demonstrating the stability and inheritance of this trait. These results open new possibilities for domestication, genetic improvement, and experimental research in citrus and other woody species.

A freezing-sensitive mutant of Arabidopsis, frs1, is a new aba3 allele.

To investigate the molecular mechanisms controlling the process of cold acclimation and to identify genes involved in plant freezing tolerance, mutations that impaired the cold acclimation capability of Arabidopsis thaliana (L.) Heynh were screened for. A new mutation, frs1 (freezing sensitive 1), that reduced both the constitutive freezing tolerance as well as the freezing tolerance of Arabidopsis after cold acclimation was characterized. This mutation also produced a wilty phenotype and excessive water loss. Plants with the frs1 mutation recovered their wild-type phenotype, their capability to tolerate freezing temperatures and their capability to retain water after an exogenous abscisic acid (ABA) treatment. Measurements of ABA revealed that frs1 mutants were ABA deficient, and complementation tests indicated that frs1 mutation was a new allele of the ABA3 locus showing that a mutation in this locus leads to an impairment of freezing tolerance. These results constitute the first report showing that a mutation in ABA3 leads to an impairment of freezing tolerance, and not only strengthen the conclusion that ABA is required for full development of freezing tolerance in cold-acclimated plants, but also demonstrate that ABA mediates the constitutive freezing tolerance of Arabidopsis. Gene expression in frs1 mutants was altered in response to dehydration, suggesting that freezing tolerance in Arabidopsis depends on ABA-regulated proteins that allow plants to survive the challenges imposed by subzero temperatures, mainly freeze-induced cellular dehydration.

Genetic relationships among biotypes of Bemisia tabaci (Hemiptera: Aleyrodidae) based on AFLP analysis.

Genetic similarities between 13 samples belonging to nine reference biotypes and two field populations of Bemisia tabaci (Gennadius), one field population of B. medinae Gómez-Menor and another of B. afer Priesner & Hosny, were evaluated using amplified fragment length polymorphism (AFLP) markers. The results indicate that B. tabaci biotypes can be grouped together with a minimum similarity coefficient of 0.32 and separated from the two other species with a similarity coefficient of 0.07. Bemisia tabaci biotypes were grouped in four clusters which comprised: (i) Near East and Indian subcontinent biotypes; (ii) B and Q biotypes plus a Nigerian population from cowpea; (iii) New World A biotype; and (iv) S biotype and a Nigerian population from cassava. These results were consistent with a previous grouping of biotypes based on RAPD-PCR analysis. The AFLP assay allowed the scoring of a total of 354 polymorphic bands in two reaction events with the use of two primer combinations.

Mutations causing defects in the biosynthesis and response to gibberellins, abscisic acid and phytochrome B do not inhibit vernalization in Arabidopsis fca-1.

The roles of gibberellins, abscisic acid and phytochrome B in the vernalization response were investigated by combining mutations causing defects in their biosynthesis and response with the Arabidopsis thaliana (L.) Heynh. fca-1 mutation. The fca-1 mutation confers a very late-flowering phenotype which can be reversed to wild-type flowering if the seedlings are vernalized. Vernalization was unaffected in ga1-3, gai, abi1-1, abi2-1, abi3-1 and phyB-1 backgrounds, suggesting that gibberellin action mediated via GA1 and GAI, abscisic acid action mediated through ABI1 and ABI2, and phytochrome B, function independently of vernalization. However, the mutations did interact with fca-1 to change flowering time in the absence of vernalization. The abi1 fca-1 and abi2 fca-1 double mutants flowered earlier than fca-1 implying a role for abscisic acid in floral repression. Combination of ga1-3 or gai with fca-1 unexpectedly resulted in opposite interactions, with gai partially suppressing the late flowering of fca-1.

Characterization of Iberian pig genotypes using AFLP markers.

The use of the AFLP (amplified fragment length polymorphism) technique for the characterization of highly inbred Iberian pig breed genotypes and the detection of strain-specific polymorphisms is demonstrated. Twelve different primer combinations were used on individual DNA samples from animals belonging to two black hairless Iberian pig strains, Guadyerbas and Coronado. These amplification reactions allowed the detection of more than 1700 amplification products of which 26 were identified as strain-specific markers, present in all individuals of one strain and absent in the other. Comparison of male and female amplification products within one strain also allowed the identification of 8 male-specific amplified bands. AFLP showed a great power of marker detection due to a high multiplex ratio and high reproducibility. Comparison of similarity and co-ancestry coefficient matrices also showed the usefulness of AFLP markers to estimate genetic relationships between individuals pigs.

Identification of genes specifically expressed in cauliflower reproductive meristems. Molecular characterization of BoREM1.

Using the meristems of the cauliflower curd as a source of tissue and a series of subtractive hybridizations and amplification reactions, we have constructed a cDNA library highly enriched in cDNAs expressed in reproductive meristems. The analysis of a sample of 250 clones from this library identified 22 cDNA clones corresponding to genes specifically expressed in these cauliflower meristems. Apart from two clones that corresponded to APETALA1, and two other ones showing similarity to different aminoacyl-tRNA synthetases, the remaining clones showed no similarity to any sequence in the databases and may correspond to novel genes. One of these clones, BoREM1, was further characterized and found to correspond to a gene encoding a protein with features of regulatory proteins that follows a expression pattern very similar to the LEAFY transcripts.

Dimerization of Arabidopsis 14-3-3 proteins: structural requirements within the N-terminal domain and effect of calcium.

The structural requirements for dimerization of RCI14A and RCI14B, two 14-3-3 isoforms from Arabidopsis thaliana, have been analyzed by testing truncated forms of RCI14A for dimerization with full-length RCI14A and RCI14B. The results show that only the fourth helix of the truncated partner is essential for dimerization, which represents a difference from what is known for animal isoforms. On the other hand, the effect of calcium has been tested in RCI14A homodimerization. Millimolar concentrations of calcium exert a negative, dose-dependent effect that involves the C-terminal domain of RCI14A and might modulate interactions with other cellular components or among Arabidopsis 14-3-3 isoforms.

Sucrose availability on the aerial part of the plant promotes morphogenesis and flowering of Arabidopsis in the dark.

Conditions to promote dark morphogenesis and flower-ing in Arabidopsis have previously been limited to liquid cultures and to a few laboratory ecotypes. We have obtained development and flowering of Arabidopsis plants under complete darkness by growing them on vertical Petri dishes containing solid agar medium with sucrose. Under these conditions, all the ecotypes tested were able to develop, giving rise to etiolated plants that flowered after producing a certain number of leaves. Dark-grown plants showed similarities with phytochrome-deficient mutants and were different from de-etiolated or constitutive photomorphogenesis mutants such as det and cop. Late- and early-flowering ecotypes, showing large differences in flowering time and leaf number under long days, flowered with a similar number of leaves when grown in the dark. Rapid dark flowering of late-flowering ecotypes was not an effect of darkness but the result of the interaction between dark and sucrose availability at the aerial part of the plant, since sucrose also had an effect when plants were grown in the light. Gibberellin-deficient and insensitive mutants were delayed in the initiation of flowers in the dark, indicating a role for these hormones in flowering promotion in the dark. The late-flowering phenotype of mutants at different loci of the autonomous and long-day-dependent flowering induction pathways was rescued in dark growth conditions. However, the late-flowering phenotype of ft and fwa mutants was not rescued by sucrose either in the dark or in the light, suggesting a different role for these genes in flowering induction.

Low temperature regulates Arabidopsis Lhcb gene expression in a light-independent manner.

Low temperature treatment of dark-grown seedlings of Arabidopsis thaliana results in a rapid increase in the amount of mRNAs encoding for the major polypeptides of the light-harvesting complex of photosystem II (Lhcb1 genes). This increase is transient and seems to be due mainly to the accumulation of Lhcb1*3 transcripts, indicating that low temperature differentially regulates the expression of the Arabidopsis Lhcb1 gene family in the dark. A 1.34 kb fragment of the Lhcb1*3 promoter is sufficient to confer low temperature regulation to a reporter gene in transgenic Arabidopsis etiolated seedlings, suggesting that the regulation is occurring at the transcriptional level. The cold-induced accumulation of Lhcb1*3 mRNA is not part of a general response to stressful conditions since no accumulation is detected in response to water stress, anaerobiosis or salt stress. The amount of Lhcb1*3 mRNA decrease in response to exogenous abscisic acid (ABA) suggesting that this phytohormone acts as a negative regulator. Moreover, the accumulation of Lhcb1*3 mRNAs in cold-treated ABA deficient etiolated seedlings is higher than that of wild-type and ABA insensitive etiolated seedlings, indicating that low temperature regulation of Lhcb1*3 is not mediated by ABA.

Isolation and molecular characterization of the Arabidopsis TPS1 gene, encoding trehalose-6-phosphate synthase.

An Arabidopsis thaliana cDNA clone, AtTPS1, that encodes a trehalose-6-phosphate synthase was isolated. The identity of this protein is supported by both structural and functional evidence. On one hand, the predicted sequence of the protein encoded by AtTPS1 showed a high degree of similarity with trehalose-6-phosphate synthases of different organisms. On the other hand, expression of the AtTPS1 cDNA in the yeast tps1 mutant restored its ability to synthesize trehalose and suppressed its growth defect related to the lack of trehalose-6-phosphate. Genomic organization and expression analyses suggest that AtTPS1 is a single-copy gene and is expressed constitutively at very low levels.

Different roles of flowering-time genes in the activation of floral initiation genes in Arabidopsis.

We have analyzed double mutants that combine late-flowering mutations at four flowering-time loci (FVE, FPA, FWA, and FT) with mutations at the LEAFY (LFY), APETALA1 (AP1), and TERMINAL FLOWER1 (TFL1) loci involved in the floral initiation process (FLIP). Double mutants between ft-1 or fwa-1 and lfy-6 completely lack flowerlike structures, indicating that both FWA and FT act redundantly with LFY to control AP1. Moreover, the phenotypes of ft-1 ap1-1 and fwa-1 ap1-1 double mutants are reminiscent of the phenotype of ap1-1 cal-1 double mutants, suggesting that FWA and FT could also be involved in the control of other FLIP genes. Such extreme phenotypes were not observed in double mutants between fve-2 or fpa-1 and lfy-6 ap1-1. Each of these showed a phenotype similar to that of ap1-1 or lfy-6 mutants grown under noninductive photoperiods, suggesting a redundant interaction with FLIP genes. Finally, the phenotype of double mutants combining the late-flowering mutations with tfl1-2 were also consistent with the different roles of flowering-time genes.