Screening of Galician grapevine varieties by SNPs, phenotypic traits, and phytopathology
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ABSTRACT:
SUBMITTER: Diaz-Fernandez A
PROVIDER: S-EPMC10904527 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Six components of partial resistance (RCs) were studied in 15 grapevine varieties with partial resistance to Plasmopara viticola: (i) infection frequency (IFR, proportion of inoculation sites showing sporulation), (ii) latent period (LP50, degree-days between inoculation and appearance of 50% of the final number of sporulating lesions), (iii) lesion size (LS, area of single lesions in mm2), (iv) production of sporangia (SPOR, number of sporangia produced per lesion, and SPOR', number of sporangia produced per mm2 of lesion), (v) infectious period (IP, number of sporulation events on a lesion), and (vi) infectivity of sporangia (INF, infection efficiency of sporangia produced on resistant varieties). Artificial inoculation monocycle experiments were conducted for a 3-year period on leaves collected at leaf development, flowering, and fruit development. Compared to the susceptible variety 'Merlot', the partially resistant varieties showed reduced IFR, longer LP, smaller LS, fewer SPOR and SPOR', shorter IP, and lower INF. At leaf development, IFR, SPOR, and INF were higher and LP was shorter than at flowering and fruit development. RCs analysis through monocyclic experiments provides reliable assessments of the resistance response of grapevine accessions. The workload required for routine assessment in breeding programs could be reduced by measuring IFR and SPOR, while producing robust results.
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Project description:Grapevine (Vitis spp., family Vitaceae) is characterized by a marked phenotypic plasticity and its ability to withstand various environmental conditions depends on the activation of highly coordinated responses, resulting from the interaction among genotypes (G) and environmental factors (E). Understanding genotype by environment (GxE) interplays is highly complex and challenging, and often the outcome of the genetic responses to field performance is not straightforward also due to the difficulties to reach a precise definition of the E component in field studies. In this work, the transcriptome of commercially ripe berries of Cabernet sauvignon and Aglianico genotypes grown in open-field at three different sites of central-southern Italy (Campania, Molise and Sicily) was analyzed by RNAseq. These transcriptomic data were integrated with a comprehensive set of climatic indices, forming an “environmentome”, through Weighted Gene Co-expression Network Analysis (WGCNA). A total of 11,887 differentially expressed genes (DEGs) have been retrieved, most of them found in the Aglianico genotype, suggesting that Aglianico transcriptome is largely influenced by the environment. Furthermore, the comparisons involving the Sicilian site exhibited the highest number of DEGs for both genotypes. WGCNA suggested that most of the climatic data (such as daily maximum air temperature, relative humidity, air pressure, dew point, hours of sun radiation) significantly correlated with “lightcyan1” module. Among these eingengenes, the low expression of ACA10 cation transporter is suggested to be indirectly related to the low anthocyanin content in Cabernet sauvignon in Campania, thus confirming WGCNA as powerful approach to identify gene of high biological interest. Similarly, transcriptome was also correlated with quality trait, such as total soluble solids and polyphenol content, leading to the discovery of hub genes that might function as markers of wine quality.
2024-04-14 | GSE261685 | GEO
Project description:Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors. Through DAPC and Bayesian population structure five groups were identified according to type of material data and reflecting the genetic basis and breeding strategies involved in their development. Phenotypic and genotypic coefficient of variation were low for kernel width (6.43%) and for grain protein content (1.03%). Highly significant differences between environments, genotypes and GEI (Genotype x Environment Interaction) were detected by mixed ANOVAs for agro-morphological-quality traits. Number of kernels per spike (h2 = 0.02) and grain protein content (h2 = 0.03) were not a heritability character and highly influenced by the environment. Nested ANOVAs revealed highly significant differences between DAPC clusters within environments for all traits except kernel roundness. Ten UPOV traits showed significant diversity for their frequencies in the two environments. By PCAmix multivariate analysis, plant height, heading time, spike length, weight of kernels per spike, thousand kernel weight, and the seed related traits had heavy weight on the differentiation of the groups, while UPOV traits discriminated moderately or to a little extent. The data collected in this study provide useful resources to facilitate management and use of wheat genetic diversity that has been lost due to selection in the last decades.
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Project description:The Italian grape germplasm is characterized by a high level of richness in terms of varieties number, with nearly 600 wine grape varieties listed in the Italian National Register of Grapevine Varieties and with a plethora of autochthonous grapes. In the present study an extended SNP genotyping has been carried out on Italian germplasm of cultivated Vitis vinifera subsp. sativa and Vitis hybrids. Several hundred Italian varieties maintained in the repositories of scientific Institutions and about one thousand additional varieties derived from previous studies on European, Southern Italy, Magna Graecia and Georgian germplasm were considered. The large genotyping data obtained were used to check the presence of homonyms and synonyms, determine parental relationships, and identify the main ancestors of traditional Italian cultivars and closely-related accessions. The parentage among a set of 1,232 unique varieties has been assessed. A total of 92 new parent-offspring (PO) pairs and 14 new PO trios were identified. The resulted parentage network suggested that the traditional Italian grapevine germplasm originates largely from a few central varieties geographically distributed into several areas of genetic influence: "Strinto porcino" and its offspring "Sangiovese", "Mantonico bianco" and "Aglianico" mainly as founder varieties of South-Western Italy (IT-SW); Italian Adriatic Coast (IT-AC); and Central Italy with most varieties being offsprings of "Visparola", "Garganega" and "Bombino bianco"; "Termarina (Sciaccarello)" "Orsolina" and "Uva Tosca" as the main varieties of North-Western Italy (IT-NW) and Central Italy. The pedigree reconstruction by full-sib and second-degree relationships highlighted the key role of some cultivars, and, in particular, the centrality of "Visparola" in the origin of Italian germplasm appeared clear. An hypothetical migration of this variety within the Italian Peninsula from South to North along the eastern side, as well as of "Sangiovese" from South to Central Italy along the Western side might be supposed. Moreover, it was also highlighted that, among the main founders of muscat varieties, "Moscato bianco" and "Zibibbo (Muscat of Alexandria)" have spread over the whole Italy, with a high contribution by the former to germplasm of the North-Western of the peninsula.
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Project description:Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.
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Project description:A controversy arose over Mendel's pea crossing experiments after the statistician R.A. Fisher proposed how these may have been performed and criticised Mendel's interpretation of his data. Here we re-examine Mendel's experiments and investigate Fisher's statistical criticisms of bias. We describe pea varieties available in Mendel's time and show that these could readily provide all the material Mendel needed for his experiments; the characters he chose to follow were clearly described in catalogues at the time. The combination of character states available in these varieties, together with Eichling's report of crosses Mendel performed, suggest that two of his F3 progeny test experiments may have involved the same F2 population, and therefore that these data should not be treated as independent variables in statistical analysis of Mendel's data. A comprehensive re-examination of Mendel's segregation ratios does not support previous suggestions that they differ remarkably from expectation. The χ2 values for his segregation ratios sum to a value close to the expectation and there is no deficiency of extreme segregation ratios. Overall the χ values for Mendel's segregation ratios deviate slightly from the standard normal distribution; this is probably because of the variance associated with phenotypic rather than genotypic ratios and because Mendel excluded some data sets with small numbers of progeny, where he noted the ratios "deviate not insignificantly" from expectation.
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Project description:The Plasmopara viticola pathogen causes one of the most severe grapevine diseases, namely downy mildew. The response to P. viticola involves both visible symptoms and intricate metabolomic alterations, particularly in relation to volatile organic compounds, and depends on the degree of resistance of a particular variety. There are numerous native grapevine varieties in Croatia, and they vary in susceptibility to this oomycete. As previously reported, in vitro leaf disc bioassay and polyphenolic compound analysis are complementary methods that can be used to separate native varieties into various resistance classes. This research used the Solid Phase Microextraction-Arrow Gas Chromatography-Mass Spectrometry method to identify the early alterations in the VOCs in the leaves after P. viticola inoculation. Based on the absolute peak area of sesquiterpenes, some discrepancies between the sampling terms were noticed. The presence of certain chemical compounds such as humulene, ylangene, and α-farnesene helped distinguish the non-inoculated and inoculated samples. Although specific VOC responses to P. viticola infection of native varieties from various resistance classes could not be identified, the response of less susceptible native varieties and resistant controls was associated with an increase in the absolute peak area of several compounds, including geranylacetone, ß-ocimene, and (E)-2-hexen-1-ol.
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Project description:IntroductionClimate change has been driving warming trends and changes in precipitation patterns and regimes throughout Europe. Future projections indicate a continuation of these trends in the next decades. This situation is challenging the sustainability of viniculture and, thus, significant efforts towards adaptation should be then carried out by local winegrowers.MethodEcological Niche Models were built, using the ensemble modelling approach, to estimate the bioclimatic suitability of four main wine-producing European countries, namely France, Italy, Portugal, and Spain, in the recent past (1989-2005), for the cultivation of twelve Portuguese grape varieties. The models were then used to project the bioclimatic suitability to two future periods (2021- 2050 and 2051-2080) to better understand the potential shifts related to climate change (modeled after Intergovernmental Panel on Climate Change's Representative Concentration Pathways 4.5 and 8.5 scenarios). The models were obtained with the modeling platform BIOMOD2, using four bioclimatic indices, namely the "Huglin Index", the "Cool Night index", the "Growing Season Precipitation index", and the "Temperature Range during Ripening index" as predictor variables, as well as the current locations of the chosen grape varieties in Portugal.ResultsAll models performed with high statistical accuracy (AUC > 0.9) and were able to discriminate several suitable bioclimatic areas for the different grape varieties, in and around where they are currently located but also in other parts of the study area. The distribution of the bioclimatic suitability changed, however, when looking at future projections. For both climatic scenarios, projected bioclimatic suitability suffered a considerable shift to the north of Spain and France. In some cases, bioclimatic suitability also moved towards areas of higher elevation. Portugal and Italy barely retained any of the initially projected varietal areas. These shifts were mainly due to the overall rise in thermal accumulation and lower accumulated precipitation in the southern regions projected for the future.ConclusionEnsemble models of Ecological Niche Models were shown to be valid tools for winegrowers who want to adapt to a changing climate. The long-term sustainability of viniculture in southern Europe will most likely have to go through a process of mitigation of the effects of increasing temperatures and decreasing precipitation.
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Project description:With the aim to characterize changes caused by grapevine leafroll-associated virus 3 (GLRaV-3) singly or in coinfection with other viruses and to potentially determine genotype-specific or common markers of viral infection, thirty-six parameters, including nutrient status, oxidative stress parameters, and primary metabolism as well as symptoms incidence were investigated in 'Cabernet Franc,' 'Merlot,' 'Pinot Noir,' and 'Tribidrag' grapevine varieties. Host responses were characterized by changes in cellular redox state rather than disturbances in nutrient status and primary metabolic processes. Superoxide dismutase, hydrogen peroxide, and proteins were drastically affected regardless of the type of isolate, the host, and the duration of the infection, so they present cellular markers of viral infection. No clear biological pattern could be ascertained for each of the GLRaV-3 genotypes. There is a need to provide a greater understanding of virus epidemiology in viticulture due to the increasing natural disasters and climate change to provide for global food production security. Finding grape varieties that will be able to cope with those changes can aid in this task. Among the studied grapevine varieties, autochthonous 'Tribidrag' seems to be more tolerant to symptoms development despite numerous physiological changes caused by viruses.
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Project description:We report the berry pericarp transcriptomic profiles of 5 red Vitis vinifera varieties: Sangiovese, Barbera, Negro amaro, Refosco and Primitivo at 4 growth stages: pea-sized berries (Bbch 75) at almost 20 days after flowering, berries beginning to touch (Bbch77) just prior véraison, the softening of the berries (Bbch 85) at the end of véraison and berries ripe for harvest (Bbch 89)
2015-01-19 | GSE62744 | GEO