Intra-varietal Diversity Research Articles

Policy dimension for promoting inter and intra-varietal diversity and evolutionary crop populations

Policy dimension for promoting inter and intra-varietal diversity and evolutionary crop populations

Evaluation of the intra-varietal diversity of ‘Tempranillo Tinto’ clones prospected in the demarcated winemaking region of Rioja (Spain)

The sustainability of traditional viticulture systems is compromised by different threats, like those derived from climate change. The use of alternative grapevine varieties is suggested as a possible solution, but different regulations limit this practice in many well-known winemaking regions. In these cases, the exploitation of clonal diversity emerges as a useful alternative of adaptation. Here, 30 ‘Tempranillo Tinto’ clones selected from a grapevine collection of 729 clones initially prospected in the demarcated winemaking region of Rioja (Spain) have been studied. The characterization of 27 traits related to phenology, agronomic performance, and oenological potential during three consecutive seasons revealed a high intra-varietal phenotypic spectrum, of interest to adapt to different growing conditions and needs. Interestingly, this diversity was markedly higher to that observed in a series of commercial clones used as controls. Further analyses revealed their clustering into four groups of clones with significant phenotypic differences. We identified a group of clones with late ripening and long veraison-to-harvest periods, of special interest to respond to projected warming conditions. In general, we proved that old vineyards in traditional winemaking regions are reservoirs of clonal diversity for ancient grapevine varieties like ‘Tempranillo Tinto’, which store useful traits to address current and future viticulture challenges.

High eugenol content of Armagnac hybrid variety Baco Blanc, an asset in combating <i>Botrytis cinerea</i>

Baco Blanc is the grape variety specific to the wine spirit Armagnac. A hybrid vine with good tolerance, particularly to Botrytis cinerea, its berries have an atypical chemical composition. Specifically, they have a high concentration of the anti-fungal compound eugenol. This research demonstrates the effectiveness of eugenol concentrations against B. cinerea and their relationship to the ripeness of Baco Blanc This study explores the intra-varietal diversity of B. cinerea tolerance, a potential source of adaptation to environmental and climate issues.

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties.

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.

Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat.

Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat.

Approaches and Advantages of Increased Crop Genetic Diversity in the Fields

Crop genetic diversity is the most important factor for a long-term sustainable production system. Breeding and production strategies for developing and growing uniform and homogenous varieties have created many problems. Such populations are static and very sensitive to unpredictable stresses. In Nepal, more than 80% of the seed system is informal, which has contributed greatly to creating and maintaining genetic diversity within the field. This paper aims to assess and present the approaches and advantages of increased crop genetic diversity in the fields, based on the experiences of implementing on-farm conservation activities carried out in Nepal for last two decades. Some of the evidence has been derived from an ongoing evolutionary plant breeding (EPB) project being implemented in Nepal. The information is supplemented with field assessments, focus group discussion, and a literature review. The major approaches to increase crop genetic diversity are evolutionary plant breeding, cultivar mixture, landrace enhancement, informal seed systems, the bulk method, diversifying the seed sources, participatory plant breeding, open pollination, etc. EPB and cultivar mixture are very simple and effective approaches to increase crop genetic diversity at field level. The involvement of farmers in these approaches helps to accelerate the population improvement, maintaining the higher degree of genetic diversity. The major advantages of increased crop genetic diversity are seed maintenance by farmers themselves, minimal risk of crop failure, resilience to unpredictable stresses, increased amount of diversified nutrition, production increment, ease of producing organically, etc. However, there are some issues and problems associated with mixtures and intra-varietal diversity; for example, not being able to harvest by machine, maturing at a different date, difficulty in maintaining seeds and registration, etc. Crop genetic diversity should be considered as a sustainable approach for a climate-resilient and self-dependent production system. The higher the genetic diversity in farming land, the more chance of receiving multiple benefits in the agriculture system.

Morphological and Genetic Clonal Diversity within the 'Greco Bianco' Grapevine (Vitis vinifera L.) Variety.

Grapevine (Vitis vinifera L.) has been propagated vegetatively for hundreds of years. Therefore, plants tend to accumulate somatic mutations that can result in an intra-varietal diversity capable of generating distinct clones. Although it is common that winemakers request specific clones or selections for planting new vineyards, relatively limited information is available on the extent, degree, and morphological impact of the clonal diversity in traditional, highly valued grapevine varieties within production areas protected by geographical denomination of origin. Here, we present a morphological and genetic investigation of the intra-varietal diversity in 'Greco Bianco', the grapevine variety used to produce the DOCG and PDO "Greco di Tufo" wine. Seventeen clones from different farms (all within the allowed production area) were phenotypically characterized using ampelographic and ampelometric traits. The clones were also genotyped with Simple Sequence Repeats (SSR) and retrotransposon-based DNA markers (REMAP). The morphological analysis indicated a uniformity in the qualitatively scored traits, and a limited variability for the quantitative traits of the bunch and of the berry composition. The molecular markers also depicted variability among clones, which was more evident with the use of REMAPs. The comparison of the discriminatory information of the three analyses indicated that they provided different estimates of the level of diversity. The evaluation described herein of the clonal variability has implications for the management and protection of clonal selections in 'Greco Bianco' and prompts for further multidisciplinary investigations on its possible role in winemaking.

Strategies and methods for conserving and exploring the intra-varietal genetic diversity of ancient grapevine varieties

The antiquity and diversity of traditional grapevine varieties guarantee a strong historical and natural character and add high economic value to viticulture and wine. A high level of intra-varietal diversity of quantitative traits was naturally created and accumulated over centuries. Nowadays, this diversity allows one to carry out selection within a variety and adapt it to the most diverse environmental, agricultural, and market contexts. However, an unusually intense process of genetic erosion of intra-varietal diversity broke out in the 1980s and threatens to destroy within a few decades the diversity created over centuries and millennia. Therefore, the definition of strategies and methods for conserving and exploring intra-varietal genetic variability is crucial for the sustainability of viticulture rich in history and traditions. Those strategies are presented in this work.

Molecular characterisation of the current cultivars of <i>Vitis vinifera</i> L. in Lanzarote (Canary Islands, Spain) reveals nine individuals which correspond to eight new varieties and two new sports

Vine was reintroduced to the volcanic island of Lanzarote (Spain) more than 300 years ago. The phylloxera plague has never reached the island; consequently, Vitis vinifera L. has evolved continuously since then due to the influence of some abiotic factors, such as low rainfall and strong winds. The aim of this study was to determine the inter- and intra-varietal diversity of the island’s vines and the potential evolution of singularity. Two hundred and twenty-three samples were genotyped with 20 SSR (Simple Sequence Repeats). The following results were obtained from these analyses: 8 new varieties (Blanca de la granja del cabildo (W), Burra chinija (W), Diego chinija (W), Lemes del Cabezo (W), Malvasia alistanada fina (W), Malvasia alistanada rustica (W) (a mutation of Malvasia alistanada fina), Sinforiano chano (Rs), Uvillón negro (R), Vijariego blanco de la granja (W)), and 2 new sports (Chasselas lajiares (Rs) and Diego de El Raso rosado (Rs)). In addition, scientific studies on varieties from the island of Lanzarote describe four local cultivars: Breval negro (Rg), Malvasia volcanica (W), Torrontes volcanico (W) and Uva de año (R), which means that a total of 12 local varieties and 2 colour mutations have been described for this Atlantic island. It should also be noted that the appearance of 100 new molecular profiles with their corresponding names represents an unprecedented lexical enrichment. Lanzarote can be considered a centre of biodiversity, as is the Canary archipelago as a whole. Their vines have evolved to such an extent that they are now genetically different from the original populations. The vines from Lanzarote could be of great interest to the wine sector, as they can act as a nursery from which better-adapted vines can be obtained to mitigate the effects of climate change.

Efficient Assessment and Large-Scale Conservation of Intra-Varietal Diversity of Ancient Grapevine Varieties: Case Study Portugal.

There are thousands of ancient grapevine varieties in Europe, each one having a high level of intra-varietal diversity with regard to important economic traits (yield, soluble solids content, acidity, anthocyanins, and others). However, this potential has become exposed to a process of genetic erosion since the middle of the last century. The main objective of this work is to present experimental strategies for conservation and utilization of intra-varietal diversity. A concrete example is given about the actions performed in Portugal since 1978. Two main approaches for the conservation of intra-varietal diversity were performed: (1) strict conservation (in pots and in the field without experimental design) for future generations; and (2) conservation and, simultaneously, evaluation of the intra-varietal variability for selection to fulfil the immediate needs of the grape and wine sector (in the field with experimental design). More than 30,000 accessions of Portuguese autochthonous varieties are conserved. Using the theory of mixed models, intra-varietal diversity of the yield was found for the 59 varieties studied. The conservation and the evaluation of the intra-varietal diversity for quantitative traits will allow to extract high economic value, as well as to ensure its utilization to meet the objectives of the vine and wine sector.

Yam (Dioscorea rotundata Poir.) Displays Prezygotic and Postzygotic Barriers to Prevent Autogamy in Monoecious Cultivars

Cultivated yam (D. rotundata) is a staple tuber crop in West Africa whose sexual reproduction control remains largely unknown despite its importance for plant breeding programs. In this paper, we compared self-pollination, intracultivar cross-pollination and intercultivar cross-pollination in three monoecious cultivars (Amoula, Heapala and Yassi). Results showed that pollen viability (49%) and stigma receptivity (40%) were similar in monoecious and dioecious plants, suggesting that autogamy could occur in monoecious plants. However, fruit and seed sets were significantly lower after self-pollination compared to cross-pollination. Overall, autogamy reached 11% and pollen lability was almost zero (<1%). The low percentage of pollen grains germinating on the stigma (37%) and pollen tubes reaching the ovules (25%) after self-pollination partly explained the low seed set. Strong inbreeding depression was observed after self-pollination and almost all fruits and about 75% of the seeds resulting from self-pollination showed malformations. Seed germination was also 20 times lower after self-pollination compared to cross-pollination. Sexual reproduction remained low in D. rotundata even after cross-pollination as fruit and seed set did not exceed 18% and 13% respectively. Moreover, comparison between intracultivar cross-pollination and self-pollination revealed intravarietal genetic diversity inside the analyzed yam cultivars. Overall, our results showed that D. rotundata has a very low tolerance to autogamy in monoecious cultivars and has developed pre- and postzygotic mechanisms to limit selfing.

DNA-Based Technologies for Grapevine Biodiversity Exploitation: State of the Art and Future Perspectives

The cultivated grapevine, Vitis vinifera subsp. vinifera L., is represented by an enormous population of varieties and clones. They arise from the accumulation of gametic and somatic mutations during centuries of sexual and asexual propagation. These varieties represent a vast reservoir of traits/alleles that could be useful in improving the berry quality as well as against environmental stresses. However, most of them are still unexploited. For this reason, an efficient characterization system is essential to define the varietal identity, avoid cases of synonymy (identical genotypes but different names) and homonymy (same names but different genotypes) and deepen our understanding of the existing diversity within the grape germplasm. The plethora of DNA-based high-throughput technologies currently available provides promising tools for the analysis of diversity, overcoming many of the limitations of phenotypic-based diversity analyses. However, the analysis of intra-varietal diversity remains challenging. In this scenario, after summarizing the causes and consequences of grapevine genetic inter- and intra-varietal diversity, we review the DNA-based technologies used for varietal genotyping, emphasizing those able to distinguish clones within a variety. This review provides an update on the technologies used to explore grapevine diversity, the knowledge of which is necessary for an efficient exploitation and conservation of the grapevine germplasm.

Potential Phenotyping Methodologies to Assess Inter- and Intravarietal Variability and to Select Grapevine Genotypes Tolerant to Abiotic Stress.

Plant phenotyping is an emerging science that combines multiple methodologies and protocols to measure plant traits (e.g., growth, morphology, architecture, function, and composition) at multiple scales of organization. Manual phenotyping remains as a major bottleneck to the advance of plant and crop breeding. Such constraint fostered the development of high throughput plant phenotyping (HTPP), which is largely based on imaging approaches and automatized data retrieval and processing. Field phenotyping still poses major challenges and the progress of HTPP for field conditions can be relevant to support selection and breeding of grapevine. The aim of this review is to discuss potential and current methods to improve field phenotyping of grapevine to support characterization of inter- and intravarietal diversity. Vitis vinifera has a large genetic diversity that needs characterization, and the availability of methods to support selection of plant material (polyclonal or clonal) able to withstand abiotic stress is paramount. Besides being time consuming, complex and expensive, field experiments are also affected by heterogeneous and uncontrolled climate and soil conditions, mostly due to the large areas of the trials and to the high number of traits to be observed in a number of individuals ranging from hundreds to thousands. Therefore, adequate field experimental design and data gathering methodologies are crucial to obtain reliable data. Some of the major challenges posed to grapevine selection programs for tolerance to water and heat stress are described herein. Useful traits for selection and related field phenotyping methodologies are described and their adequacy for large scale screening is discussed.

Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety.

Olea europaea ‘Galega vulgar’ variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. ‘Galega vulgar’ is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of ‘Galega vulgar’, 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the ‘Galega vulgar’ intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the ‘Galega vulgar’, with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of ‘Galega vulgar’. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of ‘Galega vulgar’).

Impact of 2100-Projected Air Temperature, Carbon Dioxide, and Water Scarcity on Grape Primary and Secondary Metabolites of Different Vitis vinifera cv. Tempranillo Clones.

The exploration of the grapevine (Vitis vinifera L.) intra-varietal diversity can be an interesting approach for the adaptation of viticulture to climate change. We evaluated the response of four Tempranillo clones to simulated year-2100-expected air temperature, CO2, and relative humidity (RH) conditions: climate change (CC; 28 °C/18 °C, 700 μmol mol-1 CO2, and 35%/53% RH) vs current situation conditions (CS; 24 °C/14 °C, 400 μmol mol-1 CO2, and 45%/63% RH), under two irrigation regimes, "well-watered" (WW) vs "water deficit" (WD). The treatments were applied to fruit-bearing cuttings grown under research-oriented greenhouse controlled conditions. CC increased sugar accumulation and hastened grape phenology, an effect that was mitigated by water deficit. Both CC and water deficit modified amino acid concentrations and accumulation profiles with different intensities, depending on the clone. Combined CC and water deficit decreased anthocyanins and the anthocyanin to total soluble solids (TSS) ratio. The results suggest differences in the response of the clones to the 2100-projected conditions, which are not always solely explained by differences observed in the ripening dynamics. Among the clones studied, RJ43 and CL306 were the most affected by CC/WD conditions; meanwhile, 1084 was globally less affected than the other clones.

High Temperature and Elevated Carbon Dioxide Modify Berry Composition of Different Clones of Grapevine (Vitis vinifera L.) cv. Tempranillo.

Tempranillo is a grapevine (Vitis vinifera L.) variety extensively used for world wine production which is expected to be affected by environmental parameters modified by ongoing global climate changes, i.e., increases in average air temperature and rise of atmospheric CO2 levels. Apart from determining their effects on grape development and biochemical characteristics, this paper considers the intravarietal diversity of the cultivar Tempranillo as a tool to develop future adaptive strategies to face the impact of climate change on grapevine. Fruit-bearing cuttings of five clones (RJ43, CL306, T3, VN31, and 1084) were grown in temperature gradient greenhouses (TGGs), from fruit set to maturity, under two temperature regimes (ambient temperature vs. ambient temperature plus 4°C) and two CO2 levels (ambient, ca. 400 ppm, vs. elevated, 700 ppm). Treatments were applied separately or in combination. The analyses carried out included berry phenological development, the evolution in the concentration of must compounds (organic acids, sugars, and amino acids), and total skin anthocyanins. Elevated temperature hastened berry ripening, sugar accumulation, and malic acid breakdown, especially when combined with high CO2. Climate change conditions reduced the amino acid content 2 weeks after mid-veraison and seemed to delay amino acidic maturity. Elevated CO2 reduced the decoupling effect of temperature on the anthocyanin to sugar ratio. The impact of these factors, taken individually or combined, was dependent on the clone analyzed, thus indicating certain intravarietal variability in the response of Tempranillo to these climate change-related factors.

Growth performance and carbon partitioning of grapevine Tempranillo clones under simulated climate change scenarios: Elevated CO2 and temperature

Atmospheric CO2 levels and global temperatures are expected to rise in the next decades, and viticulture must face these changes. Within this context, exploiting the intra-varietal diversity of grapevine (Vitis vinifera L.) can be a useful tool for the adaptation of this crop to climate change. The aim of the present work was to study the effect of elevated temperature and elevated levels of atmospheric CO2, both individually and combined, on the growth, phenology and carbon partitioning of five clones of the cultivar Tempranillo (RJ43, CL306, T3, VN31 and 1084). The hypothesis that clones within the same variety that differ in their phenological development may respond in a different manner to the above mentioned environmental factors from a physiological point of view was tested. Grapevine fruit-bearing cuttings were grown from fruit set to maturity under two temperature regimes: ambient (T) vs elevated (ambient + 4°C, T + 4), combined with two CO2 levels: ambient (ca. 400 ppm, ACO2) vs elevated (700 ppm, ECO2), in temperature-gradient greenhouses (TGGs). Considering all the clones, elevated temperature hastened grape development and increased vegetative growth, but reduced grape production, the later most likely associated with the heat waves recorded during the experiment. Plants in the elevated CO2 treatments showed a higher photosynthetic activity at veraison and an increased vegetative growth, but they showed signs of photosynthetic acclimation to ECO2 at maturity according to the C:N ratio, especially when combined with high temperature. The combination of ECO2 and T + 4, mimicking climate change environmental conditions, showed additive effects in some of the parameters analyzed. The clones showed differences in their phenological development, which conditioned some responses to elevated CO2 and temperature in terms of vegetative production and C partitioning into different organs. The work adds new knowledge on the use of different grapevine clones, that can be useful to improve the viticultural efficiency in future climate change scenarios.

Embedding Cultivated Diversity in Society for Agro-Ecological Transition

Agroecology calls for a global approach, integrating scientific, practical, and advocacy dimensions, to redesign agricultural systems based on ecological and socio-cultural processes and emphasizing biodiversity. This review is grounded on the results of DIVERSIFOOD, a European H2020 multi-actor research project, and explores the concept of cultivated diversity using various dimensions relevant to foster sustainable organic food systems and agro-ecological transition. From the evaluation of underutilized genetic resources and forgotten crops, DIVERSIFOOD has proposed plant breeding strategies, on-farm experimentation, and statistical tools to create new populations, landraces, and organic cultivars with intra-varietal diversity. The added value of Community Seed Banks and forms of collective seed management in Europe have been described in terms of goals and activities, and their value for improving seed regulations, treaties, and genetic resources management is discussed. In the context of the current agro-food system characterized by standardization, DIVERSIFOOD raised awareness of qualities of ‘biodiverse food systems’ in which all actors have a role to play. It highlighted the critical capacity to preserve a diversity of cultural values embodied in ‘biodiverse products’, thereby involving consumers in collective strategies for reviving diversity, and empowering all actors of organic food systems to really and efficiently implement research within their farms and networks.

Assessment of quality parameters and phytochemical content of thirty ‘Tempranillo’ grape clones for varietal improvement in two distinct sub-regions of Douro

Genetic improvement in grapevine (Vitis vinifera L.) is performed mainly through clonal selection processes. This procedure takes advantage of the intra-varietal genetic variability existing in ancient varieties. It focuses on the selection of the most promising genotypes for certain quantitative characteristics, such as yield, soluble solids content, acidity, anthocyanins, tannins, among others, always preserving the intra-varietal diversity. In the present work, we evaluated the performance of 30 clones of 'Tempranillo' grape in two distinct trial sites at the Douro Demarcated Region (DDR), Cavernelho and São Luiz, during two consecutive years, measuring phytochemical content and oenological potential parameters.Significant differences between clones related to phytochemical content and antiradical activity, were observed in the Cavernelho and São Luiz fields, besides some oenological parameters in São Luiz. Among years, significant differences for clones, in total phenols and antiradical activity by the DPPH method were observed in both fields. In São Luiz, such differences were also found for the contents in anthocyanins, flavonoids and ortho-diphenols. Concerning the differences between samples from the same clone in the two fields, the greatest number of significant differences was observed for the anthocyanins content in 2016.A set of ten 'Tempranillo' grape clones displayed behavioral stability associated with appropriate values of soluble solids, titratable acidity and phytochemical content.

Unravelling the hidden inter and intra-varietal diversity of durum wheat commercial varieties used in Portugal

AbstractAssessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological traits and repetitive sequences. As expected, reduced variability was observed regarding low molecular weight glutenin subunits (LMW-GS) but a specific LMW-GS allelic form associated with improved pasta-making characteristics was absent in one variety. Contrastingly, molecular markers targeting repetitive elements like microsatellites and retrotransposons – Inter Simple Sequence Repeat (ISSR) and Inter Retrotransposons Amplified Polymorphism (IRAP) – disclosed significant inter and intra-varietal diversity. This high level of polymorphism was revealed by the 20 distinct ISSR/IRAP concatenated profiles observed among the 23 individuals analysed. Interestingly, median joining networks and PCoA analysis grouped individuals of the same variety and clustered varieties accordingly with geographical origin. Globally, this work demonstrates that durum wheat breeding strategies induced selection pressure for some relevant coding sequences while maintaining high levels of genomic variability in non-coding regions enriched in repetitive sequences.