Cultivated Landraces Research Articles

Assembly and comparative analysis of the mitochondrial genome in diploid potatoes.

We report the mitochondrial genome of 39 diploid potatoes and identify a candidate ORF potentially linked to cytoplasmic male sterility in potatoes. Potato (Solanum tuberosum L.) holds a critical position as the foremost non-grain food crop, playing a pivotal role in ensuring global food security. Diploid potatoes constitute a vital genetic resource pool, harboring the potential to revolutionize modern potato breeding. Nevertheless, diploid potatoes are relatively understudied, and mitochondrial DNA can provide valuable insights into key potato breeding traits such as CMS. In this study, we examine and assemble the mitochondrial genome evolution and diversity of 39 accessions of diploid potatoes using high-fidelity (HiFi) sequencing. We annotated 54 genes for all the investigated accessions, comprising 34 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. Our analyses revealed differences in repeats sequences between wild and cultivated landraces. To understand the evolution of diploid maternal lineage inheritance, we conducted phylogenetic analysis, which clearly distinguished mitochondrial from nuclear gene trees, further supporting the evidence-based of clustering between wild and cultivated landraces accessions. Our study discovers new candidate ORFs associated with CMS in potatoes, including ORF137, which is homologous to other CMS in Solanaceae. Ultimately, this work bridges the gap in mitochondrial genome research for diploid potatoes, providing a steppingstone into evolutionary studies and potato breeding.

Maize pollen carry bacteria that suppress a fungal pathogen that enters through the male gamete fertilization route.

In flowering plants, after being released from pollen grains, the male gametes use the style channel to migrate towards the ovary where they fertilize awaiting eggs. Environmental pathogens exploit the style passage, resulting in diseased progeny seed. The belief is that pollen also transmits pathogens into the style. By contrast, we hypothesized that pollen carries beneficial microbes that suppress environmental pathogens on the style passage. No prior studies have reported pollen-associated bacterial functions in any plant species. Here, bacteria were cultured from maize (corn) pollen encompassing wild ancestors and farmer-selected landraces from across the Americas, grown in a common field in Canada for one season. In total, 298 bacterial isolates were cultured, spanning 45 genera, 103 species, and 88 OTUs, dominated by Pantoea, Bacillus, Pseudomonas, Erwinia, and Microbacterium. Full-length 16S DNA-based taxonomic profiling showed that 78% of bacterial taxa from the major wild ancestor of maize (Parviglumis teosinte) were present in at least one cultivated landrace. The species names of the bacterial isolates were used to search the pathogen literature systematically; this preliminary evidence predicted that the vast majority of the pollen-associated bacteria analyzed are not maize pathogens. The pollen-associated bacteria were tested in vitro against a style-invading Fusarium pathogen shown to cause Gibberella ear rot (GER): 14 isolates inhibited this pathogen. Genome mining showed that all the anti-Fusarium bacterial species encode phzF, associated with biosynthesis of the natural fungicide, phenazine. To mimic the male gamete migration route, three pollen-associated bacterial strains were sprayed onto styles (silks), followed by Fusarium inoculation; these bacteria reduced GER symptoms and mycotoxin accumulation in progeny seed. Confocal microscopy was used to search for direct evidence that pollen-associated bacteria can defend living silks against Fusarium graminearum (Fg); bacterial strain AS541 (Kluyvera intermedia), isolated from pollen of ancestral Parviglumis, was observed to colonize the susceptible style/silk entry points of Fg (silk epidermis, trichomes, wounds). Furthermore, on style/silk tissue, AS541 colonized/aggregated on Fg hyphae, and was associated with Fg hyphal breaks. These results suggest that pollen has the potential to carry bacteria that can defend the style/silk passage against an environmental pathogen - a novel observation.

SSR-marker assisted evaluation of genetic diversity in local and exotic pigeonpea cultivars in Benin for parental genotypes selection

Pigeonpea production is limited in Benin due to the undesirable agronomic and organoleptic characteristics of cultivated landraces. For a breeding program, some exotic cultivars were introduced for improving the available genepool in the country. The present study aims to assess the genetic diversity within a collection comprising of 32 local and 28 exotic cultivars, with the objective of selecting suitable parental lines for pigeonpea genetic improvement. All of the 60 accessions were genotyped with 14 SSR makers and a total of 38 alleles were detected with an average of 2.71 alleles per locus. The mean value of PIC (Polymorphism Information Content) and overall gene diversity were 0.37 and 0.43, respectively, while the mean value of heterozygosity was 0.11, indicating moderate genetic diversity within the 60 accessions with a deficit of heterozygous genotypes. As expected, the diversity was higher in exotic cultivars than in local landraces. Based on the genetic relationship among accessions, the entire collection formed 3 clusters, one of which comprised four specific exotic accessions. Population structure analysis using model-based and DAPC (Discriminant Analysis for Principal Components) methods subdivided the 60 accessions into two major groups reflecting their geographic origins with a minimal number (02) of admixtures. This indicates significant genetic divergence between local and exotic cultivars. Analysis of Molecular Variance (AMOVA) results with an overall Fst value of 0.13 confirmed the significant genetic divergence between the two collections. The findings of this study will significantly benefit for pigeonpea breeding programs in Benin. For practical applications, selected exotic cultivars, particularly those within the specific cluster can immediately serve as donor parents in crossbreeding schemes with the local landraces, for developing new varieties.

Genome evolution and diversity of wild and cultivated potatoes

Potato (Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1–4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.

Analysis of consumer-oriented quality characteristics of raw and boiled plantains in Cameroon: implication for breeding.

This study aimed at understanding users' demand for raw and boiled plantains in rural and urban areas in West and Littoral regions of Cameroon. Surveys conducted in eight rural localities consisted of key informant interviews, gender-disaggregated focus group discussions, market and individual interviews. Processing and cooking diagnoses were done with restaurant cooks in urban areas, to know the details of plantain processing and boiling and to understand the quality characteristics of raw plantain that give a most-liked boiled plantain. Local favourite landraces, most cultivated landraces in Cameroon (Batard and Big ebanga) and a new CARBAP/CIRAD hybrid (CARBAP K74) were used. The preference for plantain cultivars was both gender and region-dependent. High-quality plantain should be mature, with big fingers and having a dark green peel colour. The fruit length and girth, pulp pH, dry matter content and firmness were found to be relevant postharvest quality characteristics for plantain breeding improvement.

Genetic structure and diversity of Iranian Cannabis populations based on phytochemical, agro-morphological and molecular markers

Hemp (Cannabis sativa) is an herbaceous, annual, and dioecious plant belongs to the Cannabaceae family and grows in some parts of Iran. In the present study, the genetic diversity between and within the populations of 10 local cultivated landraces from Iran was evaluated, using multiple datasets (agro-morphological and biochemical traits, seed oil fatty acid compositions, and ISSR (Inter simple sequence repeats) markers. The analysis of variance based on the morpho-biochemical traits and oil compositions indicated significant differences among studied hemp populations (P < 0.01). Of the identified fatty acids, linoleic acid (53.02 %), α-linolenic acid (18.98 %), oleic acid (15.20 %), palmitic acid (6.61 %), and stearic acid (2.96 %) composed 77.79 % of total seed oil content. The content of major fatty acids varied greatly among the populations. Kermanshah had the highest proportion of linoleic acid (54.03 %), Hamedan; α-linolenic acid (21.47 %), Alborz; oleic acid (16.75 %), Kohkylouih-and-Boyerahmad; palmitic acid (6.82 %), and Khuzestan; stearic acid (3.23 %). In this study, 14 ISSR primers, produced 231 high-resolution bands, of which 198 (85 %) were polymorphic. Population structure inference showed that the hemp single plants in populations were distributed into six genetic clusters that were matched with UPGMA clusters. The results showed that the highest genetic distance was observed between Kerman and Markazi populations. The findings of this study can be used in future programs for the breeding of Iranian hemp landraces.

Sorghum Landraces Production Practices in Nyanza, Coast and Eastern Regions, Kenya

Sorghum Sorghum bicolar L. is an important cereal crop grown in the semi-arid areas. It is rank as the fifth key cereal crop worldwide. The ability of sorghum to adapt to drought, salinity, infertile soils, and high temperatures makes it a critical crop in the dry regions. However, farmers grow many landraces some of which do not perform well since the majority cannot afford nitrogenous fertilizers to boost their harvest. Therefore, a baseline survey was conducted in Eastern, Nyanza and Coastal regions to assess the production systems for sorghum. Structured questionnaires were used to gather information from a total of 76 randomly selected farmers in the study regions. Data on socio-economic characteristics, sorghum varieties, use of farm inputs, and source of seeds, farming systems, traits preference, farm sizes, yields and constraints in production of the crop was collected. Parameters studied were analyzed using Statistical Programmes for Social Sciences (SPSS) (IBM SPSS Statistics 20). Results showed that majority of respondents in Eastern (99%), 80% in Nyanza and all respondents in the coastal region cultivated landraces. Most of the respondents had farm sizes between 0.5-5acres. A larger proportion of respondents in the three regions reported low harvests from their farms, recording below 5 bags every season. Most of the farmers across the three regions intercrop sorghum with other crops with all respondents in Eastern, 80% in Coast and 68% in Nyanza. Some farmers plant sorghum without fertilizers, others used either inorganic or organic fertilizers while the rest use both organic and inorganic. The traits desired by farmers in the region included high yields, early maturity, resistance to pest and diseases, sweetness and tolerance to drought. Farmers cited pests and diseases, weeds such as striga, and drought as the key constraints to sorghum production in the regions. Key words : drought, landraces, sorghum, tolerance, traits DOI : 10.7176/JESD/10-10-16 Publication date :May 31 st 2019

Genetic Diversity in broccoli rabe (Brassica rapa L. subsp. sylvestris (L.) Janch.) from Southern Italy

Broccoli rabe (Brassica rapa L. subsp. sylvestris (L.) Janch.) is a vegetable crop cultivated in southern Italy where it is part of local traditional recipes and heritage. Despite its economic importance, there are no cultivars patented, giving rise to many cultivated landraces that are characterized by wide phenotypic variability and named according to their harvesting time or the size and shape of their primary inflorescence. We report the first study of genetic diversity of 67 landraces of broccoli rabe collected in Apulia region and genotyped by means of 18 very informative SSR markers. A total of 243 alleles were detected in 552 genotypes, with a mean of 13.5 alleles per locus. The molecular variance was partitioned for 64% within accessions and for 36% among accessions, revealing a high level of genetic variation within landraces and a significant genetic differentiation across themselves. Remarkably, the results of genetic structure inference, as well as principal coordinates analysis and hierarchical clustering indicated as the clustering was largely in accordance to the germplasm origin, highlighting the presence of geographic stratification. We established a comprehensive germplasm collection of Apulian broccoli rabe landraces, currently stored at the Genebanks of IBBR-CNR and University of Bari. Finally, our study lays a foundation for future bio-agronomic characterizations addressing the identification of superior accessions for breeding purposes and solving cases of homonymy and synonymy.

Gene flow signature in the S-allele region of cultivated buckwheat

BackgroundBuckwheat (Fagopyrum esculentum Moench.) is an annual crop that originated in southern China. The nutritious seeds are used in cooking much like cereal grains. Buckwheat is an outcrossing species with heteromorphic self-incompatibility due to its dimorphic (i.e., short- and long-styled) flowers and intra-morph infertility. The floral morphology and intra-morph incompatibility are both determined by a single S locus. Plants with short-styled flowers are heterozygous (S/s) and plants with long-styled flowers are homozygous recessive (s/s) at this locus, and the S/S genotype is not found. Recently, we built a draft genome assembly of buckwheat and identified the 5.4-Mb-long S-allele region harbored by short-styled plants.In this study, the first report on the genome-wide diversity of buckwheat, we used a genotyping-by-sequencing (GBS) dataset to evaluate the genome-wide nucleotide diversity within cultivated buckwheat landraces worldwide. We also investigated the utility of the S-allele region for phylogenetic analysis of buckwheat.ResultsBuckwheat showed high nucleotide diversity (0.0065), comparable to that of other outcrossing plants, based on a genome-wide simple nucleotide polymorphism (SNP) analysis. Phylogenetic analyses based on genome-wide SNPs showed that cultivated buckwheat comprises two groups, Asian and European, and revealed lower nucleotide diversity in the European group (0.0055) and low differentiation between the Asian and European groups.The nucleotide diversity (0.0039) estimated from SNPs in the S-allele region is lower than that in genome-wide SNPs. Phylogenetic analysis based on this region detected three diverged groups, S-1, S-2, and S-3.ConclusionThe SNPs detected using the GBS dataset were effective for elucidating the evolutionary history of buckwheat, and led to the following conclusions: (1) the low nucleotide diversity of the entire genome in the European group and low differentiation between the Asian and European groups suggested genetic bottlenecks associated with dispersion from Asia to Europe, and/or recent intensified cultivation and selection in Europe; and (2) the high diversification in the S-allele region was indicative of gene flows from wild to cultivated buckwheat, suggesting that cultivated buckwheat may have multiple origins.

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene.

Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia.

Agricultural weeds serve as productive models for studying the genetic basis of rapid adaptation, with weed‐adaptive traits potentially evolving multiple times independently in geographically distinct but environmentally similar agroecosystems. Weedy relatives of domesticated crops can be especially interesting systems because of the potential for weed‐adaptive alleles to originate through multiple mechanisms, including introgression from cultivated and/or wild relatives, standing genetic variation, and de novo mutations. Weedy rice populations have evolved multiple times through dedomestication from cultivated rice. Much of the genomic work to date in weedy rice has focused on populations that exist outside the range of the wild crop progenitor. In this study, we use genome‐wide SNPs generated through genotyping‐by‐sequencing to compare the evolution of weedy rice in regions outside the range of wild rice (North America, South Korea) and populations in Southeast Asia, where wild rice populations are present. We find evidence for adaptive introgression of wild rice alleles into weedy rice populations in Southeast Asia, with the relative contributions of wild and cultivated rice alleles varying across the genome. In addition, gene regions underlying several weed‐adaptive traits are dominated by genomic contributions from wild rice. Genome‐wide nucleotide diversity is also much higher in Southeast Asian weeds than in North American and South Korean weeds. Besides reflecting introgression from wild rice, this difference in diversity likely reflects genetic contributions from diverse cultivated landraces that may have served as the progenitors of these weedy populations. These important differences in weedy rice evolution in regions with and without wild rice could inform region‐specific management strategies for weed control.

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal.

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early- and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping.

Enhancing Integrated Pest Management in GM Cotton Systems Using Host Plant Resistance.

Cotton has lost many ancestral defensive traits against key invertebrate pests. This is suggested by the levels of resistance to some pests found in wild cotton genotypes as well as in cultivated landraces and is a result of domestication and a long history of targeted breeding for yield and fiber quality, along with the capacity to control pests with pesticides. Genetic modification (GM) allowed integration of toxins from a bacteria into cotton to control key Lepidopteran pests. Since the mid-1990s, use of GM cotton cultivars has greatly reduced the amount of pesticides used in many cotton systems. However, pests not controlled by the GM traits have usually emerged as problems, especially the sucking bug complex. Control of this complex with pesticides often causes a reduction in beneficial invertebrate populations, allowing other secondary pests to increase rapidly and require control. Control of both sucking bug complex and secondary pests is problematic due to the cost of pesticides and/or high risk of selecting for pesticide resistance. Deployment of host plant resistance (HPR) provides an opportunity to manage these issues in GM cotton systems. Cotton cultivars resistant to the sucking bug complex and/or secondary pests would require fewer pesticide applications, reducing costs and risks to beneficial invertebrate populations and pesticide resistance. Incorporation of HPR traits into elite cotton cultivars with high yield and fiber quality offers the potential to further reduce pesticide use and increase the durability of pest management in GM cotton systems. We review the challenges that the identification and use of HPR against invertebrate pests brings to cotton breeding. We explore sources of resistance to the sucking bug complex and secondary pests, the mechanisms that control them and the approaches to incorporate these defense traits to commercial cultivars.

SSR genetic diversity assessment of popular pigeonpea varieties in Malawi reveals unique fingerprints

Background: Pigeonpea ( Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family and the only cultivated species in the genus Cajanus . It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, it is grown as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant quality reduction and yield losses. In this study, 48 polymorphic SSR markers were used to assess the diversity amongst all pigeonpea varieties cultivated in Malawi to determine if a genetic fingerprint could be identified to distinguish the popular varieties. Results: A total of 212 alleles were observed with an average of 5.58 alleles per marker and a maximum of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC), ranged from 0.03 to 0.89 with an average of 0.30. A neighbor-joining tree produced 4 clusters. The most commonly cultivated varieties, which include released varieties and cultivated land races, were well-spread across all the clusters observed, indicating that they generally represented the genetic diversity available in Malawi, although substantial variation was evident that can still be exploited through further breeding. Conclusion: Screening of the allelic data associated with the five most popular cultivated varieties, revealed 6 markers - CCB1, CCB7, Ccac035, CCttc003, Ccac026 and CCttc019 - which displayed unique allelic profiles for each of the five varieties. This genetic fingerprint can potentially be applied for seed certification to confirm the genetic purity of seeds that are delivered to Malawi farmers.

Morphological diversity of local land races and wild forms of mungbean

A set of genotypes comprising 81 local land races, four wild forms and four improved varieties of mungbean were grouped into 15 genetic clusters. The genotypes revealed wide variation in stable morphological characters as well as agronomic traits which provided the necessary base for genetic divergence. The wild forms TCR 192, TCR 213 and TCR 243 were viny with late maturity and had distinctly different leaflet, inflorescence and pod characteristics. Whereas, a wild accession TCR 20 was erect with sturdy stem, vigorous growth, broad ovate leaflets, long pods, profuse poding with high yield potential and resistance to biotic (bruchids, CLS, PM and YMV) and abiotic(drought) stresses. Clustering pattern confirmed more proximity of TCR 20 with cultivated forms and therefore, it may be amenable for hybridization with cultivated land races and improved varieties for transfer of its desirable traits. Balarampur Keonjhar local was quite distinct from other land races owing to its vigorous growth, broad leaves and long pods with very bold seeds, but worst affected by YMV. In contrast, TARM 1 had high field resistance to diseases including YMV. Nipania munga -an elite land race of Kalahandi district of Odisha was highly drought tolerant with dwarf plant type and good initial vigour. These above genotypes being morphologically unique and having unique desirable agro-economic traits, formed small divergent clusters and hence, may serve as valuable material for genetic improvement in mungbean through hybridization.

Molecular analysis and validation of primitive races peach palm (Bactris gasipaes) by means of markers RAPD

Molecular markers were used to examine the genetic variability of eight landraces of peach palm (Bactris gasipaes var. gasipaes) and two wild populations (Bactris gasipaes var. chichagui), their relationships and genetic structures. Two hundred plants of these 8 races were used and 18 plants of the two wild populations, one from the Magdalena River, Colombia, and the other from the Xingu River, Para, Brazil. Eight primers were used to generate RAPD markers, of which 124 markers with 101 polymmorphic. The observed heterozygosity was 0.38, with 93% polymorphism, both slightly greater than in earlier studies. The gene flow medium was 1.12 among the races of peach palm, which is explained by the distance between most breeds analyzed. These values are significantly larger than those of [1], because it is a less accurate marker for this type of analysis. The Amazonian landraces had greater heterozygosity and % polymorphism than the Central American race. The structure of the dendrogram with the four previously studied landraces, essentially validating it and confirming two landrace groups - one Occidental and one Oriental. When the Jurua landrace was added to the analysis, it joined the other Occidental races, as expected by its geographic position. When the other landraces were added to the analysis, a consistency and some problems were observed. The consistency was that all the landraces joined the Occidental group, expected by their geographic positions. The problems were the grouping of the Vaupes landrace with the Jurua landrace, which are geographically distant and have different fruit sizes and shapes. The relationship between the Cauca landrace and the Inirida landrace was also problematic, since they are geographically separated. The two wild populations joined the landraces at a great distance, suggesting that they did not participate in the domestication of the cultivated landraces and indirectly reenforcing the hypothesis of a single origin in southwestern Amazonia.

SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato

BackgroundThe tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.ResultsWith the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.ConclusionsOur work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.

The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis.

BackgroundThe genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus.Results3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum.ConclusionsThese data provide a clear picture of the major distinct gene pools into which the genus Pisum is partitioned and their geographical distribution. The data strongly support the model of independent domestications for P. sativum ssp abyssinicum and P. sativum. The relationships between these two cultivated germplasms and the various sub-divisions of wild Pisum have been clarified and the most likely ancestral wild gene pools for domesticated P. sativum identified. Lastly, this study provides a framework for defining global Pisum germplasm which will be useful for designing core collections.

BAMLINK - A CROSS DISCIPLINARY PROGRAMME TO ENHANCE THE ROLE OF BAMBARA GROUNDNUT (VIGNA SUBTERRANEA L. VERDC.) FOR FOOD SECURITY IN AFRICA AND INDIA

The successful development of any underutilized crop requires a multidisciplinary approach. BAMLINK, the third EU-funded project on bambara groundnut (Vigna subterranea L. Verdc.), spans research from molecular genetics through field evaluation to product development incorporating end-user needs. Partners include four African, three Indian, and three European institutions that are evaluating the crop for both drought-prone African environments, where it is currently cultivated, and for potential new production environments in India. Underpinning this effort is a genetic analysis of the species. This is not only for specific agronomic traits but also in terms of domestication history and to establish the existing genetic structure available within cultivated and wild material that could be used for breeding. We present data on the underlying genetic structure of bambara groundnut and initial results from Diversity Arrays Technique (DArT) and Massively Parallel Signature Sequencing (MPSS) to investigate changes in gene expression under drought. We also describe microsatellite development, genetic mapping, and QTL analysis in a cross derived from a cultivated landrace and a wild relative. Underpinning all BAMLINK research is an analysis of domesticated bambara groundnut landraces from contrasting environments. The subsequent need to evaluate and accommodate the genetic variability which exists between genotypes of the same landrace in any phenotypic evaluation of that landrace is discussed. Genetic research is presented within an approach that integrates physiology, agronomy, nutrition, modelling, and end-user preferences to identify and overcome bottle-necks to further exploitation of this crop so that the full food security potential of bambara groundnut, especially for water-scarce environments, can be evaluated.

The Canon of Potato Science: 1. Genetic Diversity and Genebanks

Genebanks manage germplasm—raw materials for breeding and research. The purview of genetic diversity and genebanks with respect to the potato crop is the wild and cultivated tuber-bearing members of genus Solanum, perhaps also some very closely related non-tuber-bearing taxa. Potato is extraordinary in its breadth of related wild species (typically populations maintained as botanical seed), that are relatively amenable to use in cultivar breeding. There is also a great diversity of primitive cultivated landraces (maintained clonally as tubers or in vitro), and, of course, thousands of named clonal cultivars, breeding and genetic stocks from nearly 200 years of modern breeding. Capturing all diversity ex situ is beyond available physical and financial resources, so the challenge of genebank managers is to find the most efficient means to maximize their service with respect to the five genebank functions: