Genetic structure and history of Swiss maize (<Emphasis Type="Italic">Zea mays</Emphasis> L. ssp. <Emphasis Type="Italic">mays</Emphasis>) landraces

Between 1930 and 2003 with emphasis on the 1940s maize landraces (Zea mays L. ssp. mays) from all over Switzerland were collected for maintenance and further use in a new Swiss breeding program. The genetic relationship and diversity among these accessions stored in the Swiss gene bank is largely unknown. Our hypothesis was that due to the unique geographic, climatic, and cultural diversity in Switzerland a diverse population of maize landraces had developed over the past three centuries. The aims were to characterize the genetic diversity of the Swiss landraces and their genetic relationship with accessions from neighbouring regions as well as reviewing their history, collection, and maintenance. The characterization and grouping was based on analyses with ten microsatellite markers. Geographic, cultural, and climatic conditions explained a division in two distinct groups of accessions. One group consisted of landraces collected in the southern parts of Switzerland. This group was related to the Italian Orange Flints. The other group contained accessions from northern Switzerland which were related to Northern European Flints in particular German Flints. Historic evidence was found for a frequent exchange of landraces within the country resulting in a lack of region-specific or landrace-specific genetic groups. The relatively large separation between the accessions, indicated by high F _ST (0.42), might be explained partly by a bottleneck during the collection and maintenance phase as well as by geographical and cultural separation of north and south of the country. Due to the high genetic diversity, the accessions here are a potential resource for broadening the European flint pool.     

Genetic diversity among Polish landraces of common oat (Avena sativa L.)

All over the world about 220,000 accessions of the genus Avena is preserved in gene banks. Polish oats collection, in the National Centre for Plant Genetic Resources, consists of about 2,500 accessions. More than 80 % of them belong to the species Avena sativa. Only 136 accessions have the landrace or traditional cultivar status and 91 of them were collected in Poland. The main objective of this study was to estimate genetic diversity of a set of 67 Polish landraces using inter simple sequence repeat (ISSR) markers. We also tried to determine whether genetic diversity depended on the region and altitude of collection site and if there was a relationship between DNA polymorphism and some morphological traits. The accessions were collected between years 1973 and 1999 from areas of Northern, Southern and Eastern Poland. The obtained results indicated a relatively low diversity (0.09–0.37) of the common oat landraces. Analysis of molecular variation (AMOVA) showed that there were no significant differences within designated geographic regions. It indicated that at the same time the altitude of collection site had significant effect on the genetic differentiation of the accessions. AMOVA also showed the presence of variance between groups formed on the basis of the colour of lemma. White lemma accessions were also characterized by highest genetic distinctiveness. Considering the evident impact of local climatic conditions on the genetic distinctiveness of Polish landraces utility of them in the Polish breeding programs should be considered.     

The Sierra Norte of Madrid: an agrobiodiversity refuge for common bean landraces

At the mountain area close to the city of Madrid, common beans were one of the main food crops present in everyday diet until 1960. This paper describes the morphological diversity, for forty-six phenological and morphological traits, found in forty-three traditional varieties of common beans collected in this area and seven commercial varieties used as reference. That comparison suggests that common bean breeding programs have led to later varieties with a higher production of straight pods. Quantitative traits showed also similar values when compared to the Iberian common bean collection, except for the phenological and seed size characters. The phenological differences could suggest an ecological adaptation of the studied landraces to the regional environmental conditions. The different seed size averages of both collections might correspond to the scarce presence of smaller seed-type common beans in Madrid collection. All the accessions collected in the Sierra Norte of Madrid belong to any of the groups included in the Spanish core collection. Madrilenian collection is also composed by indeterminate growth habit varieties, while the presence of bush accessions is relatively uncommon. Most of the Madrilenian landraces have a remarkable fitness for green-pod consumption (42 %) and their seeds are mainly white (30 %), ovate-shape (49 %) and medium-large (40 %). The study of seed storage protein allowed to classify the landraces according to their domesticated gene pools. Most of them (72 %), with T and C phaseolin type, seem to belong to Andean germplasm, while the remaining (28 %), with S and B phaseolin type, to Mesoamerican one. The remarkable morphological diversity of common beans found in this small area is a symptom of a broad genetic base despite genetic erosion, what indicates a widespread crop in the past. Therefore, it is advisable to design agro-environmental policies to promote the production and commercialization of common bean landraces in Sierra Norte of Madrid.     

AFLP analysis of genetic diversity in leafy kale (<Emphasis Type="Italic">Brassica oleracea</Emphasis> L. convar. <Emphasis Type="Italic">acephala</Emphasis> (DC.) Alef.) landraces,cultivars and wild populations in Europe

AFLP markers were used to characterize diversity and asses the genetic structure among 17 accessions of kale landraces, cultivars and wild populations from Europe. The range of average gene diversity in accessions was 0.11–0.27. Several landraces showed higher levels of diversity than the wild populations and one cultivar had the lowest diversity measures. The landraces that were most genetically diverse were from areas where kales are known to be extensively grown, suggesting in situ conservation in these areas as a supplement to storage of seeds in gene banks. An analysis of molecular variance (AMOVA) showed that 62% of the total variation was found within accessions. For most accessions, genetic distance was not related to geographic distance. Similarities among accessions were probably not caused by recent gene flow since they were widely separated geographically; more likely the relationship among them is due to seed dispersal through human interactions. Our results indicate that a kale population found in a natural habitat in Denmark was probably not truly wild but most likely an escape from a cultivated Danish kale that had subsequently become naturalized.     

Genetic Diversity Among Brazilian Cultivars and Landraces of Tomato Lycopersicon Esculentum Mill. Revealed by RAPD Markers

Random amplified polymorphic DNA markers (RAPD) were used to estimate the variability of 35 tomato accessions (Lycopersicon esculentum Mill.). A total of 257 reproducibly scorable bands were obtained from 20 primers, 78.6% of which were polymorphic. The percentage distribution of RAPD markers shows a bimodal distribution, and the frequency of rare alleles is similar in commercial and landrace accessions. Genetic distances among accessions were calculated and a dendrogram showing the genetic relationships among them was constructed allowing for the separation of four groups. Twenty out of 23 Brazilian landraces fell within one group, whereas commercial cultivars were distributed in the four groups. AMOVA analysis of RAPD data showed that, despite the high within Brazilian landraces and commercial cultivars variation, these two groups are significantly different, indicating that landraces can be a source of variation for breeding programs.     

Relationships Among <Emphasis Type="Italic">Brassica napus</Emphasis> (L.) Germplasm from Spain and Great Britain as Determined by RAPD Markers

The genetic diversity and the relationships among a collection of Brassica napus L. European populations were evaluated using random amplified polymorphic DNA markers. The study included 33 accessions of B. napus collected from Galicia (northwestern Spain) and 18 British cultivars, 16 accessions of B. napus and two accessions of Brassica oleracea L. used as controls. DNA from 25 individuals per population was analyzed using 18 decamer primers. One hundred thirty-eight amplification products were scored of which 105 were polymorphic. These bands ranged in size from 350 to 2500 base pairs. Similarity coefficients and cluster analysis were computed and six groups were obtained. Cluster I was the largest and included all the landraces from northwestern Spain, except two accessions that grouped separately into Clusters III and IV, respectively. A low level of genetic variability was detected among the B. napus Spanish genotypes, while considerable diversity was present among the British ones, which grouped into three groups, two main clusters and one group formed by one accession. Cluster II included all commercial varieties grown in Great Britain whereas Cluster V grouped local varieties maintained by the growers for many years. Cluster VI was a singularity formed by one entry. British accessions of B. oleracea had the greatest dissimilarity with all the other populations and grouped separately in Clusters VII and VIII. As conclusion, B. napus landraces used in northwestern Spain as leafy-green vegetable probably have an independent origin from B. napus crops grown in other European regions. Besides, separate domestication in northwestern Spain and Great Britain for a different end use might have led to two distinct gene pools.     

Genetic diversity of carrot (<Emphasis Type="Italic">Daucus carota</Emphasis> L.) cultivars revealed by analysis of SSR loci

Polymorphism of simple sequence repeat (SSR) loci was assessed in a collection of 88 carrot (Daucus carota L. subsp. sativus Hoffm.) accessions. The collection comprised cultivars and landraces mainly from Asia, Europe, and North America. Plants were grown in the glasshouse and characterized for root color and shape. Thirty SSR loci were fully characterized using parameters derived from allele frequencies, i.e. the number of total, effective and rare alleles, the observed and expected heterozygosity, and fixation index. Using a Bayesian approach, two clusters of 17 and 61 accessions were distinguished, which comprised the Asian and Western type accessions, respectively. Genetic diversity of the Asian gene pool was higher than that of the Western gene pool. The results of SSR analysis were supported by morphological characterization, and are congruent with current knowledge on the history of carrot domestication and breeding.     

SSR Diversity of Vegetable Soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Edamame [Glycine max (L.) Merr.] is a type of soybean selected for fresh or frozen vegetable use at an immature stage. Since edamame has a similar protein content, milder flavor, nuttier texture, and is easier to cook when compared to grain soybean, it is being promoted as a new vegetable for global consumption. Global production will require breeding programs for local adaptation; however, limited research has been published on genetic diversity of edamame varieties for the assessment of genetic resources. Simple sequence repeats (SSRs) were used to study the genetic diversity among 130 accessions, including edamame cultivars and landraces from Japan, China and the US, and also the new breeding lines in the US. Although it is assumed that elite edamame cultivars would have narrow genetic diversity, seventeen SSRs detected polymorphism to distinguish 99 of the 130 accessions. The cluster analysis generated nine clusters and 18 outliers. Genetic diversity within Japanese edamame was lower than that within Chinese vegetable soybean accessions (maodou), even though only 10 Chinese maodou were analyzed compared to 107 Japanese edamame. Cluster analysis revealed that the patterns of SSR diversity in edamame can generally distinguish maturity classes and testa color. We concluded that Japanese edamame have a narrow genetic base different from others and that SSRs can describe the patterns of genetic diversity among the elite vegetable soybean.     

Genetic diversity of <Emphasis Type="Italic">Nelumbo</Emphasis> accessions revealed by RAPD

Total 65 lotus accessions in genus Nelumbo mainly collected from China, were subjected to random amplified polymorphic DNA (RAPD) markers to estimate the genetic diversity and to test the genetic basis of the relationships between morphotypes and molecular markers. Seventeen primers generated a total of 195 highly reproducible and discernible loci, among which 173 were polymorphic. Percent polymorphism varied from 66.7 to 100 with an average of 88.72, and five primers out of them, OPC05, OPG10, OPN20, OPP09 and OPS17, showed 100% polymorphism. A relatively high genetic diversity was detected among all the samples with the similarity coefficient values ranging from 0.45 to 0.85, and Nei’s gene diversity (h) 0.30, and Shannon index (I) 0.46. The UPGMA dendrogram clustered 65 accessions in four clusters and the clustering pattern showed two groups, N. nucifera ssp. nucifera and those accessions related to the American lotus, and some special cultivars, landraces, hybrids and the American lotus. Principal Coordinate Analysis (PCA) further indicated that the genetic diversity of Nelumbo accessions was not evenly distributed, instead, was presented by a clustered distribution pattern. Similar to the results revealed by the dendrogram, two main groups representing the two subspecies of N. nucifera, as well as some special landraces, cultivars of Chinese lotus, the Japanese lotus and hybrids out of the two groups were obtained. Neither the UPGMA dendrogram nor the PCA analysis exhibited strict relationship with geographic distribution and morphotypes among the accessions.     

Evaluating landraces of bread wheat <Emphasis Type="Italic">Triticum aestivum</Emphasis> L. for tolerance to aluminium under low pH conditions

Bread wheat (Triticum aestivum L.) landraces held within ex situ collections offer a valuable and largely unexplored genetic resource for wheat improvement programs. To maximise full utilisation of such collections the evaluation of landrace accessions for traits of interest is required. In this study, 250 accessions from 21 countries were screened sequentially for tolerance to aluminium (Al) using haematoxylin staining of root tips and by root regrowth measurement. The staining test indicated tolerance in 35 accessions, with an intermediate response to Al exhibited in a further 21 accessions. Of the 35 accessions classified as tolerant, 33 also exhibited increased root length following exposure to Al. The tolerant genotypes originated from Bulgaria, Croatia, India, Italy, Nepal, Spain, Tunisia, and Turkey. AFLP analysis of the 35 tolerant accessions indicated that these represent diverse genetic backgrounds. These accessions form a valuable set of germplasm for the study of Al tolerance and may be of benefit to breeding programs for expanding the diversity of the gene pool from which tolerant cultivars are developed.     

Genetic Relationship and Diversity of Four MangiferaSpecies Revealed through AFLP Analysis

We used AFLP analysis to explore the genetic relationship and diversity between and within 4 Mangifera species. We analyzed 35 accessions comprising 8 cultivars and 3 landraces of M. indica L., 11 landraces of M. odorata Griff., 7 landraces of M. foetida Lour., and 6 landraces of M. caesia Jack. Using 8 primer combinations produced a total of 518 bands, 499 (96.3%) of which were polymorphic among the 35 accessions. Clustering analysis showed that all 35 accessions were basically classified into 4 groups corresponding to the 4 Mangifera species. Our results indicate that the genetic relationship of these 4 Mangifera species based on AFLP analysis is in good agreement with their classification by classic methods. In addition, it was clearly revealed the genetic diversity between and within 4 Mangifera species. The findings obtained in this study are useful for the breeding in Mangifera species.     

Assessment of genetic diversity among African cassava Manihot esculenta Grantz accessions resistant to the cassava mosaic virus disease using SSR markers

A study was conducted to determine the extent of genetic diversity among African cassava (Manihot esculenta Crantz) accessions resistant to the cassava mosaic virus disease (CMD), using simple sequence repeat (SSR) markers. The accessions included a breeding stock (clone 58308), five improved lines, 62 CMD resistant and 10 CMD susceptible landraces. Genetic diversity was assessed among accessions in five cluster groups derived from UPGMA analysis on data from 18 SSR primer pairs. Average gene diversity, He, was high in all cluster groups, with an average heterozygosity of 0.591 ± 0.061. The estimator of inbreeding Fis revealed a low level of inbreeding within groups and averaged −0.262 ± 0.142. Gene diversity among all accessions was 51.4% and gene diversity within cluster groups was 46.6%, while 4.8% was due to diversity between the different cluster groups. The amount of genetic differentiation measured by Gst and Fst were 9.6% and 12.1% respectively, indicating a weak genetic structure.     

Variation in primitive landraces of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) from Argentina

The phenotypic variation found in four common bean (Phaseolus vulgaris L.) complex primitive landraces, among a group of accessions collected in Northwestern Argentina in several missions is described, with particular attention to the wide diversity found in some small areas. It is presented a hypothesis about the maintenance of such diversity in bean mixtures or complex primitive landraces that grow close to their wild relative. Wide diversity regarding to seed type and plant characteristics was displayed by the landraces MCM-SV (composed of 11 lines), MCM-292 (14 lines), MCM-298 (5 lines) and VAV-3716 (14 lines). Food uses of dry seed and fresh pod seemed to be more relevant than the aesthetic use although all of them were presumably considered by humans for centuries resulting in the current phenotypes of these complex primitive landraces. Additionally, some weedy types (intermediate between wild and domesticated types) were detected in the landracesMCM-292 and MCM-298. The four complex landraces described consisted of highly diverse mixtures and they could play a role in breeding to enlarge the genetic basis of domesticated bean varieties belonging to the Andean gene pool.     

Genetic diversity and population structure of a common bean (Phaseolus vulgaris L.) collection from Calabria (Italy)

Eighty-seven Phaseolus vulgaris landraces, still cultivated in Calabria (Italy), were investigated in order to study the patterns of common bean genetic diversity in this region, to better understand the evolutionary development of beans in Europe and to properly manage these genetic resources. Four American accessions and five Italian varieties were also included. Different markers, such as 12 microsatellites, seed traits, phaseolins and 100-seed weight were combined with different statistical approaches. For each microsatellite, expected (H _e ) and observed (H _o ) heterozygosities, polymorphism information content (PIC), probability of identity (PI) and homozygosity were calculated. Furthermore, in Calabrian group of bean landraces, total (N _a ) and private (N _pa ) number of alleles, observed (H _o ), expected heterozygosities (H _e ) and allelic richness (AR) were calculated. Genetic distances among landraces were estimated using Nei’s coefficient and a cluster analysis using the UPGMA algorithm was performed. The results clearly indicated that: (1) Calabrian germplasm showed a high level of diversity (H _e  = 0.595); (2) Mesoamerican and Andean gene pools were clearly distinguished in Calabrian germplasm, with the Andean gene pool predominating (83 %); (3) Calabrian landraces were largely hybridized within and between the gene pools. A model-based approach, using the STRUCTURE software, was adopted. Six groups, including 4 of Andean origin and one of Mesoamerican origin were identified. Even more interesting, a small group (8 %) showed a distinct genetic structure, in which interspecific hybridizations with runner bean (Phaseolus coccineus L.) could have occurred. Nevertheless, a relatively high proportion of Calabrian bean landraces (12.6 %) was derived from intra and interspecific hybridizations.     

Phenotypic Variation and Relationships in Landraces and Improved Varieties of Rye (Secale cereale L.) from Northern Europe

Phenotypic diversity for agronomic characteristics was determined in an experiment with 29 landraces and 14 improved varieties of rye from the Nordic area, Germany and Poland. The accessions were scored for 12 characters. Effects of the location, year, type, and country of origin for landraces were investigated with analysis of variance. Phenotypic variations for the traits were estimated using the Shannon–Weaver diversity index. The genetic variation was high, with an average of H ₀ = 0.566. The landraces from Norway, Sweden and Finland showed the highest variation, whereas the improved varieties had the lowest. The German material also had low variation but the status of this material is uncertain. The genetic diversity showed that 70% of the variation was found within the accessions. A cluster analysis was carried out to identify the relationship between the accessions. The material grouped into eight clusters, where clusters I to V included landraces from Sweden, Finland and Norway, except for cluster III, which included one improved variety from Denmark. Cluster VI comprised a single Swedish landrace from Gotland. Most of the improved varieties were in cluster VII and the last cluster contained accessions from Germany and Sweden.     

Assessing genetic diversity in 23 early Polish oat cultivars based on molecular and morphological studies

In Poland oat breeding began at the late nineteenth century. During the World War II almost all of Polish breeding materials were lost, and then were replaced by German cultivars. The main aim of this paper was to show the level of genetic diversity of Polish oat cultivars which were bred before 1939. Simultaneously usefulness and informativeness of molecular and morphological methods were tested and compared. This study involved 23 cultivars, which were described by 25 morphological traits and three types of molecular markers (AFLP, ISSR and RAPD). Based on Dice coefficient, genetic distance between cultivars ranged from 0.17 to 0.44. The degree of morphological differentiation within the collection varied depending on trait. Nei’s genetic diversity for the combined results for the whole collection was equal to 0.202. Neither unweighted pair group method with arithmetic mean nor principal coordinate analysis showed any discrimination of cultivars according to breeding period and morphological trait. Part of morphological diversity has been preserved in the Polish early oat cultivars, do not exist anymore in contemporary cultivars, and also in landraces. The interest of breeders in early cultivars germplasm stored in genebank was and still is negligible. Breeding is confined to a few preferred by market morphotypes. So, it is very probable that the gene pools of early and contemporary cultivars could be separable.     

Into the vault of the Vavilov wheats: old diversity for new alleles

Intensive selection in wheat (Triticum aestivum L.) breeding programs over the past 100 years has led to a genetic bottleneck in modern bread wheat. Novel allelic variation is needed to break the yield plateau, particularly in the face of climate change and rapidly evolving pests and pathogens. Landraces preserved in seed banks likely harbour valuable sources of untapped genetic diversity because they were cultivated for thousands of years under diverse eco-geographical conditions prior to modern breeding. We performed the first genetic characterisation of bread wheat accessions sourced from the N. I. Vavilov Institute of Plant Genetic Resources (VIR) in St Petersburg, Russia. A panel comprising 295 accessions, including landraces, breeding lines and cultivars was subject to single seed descent (SSD) and genotyped using the genotyping-by-sequencing Diversity Arrays Technology platform (DArT-seq); returning a total of 34,311 polymorphic markers (14,228 mapped and 20,083 unmapped). Cluster analysis identified two distinct groups; one comprising mostly breeding lines and cultivars, and the other comprising landraces. Diversity was benchmarked in comparison to a set of standards, which revealed a high degree of genetic similarity among breeding material from Australia and the International Maize and Wheat Improvement Center (CIMMYT). Further, 11,025 markers (1888 mapped and 9137 unmapped) were polymorphic in the diversity panel only, thus representing allelic diversity potentially not present in Australian or CIMMYT germplasm. Open-access to DArT-seq markers and seed for SSD lines will empower researchers, pre-breeders and breeders to rediscover genetic diversity in the VIR collection and accelerate utilisation of novel alleles to improve wheat.     

Genetic relationships and diversity among Brazilian cultivars and landraces of common beans (Phaseolus vulgaris L.) revealed by AFLP markers

The genetic variation and relationships among 31 accessions of Phaseolus vulgaris L., and two representatives of Vigna unguiculata L., were evaluated by AFLP analysis. A total of 263 DNA fragments across all materials were scored using nine primer combinations, averaging 32 per primer. More than 95% of the amplification products showed polymorphism, indicating high variation at the DNA level among these accessions. Pair-wise genetic similarity (Jaccard's coefficient) ranged from 0.553 to 0.840, with a mean of 0.765. Twenty-three accessions (70%) clustered into three groups. A majority of the commercial cultivars (91%) clustered within a single group, whereas the landraces were distributed along all the variation. An apparent correlation with phaseolin types was detected. Results of this study suggest that Brazilian landraces truly represent the overall genetic variability of Phaseolus vulgaris, confirming the multiple origins of these materials, and their potential as a source of variation for breeding programs.     

Genetic diversity within a range of cultivars and landraces of flax (Linum usitatissimum L.) as revealed by RAPDs

Analysis of the extent and distribution of genetic diversity incrop plants is essential for optimizing sampling and breedingstrategies. We used random amplified polymorphic DNA (RAPD)markers to assess genetic diversity and relationships in 22 Canadiancultivars, 29 selected world cultivars and 10 landraces of flax(Linum usitatissimum L.). RAPDvariation was generally low and more variation was detected among,than within, the investigated flax accessions. Based on 53 variableRAPD loci observed for the 61 accessions, the landraces had a lowerproportion of fixed recessive RAPD loci (0.427) (i.e.,more genetic variation) than all of the flax cultivars examined(0.492). The linseed cultivars had a lower proportion ofrecessive loci (0.469) than the fiber flax cultivars(0.529). Canadian linseed cultivars had a lower proportionof recessive loci (0.465) than the selected world flaxcultivars (0.512). A trend was also observed that the rateof loss in genetic variation in Canadian flax breeding programs overthe last fifty years was approximately two variable loci per 100 lociper 10 years. Clustering analyses based on similarity estimatesshowed that the fiber cultivars were more related (or similar toeach other) and were classified as a homogeneous group. All ofthe linseed cultivars were clustered in diverse groups with the ninelandrace accessions. Implications of these findings for flax breedingand germplasm management are discussed.