Genetic diversity of the African wild rice (Oryza longistaminata Chev. et Roehr) from Ethiopia as revealed by SSR markers

Data from microsatellite markers have been extensively used for both in situ and ex situ conservation strategies by determining the level of genetic diversity of natural populations that can widen the gene pool of cultivated plants. Such conservation practices are based on understanding of the between and within population genetic variations and partitioning populations on the basis of geographic origin. Therefore, the objective of this study was to assess the genetic diversity of Oryza longistaminata Chev. et Roehr and how this variation is partitioned within and between the eight O. longistaminata populations found in the different geographic regions of Ethiopia using simple sequence repeat markers. Five microsatellite markers in 320 samples generated 64 alleles that revealed the presence of large amount of genetic variability (Ho = 0.225; He = 0.768; Na = 7.375; Ne = 6.565 and P = 0.744). The F-statistics detected by the microsatellite loci showed Fst = 0.064 and Fis = 0.743 and there was no population in Hardy–Weinberg equilibrium. The genetic diversity results obtained from this data indicated that there are high levels of genetic diversity in the populations of O. longistaminata studied and it is higher within than between populations. Among the eight populations sampled, five populations were identified as priorities for conservation strategies. Thus, national collection and conservation strategies need to consider these populations.     

Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers

Indica–japonica variation represents the most significant genetic differentiation in Asian cultivated rice (Oryza sativa L. subsp. indica Kato or subsp. japonica Kato). Understanding the differentiation and distribution patterns of cultivated rice along altitude gradients will facilitate strategic utilization and conservation of rice germplasm from mountainous regions. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the “InDel molecular index” developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region: indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indica–japonica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.     

Genetic diversity associated with conservation of endangered Dongxiang wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis>)

The wild progenitor species (Oryza rufipogon) of Asian cultivated rice (O. sativa L.) is located in Dongxiang county, China which is considered its the northernmost range worldwide. Nine ex situ and three in situ populations of the Dongxiang wild rice (DXWR) and four groups of modern cultivars were genotyped using 21 SSR markers for study of population structure, conservation efficiency and genetic relationship. We demonstrated that the ex situ conservation of the DXWR failed to maintain the genetic identity and reduced genetic diversity. Therefore, in situ conservation is absolutely necessary to maintain the genetic identity, diversity and heterozygosity. Also, in situ conservation is urgently needed because natural populations in DXWR have decreased from nine to three at present due to farming activity and urban expansion. In DXWR, the three surviving in situ populations had greater expected heterozygosity than any cultivated rice, and were genetically closer to japonica than either the male-sterile maintainer or restorer lines, or indica. Japonica has the lowest genetic diversity of cultivated rice. As a result, DXWR is a rich gene pool and is especially valuable for genetic improvement of japonica rice because these O. rufipogon accessions are most closely related to the japonica as compared to O. rufipogon collected anywhere else in the world.     

ISSR analysis shows low genetic diversity versus high genetic differentiation for giant bamboo, Dendrocalamus giganteus (Poaceae: Bambusoideae), in China populations

Dendrocalamus giganteus Munro is a high-value woody bamboo widely grown in Southeast Asia and China’s Yunnan Province. We investigated its genetic diversity in Yunnan as a prelude to considering effective breeding programs and the protection of germplasm resources. Inter-simple sequence repeat (ISSR) markers were used to assess the genetic structure and differentiation of seven populations. Seven ISSR primers generated 140 bands, of which 124 were polymorphic (88.57%). Genetic diversity within populations was relatively low, averaging 11.33% polymorphic bands (PPB), while diversity was considerably higher among populations, with PPB = 88.57%. Greater genetic differentiation was detected among populations (G _ST = 0.8474). We grouped these seven populations into two clusters within an UPGMA dendrogram—one comprised the Xinping and Shiping populations from central Yunnan, the other included the remaining five populations. Mantel tests indicated no significant correlation between genetic and geographic distances among populations. Breeding system characteristics, genetic drift, and limited gene flow (N _m = 0.0901) might be important factors for explaining this differentiation. Based on the overall high genetic diversity and differentiation among D. giganteus populations in Yunnan, we suggest the implementation of in situ conservation measures for all populations and sufficient sampling for ex situ conservation collections.     

Comparative genetic structure within single-origin pairs of rice (Oryza sativa L.) landraces from in situ and ex situ conservation programs in Yunnan of China using microsatellite markers

The genetic structure and diversity of eight pairs of rice landraces from in situ (collected in 2007) and ex situ (collected in 1980) conservation programs were studied using 20 pairs of microsatellite markers with high polymorphism. Each pair of rice landraces shares a name and origin and has similar seed and plant traits. The number of alleles detected in the populations from in situ conservation ranged from 43 to 88 with the mean number of alleles per locus ranging from 2.15 to 4.40, while the number of alleles detected in the populations from ex situ conservation ranged from 33 to 65, and the mean of alleles per locus ranged from 1.65 to 3.25. Compared to the ex situ populations, the number of alleles, the number of specific alleles and the genetic diversity index showed a significant increase in the in situ populations. Further, the numbers of specific alleles from in situ populations were 2.1–5.0 times greater than in ex situ populations except for rice landrace ‘Qitougu’. An AMOVA showed that the within-landrace genetic structure differed significantly between in situ and ex situ conservation treatments with differences exceeding 20%. The analysis of genetic similarity reached similar conclusions to those of the AMOVA. Compared with ex situ conservation programs, the rice landraces under in situ conservation programs had more alleles and higher genetic diversity in Yunnan of China.     

Rice landrace diversity in Nepal. Socio-economic and ecological factors determining rice landrace diversity in three agro-ecozones of Nepal based on farm surveys

In Nepal, in traditional rice farming systems many diverse landraces are grown in all of the rice agro-ecosystems from low to high altitude. Three case study sites were selected to represent the major rice agro-ecozones: Bara (100–150 m) for the low-altitude terai (plain); Kaski (700–1,206 m) for the mid-hill zone; and Jumla (2,200–3,000 m) for the high-hill zone. The diversity in rice varieties was compared in these three sites and nine survey villages in a series of surveys conducted in 1998, 1999 and 2006. The level and distribution of diversity on farm varied with the physical and socio-economic settings of the farming communities. The mid-hill site (Kaski) had the highest rice landrace diversity. This was adapted to the diverse agro-ecosystems found there and there was equal diversity in Kule khet (irrigated lands by seasonal canals) and Sim khet (marshy wet land). The next most diverse system was Nicha khet (irrigated lowlands) in Bara, the low-altitude site. The high-hill site (Jumla) had the lowest rice diversity. Across all sites many of the landraces were rarely grown and then only in small areas, reflecting the specialized uses to which they were put. At all sites the most common single landrace occupied less than half of the rice area. Resource-rich farmers were the more important custodians of on-farm rice varietal diversity across the sites. There was more rice diversity in favourable environments than in less favourable ones. This was true whether diversity was measured across sites or across rice domains within sites.     

The diversity and sustainable development of crop genetic resources in the Lancang River Valley

This paper reviews the status of crop genetic resources in Yunnan province of China from 1978 to 1999. Results are presented of same research in the field of the diversity of cultivated and wild crop. Yunnan is one of the centre of origin or genetic diversity of more than 200 cultivated and wild crops. There are over 500 cultivated plants which account for over 80% of the total in China and more than 650 species of wild crops. In addition, there are more than 440 species of main wild flowers. According to our recently researches there are abundant species, subspecies and varieties of crop genetic resources in Yunnan Province. The Lancang River Valley is the richest genetic diversity centre of rice, maize, wheat, barley, buckwheat, legumes, ramie, sugarcane, vegetable, tea, actinidia and so on. For example, there are 59 varieties (including all varieties of Oryza sativa L. in China) in 5933 accession of Yunnan indigenous rice. The Lancang River Valley is one of the centre for genetic diversity of rice resources and a rich region for elite and rare rice resources of Yunnan, too. In order to protect the highly endangered crop genetic resources in the Lancang River Valley, it is necessary and very important to set up a collection, conservation, utilization and research system, enhancing their protection and utilization, in situ- and ex situ-conservation, farm management and sustainable production.     

A measure of genetic diversity of goldenseal (Hydrastis canadensis L.) by RAPD analysis

Goldenseal (Hydrastis canadensis L.) is a medicinal plant valued for the treatment of sore eyes and mouths. Although cultivation of the plant has helped meet growing demand, goldenseal is still considered a threatened or endangered species throughout much of its range in North America. In an effort to assess possible conservation strategies for goldenseal genetic resources, levels of genetic diversity within and among cultivated and wild populations were quantified. RAPD analysis was used to examine six cultivated and 11 wild populations sampled from North Carolina, Ohio, Pennsylvania, and West Virginia. The average percentage of polymorphic bands in cultivated and wild populations was low (16.8 and 15.5 %, respectively), and geographic range did not predict the level of genetic diversity. Most of the genetic variation (81.2 %) was within populations; only 3.6 % was partitioned between cultivated and wild populations. Our results differed from a previous study which concluded that genetic differences were greater among than within populations. The results of the current study indicate that, although goldenseal grows clonally and in dense patches, a mixed mating system in which both selfing and outcrossing occur is also operating. We therefore suggest that the ex situ conservation of individual plants within populations, chosen carefully to account for clonal propagation in situ, is an appropriate strategy for sustaining the genetic diversity of goldenseal.     

Evaluation of genetic diversity in a Camelina sativa (L.) Crantz collection using microsatellite markers and biochemical traits

A genomic DNA library enriched with GA/TC repeats from Camelina sativa variety Calena has been analysed. After sequencing of about 200 randomly selected clones, approximately 60 % of them showed to contain simple or compound microsatellites with a high number of repeats. Among all microsatellite markers analysed 15 primer pairs amplified polymorphic fragments. Forty C. sativa accessions of different origin were genotyped with 15 microsatellite markers that generated 134 alleles with an average of 8.93 alleles per locus. The observed heterozygosity (Ho) among the accessions ranged from 0.0 to 0.15 with an average of 0.0370, whereas the average of expected heterozygosity (He) among accessions was 0.2769. The analysis of the average total heterozygosity (H_T = 0.651), the intrapopulation genetic diversity (H_S = 0.260), the interpopulation genetic diversity (D_ST = 0.391) and the coefficient of genetic differentiation among populations (G_ST = 0.574) demonstrated that 57.4 % of the genetic diversity is among the accessions, while 42.6 % resides within them. Phylogenetic tree of the 40 C. sativa accessions was constructed based on Nei’s genetic distance. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram shows, except for CAM108 and CAM170, a clear discrimination among C. sativa accessions grouping them in five subgroups. ANOVA analysis indicates significant differences in some biochemical and agronomic parameters among the C. sativa accessions grouped according to Nei’s genetic distance. The result of the Tukey HSD test demonstrated that the A4 subgroup showed a significant higher TWS and linoleic acid (LA) content, while the subgroup A1 showed a significant higher linolenic and lower LA content compared to the remaining groups.     

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.     

Morphological and genetic diversity and seed germination behavior of a snow lotus (<Emphasis Type="Italic">Saussurea involucrata</Emphasis>, Asteraceae) from the Mongolian Altay Mountains,Western Mongolia

Different conservation measures including domestication approaches are needed to preserve rare and extensively used plant species and to satisfy future market demands. Snow lotus (a common name used for a number of high altitude species in central Asia) species in Mongolia are important medicinal plants, mostly endangered at the regional level due to the extensive use for medicinal purposes and naturally limited distribution ranges. In order to develop effective conservation and cultivation approaches we studied the morphological and genetic diversity as well as the seed germination behavior of three populations of Saussurea involucrata in the Altay Mountains of Western Mongolia. Plant height and leaf length were measured on 41–53 randomly selected individuals in each population. Enhancement of seed germination was studied using either mechanical or chemical scarification with potassium nitrate and gibberellic acid. Genetic diversity within and among three populations of the species was analyzed using Amplified Fragment Length Polymorphisms. Plants in three populations differed in height and leaf length (P < 0.001). Plant size tended to be negatively correlated with habitat altitude. Seed germination rate was low and increased with seed soaking in gibberellic acid. However, the response of seeds to different treatments was rather population-specific. Most treatments did not significantly affect mean days to germination and the ratio of shoot to root dry weight of 2-weeks old seedlings. The level of genetic diversity in the studied populations was lower than the average value for other long-lived perennial herbs. Analysis of molecular variance revealed a high differentiation within populations (92 % of total variation) indicating sufficient gene flow among populations.     

Population baseline data for monitoring genetic diversity loss for 2010: A case study for Brassica species in the UK

The Convention on Biological Diversity and the subsequent International Treaty on Plant Genetic Resources for Food and Agriculture have proved a watershed in plant genetic resources (PGR) conservation and consequent initiatives have set various PGR conservation targets to be met by 2010. The aim of our paper is to develop ideas and issues concerning the monitoring of natural genetic resources: particularly in terms of developing a baseline from which to measure levels of genetic diversity. Three species of Brassica (B. nigra, B. oleracea, B. rapa) found wild in the UK were assessed for levels of genetic diversity using AFLP. The relationship between genetic distribution and ecogeographic distribution was considered for each species to determine patterns that may be useful in formulating conservation strategies. Genetic distance between populations of B. nigra and B. rapa were correlated to geographic distance. Levels of genetic polymorphism in B. oleracea were correlated to soil pH while in B. rapa they were correlated to soil coarseness. In terms of PGR conservation these findings may suggest an emphasis toward in situ conservation of a selection of disparate populations would be appropriate where possible as such adaptations may be lost in ex situ collections.     

Rice genetic diversity at farm and village levels and genetic structure of local varieties reveal need for in situ conservation

Rice genetic diversity partitioning between farms, varieties and, within-variety diversity, were analysed in two villages of Maritime Guinea with contrasted agroecological conditions. One thousand and two hundred individual plants belonging to 45 accessions collected in eight farms were genotyped using 10 SSR markers. The molecular variance was evenly shared between and within accessions, while the farm effect was almost nil. Local varieties had a multi-line genetic structure. The number of multilocus genotypes was proportional to the utilisation rate of the variety in the village. The F _ST values between different accessions of each variety were significant which indicated low genetic consistency in the variety names. This varietal structure could mainly be explained by the migration phenomenon and the high varietal turnover. Compared to allelic diversity, multilocus genotypic diversity seemed to be the most suitable indicator of the quantitative distribution of diversity at different management scales (accession, farm and village). The within- and between-farm F _ST values were in the same order of magnitude. The within-farm diversity was not farm-specific but quantitatively high, i.e. up to 50% of the total genotypic diversity of a given village. Given the relative importance of the within-variety diversity, the in situ approach stands out as the most effective solution. As farms do not host specific diversity the in situ approach could be implemented by working with a small number of farms.     

Genetic diversity,population structure and differentiation of rice species from Niger and their potential for rice genetic resources conservation and enhancement

Rice genetic resources conservation and evaluation is crucial to ensure germplasm sources for further crop breeding. We conducted a wide collection of Oryza species in Niger and characterize its diversity with microsatellites (or simple sequence repeats, SSR). The aims of this research were to get a better understanding of the extent of genetic diversity, its structure and partition within rice eco-geographical zones of Niger. There were 264 accessions found in farmers’ and other fields: 173 O. sativa (Asia’s rice), 65 O. glaberrima (Africa’s rice), 25 O. barthii, and 1 O. longistaminata (weedy perennial rice), which were genotyped with 18 SSR. A total of 178 alleles were detected, with a mean of 9.89 alleles per locus. The polymorphism information content was 0.65 and heterozygosity was estimated as 0.14. Two main well-differentiate genotypic groups, which correspond to Asian and African rice species, were identified. The SSR set divided the Asia’s rice group (solely indica) into irrigated and floating rice, with rainfed lowland rice in between. The African rice species group was composed of O. glaberrima, O. longistaminata and O. barthii accessions, but without any clear genetic differentiation among them likely due admixtures within the samples of O. barthii. Five accessions that could be natural interspecific hybrids were too admixed for assigning them to any of the two well-differentiated groups. The partitioning of the overall diversity showed that maximum variation was within genotypic groups and subgroups or cropping ecologies, rather than between eco-geographical zones. The eco-geographical distribution of the diversity suggests germplasm exchange in Niger. Next-steps for conserving rice and crop wild relatives in Niger could be taken using the findings of this research.     

Population structure of the primary gene pool of Oryza sativa in Thailand

The gene pool of cultivated Asian rice consists of wild rice (Oryza rufipogon Griff.), cultivated rice (O. sativa L.) and a weedy form (O. sativa f. spontanea). All three components are widespread in Thailand, frequently co-occurring within fields and providing the opportunity for gene flow and introgression. The purpose to this study is to understand the on-going evolutionary processes that affect the gene pool of rice by analysis of microsatellite variation. Results indicate that O. rufipogon, the wild ancestor of rice, has high levels of genetic variation both within and among populations. Moreover, the variation is structured predominantly by annual and perennial life history. High levels of variation are detected among cultivars indicating Thai cultivated rice has a broad genetic base with only a 20 % reduction in diversity from its wild ancestor. The weedy rice populations reveal varying levels of genetic variation, from nearly as high as wild rice to near zero. Weedy rice is genetically structured into 2 groups. Some populations of invasive weedy rice are the result of hybridization and gene flow between local wild rice and local cultivated rice in the regions of co-occurrence. Other populations of weedy rice are genetically nearly identical to the local cultivated rice. The diversity analysis indicates that the rice gene pool in Thailand is a dynamic genetic system. Gene flow is ongoing among its three main components, first between cultivated and wild rice resulting in weedy rice. Weedy rice in turn crosses with both cultivated varieties and wild rice.     

Allelic diversity of high molecular weight glutenin subunits (HMW-GS) in Iranian Aegilops tauschii Coss. accessions by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE)

Variation of high molecular weight glutenin subunits (HMW-GS) in 28 Iranian Aegilops tauschii (2n = 2x = 14, DD) accessions studied by sodium dodecyl sulphate electrophoresis method (SDS-PAGE). The results showed high variation of HMW-GS in the accessions. The range of frequency in 14 HMW-GS combinations was 3.57–25 % in the accessions. AMOVA showed the molecular variance between the geographic areas was lower than within the geographic areas. According to Nei’s genetic diversity, the highest diversity levels were in Semnan, Golestan and Azarbayjan, on the other hand the lowest levels of diversity were found in Khorasan, Gilan and Mazandaran accessions. Hence, the Caspian Sea South East accessions also Azerbayjan in Iran have more diversity. AMOVA did not show variance between strangulata and tauschii but there was more genetic diversity in ssp. tauschii subspecies in comparison of ssp. strangulata according to Nei’s gene diversity and Shannon information index. It showed Iranian Ae. tauschii have a good potential for bread making quality improvement in bread wheat.     

Genetic diversity analysis of yams (Dioscorea spp.) cultivated in China using ISSR and SRAP markers

Yam (Dioscorea spp.) is widely cultivated in China and many landraces are maintained by local farmers. However, there is little information available about their diversity and species identity. In this study, inter simple sequence repeat (ISSR) and sequence related amplified polymorphism (SRAP) techniques were used to assess genetic diversity within 21 yam landraces from seven cultivated populations. We observed high level of polymorphism among these landraces, specifically, 95.3 % for ISSR and 93.5 % for SRAP. Analysis of molecular variance revealed a significantly greater variation among the four yam species (40.39 %) and their populations (35.78 %) than within the populations (23.83 %). The unweighted pair group method arithmetic averages clusters and principal component analysis for 21 landraces formed four well-separated groups containing landraces of each of the four species, namely, Dioscorea opposita Thunb., Dioscorea alata L., Dioscorea persimilis Prain et Burkill, and Dioscorea fordii Prain et Burkill. The ISSR and SRAP primers were highly discriminatory among the 21 landraces; all 21 landraces could be easily differentiated using these primers. The average mean of gene flow (Nm = 0.1081) estimated from high genetic differentiation (Gst = 0.8222) suggested that gene flow among the populations was relatively restricted. The lack of genetic diversity within individual yam species suggests that it is critical to develop long-term strategies for enhancing genetic diversity within various yam species.     

Capturing genetic diversity of wild populations for <Emphasis Type="Italic">ex situ</Emphasis> conservation: Texas wild rice (<Emphasis Type="Italic">Zizania texana</Emphasis>) as a model

Genebanks complement other conservation programs because they preserve genetic diversity needed for future breeding and restoration. We evaluated efficiency of capturing genetic diversity, using endangered Zizania texana (Texas wild rice) as a model for plants with recalcitrant seeds. This perennial aquatic grass is restricted to 4 km of the San Marcos River in Texas. An early conservation collection included plants from stands throughout the river, based on the assumption stands would be unique genotypes. Using microsatellite markers, we found that genetic diversity was concentrated in five of 15 large, demographically stable stands; 96 stands smaller than 2 m² contributed no unique alleles. High heterozygosity and few duplicate genotypes suggested that sexual reproduction occurs more often than presumed. Simulations of stratified sampling of large stands captured all alleles in only 45 individuals, while random sampling along the river captured much less diversity. The early conservation collection captured as much diversity as expected from random sampling. Texas wild rice stands resemble a mainland-island metapopulation; our analyses suggest that stratified sampling maximizes genetic diversity for this population dynamic. Demographic and genetic information is important for validating the design of efficient ex situ collections and guiding in situ conservation.     

Spatial and temporal dynamics in genetic diversity in upland rice and late millet (<Emphasis Type="Italic">Pennisetum glaucum</Emphasis> (L.) R. Br.) in The Gambia

Ambiguity exists about the level of genetic diversity represented by farmer crop varieties, how it develops over time and how it relates to the diversity comprised by formal varieties. As part of an interdisciplinary technological/sociological study on farmer management of gene flow, upland rice (Oryza sativa L.) and late millet (Pennisetum glaucum (L.) R.Br.) from The Gambia were investigated for morphological and molecular variation. The goal of these analyses was to obtain insight into the level of crop genetic diversity of farmer’s materials planted in several case study villages in The Gambia. For both crops, samples were collected from villages and various research institutes. Based on variety names, different rice and millet varieties were expected to be used in different villages. In fact, there was a large overlap in genetic diversity for both crops, masked by the use of synonyms. The considerable similarity in rice genetic diversity between villages most likely results from the exchange of varieties between farmers. For millet this seems the result of development of varieties from the same gene pool. Some farmer varieties of rice, however, are apparent hybrid forms between the species O. sativa and O. glaberrima Steud., and farmer varieties in general displayed higher levels of genetic diversity than formal varieties. This indicates that, for rice, genetic diversity develops in farmers’ fields and may have potential use in formal breeding programs.     

Italian common bean landraces: diversity and population structure

Phaseolus vulgaris L. is an important species that originated in Mesoamerica. A Mesoamerican and an Andean gene pool are usually distinguished in the domesticated forms. Many bean landraces are still cultivated in Italy and the Department of Applied Biology maintains an ex situ collection of 146 landraces. Although protection schemes are being developed in Italy, most landraces are extinct or at risk of extinction. To facilitate their conservation and use, geographical, morphological, biochemical and molecular (SSR) data were collected and analysed to estimate the diversity and the genetic structure of the collection. Data confirmed that both the Mesoamerican and the Andean gene pools were introduced in Italy and, although a distinction between the two gene pools exists, the Italian landrace diversity is clearly structured in three clusters that are not simply ascribable to the original gene pools. The observed structure appears also to be due to adaptation to the different environmental conditions determined by altitude. This was confirmed by assessing the presence of selective effects for some of the SSR used in this study. Finally, a certain extent of admixture in Italian landrace diversity suggests past (or recurring) hybridisation events among gene pools. The combined use of morphological, biochemical and molecular data clearly distinguished almost all the landraces. The data gathered here can assist landrace in situ protection schemes that are being developed in Italy, be used to register landraces in the European common catalogue of ‘conservation varieties’ for seed commercialisation and contribute to a better use of Italian common bean diversity in breeding for organic and conventional production systems.