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.     

Differentiation and structure of an Italian landrace of celery (Apium graveolens L.): inferences for on farm conservation

The “Sedano Nero di Trevi” (Black Celery from Trevi) is a landrace grown in Umbria (Italy) at risk of extinction. A morpho-physiological and molecular characterisation of the landrace and a detailed investigation of its cultural and cultivation context were carried out with the aim of facilitating a request for a quality mark, implement in situ (on farm) conservation schemes that are being developed in Italy and register the landrace in the European common catalogue of ‘conservation varieties’. These actions can help the landrace survive. Six farmer populations of the landrace and four élite varieties were characterised for thirteen morpho-physiological traits and nine AFLP primer combinations. The “Sedano Nero” farmer populations were better performers than élite varieties for important agronomic traits, such as yield, under the local agronomic conditions. Both morpho-physiological traits and molecular markers clearly distinguished the landrace from the élite cultivars. In addition, a structure was detected in the landrace with farmer populations being characterised by specific alleles. These results are discussed in connection with the local seed system and possible in situ conservation strategies for landraces.     

Diversity characterisation of broccoli (Brassica oleracea L. var. italica Plenck) landraces for their on-farm (in situ) safeguard and use in breeding programs

Brassica oleracea L. is an important species that originated in the eastern Mediterranean area. From there, B. oleracea L. subsp. capitata (L.) DC. convar. botrytis (L.) Alef. var. italica Plenck (broccoli) was introduced into Italy where considerable diversification took place. Several landraces of broccoli, which are highly appreciated by local people for their organoleptic traits, are presently cultivated in both large fields and home gardens. In this study, 10 landraces, 4 synthetics derived from landraces and 4 of the most used F1 hybrids were characterised for morpho-physiological and molecular traits with the principal aim of feeding information into the landrace protection schemes being developed in Italy and into breeding programs. The landraces and derived synthetics are well differentiated from each other and from the F1 hybrids for important agronomic and genetic traits. The principal component analysis based on analysis of morpho-physiological traits showed that overall the 2 main components accounted for 67.74 % of the total variation. The neighbour joining tree, based on 23 microsatellite markers, grouped accessions into 2 main clusters. One includes one synthetic variety and 2 F1 hybrids, while the other cluster includes all the other accessions. There were also several sub clusters. Most of the materials examined showed within-accession diversity. The information gathered in this study can be used to protect landraces through the schemes presently being developed in Italy and to register them in the European common catalogue of “conservation varieties”. In situ (on-farm) conservation of landrace diversity is discussed with reference to landrace use.     

Assessment of genetic variation in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) from Nebrodi mountains (Sicily,Italy)

This study was carried out to estimate the level of diversity existing within some common bean landraces still cultivated in Nebrodi mountains, North-western area of Sicily. The multidisciplinary approach adopted to reach this goal involved the characterisation of collected material through morphological, biochemical and molecular marker analyses. The nutritional quality of seeds was also investigated in view of the proposition of the best landraces as niche products. Results showed that those bean landraces retain a considerable level of heterogeneity. The use of both biochemical and molecular markers showed that all landraces clustered into two main groups, corresponding to the Andean and Mesoamerican gene pools. Our results suggest that the best strategy for preserving the diversity of common bean from a restricted area such as Nebrodi mountains, necessitates of a deep knowledge of germplasm to avoid the loss of precious genetic resources or, on the contrary, the safeguard of populations genetically redundant.     

Molecular characterisation of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) accessions from Southwestern Uganda reveal high levels of genetic diversity

Common bean (Phaseolus vulgaris L.) was introduced to East Africa over 400 years ago and is today a fundamental part of food and income security of many smallholder farmers in the region. East Africa is among the top three bean producing and consuming regions of Africa with Uganda, Rwanda and Kenya being leaders in production. The leading common bean producing region in Uganda is the Southwestern (SW) highlands. Production is subsistent and farmers grow mixed varieties (accessions) to minimize losses. The aim of this study was to investigate the impact of farmer selection and production practices on genetic diversity of common bean in SW Uganda. 100 accessions were assembled from SW Uganda and assayed with 6 DNA simple sequence repeat (SSR) markers. A total of 41 alleles were detected giving an overall average gene diversity of 0.299 (30%) in both districts. The accessions clustered into two major gene pools i.e., Mesoamerican and Andean. Within each gene pool there was evidence of clonal populations suggesting wide distribution of certain accessions. Kabale district had a higher average gene diversity (38%) compared to Kisoro district (22%). Detection of Andean phaseolin in a clone set of Mesoamerican gene pool suggests introgession between the two groups.     

Genetic erosion and in situ conservation of Lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center

Lima bean (Phaseolus lunatus L.) is an important crop in traditional Mayan agriculture of the Yucatan Peninsula, Mexico, its Mesoamerican center of diversity. Genetic erosion in this species is currently a threat in this region out of 3 of 21 landraces dominate 71.24% of the cultivated area, and 12 are rare landraces grown only in 6.29%. Using 90 ISSR loci, we estimated the diversity and genetic relationships for 21 landraces to analyzing their risk of genetic erosion, and generate data for their in situ conservation. Total genetic diversity was high (h = 0.29), however it was lower than wild gene pool reported (h = 0.69). The abundant landraces had genetic diversity values lower (h = 0.13, I = 0.17) than the common (h = 0.26, I = 0.33) and rare landraces (h = 0.24, I = 0.27). However, the rare landraces are in a higher risk of genetic erosion due to local extinction. The cluster analysis showed no groups corresponding to morpho-phenological characteristics, geographic origin or traditional classification, which resulted from high inter-landraces gene flow levels. The molecular data confirmed that the domesticated Lima bean pool of the Yucatan Peninsula has a high risk of genetic erosion. If current tendencies in landrace cultivation continue, many will no longer be planted within two to three generations, with a consequent loss of their alleles. Programs urgently need to be established for in situ conservation of Lima bean landraces in this region.     

Genetic diversity analysis in Phaseolus vulgaris L. using morphological traits

Common bean (Phaseolus vulgaris) is an important export crop in Kyrgyzstan since the end of the twentieth century. Genetic diversity analysis of common bean populations is useful for breeding programs, as it helps to select genetic material to be used for further crossing. Twenty-seven common bean accessions were analyzed using 13 qualitative morphological traits. In some cases, obtained morphological data were combined with previously published results based on microsatellite markers. The similarity matrices generated from the molecular and morphological data were significantly correlated (r = 0.49, P < 0.01). Cluster analyses based on Dice’s similarity coefficient were constructed based on morphological data and the combined data set of morphology and microsatellite, and both grouped the 27 accessions according to their origin: 15 belonged to the Andean and 12 to the Mesoamerican gene pool. On average, the Andean accessions were less diverse than the Mesoamerican accessions. The average diversity based on the Shannon diversity index for the 13 qualitative morphological traits was 0.05. Overall, this study revealed that qualitative morphological markers are efficient in assigning modern cultivars to their gene pools of origin.     

Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection

Genetic diversity data were collected from a large population of common bean (Phaseolus vulgaris L.) landraces representing the United States Department of Agriculture core collection. The data were based on microsatellite data from all linkage groups. A procedure was developed to determine if we collected sufficient marker data to adequately estimated pairwise diversity. The diversity data were used to define populations using distance and model-based approaches. Genetic differentiation and genetic isolation by distance data were collected. Diversity was also compared for markers linked and unlinked to domestication loci. Using a model-based approach, the landraces were divided into the traditional Middle American and Andean gene pools. Diversity was greater for the Middle American gene pool. Six Middle American and three Andean subpopulations were defined, and the Middle American subpopulations exhibited strong geographic identity. Unlike other studies, seed size varied considerably with subpopulations, and a number of the subpopulations contained landraces from multiple common bean races. All of the subpopulations were highly differentiated, with the Middle American subpopulations showing the greatest differentiation. Genetic isolation by distance was observed among the Middle American and Andean subpopulations but not among subpopulations within a gene pool. Within each gene pool, diversity was lower for markers linked to domestication loci.     

Temporal variation of diversity in Italian durum wheat germplasm

The aim of this work is to analyse the temporal change of genetic diversity in Italian durum wheat germplasm. The germplasm deployed in this study (158 accessions), belonging to 5 different historical classes, was characterised for its microsatellite and gliadin markers. The level of genetic diversity (He), based on gliadin and SSR markers results – on average – greater in indigenous landraces present in Italy before 1915, with the exception of pure line material which had been selected from landraces (showing highest level of heterozigosity for gliadin markers). Genotypes obtained from crosses or mutagenesis (referring to the 1950–1960 period) along with those resulting from crosses between CIMMYT lines and old materials (1970s and beyond) were also genetically more diverse. Forty-nine percent of indigenous landraces were genetically heterogeneous. Nine out of 53 landrace accessions were able to capture 4 different SSR private alleles. It is speculated that the reduction of allele richness is an indicator of the genetic erosion of the pre-breeding germplasm and it is pointed out that the implementation of appropriate methods of genetic conservation of this germplasm is a priority for breeding and food safety.     

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.     

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.     

Investigation of the genetic structure of some common bean (Phaseolus vulgaris L.) commercial varieties and genotypes used as a genitor with SSR and SNP markers

Common bean is a species belonging to the Phaseolus genus of the Leguminosae family. It has economic importance due to being rich in protein, vitamin A and C, and minerals. Being one of the most cultivated species of legumes, the determination of genetic diversity in bean genotypes or populations has an important role in terms of our genetic resources. The objective of this study was to evaluate the genetic structure of 94 genotypes which were cultivated in different parts of the world and our country with SSR and SNP markers. 10 SSR loci and 73 SNP primers were used for the determination of genetic structure in commercial cultivars and breeding lines. All of the SSR and SNP loci used in the study were found to be polymorphic. A total of 89 alleles were identified for 10 SSR loci. Mean number of alleles per locus (Na?=?8.9), effective allele number (Ne?=?3.731), Shannon information index (I?=?1.468), observed heterozygosity (Ho?=?0.023), and expected heterozygosity (He?=?0.654) were calculated based on SSR analysis. According to the results of Bayesian-based STRUCTURE analysis using SSR and SNP data, 94 bean genotypes were genetically divided into three main clusters. According to genetic distance based UPGMA dendrogram obtained from SNP analysis, 94 bean genotypes were divided into 2 main clusters corresponding Mesoamerican and Andean gene pools. The obtained results provide important information about the genetic structures of the studied bean cultivars and breeding lines. With the obtained results, it will be possible to develop breeding programs to develop new cultivars by using our gene resources.

     

Compatibility of crosses between gene pools and evolutionary classes in the common bean (Phaseolus vulgaris L.)

The extent of genetic divergence between the Mesoamerican and Andean gene pools and between evolutionary classes (wild, landrace and bred) in Phaseolus vulgaris was explored. The compatibility of crosses was assessed by the frequency with which pollination was successful and the number of seeds in the resulting pod. Mesoamerican genotypes were more effective as pollinators than Andean genotypes, regardless of the gene pool of the female parent. Though certain individual genotypes were more easily pollinated by genotypes of one or other of the gene pools, there was no consistent tendency for pollinations between genotypes within a gene pool to be more successful than those between gene pools. In crosses among wild and landrace genotypes, the landrace genotypes were more easily pollinated. In those among wild and bred genotypes, the bred genotypes were more effective as pollinators, and the number of seeds per pod was greater in crosses between the evolutionary classes than in those within classes. In crosses among landrace and bred genotypes, those within evolutionary classes had higher success rates than those between classes (47.2% vs. 38.9%), and produced more seeds per pod. However, these results do not represent a major barrier between the evolutionary classes. The hypothesis that dwarf-lethal incompatibility in inter-gene pool crosses is controlled by two complementary dominant genes (the DL-gene hypothesis) was tested by comparing the numbers of normal and abnormal plants in the progeny of three-way crosses, and the ratios obtained were consistent with the hypothesis. It is concluded that there is no biological barrier between the two gene pools and that they are distinct because, by accident of ancestry, they are located in geographically isolated and ecologically distinct areas, with different cultural practices and preferences. Research programmes aimed at transferring desirable traits between the gene pools should therefore be encouraged.     

Characterization of Italian lentil (Lens culinaris Medik.) germplasm by agronomic traits, biochemical and molecular markers

Genetic relationships, agronomic, nutritional and technological traits of ten Italian landraces, two improved lines and two cultivars of lentil (Lens culinaris Medik.) were investigated using a multi-disciplinary approach. Seed storage proteins, used as biochemical markers, were able to detect polymorphisms with variability mainly related to the polypeptide abundance. Microsatellite (SSR) molecular markers provided very useful information on genetic variation and relationships among landraces, with polymorphic fragments able to discriminate all the accessions. Lentil landraces were grouped in different clusters and sub-clusters principally on the basis of their geographical origin. The highest levels of genetic diversity were observed for lentils from ‘Castelluccio di Norcia’, ‘Colliano’ and ‘Villalba’. Field trials, performed in two locations of Southern Italy, revealed a high influence of location on yield. Comparing performances at both tested locations, the best landraces were ‘Linosa’ and ‘Valle di Nevola’ suggesting that these have the highest adaptability. Technological and nutritional data together with the agronomic ones evidenced that ‘Linosa’ lentil is the best landrace, however also ‘San Gerardo’ deserves some attention.     

Common Bean (Phaseolus vulgaris L.) Landraces from Abruzzo and Lazio Regions (Central Italy)

Marginal areas of Central Italy, i.e., areas where socio-economic conditions are weak and agriculture is carried on with traditional farming methods, are known to retain highly interesting local legume populations. The variation within a collection constituted by 44 populations belonging to 19 common bean (Phaseolus vulgaris L.) landraces, recently collected in Central Italy, was studied. Most landraces from the Lazio region were collected in the inner valleys of Aniene river basin, those from the Abruzzo region were collected in the Valley Peligna and the basin of the Aterno–Pescara river. Some morphological traits of plant and seeds and the phaseolin pattern were analysed to evaluate the degree of genetic variation among and within the landraces. Both common bean gene pools were represented in the investigated collection, the populations belonging to Andean gene pool were predominant. The landraces ‘Cioncone’, from Lazio and ‘Fagiolo pane aquilano’, from Abruzzo showed the rare A phaseolin type. All the collected data were submitted to cluster analysis. Two main subgroups were identified, the former included mainly populations from Abruzzo region and the latter including all the others. Despite this, a considerable resemblance exists between the common bean landraces from Abruzzo and Lazio, as proved by the low rankings on the tree among the populations. The observed similarity is discussed also on the basis of historical relationships between the two sides of the Apennine ridge. Contribution n. 40 from Institute of Plant Genetics-CNR, Bari, Italy.     

Variation and genomic polymorphism of lectin-related proteins in Lima bean (Phaseolus lunatus L.) seeds

Variation of the lectin and the two lectin-related proteins, AIL (-amylase inhibitor-like) and ARL (arcelin-like) was examined in wild and cultivated accessions of Lima bean (Phaseolus lunatus L.) using electrophoresis of total seed proteins, immunoblot and RFLP analysis of lectin-related genes. Results confirm that divergence of the two major Lima bean gene pools, Andean and Mesoamerican, also apply to this protein family. All three members of the family are present in both gene pools, with differences in size, abundance and composition between gene pools, giving the possibility to distinguish Andean from Mesoamerican lectin pattern types. Both patterns show some variants, such as lack of lectin or its presence as an abundant protein. The observed variation reflects, at least in part, into genomic polymorphism. The presence of arcelin- and -amylase-related proteins in Lima bean could represent a tool to increase our knowledge in the evolution of the lectin family in Phaseolus species.     

Characterization of Some Italian Common Bean (<Emphasis Type="Italic">Phaseolus Vulgaris</Emphasis> L.) Landraces by RAPD,Semi-random and ISSR Molecular Markers

Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and a semi-random PCR system were used to analyze the genetic diversity of 16 Italian common bean landraces and their relationship to four commercial cultivars. Of the primers tested, 8 ISSR, 6 RAPD and 7 semi-random primers produced polymorphic and reproducible DNA fragments. A higher proportion of polymorphic bands were observed using ISSR (85%) and semi-random (90%) primers than RAPD (69%) method. The combination of any two semi-random markers allowed the identification of all 20 bean genotypes. In contrast ISSR (except for primer (CAC)₃GC) and RAPD markers appeared to be less informative as more than two markers were necessary to achieve the same diagnostic level. Moreover, 7 ISSR, 2 RAPD and 8 semi-random exclusive bands were identified as putative population-specific markers. Semi-random and ISSR derived dendrograms showed similar tendencies in terms of genetic relatedness, whereas clustering of genotypes within groups was not similar when compared with the RAPD technique. Despite the different ability to resolve genetic variation among the investigated landraces, two major clusters with less than 60% (ISSR) and 40% (RAPD and semi-random) genetic similarity were formed with all three marker systems. The two groups were correlated with the phaseolin patterns and seed size of the landraces. The analysis showed that the cultivar ȁ8Lingua di Fuocoȁ9 and most of the landraces (13 out of 16) collected in Italy belong to the Andean gene pool, whereas only the three populations from Pratomagno belong to the Middle American gene pool.     

The European seed legislation on conservation varieties: focus, implementation, present and future impact on landrace on farm conservation

After a brief presentation of the European Directives on seed marketing of conservation varieties, data relative to their implementation status are given and discussed in relation to on farm conservation of landraces. Although generally aimed to ensure in situ conservation and the sustainable use of plant genetic resources, the Directives focus on seed production and marketing instead of genetic resource conservation per se. At present, their application has only partially favoured the registration of landraces maintained on farm or preserved in ex situ collections. They can be estimated in thousands in Europe, while only a few landrace with a verified status (51 out of a total of 184 conservation varieties) are presently included in the Common Catalogue. Reasons for this scarce registration are discussed. The European Directives on seed marketing of conservation varieties are a tool to promote on farm conservation of landraces that should be used to a greater extent than at present. Registration of landraces should be strongly and principally promoted by public bodies as a measure to give access to the genetic resources, preserve them on the long term and favour the economic profit of the farmers maintaining them.     

Genetic structure of Lima bean (<Emphasis Type="Italic">Phaseolus lunatus</Emphasis> L.) landraces grown in the Mayan area

Lima bean (Phaseolus lunatus L.) is an important crop in the Mayan culture. The Mayan area, considered as a main center of Mesoamerican diversity, has been divided into two subareas: the Mayan lowlands and the Mayan highlands. The Yucatan Peninsula is part of the Mayan lowlands and holds the highest number of Lima bean landraces of Mexico, but Lima beans are in high risk of genetic erosion due to intensification of the traditional Mayan agriculture. However, information on genetic diversity of Lima beans of the Mayan highlands is lacking. By using 46 landraces collected in the Mayan area (23 from each subarea) and 73 ISSR loci (inter-simple sequence repeats), we analyzed the structure, diversity and genetic relationships of Lima beans of this part of Mesoamerica. High levels of diversity (H _BAY = 0.45) and genetic structure (F _ST = 0.66) were found for the whole Mayan area. Genetic diversity in the Mayan lowlands was apparently higher than the Mayan highlands (H _BAY = 0.44 and 0.36, respectively); but differences were not statistically significant. Genetic structure between the subareas was high (AMOVA = 30% of total variation), most landraces grouping according to their geographic origin. This study shows the importance of the Mayan culture in the diversification and conservation of Lima beans. The results provide important information that should be considered when implementing strategies to collect Lima bean landraces and planning in situ and ex situ programs to conserve these landraces in the Mayan region.     

Wholesale replacement of lima bean (<Emphasis Type="Italic">Phaseolus lunatus</Emphasis> L.) landraces over the last 30 years in northeastern Campeche,Mexico

Genetic erosion has been evaluated at the landrace level in the past, principally because the loss of landraces is believed to generate erosion at the allelic level; however, few studies had tested this hypothesis in the crop’s centers of diversity and domestication. Using microsatellite markers, we analyzed for genetic erosion in lima bean (Phaseolus lunatus) landraces over time in samples collected in 1979 and in 2007 in northeast Campeche, in the Yucatan peninsula, Mexico, an important diversity center and part of the putative domestication area for this crop. We found that the lima bean genetic pool from 1979 had a higher genetic diversity than the one for the 2007 pool (Nei’s diversity, H = 0.18 and 0.05, respectively). Although this result could not to be explained using a bottleneck analysis, a cluster analysis showed that the alleles present in 1979 were not the same as those found in 2007, indicating an allelic displacement in the genetic pool of the lima bean landraces in the last 30 years. This displacement could be due to the introduction of improved varieties or landraces, resulting in a displacement of local varieties or to changes in the Mayan criteria for selection of germplasm or both. This study showed that the loss of landraces can generate both quantitative and qualitative changes in the genetic pool of the domesticated species. Such changes are very important to consider when planning ex situ and in situ programs to conserve crop diversity in their domestication areas.