Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region

The Capsicum genus is native to tropical America and consists of 27 species, five of which are used as fresh vegetables and spices: Capsicum annuum L., Capsicum chinense Jacq., Capsicum frutescens L., Capsicum baccatum L. and Capsicum pubescens R. et P. The study of the relationships among species of cultivate Capsicum species will be useful for breeding new cultivars or hybrids. This study is focused on the genetic diversity and relationships of these species that were collected in the Andean region. Ten microsatellites and four AFLP combinations were used to characterize 260 Capsicum accessions. The AFLP tree turned out to be informative regarding relationships among species. The data clearly showed the close relationships between C. chinense and C. frutescens. Moreover, C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Our data showed C. baccatum and C. praetermissum to be distinct species that form a compact group. In the present work, AFLP fingerprinting indicated that C. chacoense was placed in the C. baccatum complex and showed C. tovarii as a separate species. In addition, SSR data indicated that there is intraspecific differentiation in the species C. chinense, C. baccatum and C. pubescens, as the PCoA-based clustering showed a clear geographic division related to country. Even though Bolivia is considered to be the nuclear area for these species, we have found similar variability in Ecuador and Peru for several Capsicum species.     

The origin of Manihot esculenta Crantz (Euphorbiaceae)

Summary Contrary to views that cassava (Manihot esculenta) is only known in cultivation an argument is made that wild accessions of the species grow over much of the American neotropics, in Brazil, Bolivia, Peru, Venezuela, Guyana, and Surinam. Three subspecies are recognized. M. esculenta subsp. esculenta is the domesticate and includes all cultivars known in cultivation. The wild M. esculenta subsp. peruviana occurs in eastern Peru and western Brazil. The wild M. esculenta subsp. flabellifolia shows a wider distribution and ranges from the central Brazilian state of Goiás northward to Venezuelan Amazonia. The large area of distribution of the two wild subspecies makes it difficult to assign a place of initial domestication.     

Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers

The present study, using RAPD analysis, was undertaken to characterize genetic variation in domesticated cowpea and its wild progenitor, as well as their relationships. The materials used consisted of 26 domesticated accessions, including accessions from each of the five cultivar-group, and 30 wild/weedy accessions, including accessions from West, East and southern Africa. A total of 28 primers generated 202 RAPD bands. One hundred and eight bands were polymorphic among the domesticated compared to 181 among wild/weedy cowpea accessions. Wild accessions were more diverse in East Africa, which is the likely area of origin of V. unguiculata var. spontanea. Var. spontanea is supposed to have spread westward and southward, with a loss of variability, loss counterbalanceed in southern Africa by introgressions with local perennial subspecies. Although the variabilty of domesticated cowpea was the highest ever recorded, cultivar-groups were poorly resolved, and several results obtained with isozyme data were not confirmed here. However primitive cultivars were more diverse than evolved cultivars, which still suggests two consecutive bottlenecks within domesticated cowpea evolution. As isozymes and AFLP markers, although with a larger number of markers, RAPD data confirmed the single domestication hypothesis, the gap between wild and domesticated cowpea, and the widespread introgression phenomena between wild and domesticated cowpea.     

Molecular Characterization by AFLPs of Capsicum Germplasm from the Amazon Department in Colombia

Using AFLPs, 71 peppers (Capsicum) accessions from the species C. chinense Jacq., C. baccatum L., C. annuum L. and C. frutescens L. from indigenous communities of the Amazon Department (Colombia) were studied to assess the genetic diversity of the collections, and delineate species gene groups. Ten additional accessions were included as a reference species group. Three clusters were identified in the Amazonian accessions by Multiple Correspondence Analyses (MCA) and a dendrogram from the UPGMA analyses of Nei – Li genetic similarity. The clusters correspond to gene groups of the species Capsicum chinense (the majority of the accessions), C. baccatum and the complex annuum - frutescens. A fourth cluster corresponds to the reference accession C. pubescens. The MCA analyses accounted for 95% of the total variation. The total genetic variation was low (Ht 0.119) and a genetic diversity index (Gst) of 0.331 was obtained. This suggests a limited genetic diversity of the accessions and a close relatedness of the species. This study is the first molecular marker assessment of genetic diversity for peppers from the Colombian Amazon, and provides information of biodiversity that can be employed in the preservation and use of Capsicum germplasm.     

Diversity of <Emphasis Type="Italic">Ullucus tuberosus</Emphasis> (Basellaceae) in the Colombian Andes and notes on ulluco domestication based on morphological and molecular data

Ullucus tuberosus (common name ‘ulluco’) is a popular tuber crop of Andean highlands. Until now attention has been focused on ulluco from Bolivia, Peru and Ecuador, but little is known about its diversity in Colombia. Thirty-six accessions of cultivated ulluco preserved in the Gene Bank of the Universidad Nacional de Colombia were studied to assess the genetic diversity and spatial genetic structure of Colombian ulluco. We used morphological characters, molecular markers (total proteins, isozymes and RAPDs) and ploidy level. High morphological variability, especially for tuber shape and colour characters, was found. Eight accessions from north-east Colombian Andes showed some typical character-states of wild ulluco, suggesting that they could be partially domesticated forms. Genetic analysis using RAPD markers indicated that these accessions were very similar to other cultivated ullucos belonging to the same region. The regional structure observed in isozyme and RAPD dendrograms was confirmed by AMOVA results (52.6% among-region variation) and the spatial correlogram, showing the presence of two gene pools of ulluco in Colombia. Our results and the accumulated data suggest that ulluco was introduced to Colombia at least two times. Initially, semi-domesticated forms would have come from the central Andes to north-east Colombian Andes, where the native inhabitants would have completed the domestication process. Again, fully domesticated ullucos might have been introduced to south-west Colombian Andes.     

Genetic diversity among varieties of Chia (Salvia hispanica L.)

Chia, Salvia hispanica L., was a staple crop in pre-Columbian Mesoamerica. Despite the great potential of the species as an oilseed crop, little research related to domesticated and wild varieties exists. A study was undertaken to assess genetic diversity among 38 wild and domesticated accessions of S. hispanica collected throughout Mesoamerica by using RAPD markers. Genetic diversity was higher among wild varieties (H _G= 0.15) than all domesticated varieties (H _G= 0.10) and modern commercial domesticated varieties (H _G= 0.02), suggesting a slight loss of diversity accompanying domestication and a near lack of diversity in modern commercial varieties. In addition, the preliminary results indicate that the center of genetic diversity is in the highlands of western Mexico.     

Genetic identity and relationships of Iranian apple (Malus?×?domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis

In order to shed light on the role of Iran in apple evolution and domestication, we chose to investigate the relationships of a collection of 159 accessions of wild and domesticated apples including Iranian indigenous apple cultivars and landraces, selected wild species, and old apple scion and rootstock cultivars from different parts of the world. The majority of the wild species belonged to M. sieversii, which is widely believed to be the main maternal wild ancestor of domestic apples, from Kazakhstan and M. orientalis, which is one of the probable minor ancestors of domestic apples, from Turkey and Russia located on the east and west of Iran, respectively. The accessions were assigned into six arbitrary populations for the purpose of generating information on genetic parameters. Nine simple sequence repeat (SSR) loci selected from previous studies in apple were screened over DNA extracted from all the accessions. Results showed that all SSR loci displayed a very high degree of polymorphism with 11–25 alleles per locus. In total, there were 153 alleles across all loci with an average of 17 alleles per locus. The SSR allelic data were then used for estimation of population genetic parameters, including genetic variation statistics, F-statistics, gene flow, genetic identity, genetic distance and then cluster analysis using POPGENE 1.32 software. The F-statistics and gene flow in particular, showed that there was more intra-population than between population variation. The genetic identity and genetic distance estimates, and the dendrogram generated from the un-weighted pair group arithmetic average (UPGMA) method of cluster analysis showed that the Iranian cultivars and landraces were more closely related to M. sieversii from Central Asia (east of Iran) and M. orientalis native to Turkey and Russia than to other accessions of Malus species. Also, the old apple cultivars from different parts of the world have a closer genetic relationship to M. sieversii, M. orientalis and the Iranian apples, than to other wild species. Based on these results, we suggest that the Iranian apples may occupy an intermediate position between the domesticated varieties and wild species. We propose that Iran could be one of the major players in apples’ domestication and transfer from Central Asia to the western countries.     

A new collection of wild populations of Capsicum in Mexico and the southern United States

An exploration and collection mission for wild populations of Capsicum was carried out in the fall of 2006 and 2007, in 13 Mexican states and in the U.S. states of Arizona and Texas. The aim of this collection was to expand the number of accessions of wild chile pepper (Capsicum annuum var. glabriusculum and Capsicum frutescens) that are publicly available for research in plant improvement and for subsequent use in an inquiry into the domestication of C. annuum. While Mexico and the United States National Plant Germplasm System both have germplasm repositories INIFAP—Instituto Nacional de Investigaciones Forestales—Agrícolas y Pecuarias and USDA GRIN—United States Department of Agriculture’s Genetic Resources Information Network) with accessions of C. annuum var. glabriusculum, the very limited number available, their age, and/or validity of the information attached to many accessions do not allow for extensive research. Four hundred and sixty-six plants were sampled over two field seasons, of which copies of the collection reside in both UAA and at UC Davis. Given the current environment with the intellectual property of varieties of crop plants and, particularly, the extreme restrictions affecting explorations and the official procuring and sharing of germplasm across national borders, this U.S.—Mexico collaboration is one of the few examples of joint U.S.—Mexico germplasm collection efforts.     

Primitive weedy forms of guar,adak guar: possible missing link in the domestication of guar [<Emphasis Type="Italic">Cyamopsis tetragonoloba</Emphasis> (L.) Taub.]

Crop domestication has lead to the selection of a wide range of traits that distinguish domesticated crops from their wild ancestors. Over the past four decades, concerted efforts by archaeologists and geneticists have provided novel insights into the domestication of crops. However, minor crops are rarely a subject for intensive domestication studies and very less is known on the domestication of guar [Cyamopsis tetragonoloba (L.) Taub.] except the trans-domestication hypothesis. The hypothesis proposes that the domestication of guar took place in recent times in the dry areas of the northwestern region of Indo-Pakistan subcontinent and the African wild species, C. senegalensis Guill. et Perr., as its ancestor. However, the process by which the wild species was domesticated is not fully understood. The present paper describes the exploration, collection and in situ characterization of the primitive weedy forms of guar that could be the missing link between the wild and cultivated species. Adak guar is found to grow along with cultivated guar as a weed and is characterized by several primitive characters, prominent among which are spreading habit, small inedible pods which shatter at maturity, hard seed coat and seed dormancy. A total of 66 germplasm collections of these primitive weedy forms of guar have been made from naturally occurring populations in the arid regions of northwestern India. Systematic studies involving these primitive weedy forms can help in understanding the domestication bottlenecks and in utilizing the genetic variation lost during the process of domestication for the improvement of cultivated guar.     

RAPD variation in wild, weedy and cultivated azuki beans in Asia

RAPD (Random Amplified Polymorphic DNA) variation was assessed in 42 accessions of azuki bean (Vigna angularis) including wild, weedy and cultivated races and in three accessions of two related species used as outgroups. A much lower level of genetic variation was observed in cultivated and weedy azuki beans compared to wild azuki bean. Wild azuki bean (V. angularis var. nipponensis) has relatively high genetic variation in subtropical highlands of Asia compared to the Far East. Although cultivated azuki bean has low RAPD variation, accessions from subtropical highlands and Southeast Asia showed different RAPD features compared to those of the Far East. It is hypothesized that the cultivated azuki bean has been derived from wild azuki bean in the Far East; the high variation in wild azuki bean has been created through its natural dissemination; and the relatively low variation in cultivated azuki bean has come about through human dissemination after genetic bottleneck reduced by domestication. In addition, high genetic diversity in wild azuki bean in subtropical highlands of Asia is regarded as an important genetic resource in azuki improvement.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Evidence for two gene pools of the Lima bean,Phaseolus lunatus L., in the Americas

Summary The lima bean,Phaseolus lunatus L., is a bean species with a broad distribution in the Americas that rivals that of common bean (P. vulgaris). In order to better understand the organization of genetic diversity and the pattern of domestication in lima bean, a review was conducted of the available information on the geographic distribution of wild and cultivated forms of this species. In addition, one-dimensional SDS polyacrylamide gel electrophoresis of seed proteins was also conducted on a sample of 84 wild, 6 weedy, and 426 cultivated forms. Results show that wild forms can be divided into two groups, one with smaller seeds and a very extensive distribution that includes Mexico, Central America, and the eastern slope of the Andes, and the other with a more circumscribed distribution on the western slope of the Andes in Ecuador and northern Peru. Electrophoretic analyses of seed proteins confirmed this subdivision and, additionally, showed that the large-seeded cultivars had been domesticated from the large-seeded wild lima beans in western South America. For the small-seeded lima bean cultivars, it was not possible to determine a domestication center as the most abundant protein pattern in the cultivars also had a widespread distribution in the small-seeded wild progenitor. Electrophoretic analyses showed, however, that domestication led to a reduction of genetic diversity in the small-seeded, Mesoamerican group, but not in the large-seeded group. The latter may be due to insufficient sampling of the larger-seeded, wild germplasm.     

Geographic variation for isozymes in cherimoya (<Emphasis Type="Italic">Annona cherimola</Emphasis> Mill.)

Cherimoya (Anonna cherimola Mill.) is a fruit tree which originated in Peru and Ecuador and is now cultivated in several subtropical areas of the world. The characterization of cherimoya cultivars at allozyme level has been previously reported, but the geographic distribution and organization of this variation have not been fully characterized. In this study, we assessed the relationships among 206 cherimoya and four atemoya (A. cherimola ×A. squamosa) cultivars based on allozyme polymorphism. We have confirmed the genetic differences between atemoya and cherimoya cultivars, and showed that cherimoya accessions from Madeira, Bolivia and Spain form homogeneous groups of cultivars. Accessions from Chile and California form heterogeneous groups, probably due to their mixed origins. Cultivars from Peru and Ecuador showed a wide range of allelic variation, as is expected for accessions from the center of origin of this species.     

Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics

Capsicum chinense Jacq., one of the five domesticated species of pepper grown in the New World, is a major contributor to both local and international markets and the economy of the Caribbean islands. The planning and implementation of germplasm conservation and breeding programs for the sustainable use of C. chinense genetic resources are hampered by the poor understanding of the genetic structure and diversity of C. chinense in the region. In the present study, the genetic structure, diversity and relatedness of C. chinense germplasm collections within the Caribbean basin and South America were assessed using nuclear microsatellite markers. C. chinense accessions (102) representing seven geographical regions were genotyped using nine polymorphic nuclear microsatellite markers along with 16 accessions representing four other species of Capsicum. The results revealed that the highest genetic diversity (He = 0.58) was found in the Amazon region supporting the postulated center of diversity of C. chinense as the Amazon basin. The cluster analysis resulted in two distinct genetic clusters corresponding to Upper Amazon and Lower Amazon regions, suggesting two independent domestication events or two putative centers of diversity in these regions respectively. The cluster analysis further revealed that populations in Central America and the Caribbean may have been primarily derived from progenitors from Upper Amazon region and later diverged through geographical isolation. Conservation and germplasm collection programs should therefore target these genetically distinct clusters and satellite populations, towards supporting breeding programs to harness heterosis.     

Phaseolin diversity in wild Lima bean (Phaseolus lunatus L.) in American centres of origin

Summary Phaseolin variability was analyzed in 86 wild Phaseolus lunatus accessions, representing a wide geographical distribution from Mexico to Argentina, to determine geographical patterns of variability. The collection can be divided into two major groups. One group consists of accessions from Mexico, Central America, Cuba, Columbia, Argentina showing two Mesoamerican (M) phaseolin pattern types, already described in cultivated materials, as well as a variety of additional banding patterns. This suggests that at least two genotypes in the Mesoamerican gene pool were involved in a domestication process and spread throughout the world. The other group, consisting of wild Andean (A) forms from Northern Peru and belonging to the Andean gene pool, showed, among others, two A pattern types comparable to those found in cultivated large-seeded accessions.     

The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.)

The Asian cultivated rice, Oryza sativa L. (spp. indica or japonica), is assumed to have originated from one or both of the two wild Asian species, O. rufipogon Griff. and O. nivara Sharma and Shastry. They occur throughout the monsoon Asia and west Oceania. Fragrance is the most important trait among the domesticated characters of basmati and jasmine rice of Asia. The gene for fragrance in a scented rice shows the presence of a mutated portion (i.e., an eight base pair deletion in exon 7) that result in its loss of fragrance. In the present study, 229 wild rice O. rufipogon accessions were genotyped for this locus using a PCR assay. The wild rice species contained the mutated allele of the fgr gene at a low frequencies of 0.23. The surveyed populations were in Hardy–Weinberg equilibrium. This observation supports the hypothesis that the allele for fragrance was already present in the wild rice, and that this trait appeared in scented rice cultivars because of selection by the farmers of genotypes possessing this character during the process of domestication.     

Foliar response of wild and domesticated Phaseolus vulgaris L. to water stress

It is surmised that domestication has reduced geneticvariability in the common bean (Phaseolusvulgaris L.). However, little is known about leaf anatomy responses to water stress in wild or domesticated forms ofP. vulgaris. In this study,anatomical variation was evaluated in watered and water stressed plants of wild and domesticated genotypes of P.vulgaris from Mexico, growing under greenhouse conditions. Five terminal leaflets of completely expanded leaves wereused to evaluate leaf area (LA) and theirmiddle-regions to evaluate leaf thickness (LT), and various anatomical features. Domesticated genotypes showed bigger LAthan that of the wild ones; there was an effect due to the origin of materials, LA being bigger in genotypes from warm and humid lands that those from dry and temperate ones. No differences were detected in LT among materials; however, in domesticated plants the palisadeparenchyma predominated over the spongy one, contrasting with thewild genotypes. Under drought conditions, stomatal abortion was observed in wild and domesticated genotypes, especially on theabaxial surface. We conclude that, in fact, there are contrasting differences in leaf anatomy among wild and domesticated forms of Mexican Phaseolus vulgaris. Results suggest that domestication not only favours the enlargement of the LA, but also an increase in palisade parenchyma, suggesting a divergence toward assimilation in domesticated forms, in contrast with a better internal gas diffusion in wild forms. Domestication seems to have accentuated stomatal abortion as means of a transpirational control mechanism to counteract the effects of drought.     

Determining Sources of Diversity in Cultivated and Wild <Emphasis Type="Italic">Lablab purpureus</Emphasis> Related to Provenance of Germplasm by using Amplified Fragment Length Polymorphism

To improve understanding of diversity of Lablab purpureus and establish relationships among 103 germplasm accessions collected from diverse geographic origins, amplified fragment length polymorphism markers were used. Four primer sets selected out of 16 produced 289 clear, repeatable polymorphisms. UPGMA analysis of similarity data clustered the accessions according to their subspecific taxonomic organization, i.e., subsp. purpureus and subsp. uncinatus, as well as to cultivated and wild forms. The well-represented landraces from Africa and Asia, belonging predominantly to subsp. purpureus, displayed moderate genetic diversity. Wild forms from Africa showed far greater levels of diversity that would justify taxonomic re-assessment of the wild subsp. uncinatus. The molecular analysis identified forms that were collected in the wild in India but were genetically placed intermediate between wild and cultivated forms. As these plant types did not exist among the African accessions, it is suggested that they might represent escapes from early attempts of domestication. These results support the suggested pathway of domestication and distribution of L. purpureus from Africa to Asia. Additional members to a previously published core collection of the species are proposed.