A-genome cotton as a source of genetic variability for Upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>)

Since Upland cotton (Gossypium hirsutum) is known to have relatively low levels of genetic diversity, a better understanding of variation and relationships among possible sources of novel genes would be valuable. Therefore, analysis of genetic variation of the genus Gossypium, especially the diploids, which are the putative donors of the A and D genomes for the commercially important allotetraploid cottons (AADD), G. hirsutum and G. barbadense, could provide important information about the feasibility of using these genetic resources for cotton improvement. The primary objective of this study was to analyze the genetic diversity in A-genome diploid cotton species, G. herbaceum (A1) and G.␣arboreum (A2) by using microsatellite markers. Forty-one A-genome germplasm accessions were evaluated with 32 microsatellite loci. Genetic similarities between A1 and A2 ranged from 0.62 to 0.86 with a mean of 0.70. Within each A-genome species similarities ranged from 0.80 to 0.97 with a mean of 0.89 for A1 and from 0.82 to 0.98 with a mean of 0.89 for A2. A UPGMA tree and principal coordinate analysis based on genetic similarity matrices showed distinct clusters consistent with the genomic groups.     

Identification of AFLP Markers that Discriminate Between Cultivated Cotton and the Hawaiian Island Endemic, <Emphasis Type="Italic">Gossypium tomentosum</Emphasis>Nuttall ex Seeman

Interspecific gene flow from crop species into wild relatives may compromise the genetic integrity of native species and in the case of transgenic crops lead to the escape of transgenes into natural populations. Approximately 72% of the upland cotton (Gossypium hirsutum L.) acreage grown in the United States in 2000 utilized transgenic cultivars. The closest relative of G. hirsutum is G. tomentosum Nuttall ex Seeman, endemic to the Hawaiian archipelago. Because these two species are fully interfertile, cultivation of transgenic G. hirsutum in the Hawaiian Islands is restricted. We investigated the possibility of identifying AFLP genetic markers that are diagnostic for each species and thus could be used in future studies to detect introgression between them. In addition, we were interested in comparing levels and geographic patterns of AFLP diversity in G. tomentosum to previous estimates using allozyme data. AFLP analysis led to the detection of 11 and 16 species-specific markers for G. tomentosum and G. hirsutum, respectively. These species-specific AFLP markers will be useful for detecting gene flow between G. hirsutum and G. tomentosum that has occurred in the past and thus might occur in the future if the restrictions on cultivation of transgenic G. hirsutum are relaxed in the Hawaiian Islands. Little genetic diversity and limited geographic patterning were discovered using AFLP markers, consistent with data from previous allozyme studies.     

Genetic Diversity of Asian Cotton (Gossypium arboreum L.) in China Evaluated by Microsatellite Analysis

Asian cotton (Gossypium arboreum L.) was once widely cultivated in China. It has also been a valuable source of genetic variation in modern cotton improvement. In this study, the genetic diversity of selected G. arboreum accessions collected from different regions of China was evaluated by microsatellite (simple sequence repeats, SSRs) analysis. Of the 358 microsatellite markers analyzed, 74 primer pairs detected 165 polymorphic DNA fragments among 39 G. arboreum accessions examined. Twelve accessions could be fingerprinted with one or more SSR markers. With the exception of two accessions, DaZiJie and DaZiMian, genetic similarity coefficients among all accessions ranged from 0.58 to 0.87 suggesting high level of genetic variation in the G. arboreum collections. The UPGMA dendrogram constructed from genetic similarity coefficients revealed positive correlation between cluster groupings and geographic distances. In addition, comparison of the microsatellite amplification profiles of the diploid G. arboreum and tetraploid Gossypium hirsutum L. found that size distribution of amplified products in G. arboreum was dispersive and that of G. hirsutum was relatively concentrated. The information on the genetic diversity and SSR fingerprinting from this study is useful for developing mapping populations for constructing diploid cotton genetic linkage map and tagging economically important traits.Diqiu Liu, Xiaoping Guo: These two authors contributed equally to this work.     

Observations on the geographic distribution, ecology and conservation status of several Phaseolus bean species in Costa Rica

Interest in bean genetic resources of Central America has resumed because of disease pressures (e.g., web blight, BGMV) and limitations of current bean varieties. As most of the diversity in landraces has been explored, focus is now on the exploration of wild forms of the primary gene pool and wild species of the secondary gene pool. A germplasm collection was carried out in the field and resulted in the collection of 29 wild populations for six Phaseolus species; it complemented field work done in 1987. Nine more populations were found for P. costaricensis, 10 for wild P. lunatus, one for P. oligospermus, one for P. tuerckheimii, four for wild P. vulgaris and four for P. xanthotrichus. Ninety-three herbarium voucher specimens were collected for 19 populations of the six species (deposited at CR). These results confirm the presence of wild P. vulgaris on both slopes of the central valley of Costa Rica, namely in the life zones bh-MB and bmh-P, and of P. costaricensis in the life zone bmh-MB. These life zones of limited range in Costa Rica have been heavily modified, thus fully justifying the germplasm collection for ex situ conservation. For both species the range of distribution in Costa Rica has been almost completely sampled. The life characteristics of each species that are relevant for their conservation in situ are briefly reviewed. Distribution ranges of each wild bean species are compared with the present extension of national parks, protected areas and fauna/flora sanctuaries, and suggestions for expanding such protected areas are made.     

Rice Diversity Collection,Conservation and Management in Northeastern India

Rice is the principal crop of northeastern region of India, where a considerable range of diversity exists. The germplasm collection has also unfold the occurrence of large number of rice landraces in the region. Between 1985 and 2002, a total 2639 accessions of rice germplasms including their wild relatives have been collected. Most of these germplasm material have been conserved in the National Gene Bank, New Delhi following their necessary characterization and evaluation. With the establishment of the Regional Gene Bank Module with medium-term storage facilities (6–7°C with 40–45% relative humidity) at Barapani, Meghalaya, the rice germplasm conservation (ex situ) have been initiated in the region.     

On the specific status of Gossypium lanceolatum Todaro

Summary Gossypium lanceolatum comprises a group of laciniate-leaved commensal cottons from the Mexican states of Oaxaca and Guerrero. This geographically restricted, morphologically distinct group of perennial cottons has been considered conspecific with G. hirsutum, with which it is sympatric. In addition to its questionable specific status, G. lanceolatum has added importance because it represents the focal point of an hypothesis that New World tetraploid Gossypium have a polyphyletic origin—an hypothesis that conflicts with the more widely accepted view that New World tetraploid Gossypium have a monophyletic origin. To reassess the systematic and genetic relationships between G. lanceolatum and G. hirsutum, historical data were reconsidered in the context of recently published molecular marker based data. Chloroplast and nuclear DNA markers fail to discriminate G. lanceolatum from G. hirsutum, uniting both into a single phylogenetic lineage. A new analysis of allelic variability at 50 allozyme loci in 11 G. lanceolatum and 527 G. hirsutum accessions demonstrates that G. lanceolatum has no unique alleles relative to G. hirsutum. Genetic identity estimates were uniformly high (> 0.96) among G. lanceolatum and geographically adjacent, mainland Mesoamerican groups of G. hirsutum accessions. Multivariate analyses demonstrated that G. lanceolatum is genetically embedded within geographically adjacent populations of G. hirsutum. These data, in conjunction with the complete interfertility between the two taxa and previous evidence for conspecificity, lead to the conclusion that G. lanceolatum does not warrant specific status. Rather, it is more properly recognized as a locally developed, domesticated form of G. hirsutum, i.e., G. hirsutum race palmeri.     

Molecular Confirmation of the Position of <Emphasis Type="Italic">Gossypium trifurcatum</Emphasis> Vollesen

Taxonomic understanding is a necessary prerequisite for intelligent germplasm maintenance and evaluation. Here, we use molecular evidence to address the generic position of the poorly known and morphologically unusual taxon Gossypium trifurcatum Vollesen. This species possesses dentate leaves, a feature not otherwise found in Gossypium L. but one that is common in Cienfuegosia Cav., a related genus in the small Malvaceous tribe Gossypieae. G. trifurcatum is a rare plant, restricted to deserts of Eastern Somalia and known from only two collections, the last in 1980. Using DNA extracted from an herbarium specimen, we amplified and sequenced the chloroplast gene ndhF. Phylogenetic analysis reveals G. trifurcatum to be cladistically nested within Gossypium. These data diagnose dentate leaves as an autapomorphy within a genetically diverse assemblage of African–Arabian species, which remain the least well-represented cottons in germplasm collections.     

Genetic Diversity in AA and CC Genome Oryza Species in Southern South Asia

The CC genome of Oryza is found in nine species of Oryza that are distributed on all continents having a tropical climate. Three diploid Oryza species with CC genome are found in Africa and Asia to Papua New Guinea. In southern South Asia these three CC genome diploid species can be found, O. eichingeri and O. rhizomatis in Sri Lanka and O. officinalis in India. AA genome wild relatives of rice are also found in the same geographic region. Germplasm of both diploid CC and AA genome Oryza germplasm has recently been collected from Sri Lanka. AFLP analysis was used to compare the genetic diversity of the two Oryza genomes from a similar geographic region in southern South Asia. In addition, the diploid CC Oryza germplasm was also analyzed by RAPD and SSR methodologies and the combined results were analyzed. The results show that in southern South Asia the diploid CC genome species have a high level of genetic diversity compared to the diploid AA genome species. Molecular marker analysis revealed that populations of O. rhizomatis from northern and southeastern Sri Lanka are genetically differentiated. One accession of O. rhizomatis was aligned with O. eichingeri. This accession was collected from the site of O. rhizomatis that is the closest to a population of O. eichingeri. O. eichingeri showed lower genetic diversity than the other two diploid Oryza CC genome species. O. officinalis accessions from Assam, India, and China were genetically less diverged from O. eichingeri and O. rhizomatis than two accessions of O. officinalis from Kerala state, India. The first two authors contributed equally to this research     

RAPD Polymorphism of the White-Flowered Gourd (Lagenaria siceraria (Molina) Standl. Landraces and its Wild Relatives in Kenya

The present study was performed to investigate genetic diversity of Kenyan landraces of the white-flowered gourd (Lagenaria siceraria), which exhibits tremendous morphological variation. RAPD analyses were performed on 53 landraces of the cultivated species L. siceraria and 42 accessions of three wild species (40 L. sphaerica, 1 L. abyssinica, and 1 L. breviflora). A total of 432 polymorphic bands were detected using 54 primers. The four species were clearly differentiated from one another. Intra-specific variations were investigated with L. siceraria and its wild relative L. sphaerica. Landraces of the cultivated species collected from different ethnic communities or regions were differentiated. Morphological variations were not associated with RAPD variations. Bitter landraces collected in Maasai communities showed two specific RAPD bands. In the wild species, accessions collected from the eastern and western sides of the Great Rift Valley were genetically differentiated from each other. In both species, genetic and geographical distance matrices computed among all pairs of accessions were significantly correlated, implying that the observed geographical variation can be explained by the 'Isolation by distance model'. Progeny plants derived from a common mother in L. siceraria showed a low level of segregation in RAPD pattern, suggesting that collected landraces are cultivated, maintaining their inherent traits although they are monoecious and insect-pollinated, whereas the wild relative L. sphaerica showed a higher level of segregation. The morphological diversity observed among landraces of L. siceraria is the result of human selection and their genetic identities are maintained by inbreeding probably resulting from frequent self-pollination.     

Collection and Characterization of Citrus indica Tanaka and C. macroptera Montr.: Wild Endangered Species of Northeastern India

Citrus indica and C. macroptera are the wild endangered species of Citrus occurring in northeastern India. Surveys were undertaken in this region for ascertaining distribution, studying variability and for collection of germplasm of these two species. C. indica, an endemic species of this region, was collected from the Citrus Gene Sanctuary located in buffer zone of Nokrek Biosphere Reserve in the Garo hills of Meghalaya. In addition, a putative natural hybrid of C. indica and C. limon was collected for the first time from the south Garo hills. C. macroptera had much wider distribution and was collected from Mizoram and Meghalaya states. In Jantia hills of Meghalaya, natural populations of this species are in a highly threatened state. The two species were unevenly distributed all over the explored territory. Morphological characterization of leaves, fruits and seeds indicated the presence of sizable variability within collected accessions of these two Citrus species. Indigenous technical knowledge gathered on the use and socio-economic importance indicated commercial potential for these two species in northeastern India. However, lack of cultivation of these species and clearing of forest cover at an alarming rate has led to an urgent need to adopt complementary conservation strategies to safeguard these species and to ensure their availability for future utilization. A major emphasis on developing methods for their propagation, multiplication and regeneration in in situ and ex situ conditions is required.     

Genetic Diversity in Accessions of Wild Rice Oryza granulata from South and Southeast Asia

Oryza granulata, an upland wild rice species, represents an unique germplasm for possessing abilities of tolerance to shade and drought, immune to bacterial blight and resistance to brown planthopper. Although low degree of genetic variability has been revealed within its populations, little genetic information at the species level is available in determining rational conservation strategies. Here we used dominant DNA marker random amplified polymorphism DNA (RAPD) to assess the genetic variability among 23 accessions of O. granulata that collected from main distribution areas worldwide. Twenty decamer primers generated a total of 243 bands, with 83.5% of them (203 bands) being polymorphic. Calculation of Shannon index of diversity revealed an average value of 0.42 ± 0.25, indicating that O. granulata maintains a relatively high degree of genetic diversity on the species level. Analysis of genetic dissimilarity (GD) showed that genetic differentiation occurred among studied accessions, which supports the feasibility of current ex situ conservation strategies. We also suggested that information based on population studies, which could be achieved by international co-operation, is needed to conserve this widespread germplasm more effectively.     

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.     

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.     

RAPD and AFLP assessment of genetic variation in a landrace of pepper (Capsicum annuum L.), grown in North-West Italy

In several regions of Italy as well as other parts of southern Europe, the heterogeneity of the land, the climate and the soil favour the survival in cultivation of a large number of landraces specifically adapted to local conditions. Knowledge on the level and distribution of their genetic variation can help to develop appropriate strategies, in order to suistainably manage in situ these germplasm resources at risk of genetic erosion. C. annuum is an herbaceous diploid species and is considered to be self-pollinating, although different rates of out-crossing have been recorded. We used random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers to assess genetic diversity within and between five populations of a landrace of Capsicum annuum L., grown in a limited area in north-west Italy and locally known as Cuneo pepper. Partitioning the genetic variation with Shannon's diversity index revealed that 41.6% occurred between and 58.4% within populations. Analogous results were obtained when the analysis was based only on RAPD or AFLP markers. However, AFLP was more reliable, since a lower range of variation was observed among primer combinations in detecting the two components of genetic variation. Notwithstanding the rather high level of within genetic variation detected, the five populations were clearly differentiated and differed in the frequency of alleles exclusive and/or present at very low frequencies. Our results show the need for accurate estimation of allele frequencies, in order to identify populations to which priority should be given for dynamic conservation of landraces.     

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.     

Assessment of EST-microsatellites markers for discrimination and genetic diversity in bread and durum wheat landraces from Afghanistan

Accurate and reliable means for identification are necessary to assess the discrimination between landraces of tetraploid wheat [T.␣turgidum L. subsp. durum (Desf.) Husn.] and hexaploid wheat (T. aestivum L. em. Thell.). In Afghanistan, farmers usually cultivate mixed landraces, and thus distinction between bread and durum is difficult. A set of 18 microsatellites derived from the DuPont EST-database were used to describe genetic diversity in a sample of 82 Afghan wheat landraces. A total of 101 alleles were detected, with allele number per locus ranging from 2 to 13, and a mean allele number of 6.31. The percentage of polymorphic loci was 89%. The EST-SSRs markers showed different level of gene diversity: the highest Polymorphism Information Content value (0.921) was observed with DuPw 221. Our results demonstrated that with a reasonable number of expressed sequences target microsatellites (EST-SSRs) it is possible to discriminate between T. durum and T. aestivum species of wheat germplasm. Our results showed that EST-databases could be a useful source for species-specific markers and have the potential for new genic microsatellites markers that could enhance screening germplasm in gene banks.     

Description of Iranian Diploid Wheat Resources

Iran is one of the primary centers of diversity for wheat and its relatives. Wild wheats, in particular diploid species, are extensively distributed in various parts of Iran. Of these, the existence of two “A" genome donor species, i.e., T. baeoticum and T. monococcum, has already been reported in Iranian floras. However, the existence of the other important “A" genome donor, i.e., T. urartu, has not been clearly reported. In a germplasm collection survey in several regions of Iran, T. urartu was identified, collected, and described, and is reported here for the first time. In a detailed and extensive taxonomic program, the collected germplasms of the above three species were studied. Morphological characters and species-specific traits of the three species were evaluated and compared. Using the monographs by Gandilyan (1980) and Dorofeev et al. (1979) for the collected germplasms, 14 varieties were identified of T. boeoticum, 3 varieties of T. urartu, 2 forms of T. monococcum. Of these 5 varieties of T. baeoticum ssp. baeoticum (var. albinigrum, var. garniense, var. zuccarinii, var. baeoticum, var. pseudobaeoticum), 3 varieties of T. baeoticum ssp. thaoudar (var. abovjanii, var. albinigrescens, var. ebrahimzadehae, var. viridinigrireuteri) and 1 variety of T. monococcum (var. mansfeldii) are new to Iran. In addition, 1 variety of T. baeoticum ssp. baeoticum (var. khorramabadicum), 3 varieties of T. baeoticum ssp. thaoudar (var. ebrehimeadena var. taleghanicum, var. ilamicum) and 2 varieties of T. urartu (var. iranicum, var. sardashticum) are new to the wheat botany.     

Genetic Diversity and Relationships of Wheat Landraces from Oman Investigated with SSR Markers

Little is known about genetic diversity and geographic origin of wheat landraces from Oman, an ancient area of wheat cultivation. The objectives of this study were to investigate the genetic relationships and levels of diversity of six wheat landraces collected in Oman with a set of 30 evenly distributed SSR markers. The total gene diversity, (H_T), conserved in the three durum wheat (Triticum durum desf.) landraces (H_T = 0.46) was higher than in the three bread wheat (Triticum aestivum L.) landraces (H_T = 0.37), which were similar to Turkish and Mexican bread wheat landraces calculated in previous studies. Genetic variation partitioning (G_ST) showed that variation was mainly distributed within rather than among the durum (G_ST = 0.30) and bread wheat (G_ST = 0.19) landraces. Based on modified Rogers’ distance (MRD), the durum and bread wheat landraces were distinct from each other except for a few individuals according to principal coordinate analysis (PCoA). One bread wheat landrace (Greda) was separated into two distinct sub-populations. A joint cluster analysis with other landraces of worldwide origin revealed that Omani bread wheat landraces were different from other landraces. However, two landraces from Pakistan were grouped somewhat closer to Omani landraces indicating a possible, previously unknown relationship. Implications of these results for future wheat landrace collection, evaluation and conservation are discussed.