To reduce the level of redundancy in a collection of cultivated lettuce, data from 160 amplified fragment length polymorphism (AFLP) fragments and 10 polymorphic microsatellites were used in combination with passport data and morphological data, the latter obtained from an experimental field trial performed for verification purposes. Based on the observed distribution of the number of marker differences between and within accessions, a minimum of three AFLP differences and two microsatellite differences were regarded as levels warranting distinction between accessions in the redundancy analysis. The strategy followed in the redundancy analysis was mainly based on the confirmation of duplication by each of two independently generated data sources. The molecular data were used for the validation as well as the identification of potential duplicates, revealing a total number of 198 redundancies, corresponding to 12.9% of the total collection. Trueness to type, number of characterization and evaluation data, and collection management considerations, such as available seed quantities and germination percentages, were used as primary, secondary and tertiary criteria to decide which accession from duplication groups to maintain in the collection. Removal of accessions showed negligible effects on total collection diversity, as quantified for AFLPs and microsatellites, characterization and evaluation traits and resistance profiles against downy mildew pathotypes, indicating that the applied strategy was effective.

The loss of variation in crops due to the modernization of agriculture has been described as genetic erosion. The current paper discusses the different views that exist on the concept of genetic erosion in crops. Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop. Two stages in this bottleneck are recognized: the initial replacement of landraces by modern cultivars; and further trends in diversity as a consequence of modern breeding practices. Genetic erosion may occur at three levels of integration: crop, variety and allele. The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level. According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following: a reduction in diversity due to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been completed.

Indian gooseberry, popularly known as amla, is harvested from two species of Phyllanthus, namely Phyllanthus emblica and Phyllanthus indofischeri. Although these two species are characterized on vegetative and reproductive features, development of reliable and authentic identification based on molecular approaches is necessary for precise identification. Most of the commercial orchards of Indian gooseberry are established with mixture of the two species. Introduction of unauthentic clones and seedlings in the establishment of orchards and differences in the growth of these two species under different elevations are the major constrains in identification. The present work aims to study the changes in vegetative and reproductive features under different elevations and to develop a simple molecular tool for precise identification of these two species based on single nucleotide polymorphisms in trnL (UAA) intron sequences of chloroplast DNA. Genomic DNA of leaf tissues of P. emblica and P. indofischeri, collected from the authentic source, was subjected to polymerase chain reaction amplification using trnL (UAA) intron gene-specific primers. The amplified product with the molecular weight of 540 bp was sequenced and used as reference for identification of these two species. The trnL (UAA) introns sequenced from 60 individual trees in three different orchards were compared with trnL (UAA) intron of authentic samples, and confirmed that these orchards have 76% population of P. indofischeri and remaining 24% is occupied by P. emblica. Thus, trnL (UAA) intron is a potential DNA marker for precise identification of these two species. The importance of the present study and its practical application in genetic improvement of Indian gooseberry are discussed.

Thirty-one accessions of Citrullus spp. belonging to Citrullus lanatus var. lanatus, C. lanatus var. citroides and Citrullus colocynthis were subjected to phylogenetic analysis using combined datasets of amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs). Tree topologies inferred by neighbour-joining analysis have resolved the phylogenic relationships among the species with special reference to established taxonomic classification. In this study, we have clearly resolved species boundaries of various taxa of citroides, lanatus and colocynthis into three well-supported clusters. Clustering pattern of principal component analysis with the shared polymorphisms using the subsets of data between any two taxon combinations helped to elucidate the introgression and interrelationships among the species. We report two major groups of C. lanatus taxa, one of which has undergone wide introgressions with the taxa of C. lanatus var. citroides and C. colocynthis. In this paper, we identified 583 AFLP bands that are polymorphic within the var. lanatus of C. lanatus, which is the largest set ever reported. The species-specific diagnostic SSRs and polymorphic AFLPs that are informative within and between the taxa reported in this paper would be immensely useful for future studies of these economically important genera.

Production of summer squash, Cucurbita pepo, can be severely limited by viral pathogens and powdery mildew. Resistance has been introgressed from Cucurbita moschata, and resistant hybrids have been commercially deployed. Our objective was to assess genetic affinities of such hybrids with susceptible, open-pollinated cocozelle and zucchini cultivars, and two disease-resistant lines derived from six generations of backcrossing to a susceptible zucchini cultivar. Amplified fragment length polymorphism (AFLP) EcoRI/MseI primer combinations were employed and, based on the resulting polymorphic bands, genetic similarities were estimated, and an unweighted pair group method using arithmetic average (UPGMA) cluster analysis was conducted. The open-pollinated cocozelle cultivars clustered with the resistant hybrids. The hybrids had greater similarities with one another than did the open-pollinated cultivars. The zucchini cultivars and their resistant backcross lines formed their own exclusive cluster. However, the resistant backcross lines showed less than 0.80 similarity with their recurrent parent. As the chromosome number of Cucurbita is high (2n = 2x = 40) and the resistances are inherited monogenically and oligogenically, these results, after six generations of backcrossing, cannot be explained by classical genetic linkage.

Cacao (Theobroma cacao L.) was domesticated in Mesoamerica and is native to the South American rainforest. Belizean Criollo is a group of relic landraces that are thought to be similar to those used by the Olmecs and Mayans during early domestication. Knowledge of genetic diversity is essential for efficient conservation and use of these relic landraces. Using 30 microsatellite markers, we characterized genetic diversity in 77 Belize Criollo accessions collected from the Maya Mountains in Belize, and assessed their relationship with 62 cacao accessions including 25 Trinitario accessions. Genetic diversity and heterozygosity were low in Belizean Criollo germplasm. Eleven distinctive genotypes were identified among the Belizean germplasm. Results of ordination and cluster analysis supported their putative ancestral contribution to the Trinitario cacao. However, results of Bayesian assignment and parentage analysis both suggested that the contribution of Criollo cacao to the Imperial College Selections Trinitario is small. Our preferred hypothesis for the genesis of Trinitario cacao is that a limited population of Criollo × Forastero hybrids emanated from the introduced Forastero population of Trinidad. The present study provides new insights into the origin of the Trinitario cacao, which will be useful in the ex situ and in situ conservation of cacao landraces from Mesoamerica.

To understand the effect of different farming systems on the dynamics of diversity of sorghum (Sorghum bicolor (L.) Moench) crop, genetic structure of widely used landraces and modern varieties collected from two contrasting agroecosystems, in eastern Sudan and western Kenya, were analysed with 16 polymorphic microsatellite markers. A total of 1104 accessions, grouped into 46 samples from individual farmers, were genotyped. Cluster analysis of the samples from the two countries displayed contrasting patterns. Most strikingly, differently named landraces from western Kenya formed widely overlapping clusters, indicating weak genetic differentiation, while those from eastern Sudan formed clearly distinguishable groups. Similarly, samples of the modern variety from Sudan displayed high homogeneity, whereas the most common modern variety from western Kenya was very heterogeneous. The high degree of fragmentation of farmlands of western Kenya, coupled with planting of different sorghum varieties in the same fields, increases the likelihood of inter-variety gene flow. This may explain the low genetic differentiation between the differently named landraces and heterogeneity of the modern variety from western Kenya. This study highlights the important role of farmers in shaping the genetic variation of their crops and provides population parameter estimates allowing forecasting of the fate of ‘modern’ germplasm (conventional or genetically modified) when introduced into subsistence farming systems.

Target region amplification polymorphism markers were used to assess the genetic diversity and relationship among 151 worldwide collected faba bean (Vicia faba L.) entries (137 accessions maintained at the USDA–ARS, Pullman, WA, 2 commercial varieties and 12 elite cultivars and advanced breeding lines obtained from Link of Georg-August University, Germany). Twelve primer combinations (six sets of polymerase chain reaction) amplified a total of 221 markers, of which 122 (55.2%) were polymorphic and could discriminate all the 151 entries. A high level of polymorphism was revealed among the accessions with an estimated average pairwise similarity of 63.2%, ranging from 36.9 to 90.2%. Cluster analysis divided the 151 accessions into five major groups with 2–101 entries each and revealed a substantial association between the molecular diversity and the geographic origin. All 101 accessions in Group V are originated from China and 13 of the 15 accessions in Group II were from Afghanistan. Thirty-two individual plants were sampled from two entries to assess the intra-accession variation. It was found that the advanced inbred line (Hiverna/5-EP1) had very little variation (5.0%), while the original collection (PI 577746) possessed a very high amount of variation (47.1%). This is consistent with the previous reports that faba bean landraces have a high level of outcrossing in production fields and thus contain larger amount variation within each landrace. One implication of this observation for germplasm management is that a relatively larger population is needed in regeneration to mitigate the possible loss of genetic variation due to genetic drift.

The treatment of traditional knowledge (TK) and plant genetic resources is timely international topics for debate with the focus on preventing the misappropriation and misuse of these resources, and on promoting the equitable sharing of benefits that arise from utilization and commercialization. In this paper, the initiatives of the Association of Southeast Asian Nations (ASEAN) and its member countries toward safeguarding TK associated with plant genetic resources are reviewed. While Malaysia, Thailand and the Philippines have national frameworks in place for the protection of TK and plant genetic resources, other ASEAN member countries do not. In addition, true regional cooperation among ASEAN countries in the area of TK and plant genetic resources has yet to be realized. After a review of these cases, this paper will argue that a single unique model or solution for all ASEAN member countries cannot meet the wide range of concerns and objectives that exist to protect TK and plant genetic resources. Instead, what is suggested is to create a mix of solutions to better handle TK and plant genetic resources issues.

A total of 54 horsegram landraces collected from three altitudinal zones (lower hills, mid hills and higher hills) of Himalayan region were characterized and evaluated for nine quantitative characters. Accessions collected from lower and higher hills were more diverse and differed significantly from mid hills accessions for characters viz., days to flowering, days to physiological maturity, plant height and grain yield per plant. The plotting of first and second principal component axes scores revealed that there was dispersion among the accessions collected from different altitudinal groups. It reveals a less variability among the landraces collected from same altitudinal group but high variability among the landraces collected from different altitudes. This suggests that the horsegram landraces are adapted to specific zone due to different selection pressure practiced by the farmers at different altitudes. Farmers in lower and higher hills select the landraces having high grain yield coupled with less reproductive phase duration and taller in nature.

Rhubarb includes approximately 60 species in the genus Rheum. It has been utilized for thousands of years for medicinal purposes, but only recently identified for its culinary use. In the mid 1700s, edible petioles were discovered on seedlings from rhubarb species. Hundreds of cultivars have since been identified for a wide range of uses from tarts to wine. Unfortunately, propagation by seed and irregular naming has resulted in a plethora of similarly named cultivars and multitude of phenotypes. Fifteen morphological characters were evaluated to differentiate rhubarb cultivars in the USDA, ARS Rheum collection in Palmer, Alaska. Two years of morphological data, focusing on horticultural characteristics indicated variation between the years. To improve cultivar resolution, the results suggest using 1 year's data instead of combining data from different years. The mean °Brix observed was 3.8, with a range from 2.2 to 6.1. Flesh colour and basal skin colour were poorly correlated (R2 = 0.462); overall skin colour was more red at the base than in the middle of the petiole. Rhubarb character categories, in particular petiole number and petiole base thickness, need to be modified to better anticipate the range of expected values, and thereby contribute improved reproducibility and reliability to separate cultivars based on morphological characters.

This is the first report on increasing yield and nutritional content of snake melon (Cucumis melo L. var. flexuosus) by exploiting intraspecific genetic variation of genetically diverse melons. Inbred snake melon ‘Punjab Long melon 1’ (PLM1) was hybridized with five genetically diverse inbred melons: KP 7 (var. momordica), AM 72 (var. acidulus), ‘Arya 1’ (var. chate), 04-02 (var. tibish) and ‘Punjab Wanga’ (unknown botanical variety). The parents and hybrids were evaluated at three locations for nine traits. Hybrids PLM1 × 04-02 and PLM1 × ‘Punjab Wanga’ exhibited significant (P0.05) heterosis for the number of marketable fruits per plant, and ascorbic acid and carotenoid contents of marketable fruits.

In India, Protection of Plant Varieties and Farmer's Rights Act (PPV&FRA, 2001) requires the registration and protection of new and notified/extant plant varieties based on the criteria of distinctness, uniformity and stability (DUS) of morphological characteristics. However, these morphological traits have not been able to resolve closely related genotypes. The molecular markers can very well support the DUS testing in such cases. In the present study, therefore, 14 varieties of rice cultivated in Punjab state of India were fingerprinted using 75 simple sequence repeat (SSR) primers. Out of these, 58 primers produced polymorphic profiles, while 13 were monomorphic, 2 revealed null allele and the remaining 2 amplified only from super basmati. In a screen of 7 cultivars, 16 SSR loci produced 17 rare/unique alleles, which provided an opportunity for their unambiguous identification. Cluster analysis based on SSR data clearly distinguished the cultivars into two dist inct groups: comprising non-basmati (group I) and basmati (group II). The cluster pattern was consistent with the pedigree and breeding history of the cultivars.

Kenya lies within sorghum centre of diversity. However, information on the relative extent of diversity patterns within and among genetically defined groups of distinct ecosystems is lacking. The objective was to assess the structure and phenotypic diversity of wild sorghum populations across a range of geographical and ecological conditions in the country. Sixty-two wild sorghum populations (30 individuals per population) sampled from four distinct sorghum growing regions of Kenya and covering different agroecologies were characterized for ten qualitative traits. Plant height, number of tillers, panicle sizes and flag leaf dimensions were also recorded. Frequencies of the phenotypic classes of each character were calculated. The Shannon diversity index (H′) was used to estimate the magnitude of diversity. Principal component analysis was used to differentiate populations within and between regions. Wild sorghum is widely distributed in Kenya, occurring in sympatric ranges with cultivated sorghum, and both have overlapping flowering windows. All characters considered displayed great phenotypic diversity. Pooled over characters within regions, the mean H′ ranged between 0.60 and 0.93 in Western and Coast regions, respectively. Wild sorghum was found to show a weak regional differentiation, probably reflecting the importance of seed-mediated gene flow in shaping the wild sorghum population structure. Trait distribution was variable among regions, but there was no conspicuous distribution of the traits studied in any given region. Spontaneous hybridization and introgression of genes from cultivated to wild sorghum seems to be likely, and may already have occurred for a long time, although undocumented. Implications for in situ and ex situ genetic resources conservation are discussed.

Graminaceous plants including staple cereals secrete certain phytosiderophores (PS) in calcareous soils with lower iron and zinc availability to enhance their uptake and translocation to the leaves and grains. A few Triticum aestivum cultivars and accessions of six Aegilops species were investigated for release of PS in vitro under iron- and zinc-sufficient and -deficient conditions, and for root and shoot iron and zinc concentrations. All the Aegilops species had three to four times higher release of PS than the wheat cultivars under both nutrient-sufficient and -deficient conditions. The maximum rate of increase of PS was observed on days 11 and 14 under iron- and zinc-deficient conditions, respectively, which levelled off rapidly among the wheat cultivars and continued to be high among Aegilops species till the end of the experiment. The absolute amount of iron and zinc expressed on dry weight basis after 18 d under iron- and zinc-deficient conditions showed nearly three times higher concentration in both roots and shoots of Aegilops species than that of the wheat cultivars. A significantly high correlation between concentrations of iron (r = 0.94) and zinc (r = 0.91) in roots and the PS released was found. The higher grain iron and zinc contents in the Aegilops species reported earlier may be attributed to their diverse and efficient mechanism(s) for PS-mediated micronutrient uptake and translocation system, which could be exploited for biofortification of wheat.

Spine gourd (Momordica dioica Roxb. ex Willd.) is a highly nutritious and underutilized vegetable containing high amount of protein as compared to other cucurbitaceous vegetables. Twenty-six accessions of spine gourd (M. dioica Roxb.), collected from eastern India, were evaluated to study the diversity and other genetic parameters. The estimates of genotypic coefficient of variation and phenotypic coefficient of variation for all the characters indicated that selection can be done on the basis of phenotype alone. On the basis of cluster analysis, spine gourd accessions can be categorized into three distinct groups. The accessions of spine gourd from eastern India showed an immense variation and can be used as a potential source of germplasm for crop improvement. The results presented here on nature and magnitude of genetic variability and diversity existing in this species will provide the foundation for designing an efficient spine gourd breeding programme. As spine gourd is distributed widely almost throughout India, further collections from Peninsular and Western India are suggested for maximum diversity sampling.

The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) genebank in India holds the world's largest collection of 21,594 pearl millet germplasm accessions including 18,447 landraces from 50 countries. West and Central Africa (WCA) region, which is considered as the centre of diversity for pearl millet, is also an important pearl millet germplasm source for resistance to biotic and abiotic stresses. A total of 7372 landraces were assembled from WCA countries. Out of which, 6434 landraces have the georeference data. The geographic origins of these landraces were analyzed using geographic information system tools to identify gaps in the collection. Geographical distribution of existing collections, type of vegetation, land cover and the high probability (>70%) for the occurrence of pearl millet estimated using the FloraMap software in different countries show that 62 districts in 13 provinces of Nigeria, 50 districts in 16 provinces of Burkina Faso, 9 districts in 6 provinces each of Mali and Mauritania, 8 districts in 8 provinces of Chad and 7 districts in 3 provinces of Ghana as the major geographical gaps in the pearl millet collection at the ICRISAT genebank. In view of this, we suggest that the final areas for exploration in these districts should be decided prior to the launch of the collection missions in consultation with local government officials and extension officers, who have the knowledge of pearl millet cultivation in the districts identified.

Genetic diversity and phylogenetic relationships among 141 cowpea (Vigna unguiculata L. Walp.) accessions collected throughout the nine geographical regions of Ghana were evaluated using simple sequence repeat (SSR) molecular markers. Twenty-five primer combinations pre-selected by their ability to polymerase chain reaction amplify SSRs from a set of test cowpea germplasm were evaluated. Of these, 20 primer combinations gave reproducible polymorphisms among 97.2% of the cowpea accessions tested, with the remaining accessions being found to be genetically identical. The informative primer combinations revealed a total of 74 alleles at 20 loci with an average of 3.8 alleles detected per locus. Variation in heterozygosity among cowpea SSRs ranged from 0.01 to 0.84 with an average occurrence of 0.19. The polymorphism information content varied from 0.07 to 0.66 with an average of 0.38. The Ghanaian cowpea accessions clustered into five main branches, each of which was loosely associated with the geographical regions from which samples were obtained. Accession GH2288 was found to be the most divergent cowpea accession compared with all others including the outgroup IT84S-2049, a breeding line from Nigeria. Our results provide a framework for future studies aimed at the conservation and management of cultivated cowpea germplasm in Ghana, and a good starting point for the selection of parental lines for genetic improvement programmes.

Genetic structure of five populations of a locally common rice (Oryza sativa L.) landrace Jaulia from parts of Uttarakhand state of India was studied using sequence tagged microsatellite site (STMS) markers. Of these, four populations were on-farm managed, assembled from different niche environments, and one population was conserved ex situ and represented static conservation. The 16 STMS primer pairs fully differentiated the inter- and intrapopulation diversity. A total of 72 alleles were recorded with a mean of 4.5 alleles per locus. Population wise, the total number of alleles ranged from 21 to 41, with maximum number of alleles for population IC 548358 and minimum number of alleles for population IC 100051 representing static conservation. A greater number of alleles specific to populations under farmer management could be recorded. Changes in yield parameters also seemed to be affected under farmer management besides other environmental adaptations for qualitative morphological characters. The marker diversity using STMS primer pairs indicates the genetic differentiation among populations resulting from joint effects of several evolutionary forces operating within the historical and biological context of the crop landrace. The variations in adaptations, on the other hand, indicate the degree to which populations are adapted to their environments and their potential for continued performance or as donors of characters in plant breeding. Both biotic and abiotic aspects of the environment are involved.

Castor (Ricinus communis L.) is an important non-edible oilseed crop that can potentially be used as feedstock for biodiesel production. There are 1033 accessions in the United States Department of Agriculture (USDA) castor germplasm collection. The range of oil content in these accessions has never been surveyed. For exploiting castor as a feedstock for biodiesel production, the entire USDA castor collection was procured from the National Plant Germplasm System (Germplasm Resources Information Network) and the oil content was measured with nuclear magnetic resonance. The variation of oil content among all castor accessions ranged from 37.2 to 60.6% with an average of 48.2%. One hundred seed weights were determined and seed-coat colour was also recorded from each accession. One hundred seed weight ranged from 10.1 to 73.3 g with an average of 28.3 g. There was a significant correlation between seed weight and oil content but the correlation value was low (r = 0.1572, P < 0.0001). Fifty accessions with a wide range of oil content were selected to be field grown for further evaluation. The results obtained from this survey will be useful for castor breeders seeking germplasm accessions with high oil content in the collection.