A study was conducted to collect and characterize the indigenous Kala zeera (Bunium persicum Boiss. Fedtsch.) accessions from the hills of northwestern Himalayan sates of Jammu and Kashmir, Himachal Pradesh and Uttarakhand. Around 1000 accessions were collected during this exploration mission, out of which diversity of 252 accessions was established through morphological characterization. The morpho-agronomic characterization and the analysis of trait data revealed significant variability in number of branches per plant, number of umbelets per umbel, number of seeds per plant, seed yield per plant and 1000 seed weight. The collection and characterization of these diverse accessions can prove useful in future Kala zeera improvement programmes in the world as this is the first such comprehensive report of the crop from northwestern Himalayan region of India.

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

A germplasm panel of 52 six-rowed barley landraces from northern Morocco was analysed by a Cleaved Amplified Polymorphic Sequences (CAPS) assay of a fragment of the elongation factor G (EF-G) gene. Forty-nine of these accessions carried allele A, and the other three carried allele D. The latter all originated from a narrow region close to the border with Algeria, whereas the former were represented across the whole collection area. Since six-rowed D allele carriers are present in North Africa, along with both two-rowed cultivated and wild barleys, it is likely that the European six-rowed barley varieties carrying the D allele have Moroccan parentage.

Farmers in local communities have a considerable amount of information on their genetic resources both at the individual and community level. The farmers' knowledge is interweaved into their daily practices as a reserve accumulated over the generations. The Farmer Field Fora approach (FFF) has been conceptualized in order to activate farmers to identify the existing resources both in the crops they cultivate and in their knowledge, to recognize its value and to start using it more consciously. The FFF approach links the use of existing diversity to the possibility of having new varieties and to improving productivity. In weekly meetings farmers observe changes in the field between varieties, debate on them and draw conclusions. In every session a theme on plant development is debated among farmers with the aid of a facilitator. Close contact with researchers allows involvement with the breeding practices and enables the aims and conduct used in research to be understood. This empowers farmers to participate in a more active way in research, to apply more precise ways of observing and managing their genetic resources, and to link their work to conservation activities at the national and local level. The results of the FFF trial, which was carried out in 10 villages in the region of San in Mali in 2001, show an increased interest among farmers to observe varieties. The appreciation criteria used is multiple including yield, earliness, strong tillers, high number of tillers, and resistance for diseases and Striga. It seems obvious that even though the goal of the approach is on-farm conservation of plant genetic resources, it must be closely linked to farmers' interest. The variation of the results between villages demonstrates variability of climatic condition in this region and a high genotype—environment interaction. Further modifications of the approach are required in order to improve equitable participation of different stakeholders and improve the institutionalization of on-farm conservation.

Knowledge of the genetic diversity of germplasm of breeding material is invaluable in crop improvement programmes. Frequently, qualitative and quantitative data are used separately to assess genetic diversity of crop genotypes. While assessing diversity based on qualitative and quantitative traits separately, there may occur a problem when the degree of correspondence between the clusters formed does not agree with each other. This study compares five different procedures of clustering based on the criterion of weighted average of observed proportion of misclassification in black gram genotypes using qualitative, quantitative traits and mixture data. The INDOMIX- and PRINQUAL-based clustering procedures, i.e. INDOMIX and PRINQUAL methods in conjunction with the k-means clustering procedure, show better performance compared with other clustering procedures, followed by clustering based on either quantitative or qualitative data alone. The use of the INDOMIX- and PRINQUAL-based procedures can help breeders in capturing the variation present in both qualitative and quantitative trait data simultaneously and solving the problem of ambiguity over the degree of correspondence between clustering based on either qualitative or quantitative traits alone.

Nine characters contributing to seed yield were measured on 20 accessions of horse gram (Macrotyloma uniflorum (Lam.) Verd), and subjected to genetic divergence analysis using Mahalanobis statistic and mapping using DIVA-GIS. The accessions were collected from two eco-geographical regions of Andhra Pradesh (India) – North Coastal and Rayalaseema. Based on D2 values the genotypes were grouped into five clusters. Genetic diversity was not related to eco-geographical distribution. The greatest inter-cluster distance separated clusters II and V, followed by clusters IV, and V, III and IV. Entries in clusters V and II appear suitable as parents for horse gram improvement. The Rayalaseema region is the source of useful variation for days to flowering, maturity and yield.

Grapevine (Vitis vinifera L.) is a major worldwide crop of high economic importance, tightly interwoven with the traditions and the culture of many civilizations. The Greek vineyard is one of the oldest in the world composed of an ample number of highly diverse indigenous landraces. However, over the last decades the local cultivated grapevine germplasm has undergone a drastic reduction of diversity, due to the established market preferences for international varieties. In the current work a combined approach involving both, ampelographic traits and microsatellite markers has been undertaken, to study the genetic diversity within and among 96 grapevine genotypes belonging to 36 V. vinifera subsp. vinifera cultivars, predominantly representing autochthonous Greek landraces. Results revealed high genetic diversity for the Greek cultivars yielding a mean number of alleles per locus 14.69 and mean polymorphic information content 0.848. Hierarchical cluster analysis, employing both, ampelographic and microsatellite data, showed a clear distinction based on the origin of the germplasm; Anatolian versus Mediterranean. Principal component analysis, based on the most informative ampelographic traits, coupled to the results from genetic structure analysis further corroborated the proposal of germplasm differentiation on the basis of geographic origin. This information can be further utilized for the reconstitution of the Greek vineyard and can significantly contribute towards a rational conservation and utilization strategy for breeding or for direct cultivation of the Greek indigenous grapevine germplasm.

Morinda reticulata Gamble and Morinda umbellata Linn. (Rubiaceae) are medicinally important climbers distributed as a mixed population in southern Western Ghats of India. A close morphological resemblance of these two species misleads the harvester in the identification of plant parts for preparation of herbal medicines. Though both species contain anthraquinone derivatives and share common medicinal properties for treating stomach disorders, each of these species has unique curative properties for treating selective diseases. Conventional methods are not reliable for identification of these species due to similarities in morphology. Thus, misidentification often leads to the deterioration of the quality of medicines. Thus, authentication utilizing conserved gene sequences in the chloroplast genome of these two Morinda spp. has been attempted for precise identification. Here we report the use of two barcoding genes (maturase kinase and ribulose 1,5-bisphosphate carboxylase large subunit) to distinguish M. reticulata and M. umbellata based on single nucleotide polymorphism. The present findings can be used for authenticating leaf samples of M. reticulata and M. umbellata.

Bananas and plantains (Musa spp.) constitute staple food for over 20 million people in Democratic Republic of Congo (DRC). Since 1960, DRC is considered as a secondary centre of plantain diversification with few unknown accessions kept in the INERA-Mulungu genebank. Through similarity coefficients, cluster (unweighted pair group method with arithmetic mean, single, complete, sequential, agglomerative, hierarchical and nested design/clustering procedure) and/or multivariate analyses, numerical morpho-taxonomy has established that this diversity is composed of 37 different accessions. Each accession expressed 98 characters among the 401 possible character states, thus providing 39,298 feature patterns (data points). The 98 characters included 32 vegetative and 66 male and female inflorescences. The accessions were clustered into three genomic groups (AAA, AAB and AABB). Subjective classification ascertained nine subgroups: AAB-Silk, AAB-Pome, AAB-Plantain, AABB-Pisang Awak, AAA-Cavendish, AAA-Ibota, AAA-Gros Michel, AAA-Green-Red and AAA-Lujugira-Mutika. Three subgroups were further divided into nine clone sets which consisted of: Dwarf and Giant Cavendish, French and Horn Plantains, and Musakala, Nfuuka, Nakitembe, Nakabululu and Beer/Mbidde within Lujugira-Mutika. Numerical morpho-taxonomy effectively indicated a relationship between the DRC and Tanzania's Musa diversity. For example, the accessions ‘Kamaramasengi’ and ‘Isangi’ were found to be similar to ‘Kisukari’ (AAB-Silk) and ‘Ngego I’ (AAB-French) common in the Tanzanian Southern Highland. Likewise, the accessions Kimalindi-fupi, Kimalindi-ndefu and Jamaica of Tanzania were duplicates of Bakurura (Kigurube), Cavendish of Butuza and Gros Michel in DRC, respectively. Moreover, numerical morpho-taxonomy confirmed the pedigree of AAB-Prata (Cibwalo) in FHIA 17 and FHIA 23 and the closeness of the ancestors of Yangambi Km5 and Gros Michel. Furthermore, numerical morpho-taxonomy established AA-Mshale malembo as one of the AAA-Lujugira-Mutika parents. Molecular investigations are finally required to confirm the genomes.

Flavour is one of the most highly demanded consumer traits of tomato at present; poor flavour is one of the most commonly heard complaints associated with modern varieties of tomato. In order to combine flavour with other desirable fruit traits in improved cultivars, it is important to determine how much variability exists in the crucial compounds that contribute most to flavour. The objective of the present study was to determine the variability of flavour-contributing components including total soluble solids (TSS) and total titratable acids (TTA) among other subjective traits related to flavour in a core collection of tomato accessions. The core collection was comprised of 173 tomato accessions with a wide genetic background from the United States Department of Agriculture (USDA), Agricultural Research Services (ARS) Plant Genetic Resources Unit repository. The TTA varied from 0.20 to 0.64%, whereas the TSS ranged from 3.4 to 9.0%, indicating the availability of broad variation for these traits. Rinon (PI 118783), Turrialba, Purple Calabash and LA2102 were among the high TTA (>0.45%) containing accessions, whereas those with high TSS (>7.0%) were AVRDC#6, Sponzillo and LA2102. A positive correlation of overall flavour with TTA (r= 0.33; P< 0.05) and TSS (r= 0.37; P< 0.05) indicated that these two components play an important role in determining the overall flavour in tomato. Subjectively measured other traits including fruity odour and fruity flavour had positive correlations with overall flavour. Overall flavour is discussed in the context of other traits including fruit firmness. Information obtained from this study may be useful for tomato breeders aiming to improve tomato flavour.

In areas with less favourable conditions for agriculture, informal seed systems permit gene flow through pollen to play a crucial role in the development of new varieties. An important factor with great impact on cross-pollination is the plant breeding system, but so far this is little studied within the context of low-input farming systems. This research studied the chances of cross-pollination within and between rice fields in The Gambia. Size and time of flowering were measured for 28 rice fields in one village. The level of mixture was measured in 90 seed lots of rice collected from four villages. Based on the results, we suggest that in general cross-pollination between different rice genotypes occurs more often within fields than between fields. No clear relationship was found between the level of within-field mixture and socio-economic status of farmers. Some comparison was made with millet, which allowed the identification of various factors influencing pollen flow between different genotypes. Effective pollen flow (between genotypes) is a function of a number of factors, such as the rate of cross-pollination of a crop, number of off-types within fields, variety distinctiveness, farmer expert knowledge, length and reliability of the rainy season, growth duration of different varieties, availability of fields, pest pressure and number of varieties grown per field or per farmer. We hypothesize that a low cross-pollination rate is more favourable for the development of new varieties in farmer fields than a high cross-pollination rate.

Protein energy malnutrition (PEM) is prevalent in south-east Asian countries including India. Breeding and introduction of grain protein-rich varieties of legumes such as dolichos bean is considered as cost-effective approach to combat PEM. Exploitation of genetic variability within germplasm accessions (GAs) and/or breeding populations is the short-term strategy for identification and delivery of protein-rich dolichos bean cultivars to cater to the immediate needs of the farmers and target population. A set of 118 dolichos bean genotypes consisting of 96 GAs and 20 advanced breeding lines (ABLs) and two released varieties (RVs) was field evaluated in augmented deign for dry grain yield per plant and their grain protein contents were estimated. The grain protein content among the genotypes ranged from 18.82 to 24.5% with a mean of 21.73%. The magnitude of estimates of absolute range, standardized range, and phenotypic coefficient of variation (PCV) for grain protein content was higher among GAs than those among ABLs + RVs. However, average grain protein contents of GAs were comparable to those of ABLs + RVs. Nearly 50% of the genotypes (mostly GAs) had significantly higher grain protein content than those of RVs, HA 3 and HA 4. The grain protein contents of the genotypes were poorly correlated with grain yield per plant. These results are discussed in relation to strategies to breed grain protein-rich dolichos bean cultivars.

‘Sikkim Primitive’ (SP) maize locally known as ‘murali makkai’ in Sikkim is a unique genetic resource exhibiting prolificacy and excellent popping capacity. Status of SP has reached extinction level due to its very small population size and neglected conservation efforts in-situ. In an initial effort to conserve and revive this landrace, characterization and documentation was carried out with 31 morphologically assayed traits recorded at different growth stages along with molecular characterization with simple-sequence repeat (SSR) markers. Plants exhibited prolificacy (5–6 cobs/plant) and excellent popping capacity along with other distinct traits. Plants were tall with thin stem, loose drooping tassel with anthocyanin coloration present at the base of glumes and in brace roots. Cobs were medium sized carrying small seeds with low test weight (87.90 g). A total of 22 SSR markers show amplification in murali makkai with markers bnlg1083, umc1353, umc1128, bnlg1017, bnlg2077, umc2298 and umc2373 amplified unique amplicons ranging from 100 to 800 bp. The characterized set of traits and molecular characterization for murali makkai will facilitate in utilization for genetic improvement and maintenance of genetic purity.

Knowledge of the genetic diversity and relationships among maize inbred lines can facilitate germplasm management and plant breeding programmes. The study investigated the level of genetic diversity among S6 lines developed from a tropical-adapted shrunken-2 (sh-2) maize population and their relationship with normal endosperm tropical inbred lines of known heterotic groups. Ninety-one sh-2 maize inbred lines (UI1-UI91) developed in the University of Ibadan super-sweet Maize Breeding Programme were genotyped at 30 simple sequence repeat (SSR) loci, alongside five normal endosperm maize inbred lines viz. TZi3, TZi4, TZi10, TZi12 and TZi15, four of which belong to two heterotic groups. Twenty-three SSR markers were polymorphic and detected a total of 61 alleles, with a range of 2–7 and an average of 2.65 alleles per locus. The polymorphic information content ranged from 0.12 in bnlg1937 to 0.77 in phi126, with an average of 0.36. The gene diversity (He) averaged 0.43. Cluster analysis resulted in five groups consisting of 16, 36, 17, 23 and 3 inbred lines, with one sh-2 line ungrouped. TZi 12 and TZi 15, both of which are of the same heterotic group, clustered with TZi 3 of another heterotic group. Considerable genetic diversity exists among the 96 inbred lines. Only two of the five normal endosperm lines shared clusters with the sh-2 lines. The clustering of the normal endosperm inbred lines is not related to their established heterotic patterns. Inbred lines in two clusters offer the possibility of guiding the exploitation of heterosis among the sh-2 lines.

Grewia tenax locally known as ‘Gangerun’, is an important multipurpose underutilized shrub and potentially threaten species of the Thar Desert of India. Owing to its importance, naturally available germplasm was collected and evaluated for its sustainable utilization in future. Data on individual mother plant, seed characters and soil profile were investigated. Habitat occurrence of G. tenax was found in patches with dominant association of Euphorbia caducifolia across the four districts of western Rajasthan. Individual plant on unprotected area portrayed far lower average height (0.95 m) and canopy area (1.75 m2) than protected area (2.63 m and 13.89 m2) signifying level of browsing pressure on this species in Jaisalmer. Soil samples belonging to Pali region have high organic carbon and low electrical conductivity content than Jaisalmer and Jodhpur. The statistical analysis of seed characters revealed the presence of high coefficient of variation (%) in 100-seed weight (HSW; 27.36) followed by seed length (SL; 8.06) and least in seed breadth (SB; 5.85). The range and mean values of HSW, SL, SB and length:breadth ratio (LBR) were (2.02–7.00 and 3.34 g), (4.36–6.15 and 5.36 mm), (3.73–4.68 and 4.25 mm) and (1.11–1.44 and 1.27), respectively. Significantly positive correlation was observed between SL and LBR (0.73) followed by HSW and SL (0.66). Along with these findings, its economic importance, utilization and conservation are detailed in this paper as to hasten further research on its various aspects for its successful conservation and utilization.

Paphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

Direct sowing of rice in a flooded paddy field is a beneficial cultivation practice for water use and labour efficiency, compared to the transplanted cultivation. However, a drastic reduction in seedling emergence under flooded paddy fields is a serious constraint especially when the seeds fell at deeper soil layers. Suitable rice germplasm for the direct sowing in flooded paddy fields could ensure the success of this cultivation practice. Instead of laborious field-based screening systems, a pot-based screening method was adopted for simplicity and efficient evaluation of seedling emergence of a subset of world rice germplasm (n = 75) at different sowing depths. As a result, two rice genotypes, ‘Vary Futsi’ (landrace from Madagascar, non-glutinous, subspecies Indica) and ‘Dahonggu’ (landrace from China, non-glutinous, subspecies Indica), with consistently better seedling emergence were identified from a wide range of rice germplasm. These genotypes could serve as excellent parents for the breeding program in developing new rice cultivars with the improved seedling emergence in flooded paddy fields. There were no significant differences in the seedling emergence rate in flooded paddy conditions among the groups from various agro-geographical regions.

Common lilac is a popular landscape plant with nearly 2000 cultivars. In the present study, nine novel polymorphic microsatellite markers were developed for common lilac using genome screening with inter-simple sequence repeat primers. Each of the nine markers revealed two to five alleles. The markers were used for genotyping of 75 common lilac shrubs, including 17 accessions that represented named cultivars. A dendrogram, based on the allele profiles of the shrubs, was generally in agreement with the grouping made on the basis of morphological traits, as well as with the pedigree information available. The novel markers appear valuable for differentiation between common lilac cultivars.

At 50% maturity, regenerating Senna species were characterized for morphological traits, seed reproduction, and evaluated for regeneration. Quality plants regenerated from all accessions produced 1018 to more than 21,215 total seeds. Principal component analysis revealed which traits contributed the greatest to variability among coffee senna accessions. Senna species have potential to produce pharmaceutical products and can be grown as medicinal plants. The flavonoids quercetin and kaempferol found in Senna species have been clinically shown to have anti-pancreatic cancer properties.