The purpose of this study is to identify key home garden species in order to address basic research questions aimed at understanding farmers' home gardens management practices. The study was conducted in two contrasting Hill and Tarai sites in Nepal with households (HHs) ranging from 355 to 634. Unlike larger production systems, home gardens harbour many species in small areas often with a few crop varieties and species that are not well represented in larger fields. Given the number of species and their small population sizes, species and genetic diversity are best studied by identifying representative key species characterizing the complex productive niches within farms. Although species diversity within community is large (172–342), 24 key species were identified for the study. There is no fixed size of a home garden. The log of home garden size and species richness was positively correlated (r = 0.42, P < 0.001). Species richness was significantly higher in vegetable followed by fodder, fruits and spices. This paper also explores the diversity in home gardens to identify the composition and characteristics of the key species and how they are managed, used and conserved. Most of the farmers save the seeds of these home garden species for their own use, but many also exchange and buy and sell seed in local weekly market. Farmers' practices for selecting seed vary according to the reproductive biology of the key home garden species. Home gardens provide the HH with fresh and diverse supply of nutritious food, which improves their self-sufficiency, while conserving diversity on-farm. Despite this, they are neglected in research and development by policy makers and researchers.

Guava (Psidium guajava) and araçá (Psidium spp.) plants are important for the Brazilian economy, as their fruit is both accepted by the consumers, and makes a beneficial contribution to the human diet thanks to their content in vitamin C, carotenoids and phenolic compounds. Here, we report the content in the fruit of free ascorbic acid, lycopene, β-carotene, flavonoids and phenolic compounds, and the total antioxidant activity present in a collection of guava and araçá accessions curated at the Embrapa Semiarido germplasm bank. Guava fruits with a red-coloured pulp flesh contained a significant amount of carotenoids, especially lycopene, and a high concentration of phenolic compounds. These compounds were largely responsible for the antioxidant activity of the araçá accessions. Among the guava accessions, phenolic compounds were also responsible for the antioxidant activity. High levels of free ascorbic acid were present in most accessions. In both guava and araçá, there is substantial potential to develop cultivars with a good level of consumer acceptability.

Eruca vesicaria subsp. sativa (syn. E. sativa) is a cruciferous vegetable and oilseed crop that is high in erucic acid. It occurs throughout the Mediterranean region and western Asia, and has been naturalized elsewhere as a crop/weed escape. It is closely related to subsp. vesicaria and subsp. pinnatifida, which are endemic to Spain and north-western Africa, respectively. This study evaluated patterns and levels of diversity in the three subspecies based on 234 amplified fragment length polymorphisms (AFLP), and evaluated agronomic and seed quality data in a field trial in western Canada. AFLP data revealed three main clusters: ‘Sativa’ (33 accessions of subsp. sativa), ‘Vesicaria’ (nine accessions of subsp. vesicaria) and a ‘Pinnatifida’ cluster (one accession of subsp. pinnatifida and three Moroccan accessions of subsp. sativa). The Sativa cluster separated into Mediterranean and Asian groups, likely reflecting differences in origin (wild versus cultivated) or primary usage, vegetable versus seed oil. The origin of the introduced Mexican population was confirmed as subsp. sativa. The highest levels of diversity were found in the Sativa cluster (88% AFLP polymorphisms) and the least in the Vesicaria (56%) and Pinnatifida (39%) clusters. Extensive variation was observed among the 159 subsp. sativa accessions evaluated in the field trial, and overall findings indicated a favourable agronomic potential.

Regional distributions of crop diversity are important to take into account for the spatial design of in situ, farmer-participatory interventions in crop genetic management. Regional seed flows are an important factor in shaping geographical distributions of crop diversity. This study contributes to the insight in these seed flows, focusing on maize (Zea mays L.) in Chimaltenango, an area in the western highlands of Guatemala. A social survey of 257 households on different aspects of seed management produced information on cultivar naming, seed sources, reasons and causes of the discontinuation of seed lots, and important explanatory variables associated with different seed sources. A small portion of the reported seed lots originated from regional seed sources. The main motivation of regional seed exchange and the discontinuation of seed lots was to achieve change in plant characteristics of the crop, especially to obtain lower plants and shorter growing cycles. It is argued that farmer selection fails to achieve such change, and in fact leads to an equilibrium with high plants and long growing cycles. Seed exchange functions as an escape to this trend. Other factors of influence on seed exchange are altitude and ethnicity. The study also highlights the issue of geographical directionality in seed exchange patterns.

Mungbean seeds, despite being protected inside the pod, are susceptible to pre-harvest sprouting (PHS) following rainfall due to lack of fresh seed dormancy (FSD), which deteriorates the quality of the seed/grain produced. Therefore, development of mungbean cultivars with short (10–15 days) period of FSD has become important to curtail losses incurred by PHS. In this study, we investigated variations in PHS, fresh seed germination (FSG) and activity of α-amylase enzyme in diverse mungbean genotypes. There was a wide variation in PHS tolerance and FSG among 163 genotypes examined and 14 genotypes were found to be tolerant (<20%) to PHS. Seed germination in a pod, a measure used to evaluate PHS, varied from 7.14% in germplasm accession Chamu 4 to 82.52% in cultivated variety IPM 2–3. There was a marked increase in α-amylase activity in genotypes showing high FSG and PHS, especially at 48 and 72 h after germination as compared with PHS tolerant genotypes. Therefore, α-amylase can be used as an effective biochemical marker to evaluate a large number of mungbean genotypes for FSD and PHS. Also, the variation in seed germinability as found in this study could be further used for mungbean improvement programme.

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

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.

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.

Soft wheat (Triticum aestivum L.) improvement could be enhanced by the identification of germplasm with superior end-use quality traits. Due to the geographic and historical separation of eastern and western US soft wheat germplasm ‘pools’, genetic differences in end-use quality may exist among cultivars arising from these two pools. To identify such differences, 30 US soft wheat cultivars were evaluated in ‘head-to-head’ trials over 3 years in Washington state. Cultivars were classified as: eastern soft red winter (SRW), eastern soft white winter (ESWW), western soft white (WSWW) and western Club. These four soft wheat cultivar classifications clearly differed systematically for some of the quality traits examined. The Club wheat cultivar group had the highest flour yield and flour ash. The Club group also had the lowest mixograph dough water absorption. Milling score (which incorporates break flour yield) was highest for Club and ESWW. Eastern soft red and white wheat cultivar groups had lower flour ash and alkaline water retention capacity (AWRC) compared to the western Club and soft white wheats; ESWW had the lowest AWRC of any classification. Cookie diameter was greatest for the ESWW group, followed by the SRW and Club groups (which were not significantly different), and then by the WSWW group. Individual cultivars with exceptional quality traits were also identified. These results indicate that the four US soft wheat germplasm pools differ, and they may be valuable genetic resources for ‘inter-pool’ wheat improvement.

A world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.

Wild and managed bees are needed to move sunflower (Helianthus annuus L.) pollen, both to create hybrid seed and to encourage high, consistent yields when those hybrids are subsequently grown. Among floral traits that influence bee preference, floret size may be critical, as the depth of the corolla affects the accessibility of nectar. Sampling and observation of inbred maintainer (HA) lines were used to assess variation in floret size, and to measure any effects of floret size on pollinator visitation. Among 100 inbreds sampled, there was significant variation among the lines, with floret lengths of 6.8–9.9 mm. Floret length, measured before anthesis, was closely related to corolla depth during anthesis and was consistent between 2 years (environments). Pollinator observations on 30 inbred lines showed floret size explained a majority (52%) of the variation in wild bee preference, with a reduction in floret length of 2 mm more than doubling pollinator activity. Though honey bee, Apis mellifera L., colonies were located ≈ 60 m from the plots, near-zero honey bee activity in the sunflowers precluded an assessment of how strongly this managed pollinator is affected by floret length. Production of inbreds and hybrids with smaller florets could enhance sunflower pollination, but genetic markers for floret size are needed to facilitate selection, and an understanding of potential trade-offs also is required. Information on variation and heritability of other traits, such as pollen and nectar rewards, could help explain residual variation in wild bee visitation to sunflowers.

Helianthus annuus and H. petiolaris (Asteraceae) are wild sunflowers native to North America but have become naturalized in central Argentina covering an area of about 5 million hectares. Wild H. annuus has been recognized as invader species in several countries, but no research has been done to study the ecological determinants of their distribution. In a survey covering seven provinces between 31°58′–38°S and 60°33′–69°W, we described the ecology of the main wild populations. Wild Helianthus populations were located in three of the 18 ecological regions of Argentina, on five Mollisol and seven Entisol soil groups. The associated plant communities were comprised 60 species belonging to 16 families, all being frequent components of the native flora. Disease symptoms were seldom observed in wild populations, with Alternariahelianthi being the most commonly observed pathogen. Population size varied from less than 100 to more than 100,000 plants, covering from 100 to more than 60,000 m2 with densities most frequently up to 3 plants/m2, but reaching 80 plants/m2 at certain sites. Intermediate plant phenotypes between wild species and cultivated sunflower were found in one-third of the populations providing evidence of intense gene flow. Hybrid swarms were found at three localities with population sizes between 100 and 10,000 individuals.

Within the cultivated peanut species (Arachis hypogaea L.), there are two subspecies comprising six botanical varieties, and the effect of botanical taxon on oil content and fatty acid composition variability is unclear. To gauge the variability, 83 peanut accessions were analyzed for oil content (expressed at 0% moisture) and fatty acid composition. We found that within the subsp. hypogaea, var. hypogaea contained a much higher amount of oil in seeds than did the var. hirsuta Köhler (520 vs. 473 g/kg, P < 0.05); within the subsp. fastigiata Waldron, the vars. aequatoriana Krapov. & W.C. Gregory and vulgaris Harz contained a similar amount of oil in seeds (491 g/kg), not significantly different from other botanical varieties, but var. fastigiata contained a higher amount of oil (500 g/kg) than the var. peruviana Krapov. & W.C. Gregory (483 g/kg). In terms of the fatty acid composition, oil from seeds of var. hypogaea contained much more oleic acid than did var. hirsuta (491 vs. 377 g/kg, P < 0.05), but much less palmitic acid (97 vs. 138 g/kg, P < 0.05%) and linoleic acid (308 vs. 402 g/kg, P < 0.05). Oil from seeds of var. vulgaris contained much more oleic acid than did var. aequatoriana (437 vs. 402 g/kg, P < 0.05), but much less linoleic acid (346 vs. 380 g/kg, P < 0.05). Significant negative correlations of oleic with palmitic and linoleic acids were detected. The information on the oil content and fatty acid composition variability among botanical varieties would be useful for peanut breeders seeking germplasm containing both high oil content and proper fatty acid composition.

To promote the utilization of West and Central African (WCA) genetic resources of pearl millet [Pennisetum glaucum (L.) R. Br.], this study aimed at agro-morphological characterization of selected accessions from the pearl millet reference collection, established by the Generation Challenge Program and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). A total of 81 accessions were included, comprising 78 landraces originating from 13, predominantly WCA countries and three improved cultivars. All 81 accessions were evaluated together with 18 checks for resistance to the parasitic weed Striga hermonthica (Del.) Benth. in an artificially infested field at one location in Niger. Determined by available seed quantity, 74 accessions were characterized together with seven checks in the rainy season 2009 in field trials under low-input and fertilized conditions in Nigeria, Niger and Mali, respectively. Wide ranges were observed for various traits. Several accessions were identified as sources for specific traits of interest, i.e. long panicles, high-grain density, earliness, Striga resistance and stable yielding across environments. The observed yield inferiority of all Genebank accessions compared with checks may indicate lost adaptation or inbreeding depression due to an insufficient effective population size during multiplication. A principal component analysis revealed an immense diversity but also strong admixture among the tested accessions, i.e. there were no clearly distinct groups. The seed of all genotypes is available from ICRISAT. The online availability of the characterization data is expected to facilitate efficient use of these pearl millet accessions by breeding programmes in WCA and worldwide.

Both stover and grain are important considerations in the adoption of the new pearl millet (Pennisetum glaucum) cultivars in crop–livestock farming system in north-west India. Local landrace germplasm contains many of the traits needed to breed new cultivars, which met such requirements. We evaluated 169 pearl millet landraces to assess their potential for breeding new open-pollinated varieties, and measured heterosis in landrace testcrosses to evaluate their potential for topcross hybrids breeding. There were significant differences among landraces in their total biomass, grain yield and stover yield. A high accumulation of biomass, followed by its efficient partitioning, was crucial in determining grain productivity under arid zone. There was also no trade-off between stover and grain productivity and several landraces outperformed check cultivars in both grain and stover yields. The manifestation of heterosis in the landrace-based topcross hybrids varied for different traits. Significant heterosis for biomass, grain yield and stover yield was observed in specific male-sterile seed parent × landrace-based pollinator combinations. Utilization of landraces in variety development and topcross hybrids breeding programmes targeting north-western India or similar regions are discussed.

To assess the genetic diversity of spinach germplasm, 250 individuals of 50 accessions collected from geographically diverse regions (West Asia, East Asia, Japan, Europe and the USA) were analysed using simple sequence repeat (SSR) markers. A total of 39 polymorphic alleles were identified, with an average of 6.5 alleles per locus for six loci. The overall gene diversity (0.62) in the entire set of individuals suggests that the germplasm has high genetic variability. The West Asian accessions showed the highest gene diversity, with a value of 0.57, followed by the East Asian accessions. These results help confirm the notion that spinach originated from West Asia. Hierarchical analysis of molecular variance revealed significant genetic differentiation among the geographical regions, which accounts for 26% of the total variation detected. Furthermore, pairwise Φst values indicate low genetic differentiation between the East Asian and Japanese germplasm accessions, both of which showed high genetic differentiation from the European accessions. The differentiation between the East Asian and European gene pools may be attributed to the founder effect associated with crop dissemination, as well as to the selection and genetic drift that occurred during the breeding process.

Snow mould caused by Microdochium nivale (Fr.) Samuels & Hallett is the most widespread seedling disease in winter cereals. Due to the complexity of the resistance mechanisms, a poorly understood genetic background and strong interaction with winter weather conditions, it is difficult to assess the resistance of triticale cultivars via conventional inoculation methods. Genetic resistance is the most economical and environmental friendly way to control M. nivale infection; therefore, the objective of this study was to detect the quantitative trait loci (QTLs) associated with resistance components of winter triticale in a mapping population derived from a cross of the ‘Modus’ (partly resistant) and ‘SaKa 3006’ (sensitive) varieties. High-resolution mapping was conducted by using 1518 molecular markers (diversity arrays technology, simple sequence repeat and amplified fragment length polymorphism). Partial resistance components assessed in this study, i.e. candidate QTLs, were detected on chromosomes 1B, 2A, 3A, 3B, 5A, 5B, 6A, 6B and 7B, whereas QTLs describing overall seedling vitality in non-infected control plants were located on chromosomes 1B, 2B, 3A, 5A, 7B and 7R.

The Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.

The present study is the first to compare the trait-level differentiation (Qst) and the molecular-level differentiation (Fst) between Malus× domestica and Malus sieversii. A set of 115 accessions representing M.× domestica (99) and M. sieversii (16) were genotyped using the International RosBREED SNP Consortium apple 8K SNP array and phenotyped for eight fruit quality traits in a clonally replicated experiment. A set of 3521 single nucleotide polymorphisms (SNPs) with an average call rate of 98% was retained following SNP data quality filters. About 86% of the total SNPs were polymorphic in M. sieversii, while all but three SNPs were polymorphic in M. × domestica. The patterns of linkage disequilibrium were different, especially at the longer distances, between the two species. No differentiation (Fst= 0) was observed for nearly 23% of the SNPs, but about 20% of the SNPs exhibited a high genetic differentiation (Fst≥ 0.15). A highly significant (P< 0.001) genome-level Fst= 0.12 was observed between M. × domestica and M. sieversii. The average estimated Qst value was 0.20 (range 0.08–0.40), and for three of the eight studied traits (crispness, flavour intensity and fruit weight), Qst value was more than twice the estimated genome-level Fst value. A higher Qst value than Fst value for four of the eight fruit quality traits indicated differential (or directional) selection for these traits in M. × domestica. The average posterior probability of assignment of M. × domestica accessions to the M. sieversii gene pool was 11%, supporting the hypothesis of M. sieversii being one of the progenitors of the domesticated apple.