Despite Capsicum's importance in the Caribbean, comprehensive diversity studies of this species in the region are limited, especially regarding its morphological variation. This study evaluated 37 traits (seedling, vegetative and reproductive) in 201 accessions among four Capsicum species. Multivariate analyses revealed that (i) 54% of the quantitative (seedling and fruit) variation and (ii) 64% of the qualitative (floral and fruit) variation were explained by the first two components. The three main clusters identified did not immediately highlight geographic and species-specific separation. However, significance testing revealed some separation based on geographic subgroups and species assignment. Most Southern Caribbean accessions were considerably similar to each other (if not identical in some cases), thus providing opportunity to identify and remove duplicates from the collection. These Southern Caribbean accessions shared their greatest similarity with Upper Amazon accessions, and least similarity with Lower Amazon accessions, suggesting movement of material primarily from the Upper Amazon into the Southern Caribbean Basin. The dominant differentiating traits displayed in these Southern Caribbean accessions are probably due to strong active selection for certain morphotypes and not to founder effects. Upper and Lower Amazon accessions were largely well differentiated from each other, highlighting key underlying genetic differences between these two populations and possible ongoing barriers to germplasm exchange. Central American, Greater Antilles/Bahamas and Guiana Shield accessions shared similarities with both the Upper and Lower Amazon populations, hinting at probable introductions from both Amazon regions. Collectively, this provides essential baseline information on the morphological (and underlying genetic) relationships among these accessions to guide future characterisation and evaluation efforts on this collection.

Rhazya stricta is an endangered medicinal plant that is under severe human pressure as a result of commercial harvesting. As a model of habitat fragmentation, we selected the Kohat Plateau in the Pakistani Himalaya, where populations are fragmented, with less than 100 individuals per population. We hypothesized that the populations may be threatened by rapid habitat fragmentation and by unsustainable utilization of the plant. We analysed P450-based analogue functional genomic markers and amplified fragment length polymorphism markers from six populations of R. stricta on the Kohat Plateau, and examined their variations both within and among the populations. Both the marker groups revealed lower genetic differentiation among the populations and higher genetic differentiation within the populations as a result of high gene flow. The results confirmed that habitat fragmentation is being caused by severe human pressure, and although signs of genetic erosion are not yet visible, they seem likely to become visible in the future. Therefore, the conservation of R. stricta populations is necessary.

Advances in sequencing technologies have made it possible to analyse large amounts of germplasm against low production costs, which has opened the door to screen genebank collections more efficiently for DNA sequence variation. The present study explores how these developments may affect the operations of genebanks and, consequently, how genebank agendas may change. It is argued that the new developments are more likely to have an impact on the user-oriented activities than the housekeeping operations of genebanks. To better facilitate the user community, genebanks may have to strengthen their core business, in particular, by improving quality management procedures and by providing access to a wider diversity of a crop's gene pool. In addition, genebanks may have to provide novel services, such as the introduction of specific user-oriented collection types, including research populations and genetically purified lines, and the development of novel information services, including plant genetic resources portals that should guide users to the information and materials of specific interest. To improve their user-oriented services, genebanks need to increase their communication and collaboration with the user community and to develop strategic alliances with this sector.

Lutein has significant nutritional benefits for human health. Therefore, enhancing soybean lutein concentrations is an important breeding objective. However, selection for soybeans with high and environmentally stable lutein concentrations has been limited. The objectives of this study were to select soybeans with high seed lutein concentrations and to determine the stability of lutein concentrations across environments. A total of 314 genotypes were screened and 18 genotypes with high lutein concentrations and five genotypes with low lutein concentrations were selected for further examination. These 23 genotypes and two check varieties were evaluated under six environments (two planting dates for 2 years at one location and two planting dates for 1 year at another location). Lutein concentrations were influenced by genotype, environment and genotype × environment interactions. Genotypes with late maturity and low lutein concentrations were more stable than those with early maturity and high concentrations. Early (May) planting resulted in greater lutein concentrations than late (June) planting. Among the genotypes evaluated, PI603423B (7.7 μg/g) and PI89772 (5.8 μg/g) had the greatest mean lutein concentrations and exhibited medium and high stability across the six environments, respectively. Thus, these genotypes may be useful for breeding soybeans with high and stable seed lutein concentrations.

Nagaland is one of the eight states in the north-eastern region of India, where a considerable diversity exists in cultivated rice. Recent exploration in this tribal-dominated state has resulted in a collection of 130 rice accessions growing under diverse agroecological conditions. The agromorphological characterization data of 124 rice landraces revealed a significant variability in plant architecture and grain morphological and quality traits. Multivariate analyses including principal component analysis (PCA) and cluster analysis were performed to assess the patterns of morphological variation. The PCA extracted 12 components, which explained 75.4% of the total variation for 38 quantitative and qualitative traits. The cluster analysis grouped 124 rice landraces into five clusters, and the number of landraces in each cluster ranged from 1 to 59. The correlations among the traits are discussed, which will be useful in considering traits for genetic improvement in grain yield and quality. The landraces have been conserved in the national genebank for further utilization.

Roselle (Hibiscus sabdariffa L.) is an economically important plant in Niger. Little is known about its genetic diversity and population structure. In this study, we performed the first diversity assessment of a collection of 124 roselle accessions and 16 accessions of its close relatives Hibiscuscannabinus and Abelmoschusesculentus. Our study was based on ten agromorphological traits and 267 amplified fragment length polymorphism markers. We identified two major distinct groups in H. sabdariffa using a Bayesian method. These two genetic groups were associated with statistical differences for three phenological characteristics: number of days to flowering, 100-seed weight and calyx size. However, the calyx colour, i.e. a morphological characteristic often used to classify different local ecotypes, did not superimpose this separation. Our findings suggested that roselle diversity is genetically structured; the two different groups were clearly associated with morphological differences but were not commonly used by farmers for their classification. The impact of the perceived ecotype structure and its consequence on farmer management is discussed.

In this study, 15 morphological traits and 16 microsatellite markers were used to assess the morphological variability and structure of 68 (33 local and 35 foreign) almond accessions (Prunus dulcis (Mill.) D.A. Webb). Extensive phenotypic diversity was found among the accessions, and results indicated a high variation in leaf and fruit traits. Varieties were separated into two distinct groups with a similarity coefficient of 0.761. Morphological traits were categorized by principal component analysis into five components, which explained 86.5% of the total variation. Nut and kernel traits were dominant in the two first components, accounting for 49.4% of the variation. By contrast, leaf traits accounted for 18.4% of the variation in the third component. The results of molecular analysis (Bayesian clustering approach) did not correspond to morphological groupings, and the second approach was more discriminate. The combination of both approaches revealed the richness among the collected plant materials, which will be useful in breeding programmes of this species.

An interspecific hybrid Jatropha curcas (Jc) × Jatropha integerrima (Ji) was developed between jatropha (Jc) from Mexico and Ji from Thailand. Jc is a large canopy plant with soft wood, while Ji is a tall plant with semi-hard wood. The F1 hybrid and their parents were grown under field conditions at a spacing of 1 m × 1.5 m. One-year-old plants were harvested and determined for biomass yield, calorific value and chemical composition of wood, as well as for heterosis (hybrid vigour) of these characters. The F1 plants gave an average fresh wood weight of 18.07 kg/plant, a moisture content of 46.56%, a dry wood weight of 9.56 kg/plant and a wood density of 0.62 g/cm3. The F1 hybrid had less ash (2.60%) than Jc (6.93%), but a higher heat value of wood (18.73 MJ/kg) than Jc (17.77 MJ/kg). Heterosis over mid-parent was very high and positive in dry wood weight, fresh wood weight and number of secondary branches at 542, 310 and 450%, respectively, while negative heterosis was found in moisture content ( − 24.86%). The desirable traits found in the F1 hybrid can be fixed by cutting propagation of the selected plants.

In this study, simple sequence repeats (SSRs) specific to marigold were developed using the inter-SSR technique and a SSR-enriched genomic DNA library. In addition, SSRs derived from sunflower (Helianthus annuus) were also tested for transferability to marigold. In total, 38 polymorphic markers with 112 observed alleles were identified in 20 African marigolds (Tagetes erecta L.) consisting of 14 commercial varieties and six Thai landraces, and six French marigolds (Tagetes patula L.). The number of alleles per locus ranged from 2 to 7. The averages of expected and observed heterozygosities were 0.48 and 0.32, respectively. Polymorphic information content values ranged from 0.10 to 0.71, and resolving power (Rp) values ranged from 0.23 to 2.77. The SSRs were successfully applied to the differentiation of the 26 marigold samples into clusters of African commercial varieties, Thai landraces and French marigold. The genetic relationship analysis revealed that the African commercial varieties were more closely related to the Thai landraces than to the French marigold. The results of the study indicate that the SSRs developed are effective for genetic diversity analysis, species classification and individual identification.

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

Yellow endosperm maize can be used to reduce vitamin A deficiency among many pre-school children and women of reproductive age in sub-Saharan Africa. Assessment of the genetic diversity of tropical yellow endosperm maize inbred lines will have genetic gains in breeding design to develop lines with an enhanced level of provitamin A. We screened 122 tropical yellow endosperm maize inbred lines with 62 simple sequence repeat (SSR) markers and 51 SSR loci were polymorphic. We detected 190 alleles with an average of 3.72 alleles per locus, and polymorphic information content values among the inbred lines varied from 0.12 to 0.74 with an average of 0.43. Genetic distance (GD) values among all the pairs of the 122 inbred lines varied from 0.02 to 0.61 with an average of 0.41 for the SSR markers. The inbred lines exhibited a substantial level of genetic diversity. Genetic diversity was also evaluated using carotenoid data. The Euclidean GDs varied from 1.00 to 9.97 with an average of 3.81 for the carotenoid data. Cluster and principal coordinate analyses revealed clear separation of maize inbred lines into SSR-based groupings and carotenoid-based groupings. Cluster based on SSR markers were predominantly consistent with known pedigree data of the inbred lines. The correlation using Mantel's test between carotenoid-based GD estimates and SSR marker-based GD estimates gave a low r value ( − 0.06). The grouping of lines will facilitate the selection of parental lines for making crosses to develop new lines with enhanced provitamin A content.

In order to highlight the genetic status and origin of Moroccan apricot populations, trees were collected from ten oasis agroecosystems and analysed with AFLP markers. A total of 87 accessions and 12 cultivars grown in Moroccan orchards, including ‘Canino’ and ‘Del Patriarca’ cultivars, were surveyed and compared with in situ Tunisian and ex situ Montfavet (France) collections. Our results highlighted a narrow genetic diversity in the Maghreb region (Tunisia and Morocco) associated with a strong differentiation from the other groups, which supports a bottleneck effect. A similar model was illustrated at a finer geographical scale, i.e. the Draa Valley in Morocco. Genetic structure appeared as two major clusters subdivided into six sub-clusters in which Moroccan germplasm constituted specific groups in comparison with other Mediterranean apricots. Moroccan germplasm was classified into three sub-clusters, two of which were formed by genotypes related to ‘Del Patriarca’ and ‘Canino’, respectively. The present study highlights the wide Moroccan apricot's diversity in traditional agroecosystems, and also suggests a substantial gene flow occurring from recently introduced cultivars (‘Canino’ and ‘Del Patriarca’) to local apricot populations, thus leading to local germplasm diversification through seedling propagation. If we consider its geographical position, the historical diffusion of the species and farming practices, Morocco could be viewed as an additional centre of secondary diversification for apricot. Understanding the origin and specificity of local apricot populations is crucial for managing local collections in regard to adaptive traits for arid and Saharan conditions as well as for introducing local genetic resources into current breeding programmes.

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

The International Crops Research Institute for the Semi-Arid Tropics conserves 335 accessions of Pennisetum glaucum subsp. monodii originated in 13 countries. In the present study, the collection was evaluated and assessed for diversity and geographical gaps. A wide variation was observed in the collection for total tillers per plant (16 to 609), productive tillers per plant (12 to 368), leaf length (21.3 to 58.8 cm) and leaf width (8.1 to 33.1 mm), indicating high fodder yield potential of the collection. The accessions of cluster 3 flowered late, grew tall with thick stems and long and broad leaves, and differed significantly from those of cluster 1 and cluster 2. The accessions of cluster 2 were found to be promising for tillering. The highly significant positive correlation (r= 0.944) between total and productive tillers per plant suggests that the selection for total tillers will result in selection for productive tillers. A total of 354 districts located in 86 provinces of eight countries in the primary centre of origin for pearl millet were identified as geographical gaps. The probability map generated using FloraMap in the present study matched quite closely to the origin of pearl millet, supporting the prediction of P.glaucum subsp. monodii occurrence in the primary centre of diversity for pearl millet. The high fodder yield potential of P.glaucum subsp. monodii germplasm and low intensity of collection in countries under study suggest the need for launching germplasm collection missions, exclusively for pearl millet wild relatives to fill taxonomic and geographical gaps in the collection.

In order to investigate further the interest of using the Chilean gene pool in potato breeding programmes, the genetic diversity and population structure of a collection of Solanum tuberosum L. genotypes including 350 worldwide varieties or breeders' lines (referred to as the modern group) and 30 Chiloé Island landraces were examined using simple sequence repeat markers. The close genetic proximity of the Chiloé Island landraces to the modern group was confirmed using several structure analysis methods: principal coordinate analysis; hierarchical clustering analysis; analysis of molecular variance; Bayesian model-based clustering analysis. The latter analysis, in particular, revealed no clear genetic structure between the modern group and the Chiloé Island landraces. The Chiloé Island germplasm appears to represent an interesting gene pool that could be exploited in potato breeding programmes using an association mapping approach.

Microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. Although several MTI responses can be measured in different plant species, their magnitude is probably plant species specific and even cultivar specific. In this study, a genome-wide transcriptome analysis of two soybean parental lines and two progeny lines treated for 30 min with the MAMPs flg22 and chitin was carried out. This analysis revealed a clear variation in gene expression, under both untreated and flg22+chitin-treated conditions. In addition, genes with potential additive and non-additive effects were identified in the two progeny lines, with several of these genes having a potential function in the control of innate immunity. The data presented herein represent the basis for further functional analysis that can lead to a better understanding of the soybean innate immunity response.

Phenotyping of genetic resources remains the bottleneck in the characterization of genetic resources, since the advent of modern next-generation sequencing technologies has made genotyping much more cost- and time-effective. This article reports on the phenotyping of agriculturally important traits in perennial ryegrass (Lolium perenne). In the present study, water-soluble carbohydrate (WSC), crude protein and dry matter contents were recorded for 1320 individuals, pooled into 132 samples from 33 perennial ryegrass ecotypes and cultivars at five different harvest time points across the 2004 growing season. While, in general, the cultivars had higher WSC contents than the ecotypes, individual ecotypes did show potential to be used in breeding programmes, as they had higher values than all other accessions at particular cutting time points. In correlation analyses, positive relationships were observed between dry matter and glucose contents both early and late in the growing season. Principal components analysis allowed the split either between cultivars and ecotypes or between tetraploid cultivars and the rest of the accessions at four of the five cutting time points. In the analysis of variance, cutting time was the most significant factor influencing the variation in traits.

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.

Triggered by the need to develop inter-seasonal, multi-cut cereal forage crops, this study aimed at the exploitation of phenotypic variations among the rich pearl millet (Pennisetum glaucum L.) collections in Sudan for possible utilization in forage-type breeding programmes. A total of 100 pearl millet accessions were used in three field trials grown in rainy, winter and summer seasons (2008–2009) at the Gezira Research Station Farm and the Gezira University Experimental Farm. Wide diversity and highly significant differences in the total dry forage yield, days to harvest, plant height, number of tillers/plant and leaf/stem ratio were found among the accessions. At an 80% morphological similarity level, the 100 accessions of pearl millet were clustered into four main groups. In the rainy and winter seasons, 71 and 56% of the accessions produced forage yield of more than 5 t/ha, respectively. In contrast, 77% of the accessions produced less than 5 t/ha in the summer season. Among the top-ranking 25 accessions, two accessions (HSD 2190 and HSD 2236) were common in dry matter yield in the three seasons, whereas 11 accessions were identified in at least two seasons. The presence of such common accessions in more than one season is encouraging for growing pearl millet as a multi-cut crop for a longer period. These results indicated the possibility of the development of forage-suited varieties of pearl millet directly through further evaluation of those common accessions or indirectly through a crop breeding programme.

The wheat landraces collected by Dr Hitoshi Kihara et al. from Afghanistan, the place of secondary origin of wheat, are an untapped genetic resource for mining novel alleles. In this study, approximately 400 landraces were collected from seven agroecological zones and characterized using diversity array technology and single-nucleotide polymorphism markers, as well as diagnostic molecular markers at important loci controlling vernalization (Vrn), photoperiod response (Ppd), grain colour (R), leaf rust (Lr), yellow rust (Yr), stem rust (Sr) and Fusarium head blight (Fhb). A genome-wide marker array revealed a large amount of genetic diversity among the landraces, 53% of which were winter types, 43% were either spring types or facultative and 4% were either unknown or had Vrn-A1c – a rare spring allele that needs to be confirmed with additional genotyping and phenotyping. At Ppd, 97% of the lines carried a photosensitive allele. In the case of grain colour, classification based on dominant or recessive allelic combinations revealed that approximately 39% of the population is characterized by white grain. Four gene-specific markers that were targeted to identify loci for rust and Fhb resistance enabled us to identify 17 unique landraces with known resistance genes.