Development of core collection representing the diversity in the entire germplasm creates a better access and enhanced utilization of the main collection thus allowing rapid evaluation in crop improvement programs. Core collections are dynamic in nature and needs revisiting when additional germplasm and information becomes available. In the current study, an attempt was made to re-define the previously developed yam (Dioscorea spp) core collection using 56 morphological traits. Information on additional acquired germplasm and presence of duplicates or mislabelled accessions in the entire collection was also used. The re-defined core collection consisted of 843 accessions and represented about 20% of the entire collection. It included six Dioscorea species, of which accessions of Dioscorea rotundata are in the majority (73.54%) followed by Dioscorea alata (21.35%), Dioscorea bulbifera (1.66%), Dioscorea cayenensis (1.42%), Dioscorea dumetorum (1.42%) and Dioscorea esculenta (0.59%). The Shannon weaver diversity index and principal component analysis revealed the maximum diversity captured in the core from the base collection. This re-defined core collection is more valuable than the original core since it represents true-to-type accessions ensuring reliability for enhanced utilization of germplasm in yam improvement programs.

Drought is the major abiotic constraint to the rice production in the rain-fed areas across Asia and sub-Saharan Africa. Wild species of Oryza offer a wide spectrum of adaptive traits and can serve as potential donors of biotic and abiotic stress tolerance. At the Punjab Agricultural University, we are maintaining an active collection of 1630 accessions of wild species germplasm (AA, CC, BBCC and CCDD) of rice. These accessions were screened to assess genetic variation for drought tolerance under field conditions. Severe water stress was imposed at the late vegetative stage by withholding water initially for 25 d and then extended further to 35 d during kharif season in the years 2013–14 and 2015–16. The tolerance score for drought stress was based on the extent of leaf rolling and leaf drying. Based on the 2 years’ data, seven accessions from Oryza rufipogon, four from Oryza longistaminata and one each from Oryza officinalis and Oryza latifolia were found tolerant to drought stress. These selected accessions were further phenotype for root morphology. The average root length among the selected accessions ranges between 36 and 80 cm and the number of primary roots vary from 30 to 87 cm. The O. rufipogon accession IRGC 106433, O. longistaminata accession IRGC 92656A, O. officinalis accession IRGC 101152 and O. latifolia accession IRGC 80769 showed approximately 2–2.5 times longer root length and number than the indica rice elite cultivar PR121. The results indicated potentiality of selected wild species germplasm for conferring drought tolerance to the elite cultivars.

A five-point drought stress screening methodology for muskmelon based on visual observation has been standardized by modifying an earlier field screening method. The scale (1 to 5), were categorized into five groups, namely, highly drought tolerant (1), drought tolerant (2), average drought tolerant (3), drought susceptible (4) and highly drought susceptible (5). To validate and standardized the technique, 48 genotypes of muskmelon were evaluated for two successive years. Important physiological parameters, i.e.: relative water content (RWC), electrolyte leakage, photosynthetic efficiency (Fv/Fm), chlorophyll concentration index (CCI), root and shoot length were measured and correlated to make screening results more reliable. Drought tolerance efficiency of genotypes was calculated based on yield, and drought-tolerant genotypes were identified with better yield efficiency and ranking on visual scale. Whereas, yield efficiency of some drought-tolerant genotypes were less, althouth they came under drought-tolerant scale. Being a tolerant genotype, these may not be economical for commercial cultivation. Under water-deficit condition a significant positive correlation was observed between drought tolerance efficiency, and RWC, Fv/Fm, CCI and root length. Out of 48 genotypes, 14 genotypes were came under highly drought-tolerant category based on 5 point scale.

The objectives of this study were to analyse the maize diversity in the southeast of Coahuila State in Mexico and to identify a representative subset that encompasses the majority of the diversity in the region of study. Seventy-seven native maize populations were first explored and given a race classification followed by a morphological description based on selected quantitative ear traits using 10 representative ears from the collected samples. The differences between maize populations from the adaptation area and the relationships between and within groups in the region of study indicate the usefulness of the ear traits to describe maize diversity. Two main groups were identified that summarized the maize diversity. The first group, the conical ear complex, includes populations adapted to highland altitudes (Conico Norteño Race). The second group, the cylindrical ear complex, represents populations adapted to lowland and intermediate altitudes (Raton and Tuxpeño Norteño). Using the phenogram, a subset of 18 out of the 77 maize populations (23.4%) was defined that accounts for the variation between and within the different race complexes. This subset also includes at least one representative population from each of the less represented types. The final subset, representing a sample of maize diversity, can be used to establish strategies for conservation and use, such as participatory conservation and management, or it can be used to develop breeding techniques for improving the land race populations within the region of study.

Seed composition, including the protein, lipid and sucrose contents of 334 accessions of wild soybean (Glycine soja) collected in Japan, was evaluated using near-infrared reflectance spectroscopy (NIRS) technology. The distribution of protein, lipid and sucrose contents and correlations among these three classes of seed components were determined. Protein, lipid and sucrose levels ranged in accessions from 48.6 to 57.0, 9.0 to 14.3 and 1.24 to 3.53%, respectively. Average levels of protein, lipid and sucrose in the accessions were 54, 11 and 2.5%, respectively. High negative correlations were observed between the protein and lipid contents, and the protein and sucrose contents. Mean levels of the three constituents were compared among collection sites classified by climatic conditions. The total protein content of accessions from regions with a high annual mean temperature was high. The protein content of accessions from the II-1 region was higher than those from the III-3 region, and the sucrose content from the II-1 region was lower than those from regions III-2 and IV-3. The lipid content of plants from the II-1 region was lower than those from other regions, and the accessions in region II had a higher protein content and lower sucrose and lipid contents than the other regions. These results provide diverse and wide-ranged protein, lipid and sucrose contents information of Japanese wild soybean resources according to climatic region; thus, providing a foundation for the future development and selection of new soybean varieties with desired traits in global environmental changes.

There is extensive duplication of accessions among collection holders globally. To save costs, unwanted duplication should be avoided. This issue has been addressed internationally. In Europe, there are currently 35 Brassica collections located in 24 countries. Duplication may be identified not only by surveying passport data and seed transactions, but also by applying morphological or genetic characterization. Our study included two collections; one at the N. I. Vavilov Institute of Plant Genetic Resources in St. Petersburg (VIR) and one at the Nordic Genetic Resource Center (NGB). A random set of 13 accession pairs or triplets of cabbage, turnip and swede were selected on the basis of identical or similar accession names. The accessions could potentially be regarded as duplicates. Morphological characterization showed that in about 50% the pair/triplet, the accessions were identical and should thus be regarded as duplicate holding. Determining the status of the remaining accessions, which were more or less distinct but had identical or similar names, was more difficult. In this paper, possible explanations for the similarities in names are discussed, as is the need to include characterization in any duplicate assessment process.

Onobrychis viciifolia (sainfoin) is a forage legume crop with many positive agronomic, environmental, nutritional and nutraceutical attributes. Farmers also benefit from its drought tolerance in areas of low rainfall and light free draining soil, mainly due to its deep taproot. It is resistant to most common pest and diseases and is a valuable resource for pollinators, specifically cultivated for honey production in some regions. It has many benefits for animals, being highly palatable and without danger of bloat, which can be life-threatening to livestock. Its decline in Northern Europe started during the Green Revolution and was impacted by changes towards more intensive farming. Unlike other forage legume crops such as red clover and lucerne, sainfoin does not respond well to inputs and is difficult to establish and maintain. Sainfoin could be classified as an ‘orphan crop’ with very little genetic improvement or agronomic studies in the past 60 years. In the past 5–10 years, however, there has been a resurgence in interest and this has given rise to a number of studies and initiation of systematic improvement of the crop, which is indispensable to its reintroduction into the farmed environment. Interest has been driven in part by considerable evidence to suggest that condensed tannins present in the legume foliage, together with other polyphenol compounds, have positive effects on animal nutrition together with anthelmintic properties. These compounds are also thought to play a role in environmental benefits. There remain many challenges to address in order to optimize the potential for cultivation of sainfoin and its use as a beneficial forage crop. This review makes particular reference to a recently completed project; ‘Legume Plus’, funded by the European Union and embracing a multi-disciplinary approach to both understand and improve the crop for farmers. The present review covers results from both this project and other studies during the past 5 years, also drawing on historic studies of etymology, taxonomy, genetics, agronomy and botany, aiming to be a useful resource for research and for practical plant breeders and agronomists.

Full potential of African tomato has not been tapped due to lack of information regarding its characterization. The aim of this work was to study the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological data collected were subjected to GenStat's and Darwin6 software. RNA was extracted from leaf samples, fruits at three ripening stages using modified Trizol method and sequencing done using Illumina sequencing platform. The raw reads were filtered and analysed using the Bioinformatics tools. Phenotypically, the landraces clustered into three clusters dendrogram representation. Clustering was attributed by phenotypic variation. Analysis of variance showed significant phenotypic variations among the landraces (P < 0.05). A total of 115,965 validated single nucleotide polymorphisms (SNPs) were mined from the 303,754,051 high-quality filtered reads. Molecular characterization showed significant variation within the landraces at fruit development stages. Unlike the phenotypic variation, phylogenetic tree representation grouped the 17 landraces according to their geographical location with some landraces from different countries grouping together. The findings of this study reveal significant morphological variation among African tomato contributed by plant height, leaf blade length, leaf blade width and fruit width. Positive correlation between fruit width and yield (r = 0.93, P < 0.01) was observed. Results of this study reveal that there is admixture of landraces from various geographical locations. Morphological characterization of African tomato can only lay a foundation but it does not reveal genetic diversity. The transcriptome SNP analysis revealed significant variation among the African tomato according to their geographical location.

Fe and Zn deficiency are widespread worldwide. As wheat is the primary food for the majority of the world people, producing wheat grains with high mineral content can ameliorate the problem of mineral hunger. However, the genetic variation available for breeders is limited. The aim of this study was to assess the genetic variation in grain Fe and Zn contents in 47 synthetic hexaploid wheats and to identify marker loci associated with Fe and Zn contents. We measured the grain Fe and Zn contents using inductively coupled plasma atomic emission spectroscopy and performed genotyping using SSR markers. The results showed considerable genetic variation for these minerals. We identified three lines with high Fe and Zn contents and six quantitative trait loci of which three were associated with Fe content and the other three with Zn content. The minerals showed positive phenotypic and genotypic correlation and high heritability (>60%). The ratio of the σ2g to the σ2g×e was ≥1 for the two mineral contents indicating that breeding for increasing mineral content within the synthetic lines is possible. The synthetic wheat lines identified in this study are valuable genetic resources, and can be utilized for breeding wheat cultivars with high mineral content.

Overexploitation in search of its valuable non-wood fragrance product has put pressure on the survival of the endangered Aquilaria trees in the wild. In this study, the pattern of genetic variation among wild populations was measured to aid in designing useful strategies for in situ conservation. We sequenced the internal transcribed spacer (ITS) of the nuclear region of 19 wild Aquilaria malaccensis populations from different states in Peninsular Malaysia, and compared the sequence with the same species residing outside of Malaysia, mainly from the Assam region in India and Sumatra in Indonesia. This widely distributed species is found in the Indomalesian region and is a major source of agarwood. In addition, we included five wild Aquilaria hirta populations for semblance purposes. Intraspecific variations were not found within A. malaccensis and A. hirta populations in Peninsular Malaysia. Interestingly, Single Nucleotide polymorphisms (SNPs) were identified when comparing A. malaccensis from three geographical regions, with a total of 25 SNPs detected. We imply that geographical segregation is a contributing factor toward genetic variation in A. malaccensis. This is the first report on utilizing the ITS region for analysing genetic variation in A. malaccensis of various geographical regions. The molecular information obtained in this study will serve as a useful reference in designing in situ programmes for this endangered species.

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.

Among domesticated traits, pre-harvest sprouting (PHS) caused by the early breakage of dormancy leads to severe economic losses. Therefore, regulating PHS is important for cereal crop improvement against changes in climate. In this study, we surveyed naturally occurring variations in seed germination in diverse rice germplasm for the available resources of this trait, and investigated the changes of abscisic acid (ABA) levels during grain development by the distinguished PHS-resistant groups. We discovered wide variations in germination among the 205 rice accessions examined and found that 90 accessions are resistant (germination <20%) to PHS. Tropical and subtropical accessions, which are subjected to long wet periods, are more resistant to PHS than the other accessions. We detected an increase in germination of detached seeds from the panicle compared with intact seeds in panicle at harvesting time. This might be attributed to a weakening of the mechanical barrier that prevents water imbibition and radical emergence. ABA levels were maximal at 10 d after flowering and decreased thereafter. Interestingly, PHS-susceptible accessions maintained higher or similar ABA levels compared with PHS-resistant accessions, suggesting that the key factors for seed dormancy and its breakage are ABA perception and signal transduction rather than total ABA content. The diversity of germination ability detected in this study could be sustainably used for crop improvement and to help unveil the genetic and physiological basis of this quantitative trait.

Faba bean (Vicia faba L.) is a valuable grain legume and a staple protein crop in many countries. Its large and complex genome requires novel approaches for its genetic dissection. Here we introduce a multi-parent population developed from four founders (ILB 938/2, Disco/2, IG 114476 and IG 132238). The selection of parental lines was based on geographic (Colombia, France, Bangladesh and China), genetic and phenotypic diversity. The parental lines were inbred and then genotyped using 875 single nucleotide polymorphism (SNP) markers. Based on molecular data, the parents had high homozygosity and high genetic distance among them. The population segregates for several important traits such as seed morphology, seed chemistry, phenology, plant architecture, drought response, yield and its components, and resistance to Botrytis fabae. The population was checked for unbiased segregation in each generation by observing simply inherited Mendelian traits such as stipule spot pigmentation (SSP) and flower colour at different generations. All 1200 four-way cross F1 plants had pigmented flowers and stipule spots. The segregation ratios for white flower colour (single gene, zt2) fit 7:1, 13:3 and 25:7 at F2, F3 and F4 generations, respectively, and the segregation ratio of SSP (two recessive unlinked genes, ssp1 and ssp2) fit 49:15 and 169:87 at the F2 and F3 generations, respectively, demonstrating unbiased generation advance. We will subject the F5 generation of this population to a high-throughput SNP array and make it available for further phenotyping and genotyping.

In many regions of the world, the cultivation of landraces is still common, in particular in centres of crop diversity. Significant effort has been put into ex situ conservation of landraces but limited data exist on the changes in genetic diversity that occur over time in farmers’ fields. We assessed temporal changes in barley landrace diversity in Jordan using seed samples collected in 1981 and 2012 from the same locations. We did not observe significant changes in the amount of genetic diversity, but samples collected in 2012 were more homogenous and less locally distinct. In two sites, we observed replacement of the old material. We observed a change in phenotype, and phenotypes were found to be more homogeneous among sites in 2012. Climate changed significantly over the study period, becoming hotter and dryer, but we did not identify any correlation between the changes in climate and genetic and phenotypic variations. While the amount of genetic diversity in terms of allelic richness and number of multi-locus genotypes has been maintained, local distinctiveness among landrace barley populations in Jordan was reduced.

This study was conducted to characterize new plant type (NPT) traits among 650 genetically diverse rice genotypes of tropical japonica and indica and to establish an initial core set for NPT traits. Analysis of variance revealed highly significant differences among the genotypes for all the traits assessed except flag length and width and leaf angles. Dendrogram categorized the genotypes into five distinct duration groups. Genotypes viz., Pumphamah, IRGC5097, IRGC37015, IRGC43741, IRGC50448, IRGC53089, IRGC39111, IRGC18021, Haorei Machang, IRGC44069, IRGC8269, Thangmoi, IRGC33130 and IRGC29772 were identified as possessing strong culm. Long panicles with a length of more than 35 cm were found in IRGC8269, IRGC9147, IRGC14694, IRGC19642, IRGC27435, IRGC39111, IRGC31051, IRGC26011and IRGC25892. Ideal leaf angle of NPT genotypes of 5°, 10° and 20° of flag leaf, 1st and 2nd leaves was not found in any genotype but with a combination of 5°, 10° and 10° was observed in IRGC63102 and IRGC66644. NPT flag leaf length and width of 50 and 2 cm, respectively, was seen in ‘Kemenya Kepeu’ and ‘IRGC29772’. High grain number of more than 350 was observed in IRGC53089, IRGC31063 and Azhoghi. A total of 72 genotypes were found with a combination of one or more ideal plant type traits of which, hierarchical cluster analysis based on genetic distances selected 32 as NPT core set. This core set will serve as an ideal genetic resource for breeding programs aimed at NPT development.

Chinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembled de novo by a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

In this study, agro-morphological and yield-related traits associated with drought tolerance in 80 barley genotypes belonging to 15 wild species together with the cultivated one, and their potential to improve adaptation to different levels of drought stress conditions (moisture environments) were studied. There was significant genetic variation among the genotypes and species for all of the measured traits, as well as differential responses of genotypes across environments. The results indicated high variation for grain yield (GY) under drought stress among the genotypes, and that some of the wild genotypes had consistently superior specific adaptation to the water stress conditions. The genotypes belong to wild barley species, especially Hordeum murinum and Hordeum marinum had lower GY but relatively higher yield stability under different environments. Traits such as number of seed per plant and hundred kernel weight were positively correlated with GY in all of the environments. High negative correlation between GY and days to ripening was observed only under intense drought environment, showing drought escape as a strategy of wild plants under highly stressed conditions. Grouping of the genotypes by principal component analysis completely separated cultivated barley and its progenitor (Hordeum vulgare ssp. spontaneum) from other wild genotypes; however, the other wild species were slightly separated from each other. In addition, the Iranian and foreign genotypes did not completely separate from each other. The identified wild barley genotypes with favourable characters and high drought tolerance could be used in genetic studies and barley improvement programmes especially for drought stress.

A total of 326 pearl millet accessions selected for fodder traits from the world collection at ICRISAT genebank, India were evaluated in rainy, postrainy and summer seasons to identify promising sources for fodder yield. In rainy season, majority of accessions grew significantly tall, produced thick stems, long and broad leaves compared with postrainy and summer seasons. Total tillers per plant were significantly more in rainy and summer seasons than in postrainy season. Significant (P = 0.05) positive correlations were observed among all traits in all seasons except total tillers, which showed significant negative correlation with all other traits but for a few cases. Accessions of cluster 1 flowered early and produced more tillers per plant, while those of cluster 3 flowered late, grew tall, produced thick stems, more leaves per plant, which were long and broad. Promising sources identified include IP 11839 and IP 11840 for plant height and number of leaves per plant, IP 15710, IP 15735 and IP 15752 for stem thickness and leaf width, and IP 3628, IP 15285, IP 15288, IP 15302, IP 15342, IP 15351, IP 15290, IP 20347 and IP 20350 for total tillers per plant. Further testing of these sources of fodder traits at different locations will be very useful.

Focusing on 116 bread wheat landraces, this study investigated high molecular weight glutenin allele polymorphism, gene diversity, genetic variation and linkage disequilibrium (LD) in Glu-1 loci. To identify gluten alleles, sodium dodesyl sulphate-polyacrylamide, gel electrophoresis was used and for statistical analyses POPGENE software was employed. The results indicated that average genetic variation (h) was the highest in Glu-B1 (0.6421) and the lowest in Glu-A1 locus (0.4548); genetic similarity ratio (I) was the highest in Glu-B1 (1.4170); the highest average genetic diversity (Ht) was observed in Glu-B1 (0.6575) and the lowest diversity was observed in Glu-A1 (0.4558). It was also observed that genetic diversity in Glu-1 locus was largely due to intra-population variations. Inter-population gene flow was also calculated as 4.0051. Marmara and Southeastern Anatolia regions, the results further indicated, had the highest (2.8691) and lowest (0.1694) heterozygosity. Genetic erosion risk for Turkish bread wheat landraces was also seen to be high. Considering the mutual analyses of subunits of nationwide wheat landraces, it is possible to speculate about a limited migration between the landraces. LD of the landraces was largely because of this limited migration and/or epistatic natural selection. Since Turkey is known as the gene centre for major cereals including wheat, barley, rye and oat, where they diversified and spread throughout the world, studying the gluten allele diversity of Turkish bread wheat landraces is important. In addition, this study has revealed the applicability of LD, and neutrality tests to gluten protein diversity for the first time.