This study is the first assessment of the entire soybean [Glycine max (L.) Merr] collection of the United State Department of Agriculture National Plant Germplasm System (USDA) reporting quantitative and population genomic parameters. It also provides a new insight into soybean germplasm structure. Germplasm studies enable plant breeders to incorporate novel genetic resources into breeding pipelines to improve valuable agronomic traits. We conducted comprehensive analyses on the 19,652 soybean accessions in the USDA-ARS germplasm collection, genotyped with the SoySNP50 K iSelect BeadChip SNP array, to elucidate the quantitative properties of existing subpopulations inferred through hierarchical clustering performed with Ward's D agglomeration method and Nei's standard genetic distance. We found the effective population size to be approximately 106 individuals based on the linkage disequilibrium of unlinked loci. The cladogram indicated the existence of eight major clusters. Each cluster displays particular properties with regard to major quantitative traits. Among those, cluster 3 represents the tropical and semi-tropical genetic material, cluster 5 displays large seeds and may represent food-grade germplasm, and cluster 7 represents the undomesticated material in the germplasm collection. The average FST among clusters was 0.22 and a total of 914 SNPs were exclusive to specific clusters. Our classification and characterization of the germplasm collection into major clusters provides valuable information about the genetic resources available to soybean breeders and researchers.

This study evaluates the agronomic and morphological traits, chemical composition and traits related to consumer perception of local tomato landraces mostly collected in the suburban area of Madrid. Results showed remarkable variability at all the studied levels in this small area – intra- and inter-accession variability, and in morphological, agronomical and quality traits – and was often dependent on the environmental conditions where the crop was grown. However, few morphotypes could be defined. Some morphological traits of the studied samples seemed to be associated. For instance, ribbed fruits ripened with green shoulder and dark flesh accumulated more soluble solids. Consumer appreciation and fruit morphology, i.e. traits related to fruit size and shape, seemed to be the main determinants of tomato-type definition, although nutrient content also played an important role. Consumers positively received heirloom tomatoes, especially when they were cultivated in the open-field near their area of selection where they express their full potential in the nutrient synthesis and sensory properties. Although total soluble solids content seems to be the main trait related to appreciation, some morphological traits could be determinant in consumers’ choice. Furthermore, some consumers were more interested in different tomato typologies and nutritional characters like acidity.

Cowpea is a major source of vegetable protein but its production is constrained by drought resulting in yield loss. Developing drought tolerance varieties can enhance yield and reduce the need for supplemental irrigation. Breeding for drought tolerance requires the knowledge of its genetic basis. Genetic basis for some seedling traits in cowpea was investigated. Seven generations (P1, P2, F1, RF1, F2, BC1 and BC2) each derived from two crosses involving two highly drought tolerant (Danilla and IT97K-499-35) and one highly susceptible parents (Tvu7778) were evaluated for drought tolerance in the screen house. Data on Seedling height (SH), Seedling terminal leaflet area (SLA), Seedling Vigour (SV) and Recovery Capacity (RC) were collected. The SV was assessed on a scale of 1 (highly-tolerant) – 9 (highly-susceptible), while RC (%) was evaluated at 5 d interval for 30 d. The hybrids F1 and RF1 showed the best performances in both crosses with SV ranged from 2.50 ± 0.00 in Danilla × IT97K-499-35 cross to 6.50 ± 1.00 in the Danilla × TVU7778 cross. In both crosses, F1 and RF1 had 100.0% RC. Both dominance (46.5–68.6%) and additive (31.4–53.5%) effects were found similar and important in all the traits under water stressed. The six-parameter model indicated few cases of gene interactions, mostly dominance × dominance. Narrow sense heritability ranged from 33.5% for SH to 50.1% for SLA in the cross Danilla × TVU7778 at terminal water stress. Inheritance of these traits in cowpea involved both additive and dominance gene action. However, dominance and/or dominance × dominance effects had a more pronounced effect in genetic control of all characters.

In order to gain an understanding of the genetic basis of traits of interest to breeders, the pea varieties Brutus, Enigma and Kahuna were selected, based on measures of their phenotypic and genotypic differences, for the construction of recombinant inbred populations. Reciprocal crosses were carried out for each of the three pairs, and over 200 F2 seeds from each cross advanced to F13. Bulked F7 seeds were used to generate F8–F11 bulks, which were grown in triplicated plots within randomized field trials and used to collect phenotypic data, including seed weight and yield traits, over a number of growing seasons. Genetic maps were constructed from the F6 generation to support the analysis of qualitative and quantitative traits and have led to the identification of four major genetic loci involved in seed weight determination and at least one major locus responsible for variation in yield. Three of the seed weight loci, at least one of which has not been described previously, were associated with the marrowfat seed phenotype. For some of the loci identified, candidate genes have been identified. The F13 single seed descent lines are available as a germplasm resource for the legume and pulse crop communities.

The conservation of pineapple in urban backyards is an innovative strategy that aims to involve city residents. A program of this nature requires careful planning and monitoring because of the involvement of people who do not have technical knowledge. This paper reports the implementation and evaluation of 30 gardens in urban backyards in Cabaceiras do Paraguaçú, Bahia, Brazil, to establish the parameters to allow creating a model for pineapple germplasm conservation cells with the collaboration of urban residents. A questionnaire was applied in two steps to people interested in participating, from which it was possible to choose and evaluate a general profile of the participants. Thirty pineapple accessions from the Active Germplasm Bank (AGB) of the Embrapa were selected for testing in the gardens. Two production cycles were considered, during which quantitative and qualitative traits of the plants and fruits were evaluated. The data were compared with the characteristics of the same accessions in the Pineapple AGB and were analysed by mixed principal component analysis. With respect to adequate maintenance, 20 gardens were well cared for until the end of the assessments, five were reasonably well tended and five were lost, due to home remodelling or lack of care by the guardians. Despite the loss of the five gardens, no accession was totally lost, thanks to the experimental design with three plants of each accession in three different gardens. The plants preserved in the gardens did not differ from those maintained by the AGB, demonstrating the effectiveness of this conservation strategy.

The present research was conducted to determine the reactions of 200 pure lines selected from bread wheat landraces collected from 18 provinces and seven regions of Turkey against bunt disease (Tilletia foetida) under field conditions for 3 years. Bunt disease reactions of pure lines were assessed based on the infected spike/total spike ratio. For visually assessed materials, the GGE-biplot method, where G = genotype effect and GE = genotype-by-environment effect, was used to group the reactions against bunt disease. Fifty-nine pure lines showed high resistance (with infection rates ranging from 0.1 to 10%); 24 in the moderate resistance (with infection rates ranging from 10.1 to 25%); 75 in the moderate susceptibility (with infection rates ranging from 25.1 to 45%); 38 in the susceptibility (with infection rates ranging from 45.1 to 70%) and finally four in the highly susceptibility (with infection rates of >70.1%). PC1 and PC2 of the GGE-biplot graph created over the years explained 76.49% of the total variation. The GGE-biplot graph provided efficient identification of resistant genotypes. The lowest PC1 values and PC2 values close to 0.0 explained the resistance of pure line to bunt disease best. The resistance of pure lines to bunt disease over the biplot decreased from the first section through the last section. Based on the results of present study, 19 pure lines (located within the first circle of the biplot graph) were selected for resistance breeding programmes against the diseases.

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.

The valorization of genetic diversities of major crops like wheat may help substantially to feed the world Population. Durum wheat genotypes consisting of 265 farmers’ varieties (FVs), which have been cultivated for many centuries in Ethiopia, as well as 24 improved varieties (IMVs) have been recently evaluated in northern Ethiopia. The evaluation has been carried out at two different locations for 2 consecutive years to verify the inherited diversity in FVs for important phenological and agronomic traits; with the intention to provide refined information to breeders and genebank managers. As a result of a careful evaluation, a very significant variation was observed between the FVs and IMVs. A large number of the former have demonstrated superior performance to the latter in terms of mean values of the major traits within the stipulated years and locations. The best performing FV has shown a gain of 20% grain yield over the best IMV. Multivariate analyses revealed that FVs displayed larger genetic diversity than in those IMVs. FVs could therefore be used as donor of useful alleles in durum wheat breeding for improvement of yield per se and other traits of agronomic and phenological importance. The identified stable superior FVs include: 8208, 226834A, 238567, 222426, 226282 could be best candidates for farmers in marginal environments. Genotypes that have shown stable performance for spatial variation such as 204493A, 214357 and 238567; and temporal variation such as 8208, 208479, 214357 and 226834A could be the best candidates for exploitation in future breeding programs.

Having knowledge on genetic similarity and DNA profile of potato genotypes facilitates a breeder's decision for parent selection and provides accurate variety identification. Fingerprinting and identification of genetic similarity among 151 potato genotypes were achieved using an inter-primer-binding sites (iPBS) retrotransposon marker system. Our study is the first application of iPBS markers for fingerprinting and distinguishing large numbers of Solanum tuberosum genotypes. Initially, 16 potato genotypes were screened using 45 iPBS retrotransposon markers to identify polymorphisms. Seventeen of these primers were selected for fingerprinting the whole set of accessions due to strong, reproducible and polymorphic bands. The 17 iPBS primers produced 290 scorable bands of which 224 were polymorphic. The number of bands per primer ranged from 10 to 26 with an average of 17.1. The number of polymorphic bands per primer was between 6 and 21. The polymorphism percentage per primer ranged from 46.2 to 100.0% with an average of 77.2% per primer. The mean polymorphism information content (PIC) values of iPBS primers varied from 0.12 to 0.31 per primer. Genetic similarity based on Jaccard's coefficient of potato genotypes ranged from 0.61 to 0.93 with an average of 0.73. The data produced herein may be used for selection of appropriate parents and variety description in the future. The findings of the present study suggest that iPBS retrotransposons are powerful and easy DNA markers for fingerprinting the large samples of potato germplasm.

Core subset selection from collections hosted by seed banks, grow in importance as the number of accessions and genetic marker information rapidly increases. A data set of 20,526 single-nucleotide polymorphism (SNP) markers characterizing 7986 Mexican creole wheat landraces, was used to test 11 methods for core subset selection, through optimization criteria containing average genetic distance and genetic diversity. Allele richness was used as an additional criterion to qualify the generated core subsets. Three replications with random samples of 1500 SNP loci, each comprising a maximum of 3000 alleles, were used to perform the method evaluations through four different objective functions. The LR greedy search (LR) and LR with random first pair (LRSemi) were consistently best across all assays for maximizing the objective functions, and they performed well even for criteria not included in those functions. The Tukey's HSD (honest significant difference) multiple comparisons grouped those methods together with the sequential forward selection (SFS) and SFS with random first pair (SFSSemi) strategies as the top set of approaches. All of them are simple heuristic maximization algorithms, and outperformed two more sophisticated optimization approaches: parallel mixed replica exchange and replica exchange Monte Carlo. For their efficiency to optimize the objective functions and computing speed, the LRSemi and SFSSemi methods demonstrated to be good alternatives for core subset selection from large collections of highly homozygous accessions characterized by many biallelic markers.

Heterosis is a main force underlying the hybrid seed industry in maize. Our experimental approach consists of a correlation study between retrotransposon-related genetic distances between parental inbred lines and hybrid performance. The assumption is that, at least for certain traits, heterosis results from genome rearrangements, largely related to retrotransposon insertions and/or removals. Fifteen maize inbred lines and one F1 hybrid, representative of the genetic diversity among sweet corn and field corn lines were screened for polymorphism by retrotransposon microsatellite amplified polymorphism markers. DNA fingerprints served as row data for estimating genetic diversity of maize inbred lines and its correlation with the heterotic effect in their hybrids. A correlation between phenotypic and molecular distances was evident only at the level of individual inbred lines. Weak correlation between genetic distances and heterosis effect was observed for the average of all inbred lines. Phenotypic distances negatively correlated with heterosis for insertion height, diameter of the ear and number of kernel rows per ear. The relative contribution of each inbred line to heterosis in its derived hybrids was also estimated. Accordingly, we identified inbred lines with increased genetic distances that mostly add to the heterosis effect in their hybrids and that we recommend as prospective to be used in maize breeding programmes.

Iron deficiency chlorosis (IDC) is common among groundnut grown in calcareous and alkaline soils in India, China and Pakistan and causes considerable reduction in pod yield. To identify genetically diverse IDC tolerant accessions, the mini-core collection of groundnut representing geographical diversity was evaluated for IDC response over 2 years in iron-deficient calcareous soils. Enormous genetic variability was evident in the mini-core collection for IDC tolerance-related traits such as a visual chlorotic rating (VCR) and SPAD chlorophyll meter reading (SCMR) across five growth stages. Several IDC tolerant sources belonging to different botanical varieties such as hypogaea bunch (ICG # 5051, 6766, 5286, 6667, 4538, 14008, 5663, 9842, 11855), hypogaea runner (ICG 10479), fastigiata (ICG 10890) and vulgaris (ICG # 11651, 118) were identified. Among the six botanical varieties of groundnut, hypogaea bunch types were found most tolerant to IDC and this is the first report in groundnut. The IDC tolerant sources identified were irrespective of their country of origin. The principal component analysis based on VCR, SCMR, pod yield and its related traits revealed five major principal components that explained 80% of the total variation. The biplot generated using PC1 and PC2 revealed a distinct separation of IDC tolerant genotypes from the susceptible ones. The hierarchical clustering using five major principal components revealed seven major clusters that were mainly based on IDC response of the accessions.

Jatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic diversity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.

Evaluating quality traits is important to the selection of elite lines in Brassica napus L. In this study, the quality traits of 488 global collections of B. napus L were evaluated for two consecutive years under central Chinese growing conditions, and a series of phenotypic data was obtained. The measured total glucosinolate content (GLC) and erucic acid content (ERU) values for 95.5% of the accessions were consistent with the original values, and large variations in quality traits were found among these accessions, thus enabling selection for these characters. In general, Chinese accessions tended to have a higher oil content (OC) than foreign accessions, while compared with winter and spring accessions, semi-winter accessions tended to have the highest OC. The mean GLC and ERU of Chinese rapeseed accessions showed gradual downward trends over time, and the genotypic variation in ERU accounted for 98.44% of the total variation, which was the highest among all 10 of the quality traits. Additionally, the heritability for ERU was largest among all 10 of the quality traits. Significant correlations were observed between different traits; OC had significantly (P < 0.01) negative correlation coefficients with oleic acid content, whereas OC had significantly (P < 0.01) positive correlation coefficients with ERU. Principal component analysis revealed that there was no clear boundary among materials of different geographic origins and different ecotypes according to the first two principal coordinates, respectively. This information about variations in quality traits revealed in this study could identify parents for improved rapeseed breeding.

Cassava brown streak disease (CBSD) remains a major threat to cassava production in Mozambique. Breeding for CBSD resistant varieties that are also preferred by farmers is an integral part of managing the disease. The main objective of the study was to determine the genetic relationship between farmer-preferred varieties from Mozambique with those from Tanzania whose resistance to CBSD is known and some of which are being used as parents in quantitative trait loci (QTL) detection studies. To achieve this, 103 genotypes collected from farmers’ field in three provinces of Mozambique were genotyped together with five varieties from Tanzania whose CBSD response is well known. Thirty-five single nucleotide polymorphism (SNP) markers with a high minor allele frequency in East African landraces were used. Results indicated that seven Mozambican genotypes were genetically similar to either one of the four Tanzanian CBSD resistant genotypes while Xino Nn'gole was genetically identical to Namikonga a CBSD resistant variety, based on the SNPs used here. Little genetic differentiation was observed in cassava between provinces, with the majority of genetic variation distributed within individual genotypes (98%) rather than among provinces (2%). Both observed (Ho) and expected (He) heterozygosity in three provinces were generally high (Ho = 0.496) and (He = 0.455). There is a high likelihood that the eight genotypes similar/identical to those from Tanzania may share the same QTL associated with CBSD resistance thus should be further evaluated for agronomic traits as well as response to CBSD.

Germplasm of common beans from the Mesoamerican gene pool races: Durango, Jalisco, Mesoamerica and Guatemala have highest genetic variation for the crop's improvement. The objective was to assign 50 common bean germplasm in Uganda into its gene pool races based on analyses of population structure. Secondly, to estimate heritability and effects of genotype × environment (GXE) interaction on common bean agronomic and yield traits in space and time. Sample genomic DNA was amplified in 2011 with 22 Simple sequence repeat markers (SSRs) and alleles separated using capillary electrophoresis. Field evaluations were conducted in 2010 and 2011 at NaCRRI and 2015 at CIAT – Kawanda. Multivariate analyses of SSRs data identified four subgroups within the germplasm: K4.1–K4.4, with corresponding Wrights fixation indices (FST) as 0.1829 for K4.1, 0.1585 for K4.4, 0.1579 for K4.2 and least for K4.3 at 0.0678. Gene pool race admixtures in the population (14%) were notable and attributed to gene flow. Four superior parents currently used in improving resistance to major diseases grouped as; Jalisco for MLB49-89A; Mesoamerica for MCM5001 and G2333; Durango for MEXICO 54. Heritability values for yield traits estimated using phenotypic data from above fixed parents, was above 0.81. Season and location had significant effect (P < 0.05) on numbers of: flower buds per inflorescence, pod formation and weight of 100 seeds. The findings will improve understanding of co-evolutionary relationships between bean hosts and pathogens for better disease management and will broaden the germplasm base for improving other tropical production constraints.

A blueberry (Vaccinium sp.) germplasm collection was screened for allelic variation in TERMINAL FLOWER 1 (TFL1) that could be used in breeding flowering or architecture traits. TFL1 has been found to repress the transition from vegetative to reproductive growth in diverse plant species, with mutations leading to altered flowering and form. The VcTFL1 gene sequence was determined from the draft genome sequence of diploid V. corymbosum line W8520. VcTFL1 is a member of a PEBP gene family and it could be distinguished from its family members by sequence comparison with PEBP family genes from other plants. High-resolution DNA melting analysis of 160 Vaccinium accessions detected VcTFL1 exons that differed in sequence from the W8520 control. DNA sequence analysis confirmed the presence of single nucleotide polymorphisms (SNPs) and identified haplotypes of tetraploid accessions. A total of 18 SNP sites were detected in VcTFL1 coding sequences of the Vaccinium germplasm screened. A SNP causing an alanine-to-valine change in exon 4 (A159V) was determined by multiple bioinformatic tools to be deleterious to VcTFL1 function. A diploid V. corymbosum accession heterozygous for the VcTFL1 mutation was identified as a candidate for breeding novel traits for blueberry.

Drought is a major constraint to oil palm plantation in many regions relying on rainfall. One strategy to overcome this problem is to develop drought-tolerant cultivars through screening and selection. Drought tolerance assessment based on growth and physiological traits provides an alternative approach for rapid screening especially in tree crops. The aims of this study were to determine the contribution of some growth and physiological parameters to drought response variation in oil palm seedling and to use those parameters to evaluate relative drought stress tolerance in tenera oil palm progenies. Eight D × P progenies were grown under well-watered, moderate and severe stressed conditions for a total of 6 months. Data on growth traits, maximum quantum yield (Fv/Fm), SPAD value and proline content were recorded. Principal component analysis (PCA) on studied traits revealed that PC1 and PC2 explained 74.57 and 76.80% of total variance in moderate and severe drought treatments, respectively. Major contributions towards the variation of control and drought-treated plants were identified and appeared to be growth traits in moderate drought stress and growth trait plus proline content in severe drought stress. According to drought tolerance index, PCA analysis and ranking method using integrated PCA values, PSU-106 and PSU-206 were identified to be relatively high tolerant to severe drought stress, while PSU-106, PSU-128, PSU-206 and PSU-208 were tolerant to moderate drought stress. Field validation of D × P progenies selected as drought tolerance is recommended to establish this indirect selection approach in oil palm breeding programme.

The Mediterranean region has a rich history of domestication and cultivation of lentil (Lens culinaris Medik.). Landraces have been grown and repeatedly selected by local farmers under different agro-environments. Characterization of molecular variation and genetic differentiation helps to ensure enhanced valorization, conservation and use of these genetic resources. Nineteen Simple Sequence Repeat DNA markers were used for molecular variance analysis (AMOVA) and population structure assessment underlying 74 lentil landraces from four Mediterranean countries: Morocco, Italy, Greece and Turkey. Based on AMOVA, presence of population structure and genetic differentiation at different levels were evidenced. Genetic diversity among Turkish landraces was higher than that of other countries. These landraces were more homogeneous as shown by low genetic differentiation among individuals within each landrace. Whereas Moroccan landraces followed by Italian and Greek provenances showed higher diversity and differentiation among individuals within landraces. The wide genetic variability of these landraces could help to better adaptation to biotic and abiotic stresses. Moreover, they could provide useful alleles related to adaptive traits for breeding purposes. Based on structure analysis, we obtained indications of possible presence of two major gene pools: a northern gene pool composed of Turkish, Italian and Greek landraces, and a southern gene pool composed of Moroccan landraces. Our results could be of interest when designing future diversity studies, collection missions, conservation and core collection construction strategies on Mediterranean lentil landraces.

Climate change forecasts point to increased frequency of droughts which may affect plant growth. For protein crops such as lentil, genetic improvement of both water use and drought tolerance is necessary. Wild lentil species are known to have evolved in drought prone areas and can be introgressed into cultivated lentil, making them candidates for the evaluation of high transpiration efficiency (TE) and drought tolerance. We assessed TE, water use and drought tolerance at the plant level for five wild lentil species and in cultivated lentil. Under fully watered and moderate drought conditions, wild lentil genotypes consumed significantly less water to fix similar or more dry matter compared with their cultivated counterparts. Under severe drought conditions, the wild lentil genotype L. ervoides IG 72815 had significantly higher TE compared with L. culinaris Eston. Lens ervoides L-01-827A, had significantly higher yield compared with all other species in the presence or absence of drought and showed significantly higher (α = 5%) TE under moderate drought. Drought susceptibility index was identified as a tool to identify drought-tolerant lentil genotypes grown under severe drought. The numerous small seeds of wild lentil made it difficult to estimate drought indices that are weight based and require formulae that incorporate seed numbers.