Assessing genetic diversity and identifying trait-specific germplasm within germplasm collections is necessary for a varietal development programme. Agronomic features were investigated in 318 diverse dry bean germplasm accessions, including check varieties. We observed a lot of genetic variability for the traits studied. A wide range of variations was noticed for days to 50% flowering, days to maturity, pod length, the number of seeds per pod and 100-seed weight (HSW). For eight of the agronomic features evaluated, the analysis of variance revealed substantial differences among the accessions. For all characters, phenotypic coefficient of variation estimations were more significant than genotypic coefficient of variation. Plant height, days to 50% flowering, seed yield (q/ha) and HSW had high heritability and genetic advance as a per cent of the mean. Association analysis revealed a significant positive relationship between HSW, plant height, pod length and seed yield (q/ha). According to a hierarchical clustering analysis based on agronomic features, the diversity of dry bean germplasm has no significant association with their geographical origin. The number of pods per plant, plant height, days to maturity, days to 50% flowering and seed yield had relatively long vectors based on principal components 1 and 2, indicating that genotypes differ significantly. Additionally, the trait-specific donors and bean common mosaic virus disease-resistant accessions, IC360831, ET4515, EC150250, IC340947, IC564797B, EC565693 and ET8409 could be of value for dry bean improvement.

Sorghum is an important staple crop in Sub-Saharan Africa. In the Sudano-Sahelian zone of West Africa, sorghum is mainly intercropped with cowpea, but these intercropping systems are facing low-productivity problems. The overall aim of this research was to identify sorghum varieties with different agro-morphological and physiological traits that could improve the performance of the intercropping systems. We followed a two-step methodology comprising (i) identification of varieties and plant traits of interest in intercropping systems, using participatory methods, and (ii) agro-morpho-physiological characterization of 50 sorghum varieties, to examine the range of variation in traits of interest. The results show that landraces are the varieties most widely used by farmers, and that 82.5% of farmers consider the variety type they choose for intercropping to be important. Farmers mentioned plant height, number of leaves and stem diameter as important traits to consider. Analysis of variance showed significant differences between varieties for half of the 24 agro-morpho-physiological traits studied. Hierarchical clustering identified three main groups of varieties, distinguished by morphological traits such as stem diameter, total number and size of leaves (group 1), root traits (depth, growth angle, dry matter) and relative chlorophyll content (groups 2 and 3). Based on this classification, we recommend several varieties from each of the three groups, exhibiting contrasting traits, for an assessment of their performances in intercropping systems.

Common bean (Phaseolus vulgaris L.) is a highly economically important crop worldwide and a particularly important source of protein and minerals for people in less developed countries. Improving yield is a vital objective to meet the increasing demand for food due to the expanding human population. The present study was undertaken to study the genetic architecture of agronomic traits of common bean in India, particularly in the north-western Himalayan region. Marker-trait association (MTA) analysis was performed in a population of 100 common bean accessions using polymorphic microsatellite markers. Population structure analysis based on SSR markers divided the accessions into three main subpopulations. Ten significant MTAs were found using general linear model (GLM) and mixed linear model (MLM) approaches. We found two markers i.e. BM142 and J04555 associated with 100 seed weight and pods per plant common in both the GLM and MLM approach markers. All the MTAs were considered as major MTAs contributing more than 25% phenotypic variation. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield and development of high yielding common beans lines.

The Dasylirion genus is highly represented in the arid and semi-arid regions of Mexico and USA, playing important ecological and economical roles. Inferring the evolutionary patterns of this group will eventually facilitate understanding biological phenomena and outlining conservation and usage strategies. We performed a molecular phylogenetic analysis based on two chloroplast DNA regions: maturase-K gene (matK) and the large subunit of ribulose-1,5-bisphosphate carboxylase gene (rbcL). We constructed a phylogenetic tree by maximum likelihood with GTR as the sequence substitution model and a relaxed clock, inferred diversification patterns by lineage through time and explored the diversification rates of Dasylirion by the Yule model. The study included 11 species of the genus, which represent 50% of all its known species. We used two calibration points to date the tree, one based on fossil records of Acorus gramineus, and the other on the estimated stem age of the Yucca genus. The combined sequences of the two partial genes comprised 1455 bp and 18 polymorphic sites. We estimated an average substitution rate of 0.0005 nucleotide per million years for the concatenated DNA sequences. The molecular dating analysis estimated that the Dasylirion genus appeared more than 5.46 million years ago, with a rate of diversification of 0.0466 net speciation events per million years. The estimated age represents a lower bound, since not all Dasylirion species are included. These findings are consistent with other origin and diversification hypotheses for arid-land Asparagaceae in the Mexican highlands as a result of geomorphological events in North America.

Muskmelon, which is an important cucurbit of the tropical and subtropical region of the world, shows great diversity, with six different botanical or horticultural groups and fifteen varietal groups. In this study, a total of fifty (50) simple sequence repeat (SSR) markers were used to investigate the genetic diversity and population structure of 46 muskmelon accessions of different horticultural or varietal groups. Thirty-eight (38) of the fifty SSR markers were highly polymorphic. A total of 99 alleles were generated by the polymorphic markers, with an average of 2.06 alleles per loci. Heterozygosity among accessions for individual loci varied from 0.00 to 0.21, with the highest (0.21) reported for the CMCTN71 marker. The gene diversity and polymorphism information content (PIC) values varied between 0.08 to 0.72 and 0.07 to 0.67, with an average of 0.47 and 0.38, respectively. The primer that showed the highest gene diversity and PIC values was DM0913. The unweighted pair-group method for arithmetic average (UPGMA)-based dendrogram classified all the 46 accessions into two major clusters. Population structure analysis classified 46 muskmelon accessions into 2 subpopulations. The subpopulation I contained 29 accessions from the cantalupensis group, and subpopulation II contained 17 accessions from momordica, inodorus and conomon groups, respectively. Analysis of variance indicated that 18 and 68% of variance was due to subpopulations and differences among individuals, respectively. The present study supports the existence of sufficient variation among musk melon genetic resources in India, and their classification based on molecular markers will be helpful to accelerate the breeding programme for specific traits.

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

High-molecular-weight glutenin subunits (HMW-GS) contribute to dough elasticity and bread baking quality in wheat. In this study, wheat varieties were classified based on their HMW-GS composition into three groups: 1Dx5 (5 + 10, Gaoyou 8901, Xinmai 28, Xinmai 19, Xinmai 26 and Jinbaoyin), 1Dx2 (2 + 12, Zhoumai 24, Xinmai 9 and Yumai) and 1Dx4 (4 + 12, Aikang 58). Sequence analysis showed that 1Dx-GY8901, 1Dx-XM28, 1Dx-XM19 and 1Dx-XM26 were similar to the 1Dx5 gene and clustered on the same branch, while 1Dx-AK58, 1Dx-ZM24, 1Dx-JBY, 1Dx-YM, 1Dx-XM9 and 1Dx-JBY were more similar to the 1Dx2 gene and clustered on the same branch with 1Dx.2.2. There was a mutation of Ser to Cys at position S2, for an extra Cys in the repeat regions of 1Dx-XM19, 1Dx-XM26, 1Dx-XM28 and 1Dx-GY8901. The wheat HMW-GS genes exhibited similar percentages of α-helix, extended strand, β-turn and random coil structure, with ranges of 13.33–13.59, 4.77–5.78, 7.08–9.18 and 72.3–73.94%, respectively. Sequence conservation and the composition of HMW-GS subunits were also analysed for a series of strong gluten wheat varieties, Xinmai 9 (1, 7 + 8, 2 + 12), Xinmai 19 (1, 7 + 9, 5 + 10), Xinmai 26 (1, 7 + 8, 5 + 10) and Xinmai 28 (1, 7 + 9, 5 + 10). The results of this work should facilitate future breeding efforts and provide the theoretical basis for wheat quality improvement.

Teosinte, the wild progenitor of maize, has immense potential for providing unique traits and is more divergent compared to inbred lines and landraces. One hundred and sixty-nine teosinte-introgressed maize backcross inbred lines were developed to widen the genetic base of maize with predomestication alleles. The population was evaluated phenotypically and genotypic data of 76 SSR markers were used to map quantitative trait loci (QTLs) governing the targeted traits. Sixty-six QTLs were detected for eight plant architect-related traits that are spread over 10 different chromosomes with phenotypic variation ranging from 2.29 to 13.97%. Maximum three stable QTLs were recorded for days to anthesis (DA) followed by two for days to silking (DS), plant height (PH) and node bearing first ear (NBE). For rest of three traits namely flag leaf length (FLL), flag leaf width (FLW) and ears per plant (E/P) only one stable QTL was detected. Among the 16 common QTLs, the marker phi328178-linked QTL governed four characters (DA, DS, FLL, FLW) simultaneously, followed by umc1622-linked (ASI, FLW, E/P), umc2341-linked (DA, DS, NBE) and phi075-linked QTLs (ASI, PH, NBE) controlling three traits each. Remaining 12 QTLs controlled two characters. Molecular association between co-localized QTLs for different traits was also validated at the phenotypic level by significant correlation estimates. For eight studied traits, 53 superior lines were identified which along with parents (teosinte and maize inbred DI-103) were grouped into 12 clusters. Therefore, lines clustered independently can be combined to accumulate desirable traits for the improvement of maize.

The members of the Aegilops genus serve as a vast pool of allele discovery for wheat improvement in abiotic and biotic stress responses. Aegilops mutica Boiss (Amblyopyrym muticum (Boiss) Eig) is an unexplored candidate with significant potential. Even though it has been used in cytogenetics applications within the last century, natural population diversity and allele discovery have been neglected. As an endemic species for Anatolia and the lower Caucasian region, it has an unexplored population structure. Here, seventy-five genotypes from five different newly collected populations from central Anatolia were evaluated with 29 polymorphic SSR loci. Significant diversity within (83%) and between (17%) the populations was obtained. Three of the populations were clearly separated, while two had some level of the mixture. Relatively easy cross-species hybridization and introgressions make Ae. mutica a good candidate for novel allele discovery and pre-breeding. Here, for the first time, representative natural populations of Ae. mutica were compared and population structures were revealed with SSR markers which may clear the misty vision that geneticists might have regarding Ae. mutica. This could be exploited in genetic resource conservation and breeding programs and maybe a point for further studies.

Being difficult to regenerate and maintain the seeds, the oleaginous bottle gourd was investigated using nine agromorphological traits and 31 amplified fragment length polymorphism (AFLP) markers. Specifically, the study was conducted to determine the intra-specific variability of a total of 173 accessions, which were identified from five agro-ecological regions from Côte d'Ivoire (Centre, East, North and South). Then, the genetic diversity and relationships within accessions were studied using AFLP markers. This characterization using both morphological and AFLP markers was realized in order to ultimately build a reliable core collection. The discriminant analysis, using nine quantitative traits, reveals plant length and seeds number per fruit as discriminating characteristics. From the accessions used for the agromorphological study, 148 were able to be differentiated by the AFLP markers. A range of 52 to 113 bands were amplified per primer combination. As revealed by the analysis of molecular variance (AMOVA), 28% of the total variation resides among accessions and 72% occurs within populations. The AMOVA computed in order to differentiate cultivars, displayed the same trends when no prior grouping of accessions was considered. The differentiation within cultivar (97%) was more than that, among cultivars (3%). Tree topologies inferred by neighbour-joining analysis reflected no clear cut off grouping.

To group accessions, we used a Bayesian clustering analysis which exhibited two clusters. Using the informativeness of the primer combinations analysed in the present study, an orientation was given for the choice of the accessions which would be used to build a core collection.

Oaks are model species due to their importance in various ecosystems, worldwide distribution, high economic value and emerging genomic resources. As such, knowledge on population differentiation across their distribution range is of high importance for sustainable forest management. As in most angiosperms, chloroplasts are maternally (via seeds) inherited in oak species and acorns are dispersed over comparably short distances. Consequently, chloroplast markers reveal comparatively high differentiation between populations, making them highly viable for the analysis of historic migration patterns and the certification of reproductive material. Despite the existence of various white oak (section: Quercus) chloroplast markers, red oak (section: Lobatae) chloroplast markers remain limited. Northern red oak is one of the most important North American oak species and a widespread non-native plantation tree species in European forests. We took advantage of chloroplast genomes of Q. rubra L. and related oak chloroplast genomes to develop a set of robust and easy-to-use chloroplast microsatellite primers for northern red oak. Furthermore, we tested transferability of those novel red oak primer pairs to Q. robur L. and Q. petraea Matt. Liebl. The new set of fifteen polymorphic chloroplast microsatellite markers revealed three additional northern red oak haplotypes after screening 80 northern red oak individuals representing seven haplotypes, identified based on formerly available markers. Therefore, they provide a higher resolution of haplotypes as compared to currently available markers.