Hulled wheats are neglected crops that have potential in plant breeding programmes of modern durum and common wheat. Among these wheats, three species were widely cultivated in Spain until the mid 20th century: Triticum monococcum ssp. monococcum (einkorn), Triticum turgidum ssp. dicoccum (emmer) and Triticum aestivum ssp. spelta (spelt). One important aspect of wheat grain quality is starch composition, which is related to the action of waxy proteins. A collection of 536 accessions of Spanish hulled wheats was analyzed for waxy protein composition using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Polymorphism was found for the Wx-A1, Wx-B1 and Wx-D1 proteins, including new and null alleles in the three species. An allelic variant with an electrophoretic mobility not previously described was found in einkorn wheat. In emmer and spelt, some alleles with different mobility were also found. A Wx-B1 null allele was detected in emmer wheat, and null alleles for Wx-A1, Wx-B1 and Wx-D1 were found in spelt wheat. The variations found could be used to enlarge the gene pool available to breeders, and to design new cultivars with different levels of amylose content.

Foxtail millet (Setaria spp.) is an ancient cereal crop, having a short cropping cycle. Drought tolerance was assessed in this crop at an early growth stage and the extent of genetic diversity was measured between the foxtail millet genotypes, applying DNA markers. Tolerance of 18 foxtail millet genotypes was studied in vitro under four levels of polyethylene glycol (0, 10, 20 and 30% PEG-6000). PEG-6000 decreased final germination percentage and led to a reduction in shoot and root length with different stress levels. The genotypes ISe 869, ISe 1851 and yellow spike show superiority in stress tolerance for germination and the growth of root and shoot traits. They also clustered together in the biplot diagram and dendrogram of the genotypes based on the morphological traits. Marker polymorphism index (PI) was 80.36% and a total of 132 polymorphic alleles (4.00 alleles/locus) were obtained from 33 polymorphic primers. Polymorphic information content (0.54–0.83) was highly informative with an average value of 0.67. A dendrogram distributed the genotypes into five distinct clusters based on simple-sequence repeat (SSR) data, independent of their geographical distribution. A relationship was established between the SSR markers and the genotypes ability to tolerate drought stress. The SSR markers used could contribute to conducting DNA profiling of foxtail millet, and facilitating their use in future breeding programmes for drought tolerance in this crop. Based on water-stress experiment, three most tolerant genotypes: ISe 869, ISe 1851 and yellow spike are recommended to be cultivated under drought conditions around the world.

Thin pericarp is one of crucial selection criteria for high-tender waxy corn hybrid development. A pericarp thickness of 2414 maize landrace accessions including 87 public waxy inbred lines was investigated to select accessions with thin pericarp and to broaden genetic diversity among waxy corn cultivars. Observed pericarp thickness of the 2414 accessions ranged from 16.0 ± 1.56 to 139.2 ± 39.55 µm with the average of 47.7 ± 13.15 µm. More than half of the accessions were below the suggested thickness of <50 µm for high-tender waxy corn hybrid development. Large sample size resulted in significant differences among endosperm types and among collection provinces. This, however, may not translate into considerable difference in tenderness since most averages of different types and collection provinces were <50 µm. Positive correlation (r = 0.55) between the average and standard deviation of pericarp thickness implied that more samples are needed to achieve same level of precision when it comes to selection for thick pericarp than that for thin pericarp. Top 10% thin-pericarped waxy landrace accessions were intercrossed to form a new waxy corn population from this result.

The genus Narcissus L. (Amaryllidaceae) provides a model system to study the evolution and maintenance of sexual polymorphisms. In this study, we characterized microsatellite markers for N. dubius, N. cuatrecasasii, N. assoanus and N. rupicola for studies of genetic diversity and paternity analyses to investigate the stability of stylar dimorphism. We proved 40 new primer pairs from a genomic library of N. papyraceus and 12 microsatellite markers characterized also for N. papyraceus in a previous study (52 primer pairs overall). Twenty markers amplified, but their transferability and variability were different among species. Polymorphism was tested at least on 74 individuals and one population per species. The number of polymorphic loci per species ranged from four to eight. The number of alleles per locus ranged from two to 19 and the observed heterozygosity and gene diversity, from 0.107 to 0.729 and 0.103 to 0.894, respectively. These markers can be used for studies of genetic diversity and paternity analyses among individuals of N. dubius, N. cuatrecasasii, N. assoanus and N. rupicola to study the stability of stylar dimorphism.

Interspecific hybrids between pearl millet (Pennisetum glaucum) and napier grass (Pennisetum purpureum) give rise to perennial fodder crops characterized by high biomass, broad clumps and good palatability. These hybrids are triploid and developed by hand pollination of napier grass pollen on pearl millet panicles. The progeny shows a high percentage of pearl millet genotype due to self-pollination in the female parent. Identification of hybrids at a young stage based on morphological characters is difficult. DNA-based molecular markers have high discriminating power and were used to assess genetic differences between hybrids and their parents. Genetic diversity was studied in 18 pearl millet × napier grass hybrids along with their parents and two released national checks using inter simple sequence repeat (ISSR) markers. Eight ISSR primers gave rise to 125 bands, of which 120 bands were polymorphic. Polymorphic information content and ISSR primer index ranged from 0.40 to 0.49 and 8.88 to 11.14, respectively. The hybrids showed the presence of unique bands, besides those shared with male and female parents. Female (pearl millet) parents formed a separate group in the dendrogram constructed based on ISSR polymorphism. The male (napier grass) parents formed a separate group along with hybrids, indicating a higher similarity of hybrids with the male parents. Principal component analysis and STRUCTURE analyses showed a similar grouping. The close resemblance of hybrids to the male parents confirmed their interspecific origin. The study revealed that ISSR marker analysis could be a quick and reliable method to identify interspecific hybrids at an early stage of growth.

The flag leaf acts as a functional leaf in rice, Oryza sativa L., primarily supplying photosynthate to the developing grains and influencing yields to a certain extent. Drought stress damages the leaf physiology, severely affecting grain fertility. Autumn rice of northeast India is called locally as ‘ahu’ rice, and is known for its drought tolerance. Exploring diverse germplasm resources at the morphological level using an association mapping approach can aid in identifying the genomic regions influencing leaf shape dynamics. A marker–trait association (MTA) study was carried out using 95 polymorphic SSR markers and a panel of 273 ahu rice germplasm accessions in drought stress and irrigated conditions. The trials suggest that at the vegetative stage, drought stress significantly affects leaf morphology. The leaf physiology of some tolerant accessions was relatively little affected by stress and these can be considered as ideal varieties for drought conditions. The phenotypic coefficient of variance and genotypic coefficient of variance values implied moderate to high variability for the leaf traits studied. Analysis of molecular variance inferred that 11% of variation in the germplasm panel was due to differences between populations, while the remaining 89% may be attributed to a difference within subgroups formed through STRUCTURE analysis. Using the mixed linear model approach revealed 11 MTAs explaining between 4.5 and 20.0% of phenotypic variance at P > 0.001 for all the leaf traits. The study concludes that ahu rice germplasm is extremely diverse and can serve as a valuable resource for mining desirable alleles for drought tolerance.

A breeding programme of aromatic vanilla, dating back to 1944, was conducted in Ambohitsara, Antalaha, SAVA (Sambava, Antalaha, Vohemara, Andapa) – Madagascar. Imported, local, wild and cultivated vanillas were used as progenitors and thousands of hybrids were generated. However, this germplasm has not undergone any genetic evaluation, and it appears that these valuable genetic resources have been dispersed or lost after the end of the programme (2000). This study aims to investigate the genetic diversity and structure of rescued genotypes currently held in a local collection in Antalaha. Double digest restriction associated-site (RAD)-seq (ddRAD)-seq protocol was applied, providing 865 million read sequences from 56 accessions. The ddRAD sequences have been deposited to the SRA archive of NCBI. From the data, 23,701 filtered concordant common Single Nucleotide Polymorphisms (SNPs) were identified using the three widely used tools (Stacks, BCFtools, Genome Analysis ToolKit - GATK) for short-read library sequencing. These SNPs were used for germplasm evaluation. Clustering analysis segregated samples into five genetic groups: Vanilla planifolia, Vanilla pompona, hybrid Tsitaitra, Vanille Banane and the phenotype Tsivaky. Our analysis revealed distinct subgroups within V. pompona and Tsitaitra, emphasizing the importance of further characterization to accurately reflect the genetic diversity and facilitate better utilization of these accessions in future research and germplasm management. The presence of private alleles in all groups (from 487 to 2866) indicated that populations were diverging and represented a large gene pool that could be useful for future breeding efforts. The genetic data obtained from this study offers valuable insights into the genetic diversity and structure of the vanilla population, with potential applications in breeding and conservation efforts.

Climate change realities such as high-temperature levels are among the causes of drought episodes affecting the productivity and yield stability of crops worldwide. Breeders, therefore, have a daunting challenge to overcome and a large gap to seal in the agricultural sector arising due to drought through the improvement of new tolerant germplasm. It is in this endeavour that the present study, which included nine winter wheat genotypes grown in the greenhouse, was conducted to evaluate their performance under well-watered and drought stress treatments for the traits: heading time, plant height, above-ground biomass, seed number/plant, grain yield/plant, harvest index, root length and root dry mass. A lower grain yield/plant was observed for each studied genotype under drought stress conditions than for those under well-watered conditions. Additionally, grain yield/plant depression varied from 69.64 to 81.73% depending on the genotype. Positive significant correlations between grain yield/plant and heading time, above-ground biomass, and seed number/plant under the drought stress treatment were obtained. Genotypes that recorded high root dry mass had both high above-ground biomass and seed number/plant under drought stress conditions. Positive correlations between grain yield/plant depression and plant height, seed number/plant, and harvest index depressions were also observed. Grain yield for each genotype under drought stress conditions was recorded, and the varieties ‘Plainsman V.’, ‘GK Berény’ and germplasm ‘PC61’, ‘PC110’ showed the best drought tolerance. These genotypes and germplasm will be used in different drought tolerance experiments and breeding programmes.

The characterisation of traditional barley varieties from North Africa is promising with respect to detect traits linked with resilience to drought. Nine Algerian barley varieties comprising the economically relevant local landraces Saïda183 and Tichedrett were genotyped by random amplifying polymorphic DNA (RAPD) and by Simple Sequence Repeat (SSR) markers to get insight into their phylogenetic relationship and to compare the efficiency of the two approaches. The SSR markers were chosen such that all chromosomes of barley were represented by at least one marker. In addition, a principal component analysis (PCA) of morpho-agronomical traits was conducted. We found that the phylogeny based on the RAPD markers reflected the geographical distribution of the tested varieties, while the phylogeny based on the SSR markers reflected the pedigree. Among the RAPD markers, the maximal polymorphism information content was obtained for BY14 with a value of 0.82, for the SSR markers, Bmg13 was most informative with a value of 0.60. The similarity matrix used to the construct the phylogenetic tree, inferred a close relationship (Jaccard Index 0.8 based on RAPD markers) between the accessions Fouara and Oued-Athmania occurring in close vicinity. The SSR markers group the autochthonous varieties Saïda183 and Tichedrett together with a Jaccard Index of 0.8. The close phylogenetic relationship between Saïda183 and Tichedrett is also supported by the PCA of morphological and agronomic traits. Our data underpin the diversity of Algerian barley varieties and lend support to the autochthonous origin of these two Algerian landraces.

The genus Lilium contains a number of ornamental crop species, which are commercially important in many countries. As they are vegetatively propagated, maintaining genetic stability is essential for their efficient conservation. In this study, we investigated the genetic stability of regenerated plants of three cultivars (L. bolanderi ‘Lenora’, L. bolanderi ‘Mount Duckling’ and L. bolanderi ‘Mount Dragon’) and one variety (L. callosum var. flavum) after cryopreservation, compared with fresh (donor) and non-cryopreserved plants using morphological traits and ISSR markers. No differences in morphological parameters including flower, stigma and pollen colour, floral spots, floral direction or polymorphic bands were observed between control (fresh and non-cryopreserved) and cryopreserved plantlets. In addition, based on the resulting UPGMA dendrogram, the four taxa were divided into different clusters. All cryopreserved, non-cryopreserved and fresh plants in each group could be grouped together in a single cluster with more than 97 or 100% similarity. The results suggest a very low level or the absence of genetic variation in terms of morphological and genetic stability among the plants regenerated after cryopreservation.

Neocinnamomum plants are evergreen shrubs or small trees belonging to the Neocinnamomeae tribe of the Lauraceae family. Their seeds are rich in fatty acids, and their leaves are often used in traditional Chinese medicine. Presently, only a few studies have been performed on Neocinnamomum plants; therefore, the genome-based phylogeny among Neocinnamomum species has not been determined, which limits the germplasm innovation of this genus. In this study, by the Illumina (next-generation sequencing) and third-generation sequencing technologies, the whole genomes of seven Neocinnamomum species samples were sequenced, their nuclear DNA (nrDNA) sequences were assembled and characterized, and their phylogeny was reconstructed. The results revealed four hypervariable regions (i.e. transcribed spacer regions) in the nrDNA sequences, among which the highest degree of variation was observed in the external transcribed spacer (ETS) region localized behind the 26S gene. A total of 27 insertions/deletions and 184 single-nucleotide polymorphisms, both localized mainly in the ETS and internal transcribed spacer regions, were identified. Phylogenetic trees were constructed based on the nrDNA sequences using the maximum likelihood (ML) and Bayesian inference (BI) methods with Caryodaphnopsis henryi as the outgroup. The ML tree divided the seven Neocinnamomum species into four clades. Clade I consisted of Neocinnamomum caudatum var. macrocarpum and Neocinnamomum caudatum, clade II included Neocinnamomum delavayi and Neocinnamomum mekongense, clade III included Neocinnamomum fargesii and a branch species of N. delavayi and clade IV included Neocinnamomum lecomtei, constituting a monophyletic and basal group. The BI tree shared the same topological structure as the ML tree, and all the support values of the BI tree were one except for that of one Neocinnamomum species (0.98). The results of this study provide new evidence regarding the phylogenetic evolution of the Neocinnamomum plants.

Sorghum (Sorghum bicolor (L.) Moench) is a dual nature crop, which is used for food as well as fodder, depending on plant ideotype. Sorghum forage is important for ruminants, but a major constraint is the anti-nutritional factor dhurrin, a hydrocyanic acid (HCN) producing glucoside. There are several additional effects of dhurrin, which reduce the nutritional value of sorghum fodder for livestock. This two-year study was aimed to evaluate the variation among diverse sorghum varieties, specifically for HCN content, forage yield and stem sugar content (brix value) under arid climate in Pakistan. Nine sorghum varieties were used for this experiment: JS-2002, Chakwal sorghum, Lines CS-17, Super late, PAK SS-2, Johar, JS-263, Sargodha-2011 and YSS-98. Results reveal that Sargodha-2011 had superior morphological traits for fresh forage and dry biomass yield, and stem brix value, compared to other varieties. Higher HCN contents were recorded in Super late compared to other varieties. Significant negative correlation of HCN with yield showed that improvement in yield will reduce the HCN content of sorghum. In conclusion, sorghum variety SGD-11 was shown best performing for higher biomass yield and brix value, and lower HCN content compared to other tested varieties under arid climate of Thal, Pakistan.

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.

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.

In the fields of agricultural, food and medical research, the potential impacts of tea on human health are of special interest because tea (Camellia sinensis (L.) Kuntze) is continuously consumed by many people in the world. The evaluation of the diversity of genotypes found in tea germplasm can aid in the improvement of the breeding programme. In this study, the genetic diversity of 30 tea genotypes from two commercial sites of tea production in Iran was investigated by using morphological and 12 ISSR markers. Morphological analysis showed that the diversity between samples of tea was limited, and the narrow matching range was calculated. In cluster analysis at level 0.63, samples were divided into four groups. The application of 12 ISSR primers produced 91 polymorphic bands. PIC test showed a range of 0.41–0.48. Based on the ISSR data, the matching range was obtained in the range of 0.24–0.93. In cluster analysis, samples at level 0.58 were divided into five groups. According to the results, it can be understood that these series of traits and primers can very well recognize genetic differences. Using these markers, genetic diversity was observed among tea genotypes, but this diversity was not such as to be able to separate genotypes of various regions from each other. The results showed that the tea genotypes in Iran had high genetic diversity. As a consequence, the findings of our study will help the development of tea germplasm conservation strategies and their sustainable use in breeding programmes.

Screening of germplasm for specific traits is a continuous pre-breeding process in deriving the drought-tolerant donors required for crop improvement. The study evaluated 17 medium-late duration finger millet genotypes under drought stress (DS) for 28 days during the reproductive stage to identify the traits and genotypes for drought tolerance using different statistical analysis. The photosynthetic rate (by 26.3%), stomatal conductance (by 26.4%), transpiration rate (by 24.8%) and grain yield (by 13.2%) were decreased and found sensitive to DS, but the leaf temperature was increased (4.7%). From the path analysis and multiple linear regression analysis, the mean ear weight and productive tillers were found to contribute to the grain yield significantly under well-watered conditions. While under DS conditions, the mean ear weight, productive tillers and threshing percentage equally contributed to grain yield. Based on the ranking of traits significantly contributing to grain yield, the genotype GE-4683 with a higher mean ear weight (10.65 g) was found superior to the popular variety, GPU-28. The Multiple linear regression equation predicts the possibility to increase the yield of GPU-28 under DS from the existing 360.0 to 459.5 g per square metre (by 29.1%) by the incorporation of three productive tillers instead of the existing two tillers per plant in the MLR equation. An additional 1.0 g of mean ear weight will be able to predict an increased grain yield from 360.0 to 392.0 gm−2, equivalent to 3.60 to 3.92 t/ha (by 9.4%).

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

Knowledge on genetic architecture and inheritance of tomato shelf life contributing traits in different genetic backgrounds is a key issue for shelf life improvement. An investigation was undertaken to estimate the nature and magnitude of variability, traits inter-relationships, third and fourth degree statistics to unravel the genetics of 18 fruit quality and yield traits governing shelflife in F2 population of ‘Arka Vikas’ × ‘Red ball’ cross. The wider standardized range and higher estimates of phenotypic coefficient of variation indicated prevalence of adequate variability for fruit quality and yield traits. Fruit firmness and pericarp thickness ranged from 1.20–3.44 kg/cm2 and 2.44–5.31 mm respectively. Pulp content and shelflife ranged from 58.59–94.70% and 10.60–26.40 days respectively. Significant positive correlation with direct effect on fruit shelf life was exhibited by fruit firmness, pericarp thickness, TSS, titratable acidity, pulp content, fruit length and locule number. Positive skewness with platykurtic distribution recorded for TSS, lycopene, ascorbic acid, titratable acidity, fruit length, weight, pericarp thickness, plant height and number of branches. Negatively skewed with platykurtic distribution observed for pH, fruit diameter, firmness, pulp content, locule number, shelf life and number of clusters which signified duplicate epistasis of dominant genes in traits inheritance. The transgressive segregants for fruit quality traits indicated complementary effects of dispersed allele combinations between parents. Additive and dominance components could be exploited in the advanced segregating population by evaluating large number of families. In addition to additive effects, predominance of dominance effects of genes are important in inheritance of fruit quality traits governing shelflife.