Walnut (Juglans regia L.) is one of the oldest and most economically important edible nut species due to its high nutritional value. Iran is known as one of the most important centres of the origin and diversity of walnuts worldwide. This research was carried out to determine the genetic relationships of some old walnut genotypes in Iran in order to select superior genotypes and better conserve them. The results of morphological evaluation of the fruits showed that the highest coefficients of variation were related to nut weight, kernel weight, percentage kernel, thickness and weight of the shell, and thickness and weight of the packing tissue in both years. The average morphological traits among the studied genotypes were different, such that the highest nut weights in the first and second years were 15.59 and 14.79 g and the corresponding lowest values were 7.37 and 7.79 g, respectively. The highest and lowest kernel weights were observed in the first years to be 8.09 and 3.80 g and in the second years were 6.94 and 2.65 g, respectively. The highest kernel percentages in the first and second years were 64.97 and 59.79% and the lowest percentages were 39.52 and 27.80% in the first and second years, respectively. Molecular evaluation results showed that the 16 start codon of target (SCoT) primers amplified a total of 166 bands with an average of 10.44 bands per primer. The number of polymorphic bands was changed from 2 to 19 in primers SCoT-19 and SCoT-15. The average polymorphism information content value was 0.30 and the highest amount of this index (0.36) was observed in SCoT-14 and SCoT-19 primers. The results of principal component analysis and analysis of molecular variance indicated the presence of relatively high diversity within the investigated genotypes. The amount of genetic diversity within the investigated regions was 84% and that between areas was 16%. Based on the obtained results, it was concluded that SCoT markers could provide helpful information on the genetic relationships among walnut genotypes, which can be used in future walnut breeding and conservation programmes.

This study aimed to investigate vetch genotypes’ responses to moderate and severe drought stress and identify stress tolerance markers in arid conditions. Ten vetch genotypes (Vicia dassycarpa Ten., V. pannonica Crantz., V. michauxii Spereng., V. sativa-Ardebil, V. sativa-Dashtyar, V. sativa-Fereydonshahr, V. sativa-Mashhad, V. sativa-Semirom, V. sativa-Shahrekord and V. villosa Roth.) were cultivated under three water-deficit conditions: control, moderate and severe drought stress. These conditions represented maximum allowable depletion levels of 30, 50 and 85% of soil available water, applied after the six-leaf stage in the 2019–20 and 2020–21 growing seasons. The findings highlight the vetch's response to drought stress is influenced by stress severity and genotype. The result indicated a wide range of genetic diversity in agro-physiological traits among the studied vicia germplasm. Vicia dassycarpa Ten. shows highest straw yield and shorter days to flowering and maturity. Vicia michauxii Spreng. demonstrates high grain yield and advantageous traits like increased water content, photochemical efficiency of photosystem II, chlorophyll b, carotenoids and membrane stability index. It has lower soluble carbohydrate, DPPH (2,2-diphenyl-1-picrylhydrazyl) and proline content. Additionally, V. michauxii Spreng. exhibits superior agronomic traits such as more seeds per pod, per plant and higher 1000 seeds weight, serving as reliable markers for drought tolerance. The results emphasize V. dassycarpa Ten. for fodder and V. michauxii Spreng. for grain production in water-limited regions. Further research on gene expression related to drought tolerance traits should enhance our understanding of vetch.

Diversity in agronomically important traits of wild emmer wheat, Triticum dicoccoides, the progenitor of most cultivated wheats, was examined in l60 genotypes representing 16 populations derived from a wide ecogeographical spectrum of climate, soil and water availability in Israel and Turkey. The analysis included 14 quantitative economic characters including heading date, culm length, biomass, grain yield and its components, and grain protein percentage.

The results led to two major conclusions: (i) agronomically important traits varied genetically: ecogeographic diversity in these traits is dramatically displayed when populations are grown in a relatively standardized environment; and (ii) genetic diversity is revealed not only between, but also within populations. Thus, genotypes excelling in some of these characters were found in several populations.

Salvia miltiorrhiza is an outcrossing and perennial herb native to China. Although well-known for its medicinal value, there is a lack of knowledge regarding its natural population genetics. Here, we used 12 microsatellite markers to investigated population genetic diversity and structure of 215 samples from populations naturally distributed in central eastern China. A moderate level of genetic diversity was detected probably due to the over-mining of its roots. The allelic richness (AR) ranged from 3.034 to 4.889 with an average of 3.891. Moreover, pairwise estimates of FST among the populations of S. miltiorrhiza varied from 0.036 to 0.312 and two clusters were obtained by STRUCTURE and discriminant analysis of principal components. It is likely that the genetic differentiation of these two clusters was formed during glacial periods. Our result provides insights into the conservation of this valuable medicinal plant.

The North East Hill Region (NEHR) of India is home to diverse maize landraces including pigmented accessions rich in antioxidants and nutritional properties. The present study attempted to characterize a representative collection of this mostly unexplored diversity. Altogether eighty-three local maize landraces from the seven hill states of the NEHR were studied with special emphasis on pigmentation diversity. For the morphological traits, a significant ANOVA indicated the presence of substantial genetic variability for which selection would be fruitful. A number of these accessions were found to have traits that help cope with moisture stress, improve stalk strength and optimize photosynthesis. Principal component analysis studies for the yield attributing traits indicated that ear weight was most variable. The bleaching/histological studies confirmed that anthocyanin pigment when present was always restricted to the aleurone layer of the kernels, typical of blue maize. Quantitative analysis for kernel anthocyanin/phlobaphene content also revealed genetic differences among the accessions. Genetic analysis using the model-based STRUCTURE indicated significant population structuring among the accessions. Specifically, for the pigmentation diversity studies both principal coordinate analysis and neighbour joining methods revealed near concurrent population structuring due in part to the high differentiation of seven of the twenty-one pigmentation specific loci studied. The results obtained provide comprehensive evidence of a significant amount of genetic differentiation among the landraces under study. Landraces are valuable reservoirs of favourable alleles for which selection can be made and, as in this study, identify accessions for breeding maize with enhanced levels of beneficial secondary metabolites.

Improvement in genetic gains of crops could be achieved by phenomics' characterization of agronomic, physiological and stress-related traits. Molecular and strategic breeding programmes require broad range of foreground and background phenotypic information for crop improvement. The current experiment was performed on 123 advanced soybean (Glycine max L.) genotypes including seven local lines belongs to four different maturity groups (000-lV) to estimate the endogenous potential of various yield-related traits. The experimental trial was repeated for two cropping seasons. Four traits out of six, yield per plant (YPP), number of seeds per plant, number of pods per plant and plant height (PH), showed maximum variation (CV%) that directly correlate with variability in the subjected population. PH, number of pods, 100-seed weight and YPP showed strong positive correlation in both years. Among the principal components, factors 1 and 2 showed maximum contribution in phenotypic variability ranges from 19 to 48.5% and 26 to 47.7% in the first and second years, respectively. Number of pods showed significant positive correlation with genotypes in both years. Dendrogram showed two distinct groups of soybean genotypes. Genetic variation and association among the accessions is indispensable for effective conservation and utilization of germplasm. Principal component analysis helps to identify the diverse genotypes that will be used as a parent for various breeding programmes. These phenotypic data will be used for detection of heat stress-related quantitative trait loci with genotypic data in genome-wide association studies experiments.

The evolutionary relationship between domesticated Oryza species and their wild relatives in North East India is not well understood. To improve the understanding of the evolutionary relationship, this study investigates the genetic diversity of 68 indigenous rice landraces from North East India, ten O. rufipogon genotypes, and nine O. nivara genotypes using chloroplast variable repeat markers which, due to non-recombination and uniparental inheritance, enable better phylogenetic inference. Reference genotypes IR64 (indica) and Nipponbare (japonica) were included to characterize various phylogenetic clusters. Using distance-based hierarchical clustering, model-based structuring and principal component analysis, selected landraces from the three North Eastern Indian states of Assam, Manipur and Arunachal Pradesh were grouped into two phylogenetically different clusters that represented the IR64 and Nipponbare groupings. Interestingly, despite the fact that a cluster analysis combining North East landraces and wild relatives likewise produced two separate clusters (cluster I: Nipponbare, cluster II: IR64), the majority of the wild relatives were only clustered in the IR64 cluster. This suggests that the two distinct evolutionary histories of the rice landraces in North East India are distinguished by their genetic affinity for wild relatives and their variation in the indica and japonica pools. These results highlight chloroplast divergence influencing the genetic diversity of North East landraces with wild relatives. Further, these findings will enable in-depth studies on the functional significance of chloroplast diversity on trait adaptation in rice landraces.

Sticta canariensis is a lichen which is rare in all parts of its range in Atlantic Europe and Macaronesia, where it occurs in laurisilva forests, a habitat highly threatened by global change. Thus, this species is of high priority for inclusion in conservation programmes where genetic diversity should be considered. We have established new microsatellite loci and generated a dataset that demonstrates the genetic diversity of the lichen-forming fungus S. canariensis from eight locations across its disjunct range, in Macaronesia, Norway and England. We genotyped 25 microsatellite loci for 65 specimens and detected five genetic clusters which resemble major geographical divisions, specifically among the Macaronesian archipelagos. The total number of observed alleles ranged from 2 to 22. These are the first microsatellite markers developed for S. canariensis and they will be useful for population genetic studies and for conservation assessments.

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.

A total of 32 sweet potato genotypes were evaluated to assess the genetic diversity based on quantitative traits and molecular markers, as well as stability for yield and related traits. Wider variability was observed for the traits like vine length (181.2–501.3 cm), number of leaves/plant (103.0–414.0 cm), internodal length (3.20–14.80 cm), petiole length (6.5–21.3 cm), leaf length (8.50–14.5 cm), leaf breadth (8.20–15.30 cm), leaf area (42.50–115.62 cm2), tuber length (7.77–18.07 cm), tuber diameter (2.67–6.90 cm), tuber weight (65.60–192.09 g), tuber yield (7.77–28.87 t ha−1), dry matter (27.34–36.41%), total sugar (4.50–5.70%) and starch (18.50–29.92%) content. Desirable traits such as tuber yield, dry matter and starch content have shown high heritability (>60%) with moderate to high genetic advance. Under molecular analysis, a total of 232 alleles were observed from all 32 microsatellite markers, which ranged from 4 to 14 with an average of 7.77 alleles per locus. In the population, the average observed heterozygosity (0.51) was higher than the expected heterozygosity (0.49). The contribution of genotype, genotype by environment interaction to the total variations was found to be significant. Based on the multi-trait stability index (tuber length, tuber diameter, tuber weight and tuber yield), genotypes X-24, MLSPC-3, MLSPC-5, ARSPC-1 and TSP-12-12 were found to be most stable. Among them, the high-yielding and stable genotypes TSP-12-10 (26.0 t ha−1) and MLSPC-3 (23.9 t ha−1) can be promoted for commercial production or used as parental material in future crop improvement programmes.

In Ethiopia, the low productivity of garlic is largely due to a shortage of high yielding and stable varieties. To address this issue, thirteen garlic genotypes were evaluated for yield stability and performance across six different environments in central and southeast Ethiopia. The genotypes were analysed using Additive Main effects and Multiplicative Interaction (AMMI) and genotype-by-environment interaction (G × E) methods. Results showed that the genotypes differed significantly for bulb yield performance and morphological traits, with G-020/03 and G-054/03 producing the highest bulb yield with 25.39% and 18.39% yield advantages over the check variety, Kuriftu, respectively. Furthermore, G-020/03 demonstrated better yield stability across most environments, while G-054/03 exhibited specific adaptability. GGE biplot analysis confirmed that these two genotypes were among the three winning genotypes in terms of yield performance and relative stability. Therefore, G-020/03 and G-054/03 have been selected as candidate varieties for release, potentially improving garlic productivity in Ethiopia.

The North-Eastern region (NER) of India falls under the Eastern Himalayan region and it is a bio-diversity hub. Diverse maize landraces with wide adaptability to extreme climatic and soil scenario like heavy rainfall, drought and acidic soil conditions have been grown in NER since time immemorial. However, maize diversity in NER region has drastically reduced due to introduction of high yielding varieties and hybrids. Modern maize breeding programmes are focused on high yield but other unique traits like stay green trait, prolificacy (more than one fertile ear per plant), self-fertilizing ability are also important and the local germplasm of the NER region can contribute with these unique traits. Prior to the selection of any lines in several breeding programmes, assessment of genetic diversity and population structure are basic requirements. Hence, in the present study assessment of genetic diversity and population structure study in 30 maize inbreds developed from different germplasm of NER was undertaken using SSR markers, selected for their broad distribution throughout the genome, in order to assess the extent of allelic diversity among the lines and whether any population structure could be established. In addition to assessing molecular diversity, the study aims to evaluate the potential for yield and other beneficial and unique alleles that have high potential to contribute in the genetic enhancement programme of maize.

Yushania anceps is a temperate woody bamboo taxon of high socio-economic importance occurring in the sub-alpine zone of the western Himalayas. This study was carried out to delineate the potential distribution of Y. anceps in the western Himalayas through species distribution modelling (SDM), and genetic characterization using sequence-tagged microsatellite (STMS) markers. The present study revealed an endemic distribution of this species in the Uttarakhand Himalayas, with an estimated area of 211.59 km2. The maximum probability of occurrence was recorded in the moderately dense forests between the altitudinal ranges of 2500 and 2700 m. The model output was well supported with high values of different statistical measures, such as the AUC (0.911) and Kappa coefficient (K = 0.513). Environmental variables related to precipitation, temperature and topography were identified as the most contributory in current SDM. In addition, diversity measures, namely allelic richness (Ar), expected heterozygosity (He), and fixation index (FST), were calculated in five sampled populations with eight STMS markers, which indicated high genetic diversity (Ar = 4.24; He = 0.689) and little differentiation (FST = 0.062). The diversity maps displayed that the populations located in the Kumaon region captured relatively more genetic diversity than the Garhwal region. Further, genetic clustering and STRUCTURE analysis revealed a substantial level of genetic admixing across the analysed populations, and as a result, no sub-structuring was detected. Due to the rare and endemic distribution of Y. anceps, it requires immediate conservation measures, and the knowledge base generated here will be of paramount importance to forest managers, researchers and policymakers.

Ilex paraguariensis A. St.-Hil. (yerba mate) (Aquifoliaceae Bercht. & J. Presl) is a plant species with great economic and cultural importance because its leaves are processed and ground to make infusions like mate or tereré. The species is distributed in a continuous area that includes Southern Brazil and part of Paraguay and Argentina. Uruguay represents the Southern distribution limit of the species, where small populations can be found as part of ravine forests. Although there are previous reports of molecular markers for this and other species in the genus, the available markers were not informative enough to represent the intra- and interpopulation genetic diversity in marginal Uruguayan populations. In this study, we developed highly informative polymorphic microsatellite markers to be used in genetic studies in I. paraguariensis. Markers were identified in contigs from the genome sequence of two individuals and then tested for amplification and polymorphism content in a diverse panel. Markers which passed these filters were tested on populations from Uruguay. They detected higher diversity within populations (in terms of number of alleles and heterozygosity) than previously reported, and levels of heterozygosity similar to those reported for two Brazilian populations. This subset of seven markers were successfully multiplexed, substantially reducing the costs of the analysis. Combined with previously reported nuclear and plastid markers, they can be used to evaluate the genetic diversity of rear-edge populations, identify genotypes for paternity studies and provide relevant information for the conservation and management of germplasm.

Plasmodium vivax is the most frequent and widely distributed cause of recurring malaria. It is a public health issue that mostly occurs in Southeast Asia, followed by the Middle East, Latin, and South Americas and sub-Saharan Africa. Although it is commonly known as an etiologic agent of malaria with mild clinical manifestations, it can lead to severe complications. It has been neglected and understudied for a long time, due to its low mortality, culturing infeasibility, and mild clinical manifestations in comparison to P. falciparum. Despite the mild clinical issues commonly rose for P. vivax, the correlation between the clinical manifestations exhibited by patients with severe and non-severe complications and the genetic diversity of parasites responsible for the disease is not clear. An investigation was carried out between 2011 and 2021 on patients referred to Avicenne Hospital for suspected P. vivax infection. Upon arrival, they underwent clinical and biological examinations. The lateral flow test and LAMP-PCR confirmed the presence of malaria parasites, Plasmodium sp‥ Microscopic examination revealed the presence of Plasmodium parasites with a parasitaemia between 0.01 and 0.38%. Conventional PCR amplifications targeting 714 bp DNA fragment of small subunit ribosomal DNA (SSU-rDNA) followed by bidirectional sequencing allowed us to identify the parasites as P. vivax. The neighbor-joining (NJ) phylogenetic tree revealed that P. vivax sequences processed in the present study clustered in two well-differentiated and supported clades. It included a bigger clade including P. vivax specimens of all our patients together with homonymous sequences from Indonesia, India, and El Salvador and the second clade encompassed the sequences from Yemen and India. In addition, the clustering displayed by the median-joining network agreed well with the topology of the phylogenetic tree generated by the neighbor-joining analysis. No correlation between the clinical manifestation of patients with severe and non-severe complications, encompassing diverse geographical origins, and the genetic diversity of parasites was observed since all sequences demonstrated a high homogeneity. These findings can be helpful in getting knowledge about the population genetics of P. vivax and taking proper control management strategies against these parasites.

Jujube is both consumed as a food source and medicinal plant in local markets. It is expected that different geographical populations of Ziziphus jujuba, differ in their genetic content as they grow in different ecological conditions. It is important to have detailed information on population genetic structure and the available genetic variability to make a proper germplasm collection of jujube. We have no data on jujube populations of Iran based on SCoT and REMAP molecular markers, and therefore we planned a population genetic study of these trees in 10 geographical areas. We used SCoT and REMAP molecular markers for our genetic investigation. We found the loci with a high value of Gst (1.00) in SCoT and REMAP markers that can be used in fingerprinting of jujube.

Common bean (Phaseolus vulgaris L.) is an important crop of family Fabaceae used as a potential source of proteins, fibres and minerals. Thus, characterization of existing germplasm is useful for improvement and conservation. The Indian Himalayan Region harbours plentiful varieties of common bean, but it is nearly unexplored till date. In the present study, physical and genetic diversity of common bean was examined. Fifteen newly designed chloroplast microsatellite (cpSSR) markers were used to assess genetic diversity and population structure in 119 common bean individuals from 20 diverse accessions gathered from Uttarakhand, India. Significantly, positive (p< 0.05) relationship of seed weight was found with seed length (r = 0.813), seed width (r = 0.692) and seed length- width ratio (r = 0.694) using Pearson correlation analysis. A total of 20 alleles were identified using eight cpSSR markers. Mean number of alleles per locus (Na = 1.55), effective allele number (Ne = 1.370), expected heterozygosity (He = 0.213), average polymorphic loci (10.9) and Shannon information index (I = 0.313) were estimated based on cpSSR data. Maximum genetic diversity (He) was recorded in the AKJ/KK/DP/Jhalla/23 accession and minimum in the AKJ/YB/PS/Supi/43 accession. Bayesian-based STRUCTURE evaluation using cpSSR-based information partitioned 20 accessions into two distinct clusters which were also supported by neighbor-joining cluster analysis. These cpSSR markers also demonstrated transferability among other members like Vigna radiata, Macrotyloma uniflorum, Glycine max, Vigna mungo of Fabaceae family, therefore can be used to monitor their genetic heterogeneity. The findings from the study might be valuable to identify elite common bean accessions for production, conservation and future breeding programmes.

The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft de novo assembly of the Siberian fir (Abies sibirica Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (Abies alba Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of A. alba and a small sample of eight Nordmann fir (Abies nordmanniana (Steven) Spach) trees.

Bambara groundnut (Vigna subterranea (L.) Verdc) has been neglected in terms of variety selection and development which has resulted in farmers growing a mixture of landraces that are not genetically characterized and are low yielding. With the need to set up a breeding programme in Malawi, it was necessary to thoroughly understand the genetic diversity (GD) present in the available germplasm. The objectives of the study were to assess Bambara genotypes GD using agro-morphological traits and SNP markers, and to identify and select high yielding Bambara genotypes. Field trials were conducted for two seasons at Bunda College. Later, genotypes were genotyped using DartSeqLD SNP markers. All data were analysed using R Package. Significant genetic variations (P < 0.001) were observed for most traits including grain yield, which suggests that genetic variability exists in Bambara groundnuts which can be exploited in breeding programmes aimed at developing high performing varieties. Based on grain yield, the study identified 18 top performing genotypes across the evaluation seasons which will be tested under farmers’ fields’ conditions. DArTseqLD grouped the genotypes into three clusters. It was noted that majority of the genotypes from the same origin clustered together. High genetic distances were observed between genotypes from Southern African and West African regions and this has important implications in parental selection for the genetic improvement of Bambara. Our results provide valuable insights about the extent of genetic variability and how parental lines can be selected for improved genetic gain in Bambara groundnuts.