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Rice false smut caused by Ustilaginoidea virens is one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from single nucleotide polymorphism-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in the Sichuan–Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. Groups I and VI were the largest, with 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. Analysis of molecular variance showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup genetic variation. The unweighted pair-group method with arithmetic means dendrogram and population structure revealed that the genetic composition of isolates collected from Santai, Nanchong, Yongchuan, and Wansheng dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

In the present study, the phenological and genetic differences/similarities of 95 walnut genotypes were considered. These genotypes had been propagated sexually from the open pollination of the maternal cultivar ‘Maras 12’. This study examined the timing of several phenological features like bud break, leafing, yellowing of the leaves and defoliation in the mother plant and in its progenies. A total of 6 ISSR primers were used for determining genetic differences among the genotypes. The differences between the maternal cultivar and the offspring genotypes included a difference of 97.89% in the bud-break date, 96.84% in the leafing date, 100% in the yellowing date of the leaves and 94.73% in the defoliation date. On average, the phenological variation stood at 97.36%. PCA analysis also confirmed the presence of genetic diversity-based phenological markers in our walnut seedling collection with PC1 58.27%, PC2 27.16%, PC3 12.16%, and PC4 2.40% of the total variation. A total of 38 bands were obtained in molecular analyses. These bands were largely polymorphic (89.47%). While the average number of alleles was 5.66, Polymorphism Information Content (PIC) varied between genotypes from 0.47 to 0.95, and the average PIC value was 0.64. The UPGMA dendrogram divided the genotypes into two main clusters and the similarity coefficient of the genotypes varied between 0.68 and 0.96. In sum, it was found that open-pollinated walnut genotypes had high degrees of phenotypic and genetic variation in comparison with their maternal cultivar ‘Maras 12’.

Key message The morpho-agronomic and genetic studies recorded variations in vegetative and reproductive traits, and in molecular information through population structure and clustering approaches among South African Phaseolus vulgaris landraces. Abstract Phaseolus vulgaris L., commonly known as common beans, is widely used for its edible leaves, immature pods, and dry seeds. Studies on variation in morphology and genetics among P. vulgaris landraces are limited in South Africa. Therefore, the current study aimed to determine the morpho-agronomic and genetic variations among P. vulgaris landraces. Thirty-eight landraces from different agro-ecological origins, planted in a randomized complete block design, had their variation in vegetative and reproductive traits determined. These landraces were studied for their genetic diversity using simple sequence repeat (SSR) markers. The landraces were clustered in a biplot and dendrogram based on their seed coats, shape, similar morpho-agronomic traits, and their areas of origin. A total of 57 alleles were produced with a mean of 3.64 per SSR locus. The polymorphism information content ranged from 0.00 to 0.58. The population structure had the highest delta value K = 2, thus the 38 landraces were divided into two subpopulations based on the Bayesian approach. The population structure showed an overlap among the landraces as several from the Mesoamerican carried some seed traits or genes from the Andean gene pool, and showed a high level of admixtures. The principal coordinate analysis and the dendrogram had a similar clustering pattern as the population structure. This study revealed the potential markers with high diversity that can be used to determine genetically homogenous/heterogeneous landraces. Therefore, the use of PV-ctt001, PV-ag001, and PV-at003 could be beneficial in future breeding, conservation, and marker-assisted selection studies.

Sage (Salvia officinalis L.) is not found in Turkey's natural flora; however, its cultivation has been increasing in recent years. The species is widely cultivated in many provinces of the Aegean and the Mediterranean regions. There has been no information regarding genetic characteristics and the intra-individual phylogeny of cultivated sage. The levels of genetic relatedness of 19 Salvia samples from Izmir were determined by molecular tools. The sequences from the internal transcriber spacer (ITS) region of 18S–28S nuclear ribosomal DNA (nrDNA) locus were amplified by PCR and sequenced. Approximately, a 710 bp single amplified product was obtained in all genotypes. Of the nineteen Salvia specimens, six were identified as Salvia x sylvestris L. and the remaining 13 specimens were S. officinalis. The sequences of both species shared no similar secondary structures. The ITS region of all specimens contains several indels and substitutions. In the phylogenetic dendrogram, three major clusters (I, II, and III) and two independent branches (IV and V) were observed. Ninety-seven percent of local Salvia specimens were clustered in two branches (I and II), indicating a high diversity of genetic relatedness. Sequence divergence was higher among the specimens of S. officinalis than the specimens of Salvia x sylvestris.

DNA fingerprints are efficient tools for the identification of known and unknown cultivars. In order to assist with the effective identification of germplasm resources of Pennisetum in China, the genetic diversity of 24 Pennisetum cultivars was analyzed and the DNA fingerprints were constructed using SSR markers in this study. 20 pairs of SSR primers with higher polymorphism were selected from 70 pairs of SSR primers for further study. The results showed that 199 bands were amplified from 24 Pennisetum cultivars by the 20 selected pairs of primers and 176 of which were polymorphic with an average of 8.8 polymorphic bands per pair of primer. The unweighted pair group method (UPGMA) with arithmetic mean dendrogram from SSR markers grouped the 24 Pennisetum cultivars into three categories. And based on two combinations of SSR markers selected, the DNA fingerprints were constructed in this study, which can be used for the classification and identification of Pennisetum cultivars.

Asian lotus (Nelumbo nucifera Gaertn.) is an aquatic plant with ornamental, cultural, economic, and ecological values. China has abundant germplasm resources of Asian lotus. However, in many areas, the wild Asian lotuses have been destroyed and the germplasms is now facing extinction. In addition, the knowledge of the genetic diversity of the wild Asian lotus in China is poor. To identify and protect the germplasms of Chinese wild Asian lotus, eleven genomic-SSR primers, three EST-SSR primers, and three chloroplast DNA primers were used to investigate the genetic diversity among 69 samples of wild Asian lotus from 25 locations in northern China. The genetic diversity of 27 samples of wild Asian lotus from southern China and other countries, the ancient Asian lotus, Asian lotus cultivars from China, and Asian-American hybrids was also compared. The genetic diversity of the wild Asian lotus from northern China was characterized as medium, and the mean values of observed heterozygosity (Ho) and expected heterozygosity (He) were 0.087 and 0.552, respectively. Based on a UPGMA dendrogram and STRUCTURE analysis, the wild Asian lotus samples in northern China were divided into three groups. The wild Asian lotus samples from northern China contained 16 haplotypes. The Nei's genetic distance between the wild Asian lotus samples from the Songhua River basin and the Liao River basin in northeastern China was relatively small, and these germplasms might be relatively primitive compared to those from other regions. This study provides essential information regarding the genetic diversity of the wild Asian lotus resources in northern China, and provides a basis for further analysis of population-level genetic evolution through high-throughput sequencing.

Winged bean (Psophocarpus tetragonolobus (L.) DC) is a nutritious tropical legume known for its high protein content in the seeds. Twenty winged bean genotypes were studied for the genetic diversity using Inter-simple sequence repeat (ISSR) markers. On ISSR analysis, 124 bands were generated by 11 informative primers, of which 76 bands were polymorphic and 3 were unique. The PIC values of ISSR primers studied ranged from 0.06 to 0.39; resolving power (Rp) values ranged from 0.9 to 4.7 and the mean number of bands per locus ranged from 9.6 to 18.2. The mean number of bands per accession ranged from 3.9 to 13.7. Narrow genetic base was revealed with the similarity values amongst genotypes ranging from 0.72 to 0.98; with 64 combinations having similarity value more than 0.90 and another 105 genotypic combinations having similarity index in between 0.80 and 0.90. The dendrogram showed two major clusters with 4 groups; with cluster-I being mono-genotypic (EC142666); while two little bit divergent groups could be clearly distinguished from highly homogenous core twelve genotypes. The principal component analysis (PCA) derived pattern was almost in accordance with the clustering pattern based dendrogram. Within the narrow base of the winged bean genotypes studied; four main groups were observed with EC142666 being most divergent; followed by two diverse groups comprising of 3 (EC-178268/EC-178269/EC-178311) and 4 (EC-121921/EC-178291/EC-178310/EC-251020) genotypes respectively; with the other genotypes were very close to each other indicating genetic bottleneck. This necessitates the need for identification of divergence germplasm for breeding to broaden the genetic base.

Fusarium yellows tolerant/resistant lines of ginger (Zingiber officinale Rosc.) var. Himgiri generated through in vitro mutation induction using gamma irradiations followed by selection on Fusarium oxysporum f.sp. zingiberi culture filtrate (FCF) were evaluated under in vivo conditions and screened at molecular level using SCoT (Start codon targeted) markers. Thirty-six primers were used to evaluate genetic variations among all the selected lines and compared to gamma-irradiated and tissue culture propagated plants taken as control. A total of forty-nine (49) amplicons were produced with thirteen primers resulting in 45.27% polymorphism. The average polymorphic information content (PIC) value for all SCoT markers was found to be 0.48 with 0.108 effective multiplex ratio (E) and 0.052 Marker Index (MI) whereas, Jaccard's similarity coefficient showed a distance range from 0.42 to 0.98. Dendrogram prepared using UPGMA clustering analysis divided the experimental lines into two main clusters. All the Fusarium tolerant/resistant lines selected at 12.5 and 15% FCF selection pressure grouped in cluster I showing high level of similarity with gamma-irradiated and tissue culture propagated controls. Cluster II comprised of all the Fusarium tolerant/resistant lines from 17.5% FCF selection. Hence, suggesting the applicability of SCoT markers for evaluation of different ginger genotypes for Fusarium resistance, in the future.

In this study, the pollen morphology of all Ferula species distributed throughout the country of Turkey was studied with light and scanning electron microscopy for the first time. The aim is to identify the pollen morphological characteristics of 23 Ferula species. The pollen is radially symmetrical, isopolar and tricolporate in all examined species. Pollen grains are prolate and perprolate with the polar axis ranging from 22.28 to 40.47 µm and the equatorial axis from 13.70 to 18.73 µm. Their polar shapes are triangular, triangular to subtriangular and circular to subcircular. Several types of exine ornamentations have been observed on pollen through the use of scanning electron microscopy. The dendrogram constructed by using Average Linkage of the examined data revealed two main groups. It was determined that some pollen characteristics are more useful for classification than others. In particular, P, E, the ratio of P/E (pollen shape) and ornamentation in the polar and equatorial views are the most valuable variables for discrimination the Ferula species.

Safflower, an important oil seed and medicinal crop has rich genetic diversity but limited genetic resources, which could be utilized for its improvement. In a bid to enrich safflower’s genetic resources polymorphic genic SSRs were identified by in silico comparisons of the de novo assembled transcriptome sequences from two safflower genotypes. Of the 145 exon-derived primer pairs, 125 produced reproducible amplifications and 44 primer pairs yielded products that showed polymorphism even between the two closely related safflower accessions. Out of the 44 primer pairs, 10 primers that were utilized for assessing the genetic diversity and cross-species transferability on a diverse panel consisting of 24 accessions, revealed high genetic diversity in the panel and cross-species transferability of the markers. The UPGMA dendrogram clustered the wild types and safflower genotypes in three major groups, of which wild types clustered in a subgroup of major group II, whereas the remaining genotypes were scattered in all three clusters with the majority (73.68%) being clustered in group I. The in silico identified polymorphic exon derived genic SSRs are an important addition to the available genetic resources and can be deployed for marker assisted breeding programs for improvement of safflower.

The collection and characterization of apricot germplasm is an important step for its utilization, conservation, and breeding programs. In the present study, the genetic diversity and population structure of 106 accessions of apricot including 82 indigenous and 24 exotic accessions collected from various geographical locations of Jammu and Kashmir, India were evaluated using 14 inter simple sequence repeat markers. The PCR amplification produced 365 loci of which 356 (97.53%) were polymorphic. The average number of alleles, effective number of alleles, expected heterozygosity, Shannon’s information index indicated high level of genetic diversity in the collected apricot accessions, and the polymorphism information content (0.82) revealed that these markers were highly polymorphic. The results of UPGMA dendrogram and model-based STRUCTURE analysis clearly divided the 106 apricot accessions into two main groups; one group included the 78 accessions of Kashmir province and the other included 28 accessions of Jammu province indicating the distinction of two genetic pools of apricot in the region. Nonetheless, PCoA also revealed a similar grouping of accessions except few exotic accessions that formed a small separate group. Moreover, analysis of molecular variance showed high genetic variation within the population (67%) and low among the population (33%). To our knowledge, this study represents the first comprehensive report on the ISSR based genetic diversity, relationship, and the structure of apricot accessions of Jammu and Kashmir. Further, the results of the present study will assist in efficient utilization, conservation, and MAS based breeding programs of apricot.

For the estimation of genetic diversity and population structure, 23 accessions of Leucaena leucocephala were characterized using morphological and molecular markers. A medium to high degree of genetic variability was calculated among these accessions based on eight quantitative traits. Furthermore, a cluster analysis based on morphological characteristics grouped the 23 Leucaena accessions into five groups based on their similarities. Furthermore, the principal component analysis revealed that eight quantitative traits contributed for 82.57% of the total variability. Eleven simple sequence repeats (SSR) markers showed a high degree of polymorphism among the 23 L. leucocephala accessions. The polymorphic information contents (PIC) for these 11 markers were estimated and revealed that SSR723 had higher PIC value (0.90). Also, the dendrogram generated based on 11 markers distinctively demarcated most of the L. leucocephala accessions into different clusters indicating its vast genetic diversity in the population. A population structure study of these 23 L. leucocephala accessions showed the existence of two gene pools. Also, analysis of molecular variance showed that there was 13% variability between populations, while there was 87% variability within the population. The first and second coordinates of principal coordinate analysis unconditionally distributed these accessions into four coordinates based on their similarity. Overall, the high degree of genetic variability described by morphological and molecular markers in L. leucocephala can be used as a basic tool for assessing genetic diversity and linkage mapping in Leucaena genetic improvement programs.

Spot blotch is an alarming disease for wheat caused by the anamorphic stage (Bipolaris sorokiniana) generally but it’s rare when it caused by telomorphic stage (Cochliobolus sativus). The present study reveals molecular identification and pathogenic variability among the isolates of C. sativus in F2 generation. Each of the C. sativus (F2 generation) isolates was identified and confirmed following ITS rDNA sequence analysis. Internal transcribed spacers (ITS) region sequence reference was KC311473.1and EF452447.1. For determining pathogenic variability a susceptible wheat cultivar “Kanchan” was used. Seven components of disease development like infection frequency, lesion size, lesion cover, necrosis, secondary spore production, disease severity and per cent disease index were studied to understand the pathogenic variability. All components of disease development showed positive co-efficient relation with each other. Non-significant relationships were observed between necrosis and secondary spore production, disease index and per cent disease index. Cumulatively infection frequency and lesion size showed 77.95% variation. According to per cent disease index and secondary spore production isolate CSF2-32 and CSF2-58 were most virulent and aggressive ones among the tested isolates. A cluster analysis indicated that the isolates exhibited distinct differential virulence patterns with five groups supported by a dendrogram figure.

The pollen morphology of 17 taxa of Gundelia, of which 13 taxa are endemic to Turkey, was investigated by light microscopy (LM) and scanning electron microscopy (SEM). In this study, the pollen morphology of 16 taxa except G. tournefortii was investigated for the first time. The quantitative data were analyzed by descriptive statistics and multivariate statistics. The pollen grains are oblate spheroidal and prolate spheroidal in shape with the polar diameter of 37.01–61.2 μm and the equatorial diameter of 31.2–63.4 μm. The smallest pollen grains were observed in G. anatolica, G. rosea and G. tournefortii, while the largest pollen grains were observed in G. vitekii, G. komagenensis and G. colemerikensis. Pollen ornamentation is echinate in LM and echinate-microperforate in SEM. Statistically, the relationships between pollen characters of the examined taxa were identified using Principal Component Analysis (PCA) and Clustering Analyzis. In addition, a dendrogram was constructed by applying UPGMA based on the determined 15 pollen morphological characters, and the degree of their relationship was discussed. Polar axis, equatorial diameter and colpus length were the major explanations of the pollen morphological characters’ total variation in PCA. Pair group method was used to divide the main pollen taxa into three groups based on the pollen morphology by using arithmetic averages analysis (PCA scatterplot and cluster analysis). As a result, the pollen shape, polar axis, equatorial diameter and spine length were important characters distingushing the taxa from each other. We found some matches and mismatches between pollen and morphological characters, whose significance requires further study.

The genetic diversity of 334 herbaceous peonies from Fennoscandia was analysed using 18 microsatellites (simple sequence repeats, SSRs). The samples included peonies mostly from Finnish home gardens (284) and nurseries (5) as well as from Norwegian (20) and Swedish (25) peony collections. The study focused on the following species and hybrids: Paeonia anomala L., P. × hybrida Pall., P. officinalis ‘Nordic Paradox’ (Marstein 2015), P. tenuifolia L., and P. × festiva Tausch. The 18 microsatellites amplified a total of 249 alleles and were used to calculate genetic distances between samples and to build a dendrogram. In the dendrogram, samples formed clear groups according to their species. The outcome from the genetic analysis was mainly confirmed by preliminary morphological observations of the Finnish home garden samples performed within the project and the previous morphological study of peonies in Norwegian clone archives. The results of the study will be used to create a Finnish genetic resources collection of the most diverse and vigorous peonies, and to update the Norwegian and Swedish collections.

Assessing the effectiveness of different molecular markers is essential for identification of appropriate ones for crop improvement and conservation, hence, inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers were used for this study. Sixty-six accessions with different genomes obtained from International Transit Center, Belgium, were used for DNA extraction, amplification with ISSR and SCoT markers and agarose gel electrophoresis. The reproducible bands were scored for analyses. We identified high allelic richness of 299 (ISSR) and 326 (SCoT). Polymorphic information contents (ISSR: 0.9225; SCoT: 0.9421) were high but SCoT exhibited higher level of informativeness. The two markers demonstrated high percentage polymorphic loci (ISSR: 91.21–100%; SCoT: 96.97–100%). Other genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon information index were higher in SCoT and further elucidated the usefulness of the markers. Intraspecific genetic diversity, interspecific genetic diversity, coefficient of gene differentiation and level of gene flow revealed extensive gene flow and larger variability within the accessions. Both ISSR and SCoT grouped the accessions via dendrogram, biplot and structure analyses. Though the two marker systems varied in their informativeness, they demonstrated high effectiveness in resolving genetic diversity (GD) of the different accessions, with higher efficiency in SCoT markers. Due to higher GD indices exhibited by SCoT, AS is the most genetically endowed one. Our study showed that SCoT markers are more informative than ISSR for GD exploration, assessment and cluster resolution of Musa species, thereby revealing the potential of SCoT markers for improved breeding and conservation.

We analised vegetation of calcareous screes in the alpine belt of Bjelašnica Mt. (Western Balkan) by the Central European phytosociological method. In total, 69 relevés were submitted to numerical analysis in R ver. 3.5.2. (UPGMA clustering with chord distance). The obtained cluster dendrogram showed differentiation in nine associations, of which Festuco xanthinae—Valerianetum montanae Trakić et al. ass. nov. and Drypido spinosae—Seslerietum wettsteinii Trakić et al. ass. nov. are new ones. In lower section of the alpine belt we described new subassociation Pseudofumarietum leiospermae helictochloetosum Trakić et al. subass. nov. which raises questions about ecological preferences of the alliance Corydalion ochroleucae. We also neotypified the association Drypidi—Heracleetum orsinii Redžić et al. ex Trakić et al. and made correction for Pseudofumarietum leiospermae Lakušić et Redžić 1991 nom. corr. The observed high diversification of the alpine screes on Bjelašnica Mt. is based upon its ecological heterogeneity and tranzitional position in the Dinarides.

Just behind wheat and rice, maize is the third most important grain crop in the world, grown in many agricultural areas. In Mozambique, rainfall is declining, posing serious threats to national food sovereignty and security, particularly in southern regions of the country. Despite this fact, few research studies have been conducted on the performance of Mozambique´s maize germplasm under drought stress conditions. A randomized design combining eight maize genotypes (six traditional Mozambican genotypes: LVA34, TCDE, G234, D456C, MABC, C123; and two commercial cultivars from DuPont Pioneer: P0023 and P9838) and three water regimes (control (irrigated), stress and recovery) was used to characterize the maize resilience to water deficit. The photochemical performance was accessed by rapid chlorophyll fluorescence induction curves (JIP-test). The use of Performance Index based dendrogram analysis allowed to explain genotypes behavior on the different experimental sets (control, drought stress and recovery). G234 and C123 presented the best performance with the lowest mortality rates, showing a better ability to cope with drought stress when compared to other genotypes from Mozambique and to the commercial cultivars from DuPont Pioneer.

Apricot (Prunus armeniaca L.) is a world-wide highly appreciated fruit, with its attractive colour, soft texture and typical flavour. In the current investigation, 68 apricot accessions collected from Jammu and Kashmir, India were analysed to determine the measure of variation using 12 qualitative and 16 quantitative traits with an aim to identify superior apricot accessions with excellent fruit quality traits. High phenotypic variability was observed among the studied apricot accessions with significant differences among most of the qualitative and quantitative traits. Fruit-related characteristics including fruit weight, fruit length, fruit ratio, fruit firmness, fruit shape, fruit suture, stone weight, kernel weight and stone shape were the most diverse with a high coefficient of variation (>30%). One way analysis of variance showed significant differences (P < 0.0001) among all the quantitative traits. Significant positive and negative correlations were observed between all the agronomically important fruit quality traits. The principal component analysis (PCA) revealed that 75.34% of the variability was defined by the first eight components. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram, based on all traits measured grouped the accessions into two main clusters with several sub-clusters. Both UPGMA dendrogram and PCA scatter plot formed a cluster of 14 accessions, having the highest values regarding most important fruit quality traits such as fruit weight, fruit length and width, fruit ratio, stone weight and kernel weight can be treated as potentially superior accessions. These accessions can be used directly for cultivation and in future apricot breeding programmes. The present findings are promising for genetic resource management, cultivar improvement and commercial applications of apricot in Jammu and Kashmir, India.

This study assessed the genetic diversity of African yam bean (AYB) accessions using morphological and molecular markers. The accessions were grown, and morphological data collected were subjected to analysis of variance and multivariate analyses. Genomic DNA extracted from the accessions were amplified with inter simple sequence repeat (ISSR) markers. The diversity analysis was conducted using MEGA4 software. The accessions varied significantly (P < 0.05) in growth, flowering and seed-related parameters. Flowering commenced early in most accessions. Weight of 100-seed range from 15.01 to 21.15 g with the mean value of 18.30 g. Significant correlations existed between stem height, the number of leaves and leaf dimensions. Also, days to flowering correlated with pod formation; likewise, seed dimension had a positive association with seed weight. The principal biplot revealed that two components accounted for 41.77% of the observed variation. Analysis of the electropherogram showed 95 loci comprising 1351 alleles were detected by the ISSR markers with 65.26% polymorphism and combined polymorphic information content of 0.85. The principal coordinate analysis placed accessions together on a plane based on their spatial relationship. The dendrogram showed accession pairs (TSs-77, TSs-95) and (TSs-111, TSs-84) are closely related. The phylogram identified three kinships with a total length of 454. Accession TSs-115 is likely the progenitor while TSs-82 and TSs-86 are the most recent. The study concluded that a combination of morphological and ISSR markers is effective for the diversity study of AYB and the existing, genetic diversity in the accessions could be harnessed for its improvement, conservation and utilization.

Sixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

The present study was conducted to differentiate pathotypes of Xanthomonas citri subsp. citri (Xcc) the causal agent of citrus canker in Iran. A collection of 29 strains were isolated from infected plant parts. In order to investigate the genetic diversity of bacterial isolates, RAPD and ISSR markers were used and discrimination power of these markers for the pathotype detection was assessed. Based on the amplified fragments of the RAPD, the dendrogram divided the strains into three main groups. In the first group, there were eight strains of both pathotypes A and A*, and all strains of A* pathotype were categorized in this group. Strains of pathotype A formed the second and third groups. Based on the results of the ISSR amplified fragments, the dendrogram classified the strains into three main groups. The resultant grouping was indicative of placement of A strains in one group, and in all groups, both A and A* pathotypes were grouped together. The electrophoresis patterns of amplified fragments with RAPD primers revealed high specificity of this marker in pathotype differentiation.

Background.Studying genetic polymorphism of the Prunus pumilaL. representatives with a wide range of variability in morphological characters will make it possible to identify promising genotypes with high combining ability for hybridization.Material and methods.The study covered 39 genotypes from the Chelyabinsk cultivated population and 6 genotypes from Khakassia, with extreme or intermediate expressions of such characters as fruit size, color and shape; stone shape and surface structure; leaf blade serration and shape; plant habitus, and some others. Genetic distances were calculated using the data matrix for binary states of presence (1) or absence (0) of amplified fragments with the Past Program (Gower). The UPGMA dendrograms were obtained in TREECON (version 1.3b).Results and discussion. The selected 5 ISSR and 2 RAPD primers demonstrated their effectiveness in detecting genetic polymorphism in the studied accessions. In individual cases, a weak connection of separate markers with leaf blade edge serration, stone surface structure, plant habitus, and geographic origin of the genotype was detected. Concurrent inclusion of all primers and genotypes in the cluster analysis failed to group the studied P. pumilasamples into clades according to the presence/absence of any traits, which may attest to their close genetic affinity. An independent clade with reliable bootstrap support (100%) was formed only for the genotypes of the taxonomically close sp. P. tomentosaThunb., analyzed as an external group. Moreover, this clade manifested (with the 86% reliability of bootstrap support) differences between the hybrid genotypes of P. pumila× P. tomentosa(F3) and the genotype of P. tomentosa. Parent pairs promising for fruit quality and shrub shape improvement through breeding were identified using the produced indices of genetic distinction.

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.

For effective varietal improvement of horticultural crops peach (Prunus persica) and nectarine (Prunus persica var. nucipersica), information about their population structure and genetic relatedness plays an important role. In this study we used retrotransposon-based markers (iPBS) to estimate the genetic diversity and population structure of 48 peach and nectarine genotypes from various distinct geographical regions of Punjab and Khyber Pakhtunkhwa, Pakistan. A total of 461 alleles were identified from PCR amplicons derived from nine iPBS primer pairs with an average of 8.5 alleles/locus. Among all four groups the genotypes collected from Swat and Hunza had the highest and the lowest expected heterozygosity, unbiased expected heterozygosity and Shannon’s information index, respectively. We constructed a Neighbour-Joining dendrogram and performed principal coordinate analysis based on the distance matrices, and both forms of analysis grouped the 48 genotypes into two distinct clusters. The STRUCTURE software distributed the forty-eight genotypes into two main populations (k = 2) indicating a low diversity between genotypes collected from Chakwal, Swat, Mansehra and Hunza.

The jute mallow (C. olitorius L.) is an important nutritious green leafy vegetable in the tropical region of Africa. This study assesses the extent of genetic diversity and intra-specific relationships among 16 cultivated jute mallows of Nigeria (14), [Ghana (1) and Togo (1), used as checks, evaluating 16 dark jute SSR markers and 16 morphological traits (quantitative and qualitative). The study reveals moderate to high variation among the cultivars in the number of pods, pod yield and plant height traits. Based on the principal component (PC) analysis of the quantitative traits, the pod length, pod width, number of pods, pod yield and plant height are important traits composing PC1. On the other hand, the pod pedicel length and days of 50% flowering traits are highly correlated variables in PC2. Pod length, pod width, pod pedicel length and plant height account for the total diversity. Two main groups (I and II) and an outgroup are identified among the 16 cultivars based on the quantitative traits. among the cultivars, leaf shapes identified are ovate (38% of cultivars), lanceolate (6%), oblanceolate (25%) and palmately lobed (31%). Three markers which have monomorphic alleles are excluded and thirteen markers are used to analyse the genetic diversity. A total of 41 alleles are amplified using the 13 polymorphic markers with an average of 2.75 per locus. The mean polymorphism information content (PIC) value is 0.42, ranging from 0.06 to 0.73. The mean gene diversity or expected heterozygosity = 0.05 (from 0.06 to 0.76). The observed heterozygosity (Ho) ranges from 0.00 to 0.88, with a mean of 0.60. The mean genetic dissimilarity is 0.35. Thus, the SSR data indicate a moderate genetic dissimilarity within jute mallow under study. Clustering using the neighbour-joining dendrogram predicated on the SSR data separates the cultivars into three major groups in which the two cultivars from Ghana and Togo show distinctiveness from the cultivars from Nigeria. Principal coordinate analysis of SSR data is consistent with neighbour-joining groupings. The study based on a set of dark jute markers and morphological traits reveals that the extent of genetic diversity of cultivated jute mallow and could be used in germplasm evaluation. In addition to the knowledge of the high genetic variability observed in the number of pod and the yield of some of the studied cultivars, further efforts are needed to characterise the cultivar pods’ nutritive values for human health.

This study was carried out to evaluate Turkish rice landraces, in 2016 and 2017. Twenty-nine morphological traits were used for morphological evolution and 10 SSR markers were used for molecular evolution in 27 varieties. Based on morphological dendrogram, the landraces were divided in to 11 groups at 5 level differences. It was found that all 27 landraces had absent or very weak pubescence of panultimate leaf blade, broad decorated seed width and non-waxy kernel, however, they were highly polymorphic for the other 26 characters studied. In total 51 alleles were produced by screening with SSRs and among the markers; RM552 and RM287 were highly polymorphic for Turkish rice landraces with 11 and 8 alleles respectively. Average allele number was 5.1 and PIC ranged from 0.36 to 0.84. The UPGMA cluster dendrogram generated by using SSRs information and cluster grouped the 27 landraces in 2 major clusters. A significant level of polymorphism on molecular levels was observed. The study shows that some landraces with same local name were very distant from each other, while some local varieties with different names were same landraces.

Dendrobium fimbriatum is an ornamental and medicinal orchid listed in the Red data book of IUCN. Phytohormones’ effect on the in vitro regeneration of the orchid was studied using Mitra medium supplemented with different growth regulators. KN produced effective shoot formation when present alone or in combination with IBA or NAA. The shooting was gradually increased when KN concentration was increased from 0.8 to 4.8 mg L−1, but the opposite response was observed with BAP at higher concentration (4.8 mg L−1). IBA either in combination with BAP or KN promoted effective root development and multiplication. Micropropagated orchids grown in the basal medium devoid of any phytohormone showed 100% monomorphism, while low genetic polymorphism of 1.52% (RAPD—Random Amplification of Polymorphic DNA), 1.19% (ISSR-Inter Simple Sequence Repeat) and 3.97% (SCoT—Start Codon Targeted) was exhibited among the regenerants propagated in the hormone enriched medium. UPGMA (Unweighted pair group method using arithmetic averages) dendrograms showed the grouping of mother plant (MP) with the in vitro regenerants. The principal coordinate analysis (PCoA) further confirmed the clustering patterns as determined by the cluster analysis. The study reported for the first time the successful in vitro propagation of Dendrobium fimbriatum and their genetic stability assessment using molecular markers.

Citrus plant species are among the most important and consumed fruit plants throughout the world. In general, genetic diversity investigations in all Citrus species and varieties are in hand in order to add to the knowledge of these important plant species. The sweet orange cultivars (Citrus sinensis), are among the most wanted among Citrus species. Various genetic diversity investigations by using different molecular markers have been performed in different regions of the world. We investigated 23 cultivars of sweet oranges available in Iran and two out-group cultivars produced by crossing Lemon and Kumquat. We used Start Codon Targeted (SCoT) molecular markers for genetic study. The studied cultivars produce 64 SCoT loci or bands. In total each cultivar studied contained 8–29 SCoT bands and six cultivars had 1–2 private/specific bands due to their peculiar genetic structure. Genetic diversity parameters were determined in these cultivars and revealed that the genetic polymorphism varied from 6.15% into 44% in the Studied sweet orange trees. We identified many loci with high discrimination power (> 0.80) in SCoT marker. Analysis of molecular variance (AMOVA) revealed significant genetic difference among these cultivars, and pair-wise AMOVA identified those sweet oranges which differed genetically from each other. Unweighted pair group method with arithmetic mean dendrogram of the studied samples separated most of the cultivars and their replicates in distinct clusters. STRUCTURE analysis revealed genetic structure of sweet oranges, showing their genetic similarities versus genetic uniqueness. We could differentiate some of Thompson cultivars, coming with different origins or locality. It held true for red blood and Jaffa oranges too. We identified few potential hybrids in the country. These findings will be used in future sweet orange conservation and breeding.

Hymenocrater comprises of 11 species throught the world. The genus is an Irano-Turanian elements, which has several usages in traditional medicine. Northeast of Iran is the main geographical region of Hymenocrater species. The aims of the peresent study was to delimit 11 species of Hymenocrater to determine the species relationships based on morphological and molecular data (cp-DNA sequence), to produce divergence time and to construct barcode gap using the internal transcribed sequence because of adulteration of this genus in local markets. According to the results, Neighbor-Net network and UPGMA dendrogram of morphological data can delimit Hymenocrater species. Meanwhile, analyses of Chloroplast sequences (psbA-trnH) revealed that the species relationship and delimitation are difficult and complicated due to gene flow, hybridization, gene duplication, reticulation and chloroplast capture. Divergence time of Hymenocrater species estimated from Bayesian Evolutionary Sampling Trees date were seven million years ago. The center origin of Hymenocrater in Iran is Razavi Khorasan. Genetic fingerprinting of correctly identified medicinal species provides standard for comparing plant specimens sold in the market with true to type medicinal plant. Therefore, ITS sequences are important for barcoding this medicinally significant plant. It is correctly identified medicinal species, which will be used as standard for evaluating market sold plants.

The cultivated strawberry (Fragaria × ananassa Duch.) is a species of temperate origin, and the extension of this crop into tropical regions is dependent on genetic breeding. Breeders in the UNICENTRO’s Strawberry Breeding Program (USBP) selected, from among 2,000 hybrids, 40 hybrids that were adapted to photoperiod and temperature conditions of tropical regions. In this study, we used inter-simple sequence repeat to characterize 40 three-way hybrids developed by USBP and evaluated the genetic relationship of these hybrids with commercial cultivars, heirloom cultivars, and single hybrids. We used nine inter-simple sequence repeat primers to genotype 14 commercial cultivars, five heirloom cultivars, five single hybrids (SH), 20 three-way hybrids with short-day behavior (SDH), and 20 three-way hybrids with photoperiod-insensitive behavior (PIH). The percentage of polymorphism (100%) and both, the Nei genetic diversity (h = 0.34) and the Shannon index (I = 0.51), showed high variability and diversity, respectively, in the evaluated strawberry genotypes. Commercial cultivars showed the highest diversity indices (h = 0.30, I = 0.46), followed by PIH hybrids (h = 0.27, I = 0.41). In the dendrogram, the genotypes were distributed into three groups (commercial cultivars, heirloom cultivars, and single hybrids; SDH and PIH). This clustering was confirmed by principal coordinate analysis and Bayesian inference analysis. The overall analysis of the data revealed the efficacy of USBP in three-way hybrid development with different genetic characteristics compared with those of available commercially cultivars. These hybrids have substantial potential in becoming new strawberry cultivars.

Pyricularia oryzae tritici, one of the most notorious pathogens of wheat, is a major biotic threat in wheat production around the globe. A total of sixteen P. oryzae tritici isolates isolated from four major wheat blast affected districts viz., Meherpur, Chuadanga, Kustia and Jhenaidaha of Bangladesh were analyzed. Considerable morphological variations in terms of colony color, texture, surface appearance, conidial size and growth pattern were observed. Molecular characterization of the isolates was done based on the sequence information of internal transcribed spacer (ITS) regions. Phylogenetic analysis based on ITS sequences of all the isolates of this study along with 18 reference Pyricularia isolates of different countries (retrieved from NCBI) revealed that isolates belonging to same district of Bangladesh did not form same cluster in the dendrogram. Again, Bangladesh—P. oryzae tritici isolates showed close relationship with other wheat infecting reference isolates from different countries. Isolates infecting other than wheat showed host specific clustering and distantly clustered in the phylogenetic tree. Findings of this study will be helpful for better understanding of this newly evolved pathogen in Bangladesh.

We aimed to study the genetic diversity, population structure, and phylogeny of Iranian orchids using inter-simple sequence repeat (ISSR) markers to find markers associated with phenotypic traits. Based on the phenotypic analysis, the inflorescence length and the flower number of studied accessions ranged from 3.92 to 27.13 cm and 5 to 50, respectively. On the other hand, the tuber length ranged from 1.80 to 9.35 cm. A total of 310 reproducible ISSR fragments with a size range of 150 to 3000 bp were amplified. ISSR primers provided an average polymorphism information content of 0.391, varied from 0.488 for UBC-876 to 0.351 for UBC-842. Os.J population showed the lowest genetic diversity (H = 0.057 and I = 0.075), while Oyst.JA population showed the highest genetic diversity (H = 0.114 and I = 0.158). At species level, the average coefficient of genetic differentiation (G(ST)) ranged from 0.265 for Orchis simia to 0.587 for Himantoglossum affine. Gene flow (Nm) varied from 1.38 (O. simia) to 0.756 (Anacamptis collina). The UPGMA genetic similarity dendrogram using Jaccard coefficients (r = 0.973) revealed six main clusters. Based on the Bayesian clustering method, the highest probability of the data was achieved when accessions were divided into eight groups. Floral and tuber-related phenotypic traits represented high correlations together, and they were associated with some ISSR bands based on the multiple association analysis. Altogether, ISSR markers proved to be useful for discrimination and clarification of the relationships among species and populations collected from geographically different locations. Furthermore, it could identify the polymorphism among accessions within each population and species. SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s12298-020-00920-0) contains supplementary material, which is available to authorized users.

The present study was designed to analyse the anatomy of the vegetative and reproductive parts of Turkish Iberis species from a systematic point of view. Samples of leaves, stems, roots, fruits, and seeds of each species were collected, fixed, and processed according to the paraffin method for light microscopy. The numerical analysis derived from 11 anatomical characteristics showed that the number and dimensions of vessels in the root, presence of aerenchyma in the leaf, number and dimensions of palisade parenchyma, and mesophyll type were useful for grouping the Iberis taxa. The testa was composed of four layers: the epidermis, subepidermis, compact tissue, and parenchyma. The testa thickness was a significant character to distinguish the investigated Iberis species. In this study, the traditional classification of Turkish Iberis species was mostly congruent with the dendrogram generated vegetative anatomical properties. Bangladesh J. Plant Taxon. 27(2): 213-224, 2020 (December)

Curcuma caesia Roxb. belonging to Zingiberaceae family is a rhizomatous perennial herb consisting of bluish black rhizome and having vast medicinal and pharmaceutical applications. It is considered as an endangered medicinal plant and native to India. The aim of this study is to assess the molecular diversity among the high rhizome essential oil yielding lines of C. caesia (> 1.5% w/w). The molecular diversity analysis was done by using 45 simple sequence repeat markers amongst the 78 high essential oil yielding lines of C. caesia. The overall percentage of polymorphism amongst the lines was found to be 53%. AMOVA analysis showed 20% and 80% variations among and within the population respectively. Dendrogram constructed using Unweighted Pair Group with Arithmetic Mean (UPGMA) for those high essential oil yielding lines sorted into five major clusters according to their different geographical locations. These five clusters were confirmed using principle component analysis (PCA), based on the Jaccard’s similarity coefficient. The results revealed that these microsatellite markers could be used as successful tool to differentiate the genetic makeup of the crop. Molecular diversity of C. caesia has not been studied till now. So, this is the first scientific report on molecular diversity analysis which may help in the further crop improvement programme and germplasm conservation also.

Study of genetic diversity and interspecific hybridizations plays an imperative role in the genetic improvement of crop plants. Microsatellite or simple sequence repeats (SSRs) markers have been the marker of choice for many genetic studies in perennial tree crops. In this study, genetic diversity of 23 cashew (Anacardium occidentale L.) germplasm accessions with unique traits was carried out using the cashew SSR (CSSR) markers. Besides, true hybridity of the interspecific hybrids of A. occidentale and A. microcarpum Ducke was investigated. Eight of the 21 CSSRs screened in 10 diverse accessions were polymorphic and used for genetic diversity analysis in 23 accessions. Major allele frequency ranged from 0.50 to 0.98; gene diversity ranged from 0.10 to 0.50, and polymorphism information content (PIC) ranged from 0.10 to 0.38 for the surveyed SSR loci. Dendrogram analysis of 23 accessions formed two main clusters with two sub-clusters in each. Clustering of the accessions had no relationship with the geographic region of collection. In tree hybridizations, early screening methods are becoming indispensable to ascertain the true hybridity of progenies to save the costs and resources. For the first time, three CSSR markers that detect the true hybridity of interspecific hybrids of cashew and its wild relative A. microcarpum were identified. Hybrid purity index of the progenies in interspecific crosses varied from 67 to 100%. These three CSSR markers capable of distinguishing the two Anacardium species could be useful in evolutionary studies involving these species and their natural hybrids in the wilds.

Clitoria ternatea (L.) is a medicinal leguminous plant and is cultivated to cater the need of herbal industries and asthetic purposes. The unavailability of steady molecular marker impedes the genetic improvement of C. ternatea. In the present study, transferability of 98 pairs of Cajanus spp. specific SSR primers were assessed among 14 genotypes of C. ternatea, varied for their flower color, floral architecture and bio-metabolite (taraxerol and delphinidin) content, and out of them 43 had successfully amplified the fragments. Among them, 36 pairs of primers showed 100% transferability, whereas rest seven varied from 42.86 to 92.85% transferability. The transferable 43 pairs of SSR primers generated 196 alleles across the 14 genotypes and the AMOVA analysis showed moderate genetic variation (55.1%) among the genotypes of C. ternatea, which was also reinforced by Nei’s genetic distance and gene identity estimates derived haplotype matrix. Similarly, both the principal coordinate analysis and dendrogram grouped these 14 genotypes of C. ternatea into two major clusters based on SSR allele distribution and frequency, and the clustering pattern is in accordance with petal color but in contrast to floral architecture. MCheza based outlier analysis revealed 16 alleles for balancing selection, which are putatively involved in the maintenance of genetic polymorphism in C. ternatea. Moreover, the estimates of molecular diversity and bio-metabolite content revealed the possible use of these genotypes in future breeding programme of this species.

Oil palm (Elaeis guineensis Jacq.) is the key vegetable oil yielded crop and widely distributed in the southern region of China. The present study aimed at analyzing the genetic diversity and population structure of 223 oil palm accessions collected from four provinces of China by using the sequence-related amplified polymorphism (SRAP) markers. A set of 33 SRAP molecular markers were employed to analyze genetic diversity as well as population structure across 223 oil palm accessions. Out of 514 amplified bands, 487 (94.75%) bands were found to be polymorphic. The PIC value (polymorphic information content) of detected bands was from 0.38 to 0.51, with 0.46 of average. The STRUCTURE analysis categorized the 223 oil palm accessions into three subpopulations. The UPGMA based clustering classified them into three major clusters. The correlation between the population subdivisions and the genetic relationships among oil palm accessions was revealed by UPGMA and Bayesian STRUCTURE analyses. The principal coordinate analysis also confirmed a similar grouping of accessions as revealed by the UPGMA dendrogram and STRUCTURE analysis. AMOVA analysis also revealed the variance of 24% among subpopulations and 76% within subpopulations. The present investigation provided valuable information on population structure and genetic diversity of oil palm populations in China for molecular breeding research in oil palm.

Red head cabbage is among the significant winter vegetables largely produced in various parts of the world and Turkey. This study was conducted for morphological characterization of red head cabbage populations supplied from different gene banks of the world and to determine similarities and differences among the genotypes. Morphological characteristics of the genotypes were defined in accordance with the criteria of International Union for the Protection of New Varieties of Plants (UPOV) and International Plant Genetic Resources Institute (IBPGR). Principle component analysis (PCA) was used to investigate variations in 27 traits of red head cabbage populations. The first nine principal component axes accounted for 73.96% of the total multivariate variation among the populations. The first principal component (PC1) were the most important component and red head cabbage traits that constitute the PC1 (plant diameter, weight of head, length of head, diameter of head and head volume) were in fact the characteristics considered by breeders to be of greatest importance in cabbage breeding. Experimental data were also subjected to cluster analysis and it was observed that red head cabbage populations were clustered in eight groups. The dendrogram generated to assess the similarities of the populations revealed a high variation among the genotypes. These results are very important for hybrid red head cabbage breeding studies and can help breeders to select genotypes with the desired traits in redhead cabbage.

Horsegram is an important drought resistant pulse crop from Fabaceae and can be easily grown in dry lands with no irrigation facilities. However, it remained neglected since long and has been considered as orphan legume which requires immediate attention for its improvement and for the development of new promising varieties in future. In the present study, 7352 simple sequence repeat (SSR) markers were developed from the transcriptome data and 150 SSR were randomly synthesized for validation and diversity analysis in a panel of 58 horsegram genotypes. The synthesized primers included all types of repeats spanning direpeats to hexarepeats. Of the validated SSR markers, 33 markers were polymorphic and produced 40 loci which were used to analyze the genetic diversity and structure of horsegram. In total, 130 alleles were produced in a range of 2–9 alleles with maximum alleles produced by primer HTSSR 155. Expected heterozygosity (He) ranged from 0.03 to 1.00 and observed heterozygosity (Ho) ranged from 0.13 to 0.81. Polymorphism information content value ranged from 0.065 to 0.78. Dendrogram based on UPGMA and principal component analysis showed four groups of the 58 genotypes of horsegram. Structure analysis showed three genetic stocks for the analyzed germplasm. Thus, the developed SSRs can be useful in future population genetics analysis, molecular breeding studies and mapping works in horsegram germplasm as well as in related legume species.

Onion (Allium cepa L.) is one of the most important bulbous vegetable used in global kitchen. Although it has various important traits but among them the high total soluble solid content (HTSS) of white onion is highly preferred by the industries for processing purpose. Looking into the broader use of the white onion; we utilized a total of 23 polymorphic simple sequence repeats (SSRs) and intron length polymorphic markers (ILPs) to characterize thirty five white onion genotypes for HTSS. Further, we also correlated these DNA fingerprint data with the TSS for identification of HTSS and LTSS lines. The total average numbers of alleles for SSR and ILP locus, heterozygosity (He) and polymorphism information content were found to be 2.4, 0.35 and 0.29 respectively. The UPGMA dendrogram revealed two distinct clusters of genotypes. Based on the TSS and DNA genotype data, our study revealed that Bhima-shweta (LTSS-12.09%, sub-cluster IAa) & WHT-12L-HT-15-Reject-M-7(HTSS- 18.02%, cluster II) are more diverse than the others. Other white onion lines including WHTB-7G-GT-15-SC-M-7 small bulb (HTSS 18.80%), WHT-2B-GT-18-SC-M-7 (HTSS 18.51%), WHTS-4D-GT-18-MC-M-7 (HTSS 18.49%), WHTB-3C-GT-18-MC-M-7 (HTSS 18.27%) and WHTS-11K-Pickle-SC-M-7 (HTSS 17.68%) were identified as superior HTSS lines. These identified diverse HTSS and LTSS lines could be useful for the mapping of HTSS coding genes for the acceleration of molecular breeding of onion through the marker assisted selection (MAS) which could be used by the industries for the larger scale processing of the white onion products required by the global community.

We evaluated and classified forty five onion cultivars according to bulb initiation, bulb and scale characteristics, minerals and organic compounds contents, and storage quality in South Korea during 2016/2017 and 2017/2018 growing seasons. Field experiment was conducted in randomized block design with three replications. Bulb initiation ranged from 153 days after transplanting (DAT, April 2) to 177 DAT (April 26). Fresh bulb weight (FBW) and bulb index (BI) were 285.5 ± 18.5 g/individual, 0.93 ± 0.05, respectively. Number of scales (NS), number of center (NC), and scale thickness (ST) were 7.6 ± 0.2, 2.3 ± 0.2, and 5.5 ± 0.2 mm/scale, respectively. Chroma and Lightness of bulb skin were 27.1 ± 1.9, 61.2 ± 2.3, respectively. Storage loss (SL) on December 12 was 19.4 ± 5.9%. Nitrogen (N), Carbon (C) and sulfur (S) contents were 1.36 ± 0.14, 37.9 ± 3.2 and 0.40 ± 0.06 mg kg−1 on a fresh weight basis. Total soluble solids (TSS) and total phenolics content (TPC) were 8.6 ± 0.6 °Bx, 164.8 ± 15.6 mg GE kg−1 on a fresh weight basis. Days from transplanting to bulb initiation was significantly positively correlated with bulb height, NC, dry matter, N, C, S, TSS, TPC, total flavonoids content (TFC) etc., while it was negatively correlated with rot loss and SL. Dry matter content was significantly positively correlated with N, C, S, TSS, TPC, TFC etc., while it was negatively correlated with SL. Storage loss was negatively correlated with N, S, Potassium and TSS. Dendrogram of agglomerative hierarchical clustering for the forty five cultivars based on bulb initiation, bulb and scale characteristics, and bulb minerals and organic compounds contents classified five cultivar groups. Cluster 1 featured the earliest bulb initiation and the greatest SL. Cluster 2 featured the fewest NS and NR, and the thickest ST. Cluster 3 featured the greatest FBW, and the most NS and NC. Cluster 4 featured the greatest BI and the thinnest ST. Cluster 5 featured the lowest SL, and the highest minerals and antioxidant compounds contents. This information should be helpful for onion growers to decide onion cultivar and for onion breeders to promote new cultivars depending on their purpose.

Background. Pea is the main leguminous crop in the Republic of Bashkortostan and widespread all over the world. The key role in the breeding of new pea cultivars is played by source material representing the phenotypic and genotypic diversity of Pisum sativum L., searched for in plant genetic resources collections. SSR markers are successfully used to study the DNA polymorphism of various genetic objects, including pea. However, the distribution of a number of microsatellite alleles in the genotypes of specific lines and cultivars of this valuable pulse crop remains practically unexplored.Materials and methods. Molecular genetic polymorphism was studied in 40 pea cultivar accessions of different ecological and geographical origin from the Vavilov Institute’s genebank of plant genetic resources or developed at regional breeding centers. Microsatellite analysis was performed using 5 SSR markers from the genomic library of microsatellites (Agrogene®, France).Results. All markers delivered good electrophoretic profiles and helped to amplify a number of alleles per locus varying from 2 (AB53) to 9 (AA355). The total number of alleles was 26, while the average number of alleles per locus was 5.2. The polymorphism information content (PIC) varied from 0.39 for locus AB53 to 0.82 for locus AA355, with the mean value of 0.60. The set of SSR markers used in the work made it possible to individualize each of the studied pea genotypes. The measured genetic distances were used to draw a dendrogram showing the distribution of genotypes according to their genetic relationship.Conclusion. Through studying the source material for pea breeding by the SSR analysis the data were obtained that provide additional information about the genetic structure of the collection and the polymorphism of the studied cultivar accessions. The results of genotyping pea cultivars and lines can be used for their genetic identification or to select parental pairs for hybridization.

META-R (multi-environment trial analysis in R) is a suite of R scripts linked by a graphical user interface (GUI) designed in Java language. The objective of META-R is to accurately analyze multi-environment plant breeding trials (METs) by fitting mixed and fixed linear models from experimental designs such as the randomized complete block design (RCBD) and the alpha-lattice/lattice designs. META-R simultaneously estimates the best linear and unbiased estimators (BLUEs) and the best linear and unbiased predictors (BLUPs). Additionally, it computes the variance-covariance parameters, as well as some statistical and genetic parameters such as the least significant difference (LSD) at 5% significance, the coefficient of variation in percentage (CV), the genetic variance, and the broad-sense heritability. These parameters are very important in the selection of top performing genotypes in plant breeding. META-R also computes the phenotypic and genetic correlations among environments and between traits, as well as their statistical significance. The genetic correlations between environments or traits can be visualized in a biplot graph or a tree diagram (dendrogram). Genetic correlations are very important for identifying environments with similar behavior or making indirect selection and identifying the most highly associated traits. META-R performs multi-environment analyses by using the residual maximum likelihood (REML) method; these analyses can be done by environment, across environments by grouping factors (stress conditions, nitrogen content, etc.) and across environments; the analyses across environments can be done with a pre-defined degree of heritability.

In this research, ‘Pedro’ walnut variety (maternal parent) was open pollinated. Offspring genotypes were compared with their maternal parent in terms of morphological and molecular features. Leafing and leaf fall dates were measured as two phenological traits. Genetic differences were identified by molecular fingerprinting using twelve Inter Simple Repetitive Sequence Polymorphism (ISSR) primers. In some progenies, leafing and leaf fall occurred later than the maternal parent (‘Pedro’). Progenies were grouped according to their similarities with the maternal parent regarding leafing date. Specifically, 14.44% of the progenies were ‘Very close’ to the parent, 16.66% were ‘Close’, 30.00% ‘Far’ and 38.89% ‘Very far’. Regarding the leaf fall date, 7.78% of the progenies were ‘Very close’ to the parent, 28.88% were ‘Close’, 36.66% ‘Far’ and 26.67% ‘Very far’. A total of 43 bands were obtained in molecular analyses. These bands were largely polymorphic (95.34%). The average number of the alleles was 3.90, while the polymorphism information content varied between 0.14 and 0.91 among the genotypes. Genetic distances were tested according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average) and by The Structure Analysis. The UPGMA dendrogram divided the genotypes into two main clusters and the similarity coefficient of the genotypes varied between 0.61 and 0.99. This study revealed that ‘Pedro’ can be used as an excellent parental variety in hybridization programs which prioritize late-leafing in walnut breeding. Furthermore, ISSR primers can be safely used for fingerprinting walnuts in general.

Among the tropical tuber crops, cassava (Manihot esculenta Crantz) deserves special attention as regards to its higher biological efficiency in terms of dry matter production which incidentally implies to the higher amount of nutrient extraction from the soil resulting in better response to the application of manures and fertilizers. Among the major nutrients, Potassium (K) is considered as the key nutrient for cassava owing to its influence both in tuber yield and tuber quality. The above facts as well as the availability of sufficient cassava genotypes in the germplasm collection of ICAR-CTCRI made us to initiate research work to screen cassava germplasm including the pre breeding lines. The objective being to identify K efficient genotypes which can yield well under limited availability of K so that the external application of K can be reduced. This paper describes the wide variation noticed during the pre evaluation of 83 elite genotypes which was done as a prelude in the screening and identification of K efficient genotypes. The characters studied were tuber yield, tuber characters, plant dry matter percentage, plant K content, tuber quality (starch, cyanogenic glucosides) attributes, physiological efficiency and plant biometric characters. The variation among the genotypes for the above traits was assessed by making some yardstick for classification which in turn helped in determining the percent distribution of genotypes in each category. The variation among the genotypes were further affirmed through principal component analysis, wherein the first five components explained more than 77% of variability and the cluster analysis performed grouped these genotypes into five clusters. The biplot showed the traits which are closely linked to the genotypes. The dendrogram constructed indicated similar genotypes to that of the clusters to the extent of more than 50% revealing the association of members with similar traits in clusters and dendrograms. The study helped in establishing the drastic variation among the genotypes along with identification of six genotypes viz., Aniyoor, 7 Sahya (2), 7 III E3-5, W-19, CR 43-8, 6-6 for further detailed experimentation to identify K efficient genotypes.

SSRs related to parent selection of D. kaki were validated by transcriptome sequencing, and genetic diversity of these markers among 76 persimmon germplasm resources was additionally investigated. The selection of hybrid parents is critical in cross-breeding plants for germplasm innovation and cultivating improved varieties. This study used a published RNA-Seq database of a persimmon cultivar ‘Zenjimaru’ to develop simple sequence repeat (SSR) markers to assist efficiently selection of appropriate persimmon cultivars for cross-breeding. A total of 154,741 unigenes with 41,999 SSR loci at a frequency of one per 2.30 kb were identified. Of the different SSR motif types, mononucleotide repeats (47.63%) were the most abundant, followed by dinucleotide repeats (38.23%). The main repeat motifs were A/T (42.26%) and AG/CT (24.72%). A total of 17,111 SSR primer pairs were designed, from which 100 selected loci were synthesized and preliminary screened with capillary electrophoresis by testing PCR products from 15 persimmon germplasm resources. The effectiveness of 13 primer pairs that produced products with distinct peaks at the predicted sizes was subsequently determined using 76 persimmon germplasm resources. A total of 111 alleles were identified by using 13 SSR markers, ranging from 2 to 17 with an average of 8.54 bands per locus. Additionally, different hybridized combinations could be selected according to a dendrogram based on these newly developed 13 SSR markers. And two androecious persimmons (“Yunjia-9” and “Luotian Yeshi-1”) were genetically closely related to Chinese pollination-constant non-astringent (C-PCNA) persimmons, which was significant for the cultivation of PCNA offspring. The identified SSR markers will not only promote persimmon cross-breeding programs by increasing the efficiency of parent selection but also assist in genetic resource identification and conservation.

Brassica carinata A. Braun (Ethiopian mustard) is an oilseed crop belonging to rapeseed-mustard group, with extensive food and industrial applications. It produces high quality oil ideal for aviation fuel, bio-jet for aircrafts and bio-diesel for airport vehicles besides its use as edible oil. In an attempt to analyze population structure and genetic diversity in a panel of 78 Ethiopian mustard accessions, 212 SSR markers had been employed. A total of 139 (65.57%) SSRs resulted into polymorphic amplicons, while 73 (34.43%) SSRs amplified monomorphic products. The allele number ranged from 1–7 with 3.03 average number of alleles per marker. PIC values were in the range of 0.02–0.53 with an average PIC value of 0.29 per marker. Gene diversity ranged from 0.02 to 0.50 with an average value of 0.37 per SSR marker. Overall, lower PIC values and gene diversity values indicated the presence of lesser genetic diversity among B. carinata genotypes. The unweighted pair group method with arithmetic average (UPGMA)-based dendrogram divided all the 78 accessions into two major groups, whereas, three subpopulations/subgroups were predicted by population STRUCTURE analysis. Further, this study provided a deeper insight into the population structure and genetic diversity of Ethiopian mustard in India and will help to improvise the breeding strategies for its genetic improvement.

A set of accessions of lettuce landrace ‘Ljubljanska ledenka’ (Lactuca sativa L.) was characterized by morphological and molecular markers and for resistance to Bremia lactucae, with the aim of assessing the variability of the collection, exploring the genetic structure and potentially identifying the characters responsible for differentiation of the accessions. Wide phenotypic variation was observed among 51 accessions screened for 26 morphological and phenological traits. UPGMA cluster analysis and principal component analysis based on phenotypic data enabled the studied accessions to be divided into four clusters. The most important character by which the largest two clusters were differentiated was anthocyanin coloration. The clustering pattern of the AFLP dendrogram where two major clusters were identified was similar but not identical to the pattern of the phenotypic dendrogram. The Mantel test showed a high correlation between the phenotypic and the molecular data obtained (r = 0.67). In spite of the weak genetic differentiation between the accessions, STRUCTURE analysis based on AFLP data provided a clear indication for the existence of sub-groups within the two clusters. Thirty-four accessions were screened for resistance to 12 races of B. lactucae. The results show that the accessions very frequently express various reaction patterns of race specificity. Expression of race-specificity was not uniform across the set of accessions and at least 11 different reaction patterns were recorded, indicating that different race-specific resistance factors (R-factors) or genes (Dm genes) could be expected. This conclusion is supported by the results obtained in morphological and molecular studies, showing that lettuce landrace ‘Ljubljanska ledenka’ is not genetically uniform and is represented by a variety of genotypes.