Diversity In Germplasm Collections Research Articles

Pseudomonas syringae pv. tomato DC3000 Induces Defense Responses in Diverse Maize Inbred Lines

Many phytopathogens translocate virulence (effector) proteins into plant cells to circumvent host immune responses during infection. One such pathogen is Pseudomonas syringae pv. tomato DC3000, which secretes at least 29 effectors into host cells, of which a subset elicits host defense responses in crop plant species. However, it is unknown whether P. syringae pv. tomato DC3000 activates immune responses in diverse maize inbreds. Here, we screened a diverse maize germplasm collection for effector-dependent recognition of this bacterial pathogen. As a control, we infiltrated P. syringae DC3000(D36E), a derivative of P. syringae pv. tomato DC3000 that lacks all endogenous effectors. In our evaluations, we observed a variety of responses to P. syringae pv. tomato DC3000 in maize and scored the phenotypes as either having no observable response (N) or exhibiting one of three responses: weak chlorosis (WC), chlorosis (C) with minimal cell death, and hypersensitive reaction (HR)-like cell death. Of the 26 maize inbreds screened, 13 were scored as N, 2 as WC, 2 as C, and 9 as HR-like cell death. Importantly, no maize line responded to P. syringae DC3000(D36E), demonstrating that the responses observed are likely dependent on recognition of one or more Pseudomonas effectors. Furthermore, the maize inbreds that recognize P. syringae pv. tomato DC3000 accumulated detectable hydrogen peroxide as well as an increase in transcript expression of a subset of maize defense genes. Collectively, our results will likely stimulate new research aimed at identifying the cognate maize disease resistance proteins that recognize the activities of one or more bacterial effectors. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Flooding stress and responses to hypoxia in plants.

In recent years, research on flooding stress and hypoxic responses in plants has gathered increasing attention due to climate change and the important role of O2 in metabolism and signalling. This Collection of Functional Plant Biology on 'Flooding stress and responses to hypoxia in plants' presents key contributions aimed at progressing our current understanding on how plants respond to low-O2 conditions, flooding stress and a combination of stresses commonly found in flooded areas. The Collection emphasises the characterisation of diverse plant responses across different developmental stages, from seed germination to fully developed plants, and under different water stress conditions ranging from waterlogging to complete submergence, or simply low-O2 conditions resulting from limited O2 diffusivity in bulky tissues. Additionally, this Collection highlights diverse approaches, including eco-physiological characterisation of plant responses, detailed descriptions of root anatomical characteristics and their surrounding microenvironments, evaluation of the seed microbiota under flooding stress, the modification of gene expression, and evaluations of diverse germplasm collections.

Genomic prediction for agronomic traits in a diverse Flax (Linum usitatissimum L.) germplasm collection

Breeding programs require exhaustive phenotyping of germplasms, which is time-demanding and expensive. Genomic prediction helps breeders harness the diversity of any collection to bypass phenotyping. Here, we examined the genomic prediction’s potential for seed yield and nine agronomic traits using 26,171 single nucleotide polymorphism (SNP) markers in a set of 337 flax (Linum usitatissimum L.) germplasm, phenotyped in five environments. We evaluated 14 prediction models and several factors affecting predictive ability based on cross-validation schemes. Models yielded significant variation among predictive ability values across traits for the whole marker set. The ridge regression (RR) model covering additive gene action yielded better predictive ability for most of the traits, whereas it was higher for low heritable traits by models capturing epistatic gene action. Marker subsets based on linkage disequilibrium decay distance gave significantly higher predictive abilities to the whole marker set, but for randomly selected markers, it reached a plateau above 3000 markers. Markers having significant association with traits improved predictive abilities compared to the whole marker set when marker selection was made on the whole population instead of the training set indicating a clear overfitting. The correction for population structure did not increase predictive abilities compared to the whole collection. However, stratified sampling by picking representative genotypes from each cluster improved predictive abilities. The indirect predictive ability for a trait was proportionate to its correlation with other traits. These results will help breeders to select the best models, optimum marker set, and suitable genotype set to perform an indirect selection for quantitative traits in this diverse flax germplasm collection.

Evaluation of castor landraces collected from N-W Rajasthan as noval geneticresources for breeding

An exploration was conducted in North-Western Rajasthan state and a total of 114 castor germplasm lines were collected from seven districts. Most of the accessions were tall in plant height. Variability for different traits viz., plant height (50-275 cm), node number (10-35), total length of primary spike (16-60 cm), length of primary spike covered by capsules (6-60 cm), 100 seed weight (7.1-53 g), total seed yield (23-416 g/plant)among the collections were very high. These 114 genotypes were grouped into 11 clusters using D2 analysis. Among the 11 clusters studied, plant height contributed highest towards genetic divergence (45.8%) followed by total seed yield/plant (36.4%). Principal component (PCA) analysis revealed that first three PC axes explained 64.7% of the total multivariate variation while the first five PC axes explaining 81.7%. Among these diverse germplasmcollections few promising accessions identified for node number RG-3840 (10), RG-3841 (11), 100-seed weight, RG-3832 (53.2g), RG-3839 (52.6 g), RG-3831(49.5 g), seed yield/plant, RG-3851-(416 g), RG-3860 (305 g) and RG-3895 (238 g). These landraces were found to be potential source of genetic diversity to castor repository.

Promoter insertion leads to polyembryony in mango — a case of convergent evolution with citrus

Abstract Sexual reproduction in plants is the main pathway for creating new genetic combinations in modern agriculture. In heterozygous plants, after the identification of a plant with desired traits, vegetative propagation (cloning) is the primary path to create genetically uniform plants. Another natural plant mechanism that creates genetically uniform plants (clones) is apomixis. In fruit crops like citrus and mango, sporophytic apomixis results in polyembryony, where seeds contain multiple embryos, one of which is sexually originated and the others are vegetative clones of the parent mother tree. Utilizing the mango genome and genetic analysis of a diverse germplasm collection, we identified MiRWP as the gene that causes polyembryony in mango. There is a strong correlation between a specific insertion in the gene’s promoter region and altered expression in flowers and developing fruitlets, inducing multiple embryos. The MiRWP gene is an ortholog of CitRWP that causes polyembryony in citrus. Based on the data, we speculate that promoter insertion events, which occurred independently in citrus and mango, induced nucellar embryogenesis. The results suggest convergent evolution of polyembryony in the two species. Further work is required to demonstrate the utility of these genes (mango and citrus) in other biological systems as a tool for the clonal production of other crops.

Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits.

Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200, Glyma.10g065700, Glyma.18g297900, and Glyma.14g009900, were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana. This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs.

A quick and precise online near-infrared spectroscopy assay for high-throughput screening biomass digestibility in large scale sugarcane germplasm

The near-infrared spectroscopy (NIRS) has been used for efficient characterization and rapid assay of biomass saccharification in other energy plants, but its application in sugarcane is not reported yet. The current study collected a total of 541 sugarcane accessions to take an online NIRS assay. Among these sugarcane collections, we observed large variations in biomass digestibility, particularly for fermentable hexose and total sugar yield from fresh sugarcane stalks, which were detected ranging from 69.88 to 239.86 kg t -1 and 66.56–228.55 kg t -1 respectively. Using the modified partial least squares method, six reliable NIRS models were obtained with a high coefficient of determination ( R 2 ) and the ratio of prediction to deviation (RPD) values during calibration, internal-cross validation and external validation. Notably, the equation for fermentable hexose exhibited the most consistently high R 2 (0.98) and RPD (6.62) values, as well as retaining relatively low root mean square error during calibration (3.74 kg t -1 ) and validation (4.19 kg t -1 ), indicating excellent predictive capacity. All models demonstrated accurate and stable prediction performance in the two-year large-scale germplasm resources evaluation, and the optima accessions with high or low biomass digestibility can be screened out consistently. Therefore, this study provides a precise and consistent NIRS assay for high throughput scanning of biomass digestibility in sugarcane. • Sugarcane is one of the significant bioenergy crops. • Diverse sugarcane germplasm collections allowing for reliable NIRS calibration. • Six excellent equations were generated for biomass digestibility characterization. • Fermentable hexoses and total sugar displayed the best prediction performance. • Model-based NIRS application screened out optima genotypes consistently from large-scale sugarcane germplasm.

Patterns of genetic variation and QTLs controlling grain traits in a collection of global wheat germplasm revealed by high-quality SNP markers

BackgroundEstablish a molecular breeding program involved assembling a diverse germplasm collection and generating accurate genotypes to characterize their genetic potential and associate them with agronomic traits. In this study, we acquired over eight hundred wheat accessions from international gene banks and assessed their genetic relatedness using high-quality SNP genotypes. Understanding the scope of genomic variation in this collection allows the breeders to utilize the genetic resources efficiently while improving wheat yield and quality.ResultsA wheat diversity panel comprising 39 durum wheat, 60 spelt wheat, and 765 bread wheat accessions was genotyped on iSelect 90 K wheat SNP arrays. A total of 57,398 SNP markers were mapped to IWGSC RefSeq v2.1 assembly, over 30,000 polymorphic SNPs in the A, B, D genomes were used to analyze population structure and diversity, the results revealed the separation of the three species and the differentiation of CIMMYT improved breeding lines and landraces or widely grown cultivars. In addition, several chromosomal regions under selection were detected. A subset of 280 bread wheat accessions was evaluated for grain traits, including grain length, width, surface area, and color. Genome-wide association studies (GWAS) revealed that several chromosomal regions were significantly linked to known quantitative trait loci (QTL) controlling grain-related traits. One of the SNP peaks at the end of chromosome 7A was in strong linkage disequilibrium (LD) with WAPO-A1, a gene that governs yield components.ConclusionsHere, the most updated and accurate physical positions of SNPs on 90 K genotyping array are provided for the first time. The diverse germplasm collection and associated genotypes are available for the wheat researchers to use in their molecular breeding program. We expect these resources to broaden the genetic basis of original breeding and pre-breeding materials and ultimately identify molecular markers associated with important agronomic traits which are evaluated in diverse environmental conditions.

Genome size, ploidy levels, and development of novel SSR primer to evaluate genetic diversity of Corylopsis Siebold & Zucc. germplasm collections

Corylopsis Seibold & Zucc. is a genus of flowering shrubs with few cultivars and little information on genome size, ploidy levels, and genetic relationships among taxa. The United States National Arboretum and collaborating gardens in North America maintain a diverse germplasm collection of Corylopsis including cultivated and wild-collected taxa. The objectives of this study were to determine genome size, ploidy, and genetic diversity in Corylopsis. Flow cytometry revealed a ploidy series of diploid, tetraploid, pentaploid, and hexaploid taxa in Corylopsis with 2C genome sizes ranging from 1.9 pg to 5.7 pg. Representative taxa were selected for root tip cytology, revealing diploid (C. platypetala Rehder & E.H. Wilson), tetraploid (C. gotoana Makino), pentaploid (unnamed hybrid selection), and hexaploid (C. willmottiae Rehder & E.H. Wilson) taxa. Seventeen genomic simple sequence repeat markers were developed and used to determine the genetic diversity of Corylopsis. These markers had an average of 7.4 alleles per locus with a range of three to 17 alleles. A dendrogram was generated by unweighted pair group method with arithmetic mean (UPGMA) cluster analysis using the Jaccard similarity coefficient to visualize genetic relationships and ploidy series within taxa. Information gained from this study will further breeding efforts and aid management of germplasm collections of Corylopsis.

Analyses of genetic diversity and population structure of sesame (Sesamum indicum L.) germplasm collections through seed oil and fatty acid compositions and SSR markers

Knowledge of the genetic profiles of diverse germplasm collections of sesame using seed oil, fatty acid contents, and molecular markers is a prerequisite to develop market-preferred cultivars with quantity and quality oil. The objective of this study was to determine the genetic diversity and relationships among Ethiopia’s sesame germplasm collections using seed oil content and fatty acid compositions and diagnostic simple sequence repeat (SSR) markers to select genetically complementary and promising parental lines for breeding. The contents of the seed oil and fatty acids of 100 lines grown under field conditions were determined using the near-infrared reflectance spectrometry. Twenty-seven polymorphic SSR markers were used to assess the genetic profile of the test lines and complement the seed oil and fatty acid data. The SSR markers revealed that the mean gene diversity and polymorphic information content were 0.30 and 0.25, respectively. Population structure analysis identified four major heterotic groups. Based on higher oil content and desirable fatty acid compositions and SSR markers the following superior and complementary lines such as: Hirhir Kebabo Hairless Sel-6 (from sub-cluster I-b), Hirhir Humera Sel-8 and NN0058–2 (sub-cluster II-a) and Bawnji Fiyel Kolet (sub-cluster II-b) are identified for sesame breeding programs or production globally.

Microsatellite markers as a tool for active germplasm management and bridging the gap between national and local collections of apple

Simple sequence repeat (SSR) microsatellite markers have been extensively used to identify duplication and analyse genetic diversity in germplasm collections of apple. Here, we present findings from the use of a standard set of SSR loci in the managed repropagation of a significant international germplasm collection: the UK National Fruit Collection (NFC). A subset of eight SSR loci was deemed sufficient to distinguish all apart from the clonal relatives across a sample of 1995 accessions, with a single exception being one pair of full siblings. In total, 99% of accessions were able to be confirmed present and correct after the replacement of trees initially identified to be incorrectly propagated. In parallel to the curation of the collection itself, through an initiative led by the UK local apple enthusiast community, 3373 SSR profiles for apples held in local collections were compared to the NFC holdings. Overall, in both sets of material, diversity remained high with average gene diversity values of 0.800 and 0.812 in the NFC holdings and local collections, respectively. Accessions in local collections were not found to differ in their overall coverage of genetic diversity to that of the NFC collection (FST = 0.0035) although significant numbers of locally valued, and genetically distinguishable individuals were identified, some of which may represent ‘lost’ cultivars.

Agro-Morphological Characterization of Lentil Germplasm of Indian National Genebank and Development of a Core Set for Efficient Utilization in Lentil Improvement Programs.

Lentil (Lens culinaris Medik.) is one of the major cool-season pulse crops worldwide. Its increasing demand as a staple pulse has led to the unlocking of diverse germplasm collections conserved in the genebanks to develop its superior varieties. The Indian National Genebank, housed at the Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India, currently has 2,324 accessions comprising 1,796 indigenous and 528 exotic collections. This study was conducted to unveil the potential of lentil germplasm by assessing its agro-morphological characteristics and diversity, identifying trait-specific germplasm, and developing a core set. The complete germplasm set was characterized for two years, i.e., 2017–2018 and 2018–2019, and data were recorded on 26 agro-morphological traits. High phenotypic variability was observed for nine quantitative and 17 qualitative traits. A core set comprising 170 accessions (137 Indian and 33 exotic) was derived based on the characterization data as well as geographical origin using a heuristic method and PowerCore software. This core set was found to be sufficiently diverse and representative of the entire collection based on the comparison made using Shannon–Weaver diversity indices and χ2 test. These results were further validated by summary statistics. The core set displayed high genetic diversity as evident from a higher coefficient of variance in comparison to the entire set for individual traits and overall Shannon–Weaver diversity indices (entire: 1.054; core: 1.361). In addition, the total variation explained by the first three principal components was higher in the core set (70.69%) than in the entire collection (68.03%). Further, the conservation of pairwise correlation values among descriptors in the entire and core set reflected the maintenance of the structure of the whole set. Based on the results, this core set is believed to represent the entire collection, completely. Therefore, it constitutes a potential set of germplasm that can be used in the genetic enhancement of lentils.

Isolation and characterization of sub-plastidial fractions from carotenoid rich fruits.

Carotenoid biosynthesis and sequestration in higher plants occurs in the plastid organelle. Among diverse germplasm collections displaying natural variation for carotenoids and outputs from metabolic engineering experiments it has become clear that plastid type and numbers can have important implications on the quantitative composition of carotenoids accumulating. Therefore, it is important to characterize these organelles to fully evaluate the potential of the germplasm to enhance carotenoids and create nutrient dense fruits and vegetables. In this article the procedures used to isolate sub-plastidial structures from carotenoid-rich Solanaceae fruits (tomato and Capsicum) are described.

Assessment of the Genetic Structure and Diversity of Soybean (Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers.

Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon’s diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.

Correlation and Path Coefficient Analysis for Seed Yield and Agronomic Traits of Newly Introduced Pigeon Pea Genotypes in South Africa

Pigeon pea is an important source of protein for smallholder farmers in South Africa. The average seed yield per hectare ranges from 0.5 to 1 tonne due to the use of un-improved varieties that succumb to both biotic and abiotic stresses. Understanding the relationship between seed yield and agronomic traits in a genetically diverse germplasm collection is a prerequisite for developing an efficient selection and breeding program. This study determined the relationship between seed yield and agronomic traits to identify key traits for selection. Two separate experiments involving seven short and six medium duration pigeon pea genotypes were planted in a randomized complete block design (RCBD), each with three replications. Agronomic traits, including yield and its components’ genotype mean data was subjected to correlation, path coefficient and stepwise regression analyses. The results showed a strong positive and significant correlation between number of pods per plant and seed yield in both medium and short duration genotypes. The number of pods per plant had a high direct effect on seed yield in both medium and short duration with values of (0.43) and (0.63) respectively. Number of branches and pod length exhibited high direct effect (0.30-0.99) for medium duration. However, seed yield per plant was an important predictor of seed yield in short duration while seed yield per plant, 100 seed weight and number of seeds per pod were key predictors of seed yield in medium duration genotypes. Therefore, these traits should be targeted for seed yield improvement in Pigeon pea.

Morphological Characterization of High Grain Iron and Zinc Concentration Bio-fortified lentil (Lens culinaris Medikus subsp. culinaris) in Nepal

Lentil (Lens culinaris Medikus subsp. culinaris) is the wonderful, most popular & preferred food legume of Nepalese people and commonly grown in the rice and maize based cropping system. Morphological characters have been frequently used in order to know the diversity in germplasm collections. The main objectives of the study were to characterize the bio-fortified lentil accessions using morphological markers and select the DUS accession for using targeted the best utilization in hybridization program. Plant breeders can use these morphological variations to make decision regarding the choice for selecting superior genotypes for improvement or to be utilized as parents for the development of future cultivars through hybridization. Furthermore, important morphological markers like, plant type, foliage color, testa color, testa pattern and cotyledon colors can also be used for testing hybridity and keeping genetic purity at genetic level. The information obtained by the identification keys at seed and plant levels may be useful for discrimination and verification of varieties, hybridity testing and maintenance of genetic purity at genetic level during seed production and certification programme. Out of 25 lentil accessions, 18 accessions were observed as erect and compact growth habit, 22 accessions had green stem color, 21 accessions had dense leaf pubescence and dark foliage, 7 accessions had prominent tendril, 3 accessions had white blue veins flower and 4 accessions had large seeded accession.

Transferability of ISSR, SCoT and SSR Markers for Chrysanthemum × Morifolium Ramat and Genetic Relationships Among Commercial Russian Cultivars.

Characterization of genetic diversity in germplasm collections requires an efficient set of molecular markers. We assessed the efficiency of 36 new SCoT markers, 10 new ISSR markers, and 5 microsatellites for the characterization of genetic diversity in chrysanthemum core collection of 95 accessions (Russian and foreign cultivars). Seven new SCoT (SCoT12, 20, 21, 23, 29, 31, 34) and six new ISSR markers ((GA)8T, (CT)8G, (CTTCA)3, (GGAGA)3, (TC)8C, (CT)8TG) were efficient for the genetic diversity analysis in Chrysanthemum × morifolium collection. After STRUCTURE analysis, most Russian cultivars showed 20–50% of genetic admixtures of the foreign cultivars. Neighbor joining analysis based on the combination of SSR, ISSR, and SCoT data showed the best accordance with phenotype and origin compared to the separate analysis by each marker type. The position of the accessions within the phylogenetic tree corresponded with the origin and with some important traits, namely, plant height, stem and peduncle thickness, inflorescence type, composite flower and floret types, flower color, and disc color. In addition, several SCoT markers were suitable to separate the groups distinctly by the phenotypical traits such as plant height (SCoT29, SCoT34), thickness of the stem and peduncle (SCoT31, SCoT34), and leaf size and the floret type (SCoT31). These results provide new findings for the selection of markers associated with important traits in Chrysanthemum for trait-oriented breeding and germplasm characterization.

Genetic diversity and phylogenetic relationships among citrus germplasm in the Western Caucasus assessed with SSR and organelle DNA markers

Characterization of genetic diversity in germplasm collections is fundamental for an efficient management and utilization. The citrus germplasm in the Western Caucasus represent one of the most northerly citrus collections. The collection contains numerous cultivars specifically selected for frost-tolerance, which are valuable as genetic resources for citrus breeding programs worldwide. Currently, the field citrus collection consists of more than 200 accessions, but their taxonomic assignment, genetic structure and diversity has not been clarified.In our study, 130 different citrus accessions including 24 species or interspecific hybrids maintained and bred at the Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences (FRC SSC RAS) were genetically investigated using 13 biparental (ncSSR) and 13 uniparental (orgDNA) markers. After STRUCTURE analysis, the single accessions were allocated to eight genetic clusters and their relationships were elucidated. This phylogenetic relationship was also confirmed by principal coordinates analysis (PCoA) and by dissimilarity analysis using DARwin. We identified twenty accessions as misclassified and reassigned them to the correct species. For the remaining 110 accessions the taxonomical assignment could be confirmed. A high genetic diversity was observed on basis of the nuclear ncSSR markers, while the detection of 19 different haplotypes allowed the distinct differentiation of the accessions within our collection. Our study showed that the combination of ncSSR and orgDNA was an efficient tool to estimate the genetic diversity, genetic structure and phylogeny in the FRC SSC RAS citrus germplasm collection. The results obtained are valuable for future management of the collection and the usage of individual accessions as genetic resource for citrus cultivar and rootstock breeding, especially in colder regions.

Genetic relationships in Saccharum complex germplasm collections based on morphological and molecular markers

and is a cross-pollinator, so information about the genetic relationship between the accessions in germplasm collections is very important for selecting the prospective parent in crossbreeding. This research aims to determine the phylogenetic relationship of 24 Saccharum complex accessions and to verify the grouping of accessions using 37 morphological and three microsatellite molecular markers. Interpretation of morphological and molecular data was obtained from the analysis using the NTYSYpc-2.02i program. The results show that within the 24 accessions analyzed using morphological markers, some accessions did not cluster as the classification at the conservation time. This difference is due to the morphological markers, descriptions of characters that do not appear are considered as the same variables though in different morphological characters, so this increases the value of genetic similarity among accessions analyzed. In contrast, the grouping of molecular markers shows that each accession was grouped according to the classification at the conservation time. These accessions had a low genetic similarity of 0.20 with a broad genetic distance of 0.80. This broad genetic distance indicates that the twenty-four accessions have a distant genetic relationship with one another, so that the genetic diversity of these accessions is relatively high. The high genetic diversity in germplasm collections improves its potential as a crossing parent to obtain a high heterosis effect.