Kale (
Brassica oleracea.
var.
acephala
) is a nutrient-rich green leafy vegetable consumed as food and used in traditional medicine worldwide. An essential step in describing the available genetic ...resources and ensuring their effective use in breeding programs is to characterize the genetic diversity of available germplasm. In this study, the genetic diversity and structure of 26 kale accessions from South-East Europe were examined using 26 agro-morphological traits collected in the field and 12 simple sequence repeat (SSR) markers. Considerable agro-morphological variability was found in most quantitative (CV = 17.26–42.42%) and qualitative (H' = 0.61–1.79) traits. Multifactorial analysis (MFA) showed that country of origin (33.01%) and morphotype (32.30%) significantly influenced kale diversification. Leaf blade shape (20.62%), leaf incision (19.43%), anthocyanin distribution (16.43%), and leaf colour (15.55%) were the traits that most clearly differentiated accessions. The three common commercial kale cultivars were identified as independent outliers that differed from the other kale accessions in both MFA and UPGMA clustering analysis. The SSR markers were highly informative with 108 alleles and polymorphic information content ranging from 0.395 to 0.856. Strong genetic diversity was detected at the accession level (H' = 0.58) while genetic differentiation was low (Fst = 0.05). Similar to UPGMA clustering, Bayesian clustering suggests that the kale collection can be divided into four clusters with a high degree of admixture and no geographic grouping pattern is apparent. Overall, the study showed that the kale collection studied represents a valuable reservoir of genetic and agro-morphological variability that could be used for future breeding initiatives.
The usefulness of genetic identification of varieties for seed quality analyses becomes important, when we suspect the presence of another variety, species or even genus, based on morphological seed ...traits in the purity analysis and germination test, With genetic analyses, the doubt about the authenticity of the naked oats (Avena nuda L.) variety 'Kamil' was successfully solved. There were atypical seeds with chaff among the samples of this variety, so it was not possible to confirm with certainty, whether these were seeds of the same species/variety or impurities of common oats (Avena sativa L.). Based on the seed phenotype of the 'Kamil' variety (two independent samples 284 and 285), four sub-samples were prepared (284AN, 284AS, 285AN, 285AS); AN label was the sub-sample with naked seeds and AS label was the sub-sample with chaffed seeds. In addition, another variety ('Noni') and four accessions of common oats (ACC378, ACC379, ACC380, ACC381) from the Slovene Plant Gene Bank were included as common oat standards. A total of 36 plant samples of Avena sp. were included in the genetic differentiation. Using a set of six highly informative SSR markers and the results of diversity parameters at individual loci and paired genetic comparisons, we were able to confirm that the analysed sub-samples belonged to the same variety, i.e. 'Kamil'. In addition, despite the morphological similarity, the chaffed seeds of naked oats variety 'Kamil' were sufficiently (genetically) different from the analysed variety and/or accessions of common oats. Keywords: genetic identification, SSR markers, oat, varietal authenticity Uporabnost genetske identifikacije sort se kae pri analizah kakovosti semena, ko se na osnovi morfolokih znakov semena pri analizi cistote in/ali klic v postopku kalivosti pojavi sum na drugo sorto, vrsto ali celo rod. Z aplikativno uporabo genetskih analiz smo uspeno reili dvom o pristnosti sorte 'Kamil' vrste golega ovsa (Avena nuda L.). Med semenom omenjene sorte je bilo namrec prisotno tudi seme s plevo, a se ni dalo z gotovostjo potrditi ali gre za seme iste vrste s plevo ali za primes semen navadnega ovsa (Avena sativa L.). Na podlagi fenotipa semena sorte 'Kamil' (dva neodvisna vzorca 284 in 285) so bili pripravljeni tirje pod-vzorci (284AN, 284AS, 285AN, 285AS), kjer AN pomeni golce, AS pa plevence. Kot standardi navadnega ovsa so bili v genetsko identifikacijo vkljucene e sorta navadnega ovsa 'Noni' in tiri akcesije navadnega ovsa (ACC378, ACC379, ACC380, ACC381) iz Slovenske rastlinske genske banke. Skupno je bilo v genotipizacijo vkljucenih 36 vzorcev rastlin rodu Avena sp. Z uporabo seta estih visoko informativnih SSR markerjev in rezultatov analize parametrov raznolikosti na posameznih lokusih ter parnih genetskih primerjav smo lahko potrdili, da so analizirani pod-vzorci pripadali isti vrsti in sorti, t.j. golemu ovsu 'Kamil'. Poleg tega so bili kljub morfoloki podobnosti plevenci sorte Kamil' genetsko dovolj razlicni od analizirane sorte in/ali akcesij navadnega ovsa. Kljucne besede: genetska identifikacija, SSR markerji, oves, vrstna pristnost DETAILED ABSTRACT Varietal authenticity and seed quality of varieties that are adapted to Slovenian production conditions are of key importance for successful agricultural production and consequently for ensuring food security and reducing the risk in agricultural production. In practice, when confirming seed crops during growing season, the problem of identifying varieties of atypical plants, especially within plant species of cereals and crosses, arises. The usefulness of genetic identification of varieties is shown in seed quality analyses, when on the basis of morphological traits of seeds in the purity analysis and germination test there is a suspicion of another variety, species or even genus. With the application of genetic analyses the doubt regarding the authenticity of the variety 'Kamil' of naked oats (Avena nuda L.) was successfully solved. Among the seeds of variety 'Kamil' there was a presence of seeds with chaff, so it was not possible to confirm with certainty whether these were seeds of the same species with chaff or impurities of seeds of common oats. Based on the verification of varietal purity and morphology of oat seeds, four sub-samples (284AS, 284AN, 285AS, 285AN) of the A. nuda variety 'Kamil' were prepared. In addition variety of the A. sativa ('Noni') and four accessions of common oats (ACC378, ACC379, ACC380, ACC381) from Slovene Plant Gene Bank were included. Each sample was represented by four individual plants (a, b, c, d) to ensure diversity within each variety/accession. A total of 36 genotypes/individual plants of Avena sp. were included in the genetic identification. DNA isolation from young plant leaves was performed on a nucleic acid isolation robot using isolation kit. The original DNA was used for genetic analysis for PCR using six specific SSR markers presented in Table 1. The results were read by GeneMapper4.0 and prepared for codominant matrices for further processing. Based on the obtained results, a detailed computer analysis was required at both, the 2n and 6n levels. Several statistical programs and software packages were used to visualize the quantitative results presented in Tables 2&3 and Figs 1-4. The overall polymorphic information content of six SSR markers was 0.710. There was also small deviation (0.126) between total expected (0.752) and observed heterozygosity (0.878). According to the principal coordinate analysis and analysis of the genetic structure, two groups of genotypes were formulated. Pairwise comparisons of Nei's genetic distance showed that genetic relatedness of AN and AS sub-samples within variety 'Kamil' was higher (>0.8) compared to the common oat variety/accessions (>0.7). Despite the high degree of genetic similarity among the studied 36 Avena sp. genotypes, based on statistical analysis and relevant genetic diversity parameters at the codominant 6n level, we were able to confirm that the analysed sub-samples belonged to the same species and variety, i.e. 'Kamil'.
The usefulness of genetic identification of varieties for seed quality analyses becomes important, when we suspect the presence of another variety, species or even genus, based on morphological seed ...traits in the purity analysis and germination test, With genetic analyses, the doubt about the authenticity of the naked oats (Avena nuda L.) variety 'Kamil' was successfully solved. There were atypical seeds with chaff among the samples of this variety, so it was not possible to confirm with certainty, whether these were seeds of the same species/variety or impurities of common oats (Avena sativa L.). Based on the seed phenotype of the 'Kamil' variety (two independent samples 284 and 285), four sub-samples were prepared (284AN, 284AS, 285AN, 285AS); AN label was the sub-sample with naked seeds and AS label was the sub-sample with chaffed seeds. In addition, another variety ('Noni') and four accessions of common oats (ACC378, ACC379, ACC380, ACC381) from the Slovene Plant Gene Bank were included as common oat standards. A total of 36 plant samples of Avena sp. were included in the genetic differentiation. Using a set of six highly informative SSR markers and the results of diversity parameters at individual loci and paired genetic comparisons, we were able to confirm that the analysed sub-samples belonged to the same variety, i.e. 'Kamil'. In addition, despite the morphological similarity, the chaffed seeds of naked oats variety 'Kamil' were sufficiently (genetically) different from the analysed variety and/or accessions of common oats.
Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. ...Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.
The genetic composition of sweet potato Ipomoea batatas (L.) Lam. (2n = 6x = 90) is reflected in different levels of genetic variation. The main objective of the present study was a comparison of ...genetic diversity parameters of different ploidy levels (2n, 4n, and 6n codominant allele determination), analyzed on two high-resolution capillary platforms. Fragment analysis was performed by applying SSR markers on a 3130XL Genetic Analyzer (ABI 3130) and QIAxcel Advanced System (QX). A high level of expected heterozygosity (He) as a measure of genetic diversity was observed for both ABI3130 (0.731) and QX (0.679). Molecular variance was 17% for ABI3130 and 10% for QX. Comparison between genetic distance matrices based on allele lengths showed a moderate Mantel correlation coefficient (rxy = 0.557) between ABI3130 and QX. Global cluster analysis using the Bayesian approach distributed the observed genotypes into two clusters on both capillary platforms. Our results show that the two high-resolution capillary electrophoreses for codominant data on 2n, 4n, and 6n levels are applicable in genetic diversity studies but their efficiency depends on in-resolution expectations, financial resources, available time, and the equipment of the laboratory.
Common buckwheat (
Fagopyrum esculentum
) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is ...becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of
F
.
esculentum
var.
homotropicum
, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (
F
.
esculentum
) and Tartary buckwheat (
F
.
tataricum
), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including
FhFAR
genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that
Fh05G014970
is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that
Fh06G015130
is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of
FhS-ELF3
contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.
Despite the high ecological and economic value of common buckwheat, the availability of high-quality genomic resources is limited for this important crop. In this study, whole-genome sequencing and population genomics approaches were used to unravel the genetic basis of varied flavor-associated flavonoid content and flower morphology. The results provide insights into the evolutionary history of buckwheat species and will accelerate the genetic gain for important agronomic and nutritional quality traits by facilitating genomics-assisted breeding.
In South-Eastern Europe, the majority of runner-bean (Phaseolus coccineus L.) production is based on local populations grown mainly in home gardens. The local runner-bean plants are well adapted to ...their specific growing conditions and microclimate agro-environments, and show great morpho-agronomic diversity. Here, 142 runner-bean accessions from the five South-Eastern European countries of Slovenia, Bosnia and Herzegovina, Serbia, North Macedonia and Romania were sown and cultivated in their respective countries and characterised using 28 quantitative and qualitative morpho-agronomic descriptors for Phaseolus spp. based on inflorescences, leaves, plants, pods and seeds. For each of these morpho-agronomic descriptors, the accessions can be classified into two or three specific groups. The highest correlations were observed within the fluorescence, seed and pod traits. The highest variability, at 76.39%, was between the different countries, representing different geographic origins, while the variability within the countries was 23.61%. Cluster analysis based on these collected morpho-agronomic data also classified the accessions into three groups according to genetic origins. The data obtained serve as useful genetic information for plant breeders for the breeding of new bean varieties for further studies of the morpho-agronomic traits of the runner bean.
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