Genetic characterisation of traditional chestnut varieties in Italy using microsatellites (simple sequence repeats) markers

European chestnut (Castanea sativa) is an important multipurpose tree that has been cultivated for wood and fruit in the Mediterranean basin since ancient times. Cultivation of traditional chestnut varieties has a long tradition in Italy, where cultivars have been selected over centuries as a function of the best nut traits. In this study, 94 grafted chestnuts corresponding to 26 representative cultivars from Italy were evaluated by seven simple sequence repeat (SSR) markers to establish whether they corresponded to varieties in the narrow sense. The results allowed 20 genotypes to be identified that corresponded to the same number of clones. In total, 52 alleles were identified, eight of which were exclusive. Cases of homonymies and synonymies were detected. Moreover, our results highlighted a considerable genetic uniformity among ‘Marrone-type’ cultivars and, on the contrary, a high genetic diversity among the evaluated cultivars demonstrating that this is a valuable germplasm and an important genetic resource to be preserved.     

中国部分板栗品种坚果表型及营养成分遗传变异分析

以中国板栗主产区山东等10个省份97个板栗品种为材料,对其坚果表型性状及营养成分进行遗传变异分析。结果显示:（1）97个板栗品种间存在广泛的遗传变异,坚果表型性状及营养成分指标品种间差异均达到极显著水平;遗传变异系数均较大,最大达到0.378,遗传潜力较大;且所有性状重复力均在0.928及以上,受自身遗传因素控制较强。（2）坚果长度等表型性状间呈极显著正相关关系,淀粉含量等营养成分指标间为正相关关系,而表型性状与营养成分指标间表现为负相关关系,据此可将坚果表型性状、品质性状作为两个相互独立又有一定关联的综合因子。（3）进一步利用坚果表型和营养成分8个指标对97个板栗品种进行主成分分析,并结合多重比较结果,综合选出具有单个或多个性状优势的43个品种。研究认为,选出的43个板栗品种具有果粒较大,或营养价值较高,或二者特性兼有,初步选择为果型或品质优良的板栗品种资源材料。     

Molecular and morphological diversity of on-farm hazelnut (Corylus avellana L.) landraces from southern Europe and their role in the origin and diffusion of cultivated germplasm

Hazelnut (Corylus avellana L.) is a traditional nut crop in southern Europe. Germplasm exploration conducted on-farm in five countries (Portugal, Spain, Italy, Slovenia, and Greece) identified 77 landraces. The present work describes phenotypic variation in nut and husk traits and investigates genetic relationships using ten simple sequence repeat (SSR) markers among these landraces, 57 well-known references cultivars, and 19 wild accessions. Among the 77 landraces, 42 had unique fingerprints while 35 showed a SSR profile identical to a known cultivar. Among the 42 unique landraces, morphological observations revealed high phenotypic diversity, and some had characteristics appreciated by the market such as nut round and caliber. Analysis of genetic relationships and population structure allowed investigation of the origin and spread of the cultivated germplasm in southern Europe. Our results indicate the existence of three primary centers of diversity in the Mediterranean basin: northwestern Spain (Tarragona) and southern Italy (Campania) in the West and Black Sea (Turkey) in the East. Moreover, the data suggest the existence of secondary gene pools in the Iberian (Asturias) and Italian (Liguria and Latium) Peninsulas, where local varieties were recently domesticated from wild forms and/or from introduced ancient domesticated varieties.     

栗树种质资源的多样性及其保存利用

本文在总结板栗(Castanea mollissima Bl.)种质资源调查研究的基础上,论述了以板栗为主的中国栗属植物遗传变异的多样性。并且从生态地理学上分析板栗种内变异的分布,提出了板栗遗传变异沿生态地理梯度变化的规律,为板栗种质资源的利用提供了依据。文中指出,当前正面临着板栗种质流失的严重问题,尤其随着良种的推广,必将带来遗传种质贫乏的后果。为此,提出了有关保存和利用的具体建议。     

Molecular genetic diversity and association mapping of nut and kernel traits in Slovenian hazelnut (<Emphasis Type="Italic">Corylus avellana</Emphasis>) germplasm

European hazelnut (Corylus avellana L.), cultivated in several areas of the world including Europe, Anatolia, and the USA, is an economically important nut crop due to its high mineral, oleic acid, amino acid, and phenolic compound content and pleasant flavor. This study examined molecular genetic diversity and population structure of 54 wild accessions and 48 cultivars from the Slovenian national hazelnut collection using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Eleven AFLP primer combinations and 49 SSR markers yielded 532 and 504 polymorphic fragments, respectively. As expected for a wind-pollinated, self-incompatible species, levels of genetic diversity were high with cultivars and wild accessions having mean dissimilarity values of 0.50 and 0.60, respectively. In general, cultivars and wild accessions clustered separately in dendrogram, principal coordinate, and population structure analyses with regional clustering of the wild material. The accessions were also characterized for ten nut and seven kernel traits and some wild accessions were shown to have breeding potential. Morphological principal component analysis showed distinct clustering of cultivars and wild accessions. An association mapping panel composed of 64 hazelnut cultivars and wild accessions had considerable variation for the nut and kernel quality traits. Morphological and molecular data were associated to identify markers controlling the traits. In all, 49 SSR markers were significantly associated with nut and kernel traits [P < 0.0001 and LD value (r ²) = 0.15–0.50]. This work is the first use of association mapping in hazelnut and has identified molecular markers associated with important quality parameters in this important nut crop.     

Genetic diversity in peach [Prunus persica (L.) Batsch] at the University of Florida: past,present and future

The University of Florida (UF) stone fruit breeding and genetics program was created in 1952 to develop early ripening stone fruit cultivars with high quality, adaptation to summer rainfall, low chilling requirements, and the ability to withstand high disease pressure. Diverse germplasm sources were used to introduce desirable traits in UF breeding pool. The main objective of this research was to determine the genetic diversity and population structure of the breeding germplasm, and to search for loci under selection. A total of 195 peach genotypes were used: UF cultivars and advanced selections (n?=?168), cultivars and selections from the UF-UGA-USDA joint breeding effort (n?=?13), landrace cultivars (n?=?4), high-chilling cultivars released by NCSU (n?=?5), and related Prunus (n?=?5) species. A total of 36 SSR markers distributed across the peach genome amplified 423 alleles. An average of 18 genotypes were detected per marker: A (number of observed alleles) of 11.43, Ae (effective number of alleles) of 2.58, Ho (observed heterozygosity) of 0.4, He (expected heterozygosity) of 0.52, F (Wright’s fixation index) of 0.25, and PIC (polymorphism information content) of 0.48. UPGMA cluster analysis based on Nei’s genetic distance represented best the known pedigree information for the germplasm pools. Two major groups were observed across the germplasm corresponding to melting and non-melting flesh cultivars/selections. Population structure results supported these two major groups. Several loci closely located to genome regions where different phenotypic traits have been previously mapped were detected to be under selection.     

Genetic structure of Argentinean hexaploid wheat germplasm

The identification of genetically homogeneous groups of individuals is an ancient issue in population genetics and in the case of crops like wheat, it can be valuable information for breeding programs, genetic mapping and germplasm resources. In this work we determined the genetic structure of a set of 102 Argentinean bread wheat (Triticum aestivum L.) elite cultivars using 38 biochemical and molecular markers (functional, closely linked to genes and neutral ones) distributed throughout 18 wheat chromosomes. Genetic relationships among these lines were examined using model-based clustering methods. In the analysis three subpopulations were identified which correspond largely to the origin of the germplasm used by the main breeding programs in Argentina.     

Seed traits,nutrient elements and assessment of genetic diversity for almond (Amygdalus spp.) endangered to China as revealed using SRAP markers

Almond (Amygdalus spp.) is one of the most important nut fruits worldwide and its seed has been recognized as a health nutrient supply for human consumption. In this study, we characterized the major seed traits and fruit nutrient elements among four Chinese wild almonds (Amygdalus mongolica Maxim., Amygdalus pedunculata Pall., Amygdalus tangutica Batal., and Amygdalus triloba (Lindl) Ricker.) in addition to commercial two cultivars (Amygdalus communis L.), as well as their genetic diversity and natural variations using SRAP marker, aiming at exploiting valuable traits for breeding new cultivars. Our results show that the wild almond species are rich in crude fat, Ca, Ma, Fe and Zn compared to the cultivars analyzed. Our study also identified a relatively high level of genetic diversity (h = 0.3363, I = 0.5075) among species analyzed as evidenced by fact that 161 out of a total of 162 bands amplified with fourteen SRAP primer combinations reveal polymorphism among species analyzed. AMOVA analysis reveals a high level of genetic differentiation among populations (Φ_ST = 0.4474) but The UPMGA cluster analysis indicates that A. communis and A. mongolica are more closely related. Potential utilization of the wild almond species and their valuable traits for breeding new cultivars is discussed.     

Bayesian genome-wide association study of nut traits in Japanese chestnut

Japanese chestnut (Castanea crenata Sieb. et Zucc.) has a long juvenile phase, so breeders have to wait many years to evaluate nut traits. Molecular markers associated with genes of interest would accelerate selection in chestnut breeding programs. We evaluated five nut traits (nut harvest date, nut weight, pericarp splitting, insect infestation, and specific gravity) in 99 Japanese chestnut cultivars and selections. A wide range of phenotypic variation was observed for each of the traits, suggesting that the collection harbored sufficient genetic diversity for breeding. A Bayesian genome-wide association study was conducted using 162 simple sequence repeat markers and 741 single nucleotide polymorphism markers. To evaluate the potential of marker-assisted selection, we examined 12 molecular markers found to be associated with nut traits: 4 for nut harvest date, 4 for nut weight, 1 for pericarp splitting, and 3 for insect infestation. The percentages of phenotypic variance explained ranged from 4.8 to 37.1%. Although insect infestation showed only medium heritability (0.672), we obtained two quantitative trait loci (QTLs) with extremely high posterior probabilities (0.93 and 1.00). Out of the 12 molecular markers, 3 of the 4 markers for nut harvest time could be validated in a breeding population. Accuracies of genomic selection were extremely high for nut harvest date (0.841) and moderate for insect infestation (0.604), suggesting that genomic selection based on Bayesian regression would reduce the cost of phenotypic evaluation of these traits and possibly others.     

Identification,development, and application of 12 polymorphic EST-SSR markers for an endemic Chinese walnut (Juglans cathayensis L.) using next-generation sequencing technology

The Chinese walnut (Juglans cathayensis L.), valued for both its nut and wood, is an ecologically important tree species endemic temperate southern China. Investigation of the genetic diversity of Chinese walnut has been limited to natural population genetics and genetic germplasm resources. Here, we describe the development of 12 polymorphic microsatellite markers using next-generation sequencing to screen 96 Chinese walnut individuals collected from 11 natural populations. The number of alleles per locus ranged from 5 to 12. The observed heterozygosity (0.288–0.748) overlapped well with the expected heterozygosity (0.337–0.751). This species has high genetic diversity and gene flow among different populations (F_ST = 0.075, Nm = 3.088). These markers will be useful for future studies on population genetic structure, evolutionary ecology, and genetic breeding of this walnut tree or other Juglans species.     

Analysis of the genetic diversity and structure of the Spanish apple genetic resources suggests the existence of an Iberian genepool

The nature and structure of genetic diversity in the Spanish apple germplasm preserved at the national level was widely unknown, since studies performed to date on this topic have been exclusively carried out at the regional scale. Here, 1453 accessions from Spanish collections of Malus × domestica were evaluated with a common set of 13 SSR (Simple Sequence Repeats) markers in order to estimate genetic diversity, to identify the underlying genetic structure and to unravel the relationships among them and among a wide set of international cultivars for reference. In total, 737 unique genotypes were identified, 581 diploids and 156 triploids. Using a model‐based Bayesian clustering procedure, two reconstructed populations were obtained for diploid genotypes; one retaining only Spanish cultivars (42% of genotypes), and a second containing all foreign cultivars the latter exhibiting evidence supporting the existence of a secondary sub‐structure. Similarly, analysis performed on the 156 triploid genotypes also revealed two reconstructed populations; one exclusively associated with local Spanish genotypes (44%). The Jaccard coefficient allowed clustering by UPGMA (Unweighted Pair Group Method) diploid and triploid genotypes, and remarkable differences in allelic composition among the different partitioning levels were found. AMOVA analyses showed moderate but significant differentiation among the main groups (0.08 ≤ F_ST ≤ 0.12). Our results highlight an important fraction of the Spanish apple germplasm that constitutes a differentiated genepool with respect to the international and commercial apple cultivars. Moreover, the extent of the Spanish genetic diversity was spatially distributed along the northern Iberian Peninsula, suggesting an extensive migration of genotypes along the country. This study is the first valuable action for genetic conservation of apple at the national scale, and constitutes a decisive step towards the definition of a Spanish core collection that will be useful for further studies in dissecting the genetic control of important horticultural traits through genome‐wide association analysis in apple.     

Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers

In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found.     

Mapping and pedigree analysis of the gene that controls the easy peel pellicle trait in Japanese chestnut (Castanea crenata Sieb. et Zucc.)

The Japanese chestnut (Castanea crenata Sieb. et Zucc.) has a pellicle that is difficult to peel, which increases the labor and cost for removing the pellicle from the nut during processing. Thus, a pellicle that is easier to peel has been an important objective of Japanese chestnut breeding programs. A newly released cultivar (“Porotan”) exhibits a unique, easily peeled pellicle. A previous study indicated that this trait is controlled by recessive gene p, and that several of the ancestors of Porotan (e.g., “Tanzawa” and 550-40) were P/p heterozygotes. Two F₁ populations from intra-specific crosses of Japanese chestnut, Tanzawa (P/p) × Porotan (p/p) and 550-40 (P/p) × Tanzawa (P/p), were used for genetic mapping of the gene that controls this characteristic. A total of 11 simple sequence repeat (SSR) markers were obtained that showed significant linkages to the p gene, and genetic linkage maps for the region around the p gene were established. Pedigree analysis was conducted for eight ancestors of Porotan around the pellicle-peeling locus using graphical genotypes based on the 11 SSR loci. The two recessive p alleles and surrounding haplotypes of Porotan were inherited through different intermediate cultivars: one allele was derived from “Otomune” (P/p) via Tanzawa and the other was derived from Otomune via Tanzawa, “Kunimi” (P/p), and breeding line 550-40. A recombination event was found in the flanking region close to the p gene in Kunimi. Molecular identification of the easy peel pellicle trait will lead to marker-assisted selection and will greatly improve Japanese chestnut breeding.     

Cotyledon storage proteins as markers of the genetic diversity in Castanea sativa Miller

This study has been to analyse the useful nut globulin proteins as a marker of the genetic diversity in Castanea sativa. The evaluated populations were highly polymorphic for the globulins, being detected up to 35 polymorphic bands with a wide distribution among all the evaluated populations. Taken together for populations from all the chestnut regions, about 39.3% of total allelic variation was distributed among the populations. The estimates of genetic similarity between populations were clearly associated with the collecting site. This method of analysis of the nut storage proteins (globulins) could be a useful tool for the evaluation of genetic diversity in this and other species of the Fagaceae.     

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.     

茄子种质遗传多样性及群体结构的SRAP分析

采用SRAP标记法对183份茄子(Solanum melongena)种质资源的遗传关系和群体结构进行分析。结果表明, 33对多态性SRAP引物组合共扩增出215条清晰稳定的多态性条带, 平均每对引物组合产生7条多态性条带。183份茄子种质的遗传相似系数介于0.276-0.813之间, 平均值为0.623, 表明茄子种质资源间遗传背景存在一定的差异。在遗传距离为0.345 6处可将183份茄子种质分为4组。通过群体结构分析可将种质划分为4个群体, 不同群体间的界限十分明显, 且群体间的基因渗透较高。     

Identification and characterisation of traditional chestnut varieties of southern Spain using morphological and simple sequence repeat (SSRs) markers

The maintenance of plant genetic resources requires the identification of places and agroforestry systems that support high levels of genetic diversity. The aim of this work was to clarify the number and names of chestnut ( Castanea sativa ) cultivars in the south of Spain. Accordingly, 100 grafted chestnut trees corresponding to 34 traditional names were evaluated using 10 qualitative morphological traits and seven simple sequence repeat (SSRs) markers. We identified 38 varieties, 12 in the Huelva region and 26 in Malaga, and synonymies and homonymies were discussed. This work demonstrated that the joint use of morphological traits and SSR markers is an efficient method to evaluate the agrobiodiversity of chestnut in this region. It was also stated that chestnut production in the south of Spain is a traditional system using varieties developed ' in situ '. This constitutes a genuine system of on-farm conservation, which is now threatened. Consequently, adopting strategies for its safeguarding are urgently recommended.     

Markers polymorphic among malting barley ( Hordeum vulgare L.) cultivars of a narrow gene pool associated with key QTLs

Barley used for malting is a fine-tuned organism, and it requires breeding within narrow gene pools for realistic cultivar enhancement. Significant phenotypic advance within such narrow gene pools has been achieved and the necessary genetic variability for breeding progress has been documented, but it was not well understood. This study was conducted to further characterize detectable genetic variability present within a select set of four closely related malting barley cultivars using three types of molecular markers: RFLP, PCR-RAPD and AFLP. The markers that identified polymorphism among the select malting cultivars tended to link with each other and to map in chromosomal regions associated with quantitative trait loci (QTLs) for agronomic and malting quality traits that differed among the four cultivars. Although RFLPs identified the least amount of polymorphism, the differences detected by the RFLPs best fit the chronology of the cultivars. These results indicate that a large amount of the genetic variability necessary for cultivar improvement may have originally been present in the breeding gene pool, but does not rule out de novo variation. Study of the populations from crosses within this narrow germplasm is needed to further elucidate the basis of the phenotypic variability found among these select barley cultivars.     

From the cradle of grapevine domestication: molecular overview and description of Georgian grapevine (Vitis vinifera L.) germplasm

Historical information and archaeological and palaeobotanical findings point Georgia, in the South Caucasus, as a cradle for grapevine (Vitis vinifera L.) domestication from its wild form (V. vinifera silvestris Beck.) and subsequent selection and development of varieties with characters suitable for human consumption. The hypothesis of Georgia being a center of domestication, combined with its distance from western countries and the importance of its viticulture and wine production, make Georgian grape germplasm particularly interesting to be investigated under the genetic point of view. Twenty nuclear microsatellite loci were used to genotype 112 Georgian grapevine accessions (V. vinifera sativa Beck.) from germplasm collections and 18 from spontaneous growing plants (V. vinifera silvestris Beck.) found in wild conditions and to compare them to a large international cultivar collection in France. Data analysis shows that Georgian grapevine germplasm has maintained distinctive traits despite arrival of international, foreign varieties and still conserve characteristics of local breeding linked to traditional wine production regions of the country. Results have identified alleles, overall loci, well represented in the Georgian germplasm (cultivated and wild) and absent or poorly represented in other countries, highlighting uniqueness and originality of traits of this viticulture. Moreover, the search for relationships between Georgian and foreign viticulture has evidenced few interesting cases linking the Georgian varieties with Western European ones and with neighboring Caucasian countries, helping to identify the real place of origin in some doubtful cases. In addition, populations or sparse individuals of wild grapevine still preserved in the Georgian natural environments present smaller genetic distances with local cultivars than in other European regions. Principal component analysis (PCA) has also identified special overlapping of the wild compartment with some cultivated varieties. This work provides a highly significant new contribution to applied aspects of Georgian grapevine genetic resources management and use. Uniqueness of the Georgian cultivated grapevine gene pool together with its close relatedness with the wild compartment makes this country a good candidate to address questions regarding domestication and grapevine genetic resource conservation.     

Genetic diversity of different Tunisian fig (Ficuscarica L.) collections revealed by RAPD fingerprints

The genetic diversity in Tunisian fig (Ficus carica L.) was studied using RAPD markers. Thirty-five fig cultivars originating from diverse geographical areas and belonging to three collections were analysed. Random decamer primers were screened to assess their ability to detect polymorphisms in this crop. Forty-four RAPD markers were revealed and used to survey the genetic diversity and to detect cases of mislabelling. As a result, considerable genetic diversity was detected among the studied F. carica accessions. The relationships among the 35 varieties were studied by cluster analysis. The dendrogram showed two main groups composed of cultivars with similar geographic origin. Moreover, the male accessions (caprifigs) were clustered indistinctively within the female ones, suggesting a narrow genetic diversity among these accessions. Our data proved that RAPD markers are useful for germplasm discrimination as well as for investigation of patterns of variation in fig. Since this designed procedure has permitted to establish a molecular database of the reference collections, the opportunity of this study is discussed in relation to the improvement and rational management of fig germplasm.