SSR markers reveal the uniqueness of olive cultivars from the Italian region of Liguria

Twenty-three important Ligurian olive accessions corresponding to 16 cultivars were studied using 12 SSR markers and 40 Mediterranean cultivars were included in the study in order to investigate the relationships between Ligurian and Mediterranean germplasm. All SSRs produced polymorphic amplifications. One hundred and forty-nine alleles were found in the 63 accessions analysed. Twenty-two alleles were specific to germplasm from Liguria and of these 12 were unique to single cultivars. Heterozygosity and discriminating power calculated in this regional germplasm were high on average (0.70 and 0.74) and not so much lower than the values in the total sample that includes cultivars from different Mediterranean countries (0.77 and 0.88 respectively). No cases of genetic identities were found between Ligurian and Mediterranean accessions. Several cases of homonyms and synonyms within the Ligurian germplasm were explained. Cluster analysis generally revealed a clear discrimination of the profiles from Liguria and Italy with respect to the cultivars from other Mediterranean countries. Only one Ligurian cultivar, “Negrea”, appeared to have a different origin, grouping with the Mediterranean cultivars.     

Genetic diversity of apricot revealed by a set of SSR markers from linkage group G1

Eight polymorphic simple sequence repeat (SSR) markers located in the G1 linkage group of apricot (Prunus armeniaca L.) were previously developed and evaluated in a small set of cultivars. Those primers were used for studying variability in 77 apricot cultivars belonging to five different geographical groups, such as Chinese, Asian (Irano-Caucasian and Central Asian), North American, Mediterranean and Western European as well as Middle European cultivars. Six of the markers were polymorphic and revealed a total of 71 alleles ranging from 5 (aprigms11) to 20 (aprigms1) alleles per locus with a mean value of 11.83 alleles per locus. In conclusion, the SSR loci located in the G1 linkage group show a level of polymorphism which is similar to loci dispersed throughout the entire genome. The total number of alleles and the number of unique alleles were the highest in Chinese apricots and the lowest in Middle European cultivars. Heterozygosity also showed a decrease from Asia and China to Middle Europe. No association could have been observed between any SSR markers tested and plum pox virus (PPV) resistant phenotype of cultivars. PPV resistant cultivars did not form a separate clade on the dendrogram obtained by UPGMA cluster analysis. Middle European and Chinese cultivars formed separate clusters while other genotypes formed smaller multiple sub-groups or scattered among different clusters. Our results support previous hypotheses on the origin of PPV resistance in North American apricots. The allele data was also presented in a form that allowed the easy observation of allele frequencies in each geographical group at each locus. Using this data field, differences and similarities between cultivar groups can be easily assessed. The analysis demonstrated the links between the North American and Mediterranean apricot germplasm and confirmed that the Chinese and Eastern European cultivars are distantly related.     

Ampelographic and genetic characterisation of ancestral grapevine (Vitis vinifera L.) accessions present in the Umbria Region (Central Italy)

Summary

During an ongoing effort to recover and preserve local germplasm, 14 accessions of indigenous minor grapevine (Vitis vinifera L.) cultivars from the Umbria Region, Central Italy, were chosen because they had been neglected and were threatened with extinction. Their phenotypic and genetic characteristics were evaluated through an ampelographic study of their shoots, mature leaves, bunches, and berries and by genomic analysis using an international set of nine microsatellite (simple sequence repeat; SSR) markers (VVS2, VVMD5, VVMD7, VVMD27, VrZAG62, VrZAG79, VVMD25, VVMD28, and VVMD32). Comparisons of the SSR profiles of all 14 accessions with grapevine accessions in several databases permitted the identification of unique genotypes, as well as possible synonyms. Information on these older, neglected cultivars will help to reduce the genetic erosion of grapevine germplasm, improve conservation and possible recovery, and assist in the future production of new, distinctive wines.     

Assessment of genetic variability in Italian heritage peach resources from Emilia-Romagna using microsatellite markers

Summary

Heritage peach (Prunus persica L. Batsch) varieties in Emilia-Romagna, Italy’s leading peach-producing region, are largely marked by melting, juicy, aromatic white-fleshed fruit with a short shelf-life and susceptibility to bruising.While these varieties have rapidly been replaced since the 1950’s by yellow-fleshed peaches from US breeding programmes with improved handling resistance, the Fruit Research Unit of the Agricultural Research Council, at Forlì, has begun an effort to safeguard and characterise the heritage varieties of Emilia-Romagna. The programme has screened 26 local heritage accessions using a set of 16 highly polymorphic microsatellite (simple sequence repeat; SSR) markers to assess genetic diversity, to elucidate inter-relationships, and to resolve any cases of homonymy. Seven international peach cultivars have been included in order to standardise allele scoring. This study resulted in 19 unique molecular profiles among the heritage accessions, and a relatively high mean observed heterozygosity value of 0.49 for a germplasm pool from a restricted region, an indicator of potential genetic diversity. The main morphological features of the heritage peaches are reported, and potential benefits for future breeding programmes discussed.     

Development and characterization of SSR markers in Chinese jujube (Ziziphus jujuba Mill.) and its related species

In order to study the extensively genetic diversities of more than 700 cultivars of Chinese jujube, it is necessary to utilize various informative DNA markers. SSR markers are highly polymorphic, co-dominant, locus-specific markers widely used in genetic studies, but less used in Chinese jujube because of no specific primers available. In this study, we used the approach of selectively amplified microsatellite (SAM) to develop SSR markers for Chinese jujube and its related species. Three cultivars (Dongzao, Dalilongzao and Jinsixiaozao) were selected to perform the approach of SAM with CT repeats. There were totally 25 primers obtained, of which we selected 16 primers available to detect the polymorphism in populations of 24 Chinese jujube cultivars, two wild jujube varieties and two Indian jujube cultivars. Based on these primers, genetic relationships of the 28 samples were constructed in a dendrogram according to the UPGMA cluster analysis. The samples were clustered into three main groups, including Chinese jujube, wild jujube and Indian jujube as expected. The 16 sequence-specific SSR primers could efficiently distinguish all the 24 cultivars of Chinese jujube, except for two cultivars, Jinsixiaozao and its ‘stoneless’ mutant, Wuhexiaozao. As a result, SAM was a very efficient method in targeted developing sequence-specific SSR primers in Chinese jujube. Furthermore, SAMs could also be used as high polymorphic molecular markers independently. The further study would focus on developing other oligonucleotide repeat types and applying more SSRs available in the genetic research of Chinese jujube.     

Microsatellite marker-based identification of mother plants for the reliable propagation of olive (Olea europaea L.) cultivars in Australia

Summary

Olive production in Australia has continued to increase in recent years, however there remains a high degree of confusion on the genetic identities of the cultivars being grown. In the present study, seven microsatellite (simple sequence repeat; SSR) loci were used to identify a set of 53 olive tree samples from different sources. The microsatellite DNA profiles of all 53 tree samples, including seven unknown trees, were compared with the SSR profiles of 14 reference olive cultivars. A total of 60 fragments (alleles), averaging 8.57 alleles per microsatellite locus, were amplified. High average values were found for the observed heterozygosity, the expected heterozygosity, and the polymorphic information content (0.73, 0.74, and 0.72, respectively). While all seven microsatellite markers proved useful for characterisation and identification purposes, a combination of three SSR primer pairs (DCA9, DCA18, and EM030) was sufficient to distinguish all 53 olive samples. The microsatellite allelic profiles allowed the 53 tree samples to be grouped into 23 genotypes. The allelic profiles of 14 of these genotypes matched with their reference cultivars, while the genetic identities of the remaining nine genotypes could not be confirmed. Some of these unknown genotypes may have been derived from feral olive trees, or were due to mislabelling and/or planting errors among Australian olive cultivars. Our results confirm the usefulness of microsatellite markers as a tool for cultivar differentiation and identification, and indicate the need for reliable identification of mother plants for commercial propagation.     

二倍体马铃薯栽培品种遗传多样性的SSR标记分析

二倍体马铃薯基因组相对简单,借助二倍体进行育种可以加速马铃薯的育种进程,因此评价二倍体马铃薯种质的遗传多样性,挖掘和有效利用优良性状显得非常必要。为了筛选多态性的SSR标记,用55对SSR引物扩增39个遗传关系相对较远的二倍体马铃薯材料。选取分布在12条染色体上的12个具有高多态性的SSR标记评价192份二倍体马铃薯栽培品种的遗传多样性,共检测到98个等位位点,其中97个为多态性位点;每对SSR引物扩增出的等位位点为6~18个,平均8.2个。用非加权配对算术平均法(UPGMA)进行聚类,显示出所有供试材料的遗传关系:12对SSR引物可以将192份材料中的186份区分开;这192份材料被划分为11个组群,其中第一个组群包含了83.3%的材料。     

The advancement of research on litchi and longan germplasm resources in China

Litchi and longan are famous southern subtropical fruits in China. Besides closely related to each other taxonomically, litchi and longan share many similarities in origin, cultivation history and environmental requirements; furthermore, the developments of research on litchi and longan germplasm resources are somewhat similar and comparable. This paper reviews the literature on origin and distribution, collection and conservation, classification and identification, selection and breeding of litchi and longan germplasm resources in China. The classification of litchi and longan can be divided into three stages: classification based on morphological traits, classification by isozyme analysis and DNA markers. The expression of morphological traits is often affected by environmental conditions; the number of loci that isozyme analysis can examine is small, cultivars, which are closely related often have identical isozyme patterns. The limitations of classification based on morphological traits and isozyme analysis are then overcome by the utilization of molecular markers. At present, most new litchi and longan cultivars are selected from superior seedlings obtained after open-pollination or sport; germplasm with desirable characteristics such as aborted seeds, rather big-fruit and rather late-bearing have not been fully exploited. In order to achieve the goal of improving fruit quality and agronomic characteristics, it is suggested that additional studies of genetic diversity on litchi and longan germplasm should be carried out with more powerful markers such as SSR and ISSR; marker assisted selection (MAS) should be employed to improve litchi and longan's cross breeding efficiency.     

Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers

Eighty-one accessions representing apricot germplasm in Tunisia were collected from different areas of cultivation and fingerprinted using amplified fragment length polymorphism (AFLP) and microsatellites (SSR) markers. A total of 339 polymorphic markers were revealed using 5 AFLP primers combinations and 24 SSR loci. AFLP and SSR markers expressed a high level of polymorphism allowing the distinction of the accessions with an efficiency coefficient of discrimination of 100% for AFLP and 97% for SSR markers. Genetic diversity structure was assessed with AFLPs and SSRs markers separately then with combined matrix data by the help of hierarchical clustering elaborated using Wards method based on Nei and Li (1979) distances. Comparison of the obtained dendrograms revealed a phylogeographic structure into two major groups with significant conservation between the observed subgroups in relation with the geographic origin of the accessions. The relative efficiency of the markers in determining the genetic relationships among apricot accessions has been assessed and a combination of AFLPs and SSRs markers was the most effective. In addition, Mantel test based on genetic distances indicated highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with Pearson correlation values of r = 0.873 and r = 0.692, respectively, revealing the higher efficiency of the combination of both molecular techniques (AFLP and SSR) to estimate the levels of genetic variability among apricot germplasm.     

The origin and dissemination of the cultivated almond as determined by nuclear and chloroplast SSR marker analysis

Sixteen nuclear and 10 chloroplast SSR markers were evaluated for 40 almond genotypes including cultivated almond, 18 related species and 5 interspecific-hybrid populations. Results establish the value of SSR (nuclear and chloroplast) markers for distinguishing different genetic lineages and characterize an extensive gene pool available to almond genetic improvement. Hierarchical analysis using integrated nuclear and chloroplast DNA markers support Prunus fenzliana, a species native to the northeast Iran, as a probable ancestor of the cultivated almond. Results also established the importance of interspecific hybridization and subsequent genetic introgression in the development of cultivated almond and demonstrate continuing value of an interspecific gene pool for modern cultivar improvement. Molecular results implicate a dissemination of the cultivated almond from Asia to the Eastern Mediterranean and subsequently the Western Mediterranean and the New World is supported by the molecular analysis of regional germplasm.     

基于SSR标记的食荚菜豆指纹图谱构建

以14个食荚菜豆品种为试材,采用SSR分子标记技术,对其进行遗传多样性研究,并建立了特异性指纹图谱,以期为今后食荚菜豆的品种鉴定建立新的参考依据,同时也为菜豆种质资源的分类和筛选提供分子生物学的参考方法。结果表明:74对SSR引物中有18对引物在供试样品中表现出多态性,筛选出其中5对具有良好多态性SSR引物(BM200、PVBR269、PVBR6、BM141、BM154)用于构建指纹图谱,并对14个食荚菜豆品种进行聚类分析。在相似系数为0.64时,14个食荚菜豆品种被分为2个类群,聚类结果显示"黑珍珠"和"黄金钩"的相似度最高,相似系数为0.98。最终构建菜豆指纹图谱,对深入挖掘菜豆种质资源,减少亲本选配的盲目性,提高育种工作效率,并对品种鉴定和知识产权保护均具有重要的应用意义。     

The Use of Dinitrocresol-Mineral Oil Sprays for the Control of Prolonged Rest in Apple Orchards

Summary

Pluots are putative hybrids between plums (Prunus salicina Lindl.) and apricots (P. armeniaca L.). The capability to distinguish among plum and pluot cultivars is important in breeding and cultivation. We investigated the genetic diversity among 14 plums, 6 pluots and one plumcot representing commercial cultivars in California, with 28 microsatellite markers. We also tested seven apricot cultivars as a reference to ®nd evidence of apricot in the ancestry of pluots and plumcot. The parental material used in the original cross that produced the pluot and plumcot was not available. Of the 28 SSR markers, 25 were from sweet cherry (Prunus avium L.) and three from peach (Prunus persica L.). Approximately 80% of the cherry primers generated ampli®cation products in plum and pluots, showing transportability between these Prunus species. One to eight putative alleles per locus were displayed by the tested SSRs in plums and pluots. In plum and pluot samples a total of 100 alleles were identi®ed with an average of 4.3 alleles per primer combination. The SSR markers were successfully used for the discrimination of all tested cultivars. In pluots, 76 alleles were found in which 63 (83%) were speci®cally coming from plum, 9 (12%) were common in plum, pluots and apricot while no allele in the pluots was observed that was contributed from apricot. In plumcot, 49 alleles were observed in which 25 (51%) were from plum, 18 (36%) were speci®cally from apricot and 6 (12%) were common in plum, plumcot and apricot. Relationships among the 28 plum, pluot and apricot cultivars were represented by a dendrogram, constructed on the basis of 168 SSR markers. The dendrogram showed the plums and pluots form a cluster distinct from the apricots, with pluot cultivars interspersed among plum cultivars and more closely related to plum than to apricot. Plumcot made a separate branch and was placed between the plum and apricot cluster. These results suggest that the SSR markers are valuable tools for identi®cation of cultivars and diversity analyses in plum.     

Genetic Identification and Conservation of Local Turkish Grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L.) Genotypes on the Edge of Extinction

In the second half of the nineteenth century, intensive renovation of vineyards took place due to the losses caused by phylloxera and local varieties were mostly replaced by several worldwide cultivars. Shift in genotypic structure in favor of modern cultivars resulted in the decrease or even disappearance of regionally typical local varieties. A total of sixty five Turkish grape genotypes, including 5 references (four cultivars and one rootstock), were genotyped with 16 SSR and 15 SRAP markers. Sixteen SSR primers generated a total of 60 SSR amplicons in which 43 were polymorphic with 73.4% average polymorphism percentage. A total of 111 well-resolved clear DNA bands were obtained from 15 SRAP primers. Of these bands, 53 were highly polymorphic with an average of 47.74%. Cluster analysis based on pooled marker data generated a well resolved grouping pattern. The analyzed genotypes grouped basing on their geographical belongings. There were many cultivar pairs on the dendrogram most of which occurred between 0.75 and 0.90 levels. SSR and SRAP data revealed a wide genetic variability as well as certain synonyms among the historical grape varieties cultivated for decades in local vineyards lengthwise the mountainous regions of Konya, Karaman and Mersin provinces. All the genotypes have been maintained in a grapevine germplasm glasshouse. Preservation and use of these endangered genotypes will be helpful to avoid genetic erosion and diversity loss in this part of Turkey. Also, the molecular data generated in this study could be of great use in determining the optimal breeding strategies to allow continued progress in grapevine breeding.     

SSR fingerprinting Chinese peach cultivars and landraces (Prunus persica) and analysis of their genetic relationships

Thirty-two Chinese peach landraces/cultivars, a major subset of the core Chinese peach collection, were fingerprinted using seven pairs of SSR primers to assess their genetic diversity and relatedness. The seven primer pairs detected eight loci and revealed an allele richness of 3.125 (average alleles per locus), an expected heterozygosity (He) of 0.450, and a Shannon index of 0.728 among the landraces/cultivars. This level of genetic diversity is lower compared to other fruit trees and Prunus congenus species (cherry and apricot), but it is comparable to previous reports in peaches. A greater level of genetic diversity was observed in landraces than in cultivars, indicating that peach landraces are valuable for germplasm collection. All cultivars and landraces, except two, were unambiguously identified based on multi-locus genotypes. Eight unique alleles were detected among this group of Chinese peaches. UPGMA clustering analysis separated the 32 cultivars/landraces into two distinct groups, which is generally in accordance with the known pedigree information. The results provide accurate genetic information for defined acquisition policy in the repositories, improving the integrity and efficiency of germplasm management and giving evidences for protection of breeder's intellectual rights.     

云南蔷薇属部分种质资源的SSR遗传多样性研究

利用简单重复序列SSR（Simple Sequence Repeat）标记技术对42份蔷薇属（Rosa L.）种质资源（包括13份野生种、变种、变型及29份栽培品种）的遗传多样性进行了研究。用筛选出的18对SSR引物对42份材料DNA进行PCR扩增,在18个位点共检测到148个等位基因,每一位点的等位基因变幅为6~14个,平均8.2个。材料间遗传相似系数变化范围为0.282~0.892,表明在分子水平上云南省蔷薇属植物具有丰富的遗传多样性。本研究发现,在相似系数为0.456时,基于SSR标记的聚类分析可以将 13个蔷薇野生种明显分为5个组,这与植物形态学分类结果大体一致。在遗传相似系数为0.43水平上,聚类分析将42份供试材料分为5大组群;同时初步探讨了野生种之间以及野生种与栽培品种之间的遗传亲缘关系。