Instant domestication process of European chestnut cultivars

This study presents the results of the first genetic analysis of ancient chestnut trees (Castanea sativa Mill.) in Italy and in the Iberian Peninsula to better understand the effect of grafting on the domestication process of chestnut and to investigate the impacts of early selection and improvement on the genetic diversity retained. We evaluated 105 giant ancient trees from Italy, Spain and Portugal and compared them with the European Union (EU) database of chestnut cultivars by using a set of 24 simple sequence repeats (SSRs; microsatellite markers). We measured the perimeter (girth) at the diameter at breast height (DBH). Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self‐rooted and which were grafted. Diversity was compared using standard metrics and model‐based approaches based on the expected heterozygosity (He) at equilibrium. We could differentiate 91 new genotypes; 9.6% matched known chestnut cultivars. We found the first evidences of cultivation, that is, grafting to produce “instant domestication” in Galicia and in the Douro Valley in trees of 14‐m perimeter (15th century) and in the Basque Country (first report in that area) in a tree of 11.5‐m perimeter (16th century). In Italy, the cultivar “Marrone Fiorentino” was found in some giant trees with perimeters of 8 and 9 m (17th‐18th centuries) in the Toscana and Umbria. Those findings matched with written references in Portugal from the 16th century and from the 18th century in Spain. “Instant domestication” could be dated back to the 15th century and was related to the wild populations existing in the same areas where cultivars are being propagated, without a different genetic structure for wild chestnut trees and with a high diversity maintained through the initiation of domestication.     

Structure of genetic diversity in <Emphasis Type="Italic">Olea europaea</Emphasis> L. cultivars from central Italy

The olive is considered one of the most important fruit crops of the Mediterranean basin where it shows a wide range of variability, with about 2,000 cultivars. Italy, with about 500 cultivars, plays a fundamental role. The ability to discriminate olive cultivars and estimate genetic variability are important factors in better management of genetic resources and in helping to understand how genetic diversity is partitioned among cultivars. The two main objectives of the present investigation were to evaluate the identity of cultivars grown in Abruzzo region, central Italy, and to study their genetic structure. We applied amplified fragment length polymorphism (AFLP) methodology on 84 genotypes belonging to the most relevant and oldest varieties cultivated in Abruzzo and on six unknown genotypes. The information content of data was evaluated using the Marker Ratio index and the Polymorphic Index Content. Moreover, STRUCTURE software was used to investigate the genetic population structure. The analysis enabled us to clearly distinguish eight cultivars within seven clusters. Additionally, one cluster was found to have various minor cultivars and showed a relatively high level of diversity. The partitioning of genetic diversity showed that the largest amount of molecular variance was within groups. Our data suggest that both sexual and clonal propagation have played an important role in the evolution of olive cultivars. In our hypothesis, some ancestral population spread in central Italy with a relevant role of seed propagation, followed by a selection of superior clones from which more traditional varieties originated. In a few cases, hybridization should be taken into consideration to explain the diffusion of recently developed cultivars.     

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.     

Differential response among chestnut traditional varieties to the attack of Cydia splendana

Fruit production of Castanea sativa Miller (Fagaceae) in southern Spain is carried out in traditional orchards using a large number of local varieties. The main areas of production are located in the Natural Park of Sierra de Aracena y Picos de Aroche (Huelva) and the Genal river Valley (Malaga). These agroforestry systems have shown a high genetic diversity and represent an example of in situ conservation. In this region, chestnut mainly suffers from attacks by Cydia splendana (Hübner) (Lepidoptera: Tortricidae), whose larvae feed on the fruits, thereby reducing their quality and economic value. The aim of this study was to evaluate the differential response between the chestnut local varieties to the attack of C. splendana. For that purpose, trees from the most representative varieties were evaluated on various farms. In cases where it was necessary, the trees were identified with a set of eight microsatellite markers. The infestation rate of C. splendana (percentage of infested fruits of the total fruits sampled per tree) differed among varieties, indicating a high genetic component in this effect. The results obtained in this study open the possibility of using this differential response in the control of C. splendana.     

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。     

The use of microsatellite markers for the detection of genetic similarity among winter bread wheat lines for chromosome 3A

Previous studies with chromosome substitution and recombinant inbred chromosome lines identified that chromosome 3A of wheat cv. Wichita contains alleles that influence grain yield, yield components and agronomic performance traits relative to alleles on chromosome 3A of Cheyenne, a cultivar believed to be the founder parent of many Nebraska developed cultivars. This study was carried out to examine the genetic similarity among wheat cultivars based on the variation in chromosome 3A. Forty-eight cultivars, two promising lines and four substitution lines (in duplicate) were included in the study. Thirty-six chromosome 3A-specific and 12 group-3 barley simple sequence repeat (SSR) primer pairs were used. A total of 106 polymorphic bands were scored. Transferability of barley microsatellite markers to wheat was 73%. The coefficient of genetic distance (D) among the genotypes ranged from 0.40 to 0.91 and averaged D=0.66. Cluster analysis by the unweighted pair-group method with arithmetic averages showed one large and one small cluster with eight minor clusters in the large cluster. Several known pedigree relationships largely corresponded with the results of SSR clusters and principal coordinate analysis. Cluster analysis was also carried out by using 22 alleles that separate Wichita 3A from Cheyenne 3A, and three clusters were identified (a small cluster related to Cheyenne of mainly western Nebraska wheat cultivars; a larger, intermediate cluster with many modern Nebraska wheat cultivars; a large cluster related to Wichita with many modern high-yielding or Kansas wheat cultivars). Using three SSR markers that identify known agronomically important quantitative trait loci (QTL) regions, we again separated the cultivars into three main clusters that were related to Cheyenne or Wichita, or had a different 3A lineage. These results suggest that SSR markers linked to agronomically important QTLs are a valuable asset for estimating both genetic similarity for chromosome 3A and how the chromosome has been used in cultivar improvement.     

Analysis of genetic diversity among persimmon cultivars using microsatellite markers

In the Mediterranean area, the production of persimmon (Diospyros kaki Thumb) [2n = 6x = 90] has increased recently as an alternative to the major fruit crops. In Spain, production relies almost exclusively on the cultivar “Rojo Brillante” which accounts for 83% of the crop. A crop based on a monovarietal culture implies several commercial risks that can compromise the future of the crop. Although the species was introduced in Europe very recently, it is well adapted to the climate of southern Europe. However, the recent introduction from Japan, the mistakes on the identity of varieties in the collections due to a bad translation of variety names from Japanese, and the lack of genetic characterization of many varieties have caused difficulties for effective management of the available genetic resources. The present paper was aimed at exploring the genetic diversity among different persimmon cultivars, including those collected in the European survey as well as Japanese cultivars. Seventy-one persimmon cultivars coming from two European collections that included accessions from Japan, Italy, and Spain were analyzed using 19 polymorphic microsatellite markers. A total of 206 alleles were obtained, with a mean value of 10.8 alleles per locus. A neighbor joining dendrogram and a principal coordinate analysis arranged the cultivars according to their genetic relationships. Analysis of molecular variance revealed significant genetic variability between and within groups, 73.3% and 85.2% for astringent-type and country origin, respectively. The simple sequence repeat markers classified the persimmon cultivars according to their genetic relationship.     

29个香蕉基因型遗传多样性的SRAP分析

采用SRAP分子标记技术对29个香蕉品种(系)的多样性进行研究,结果显示,64对SRAP引物中筛选出25个多态性较高的引物组合,共扩增出324条条带;UPGAM聚类图显示所有供试的29个香蕉品种(系)可分为2个类群且与基因型相一致;实验结果与形态、农艺性状标记分类基本一致。研究表明,SRAP技术可有效运用于香蕉基因型的遗传和育种研究。     

Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice

Sheath blight caused by Rhizoctonia solani Kühn is one of the important diseases of rice, resulting in heavy yield loss in rice every year. No rice line resistant to sheath blight has been identified till date. However, in some rice lines a high degree of resistance to R. solani has been observed. An indica rice line, Tetep, is a well documented source of durable and broad spectrum resistance to rice blast as well as quantitative resistance to sheath blight. The present study identified genetic loci for quantitative resistance to sheath blight in rice line Tetep. A mapping population consisting of 127 recombinant inbred lines derived from a cross between rice cultivars HP2216 (susceptible) and Tetep (resistant to sheath blight) was evaluated for sheath blight resistance and other agronomic traits for 4 years across three locations. Based on sheath blight phenotypes and genetic map with 126 evenly distributed molecular markers, a quantitative trait loci (QTLs) contributing to sheath blight resistance was identified on long arm of chromosome 11. Two QTL mapping approaches i.e., single marker analysis and composite interval mapping in multi environments were used to identify QTLs for sheath blight resistance and agronomical traits. The QTL qSBR11-1 for sheath blight resistance was identified between the marker interval RM1233 (26.45 Mb) to sbq33 (28.35 Mb) on chromosome 11. This region was further narrowed down to marker interval K39516 to sbq33 (~0.85 Mb) and a total of 154 genes were predicted including 11 tandem repeats of chitinase genes which may be responsible for sheath blight resistance in rice line Tetep. A set of 96 varieties and a F₂ population were used for validation of markers linked to the QTL region. The results indicate that there is very high genetic variation among varieties at this locus, which can serve as a starting point for allele mining of sheath blight resistance.     

Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers

To quantify genetic diversity among modern and earlier maize cultivars, 133 varieties, representative of the maize grown in France during the last five decades, were fingerprinted using 51 SSR. The varieties were grouped into four periods. For each period, allelic richness, genetic diversity and genetic differentiation among periods were computed. A total of 239 alleles were generated. Allelic richness, in terms of number of alleles per locus, for each period was 4.5, 3.6, 3.9 and 3.6 respectively. Genetic diversity corresponding to Neis unbiased heterozygosity was calculated, based on allelic frequencies. Values ranged from 0.56 to 0.61. Period I presented the highest genetic diversity, whereas the three other periods all presented a similar value. A great proportion of the total genetic diversity (H_T=0.59) was conserved within all periods (H_S=0.57), rather than among periods (G_ST=0.04). The analysis of molecular variance showed that the variation among periods represented only 10% of the total molecular variation. However, the differentiation among periods, although low, was significant, except for the last two periods. Our results showed that the genetic diversity has been reduced by about 10% in the maize cultivars bred before 1976 compared to those bred after 1985. The very low differentiation (G_ST=0.21%) observed among cultivars of the last two decades should alert French maize breeders to enlarge genetic basis in their variety breeding programmes.     

Microsatellite analysis of Latial Olea europaea L. cultivars

Olea europaea L. is one of the oldest domesticated tree species. O. europaea varieties cannot be confused because they are very different in morphology, genetics, and secondary metabolite content. It is important to study and establish the genetic structure of vegetal cultivars to better distinguish them, to solve past misclassification, to preserve plant biodiversity, and to increase their use, diffusion, selection, resistance to adversities, marketing, and scientific applications. Five simple sequence repeat loci (DCA-3, DCA-9, UDO99-9, UDO99-35, and EMO-3) were used to differentiate 39 individuals, representing 13 olive cultivars sampled in Latium (Central Italy). The markers showed a high discrimination power and were able to differentiate 39 alleles. Observed heterozygosity ranged from 0.538 at locus UDO99-9 to 1 at locus UDO99-35, with a mean value of 0.784. DCA loci were the most informative ones. Sample clustering, based on their genetic distance and similarity values, produced a phylogenetic network that has shown a unique major group of cultivars, composed of two sub-branches, and two independent taxa.     

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.     

Structured diversity in octoploid strawberry cultivars: importance of the old European germplasm

Understanding genetic structure and diversity information is critical for genetic association studies. In the octoploid cultivated strawberry (Fragaria×ananassa), genetic analyses were focussed on diversity, whereas genetic structure has been poorly explored. This study investigated the genetic structure in a genetic resources collection representing a wide range of the octoploid strawberry cultivars released mainly by North America and western and southern Europe, at different breeding periods and with various pedigrees. The relationship between varieties was examined using 23 microsatellite (simple sequence repeat, SSR) markers. Eight SSR markers were diploid, useful for cultivar discrimination with polymorphic information content (PIC) values between 0.29 and 0.74. Bayesian analyses of genetic structure identified four subpopulations. Three of them, American and modern northern European cultivars (AMNECs), American and modern southern European cultivars (AMSECs) and old European cultivars (OECs), reflected the European breeding history of the cultivated octoploid strawberry. The fourth subpopulation, ‘Intermediate’ group cultivars (IGCs), comprised various origins including OECs that were introgressed with wild species such as Fragaria chiloensis or Fragaria moschata. The OEC group gathered cultivars dating before 1960s, forming the most homogenous and stable subpopulation. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on modified Nei and Li distance confirmed the separation of the AMSEC, AMNEC and OEC groups. In addition, significant differences were observed among the four subpopulations (AMNEC, AMSEC, OEC, IGC), with high variability within groups and between AMSEC and IGC. Our work underlined that the structure within the studied collection was mainly explained by the pedigree and the year of release than the geographical origin of cultivars. In addition, the important loss of diversity observed in the modern European cultivars and a trend towards using mainly American cultivars for breeding programmes led to the progressive abandonment of old European germplasm, which was revealed as a relative distinct and rich group. This European material should be protected and maintained, because it represents a potential source of original traits for broadening the genetic base of cultivated strawberry. In addition, diploid markers we identified can be used without ambiguity in phylogenetic and diversity studies, because they are genome‐specific. This study is the first step for further association studies in strawberry.     

Assessment of genetic diversity in Italian rice germplasm related to agronomic traits and blast resistance (<Emphasis Type="Italic">Magnaporthe</Emphasis><Emphasis Type="Italic">oryzae</Emphasis>)

Italy is the only country in Europe with a significant land area used for rice production. In this paper, the genetic diversity of 172 national varieties and 47 foreign accessions (ITALORYZA collection) was investigated using a set of neutral markers evenly distributed throughout the 12 chromosomes. Out of the 218 alleles detected in our analysis, 17 and 29% were specific to the Italian and foreign accessions, respectively. From the neighbour-joining tree generated, six sub-groups of temperate japonica germplasm were identified. Plant height and grain type measured in the source collection were fitted to the phylogenetic tree, along with the period of variety registration. This integrated genotype–phenotype analysis revealed that specific sub-groups are characterized by uniform classes of grain type, or by similar plant size, or by period of release in the market. The whole collection was also evaluated for leaf blast resistance by inoculating the plants with three strains of Magnaporthe oryzae, representing the pathogen genetic diversity existing in Italy. Only 15 out of 172 Italian accessions (8.7%) were resistant to all three fungal strains. The correlation between genotype and leaf blast phenotype revealed that the most highly resistant Italian varieties are included in a single germplasm sub-group derived from US varieties. This study represents the starting point for carrying out detailed phenotype–genotype whole-genome association studies and identification of the genetic basis of important agronomic traits for rice cultivation in temperate climates.     

Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years

It has been claimed that the system that delivers the products of plant breeding reduces the diversity of cultivated varieties leading to an increased genetic vulnerability. The main goal of our study was to monitor the temporal trends in genetic diversity over the past five decades among maize cultivars with the largest acreage in Central Europe. Our objectives were to (1) investigate how much of the genetic diversity present in important adapted open-pollinated varieties (OPVs) has been captured in the elite flint germplasm pool, (2) examine changes in the genetic diversity among the most important commercial hybrids as well as in their dent and flint parents, (3) analyze temporal changes in allele frequencies between the dent and flint parental inbreds, and (4) investigate linkage disequilibrium (LD) trends between pairs of loci within the set of parental dent and flint lines. We examined 30 individuals of five prominent OPVs from Central Europe, 85 maize hybrids of economic importance, and their dent and flint parental components with 55 SSRs. LD was significant at probability level P=0.01 for 20.2% of the SSR marker pairs in the 82 dent lines and for 17.2% in the 66 flint lines. The dent and flint heterotic groups were clearly separated already at the beginning of hybrid breeding in Central Europe. Furthermore, the genetic variation within and among varieties decreased significantly during the five decades. The five OPVs contain numerous unique alleles that were absent in the elite flint pool. Consequently, OPVs could present useful sources for broadening the genetic base of elite maize breeding germplasm.     

Use of population structure and parentage analyses to elucidate the spread of native cultivars of Japanese chestnut

The Japanese chestnut (Castanea crenata Siebold et Zucc.) is naturally distributed throughout Japan and is cultivated for its fruit (nuts) throughout the country. Many native cultivars have cultivation records going back more than 100 years. Researchers have speculated that native cultivars that originated in the Tanba region, the most important region of cultivation, were spread throughout Japan. To clarify the breeding history and spreading pattern of Japanese chestnut cultivars, we estimated the population structure of a set of 60 native chestnut cultivars via hierarchical clustering and Bayesian model-based clustering. Both analyses gave similar results. The cultivars were divided into two main clusters: one with cultivars from the Tanba region, the other with cultivars from other areas of Japan. However, there were some exceptions to this pattern, suggesting that propagation of clones and seeds by humans was a part of the spreading process. Additionally, parent–offspring relationships were estimated from the data obtained for 175 simple sequence repeat markers. Out of the 60 genotypes, nine putative parent–offspring pairs and eight putative parent–offspring trios were identified. These results suggest that native cultivars are likely to have been selected from crosses of older native cultivars. In particular, some native cultivars from outside the Tanba region had parent–offspring relationships with cultivars from the Tanba region. This result suggests that cultivars from outside the Tanba region had been crossed with cultivars from the Tanba region and then selected as a means of introducing favorable traits from the Tanba cultivars.     

成都地区19个木芙蓉品种的孢粉学研究及其分类学意义

为了解成都地区木芙蓉(Hibiscus mutabilis)品种间的亲缘关系,采用扫描电镜观察了19个木芙蓉品种的花粉显微结构,并探讨其分类学意义.结果表明,19个木芙蓉品种的花粉均为大粒,主要为圆球形,具散孔,外壁纹饰均为刺状纹饰,表面具有颗粒状突起.木芙蓉品种间在花粉粒大小、外壁纹饰上具有一定差异,可以作为品种分类...     

Stripe rust analysis of D-genome synthetic wheats (2n = 6x = 42, AABBDD) and their molecular diversity

Stripe or yellow rust caused by Puccinia striiformis f. sp. tritici is a threat to many of the existing cultivars of Pakistan. Many attempts are being made to evolve new varieties resistant to stripe rust to reduce the losses caused by this disease. For this purpose, novel genes are needed to incorporate into the existing cultivars. These genes are found in the wild progenitors of wheat that are D-genome donors to wheat. As a result of extensive research, wheat synthetic hexaploids have been developed. These synthetics have resistances against biotic as well as abiotic stresses including the yellow rust. A group of such synthetics has been identified which seems resistant to this destructive disease. This group was tested under field conditions to identify resistance against stripe rust. The same population was analysed at molecular level to explore the genetic diversity for rust resistance. Genetic diversity among 34 selected synthetic hexaploid wheats was studied by random amplified polymorphic DNA (RAPD) analysis. A set of 12 RAPD primers was applied, and the level of polymorphism was found to be 46.67%. The coefficients in the range of 71–100% were detected by genetic similarity matrix based on Nei and Li's index. These coefficients were used for constructing a dendrogram using unweighted pair group of arithmetic means. Synthetic hexaploid line 34 was found to exhibit maximum genetic distances among the 34 selected lines. The same accession also showed excellent phenotypic characters with above average grain weight. These synthetic hexaploids carrying genetic potential for stripe rust resistance and morphological traits should be useful for improvement of existing wheat cultivars.