Genetic variability measures among Bromus catharticus Vahl. populations and cultivars with RAPD and AFLP markers

The objectives of this study were to optimize RAPD and AFLP techniques in B. catharticus, and to determine the genetic variability of populations and commercial prairie grass cultivars with the aforementioned molecular markers. Two populations with contrasting morphological characteristics were evaluated from individual and bulked DNA samples using RAPD markers. Both analyses showed a similar information about inter population variability. Each accession was sampled by a single leaf bulk of 10 plants. Accession similarities were established with 276 RAPD and 714 AFLP bands using Jaccard similarity coefficient. The dendrogram of the accessions using RAPD markers showed that they shared high similarity values (>94%). A similar result was obtained with AFLP markers (similarity values >98%), revealing a narrow genetic basis in the analyzed accessions. Consequently, molecular characterization of germplasm should be considered in addition to morphological criteria, to choose the parental genotypes for breeding programs of this forage crop. The AFLP technique was more efficient to detect DNA polymorphism in our experiments and unique fingerprints were detected for all the accessions. RAPD is a simple and non expensive technique, suitable to estimate genetic similarity. This revised version was published online in August 2006 with corrections to the Cover Date.     

草莓抗炭疽病遗传图谱及其QTL初分析

为获得与草莓炭疽病密切相关的分子标记,需构建高密度与抗病相关的遗传连锁图,本研究以易感草莓炭疽病品种宝交早生（Hokowase）与高抗草莓炭疽病品种甜查理（SweetCharlie）杂交的210个F2代群体材料为作图群体,构建了包含34个AFLP标记和109个SSR标记的分子遗传图谱,并对抗草莓炭疽病相关因素进行了QTL分析。该图谱共包括7个连锁群和133个遗传标记,平均每个连锁群有19个遗传标记。遗传图谱总覆盖长度为451．8cM,标记间平均距离为3．4cM。经复合区间作图法分析得到3个与草莓炭疽病抗性相关基因座（QTL）,其中2个与Colletotrichumacutatum抗性相关,分布在LG3和LG5连锁群上,可解释表型变异的31．6％;1个与Colletotrichumgloeosporioides抗性相关,分布在LG6连锁群上,可解释表型变异的68．4％。     

Genetic structure of plantations and the conservation of genetic resources of Brazilian pine (Araucaria angustifolia)

With growing concern about maintenance of genetic variation and conservation of gene resources, the question arises on the extent to which a planted population should be considered a resource able to preserve the gene pool of a species. In this study, levels of genetic diversity were assessed in natural and planted populations of Araucaria angustifolia using AFLPs and nuclear microsatellites, in order to assess the usefulness of planted forests in programs of species’ genetic resource conservation. In general, the genetic structure of the plantations was not strongly differentiated from the natural populations. For microsatellites, gene diversity (H) and allelic richness were significantly higher in plantations, while inbreeding was not different between planted and natural populations. For AFLPs, no significant difference was found between groups in the measures of genetic diversity. In the cluster analysis based on microsatellite data, plantations and natural populations from Santa Catarina State were grouped together, suggesting that plantations preserved genetic information very similar to natural populations. The cluster analysis of populations based on AFLP data differentiated plantations from natural populations. This pattern may be a result of genetic hitchhiking of AFLP fragments with genes under selective pressure due to plantations establishment and management. We suggest that the moderate to high level of genetic diversity retained in A. angustifolia populations after the intense fragmentation of the natural forest has the potential to supply plant material with sufficient genetic diversity for the species conservation through the establishment of planted forests. A sustainable management of the extant forest remnants and forestation/reforestation enterprises should additionally attend to trends revealed in previous studies concerning population structure and gene flow.     

Assessment of genetic diversity in bread wheat genotypes for tolerance to drought using AFLPs and agronomic traits

Moisture stress greatly limits the productivity of wheat in many wheat-growing regions of the world. Knowledge of the degree of genetic diversity among parental materials for key selection traits will facilitate the development of high yielding, stress tolerant wheat cultivars. The objectives of this study were to: (i) use amplified fragment length polymorphisms (AFLPs) to assess genetic diversity among bread wheat lines and cultivars with different responses to drought stress in two distinct environments and, (ii) compare genetic diversity estimated by AFLPs with diversity evaluated on agronomic performance under drought stress. Twenty-eight genotypes, 14 from Iran and 14 developed or obtained by CIMMYT, were evaluated in the study. Phenotypic data on the 14 Iranian lines were obtained in Iran, and data on the 14 CIMMYT lines were collected in Mexico. Ten AFLP primer pairs detected 335 polymorphic bands among the 28 cultivars. At the 5th fusion level of the resulting dendrogram, 6 genotype clusters were identified. Thirteen of the 14 CIMMYT genotypes grouped into one cluster while 4 of the remaining groups were comprised only of Iranian genotypes. When the agronomic performance of the Iranian materials was compared with the AFLP diversity analysis, 5 of the 6 drought susceptible genotypes clustered together in the agronomic dendrogram, and were located in the same cluster in the AFLP dendrogram. However, the drought tolerant Iranian materials did not show the same degree of relationship. The CIMMYT materials did not demonstrate a significant association between agronomic performance and genetic diversity determined using AFLPs. Clearly these data show that there are genotypes with similar agronomic performance and different genetic constitutions in this study that can be combined in a breeding program to potentially improve tolerance to drought stress.     

Assessment of genetic diversity in synthetic hexaploid wheats and their Triticum dicoccum and Aegilops tauschii parents using AFLPs and agronomic traits

Synthetic hexaploid wheats are of interest to wheat breeding programs, especially for introducing new genes that confer resistance to biotic and abiotic stresses. A group of 54 synthetic hexaploid wheats derived from crosses between emmer wheat(Triticum dicoccum, source of the A and B genomes) and goat grass (Aegilops tauschii, D genome donor) were investigated for genetic diversity. Using the AFLP technique, dendrograms revealed clear grouping according to geographical origin for the T. dicoccum parents but no clear groups for the Ae. tauschii parents. The geographical clustering of the T. dicoccum parents was also reflected in the dendrogram of their derived synthetic hexaploids. Diversity of the T. dicoccum parents and their derived synthetic hexaploids was further evaluated by measuring 18morphological and agronomic traits on the plants. Clustering based on morphological and agronomic data also reflected geographical origin. However, comparison of genetic distances obtained from AFLP and agronomic data showed no correlation between the two diversity measurements. Nevertheless, similarities among major clusters with the two systems could be identified. Based on percentage of polymorphic markers, the synthetic hexaploids had a considerably higher level of AFLP diversity (39%) than normally observed in cultivated hexaploid wheat (12–21%). This suggests that synthetic hexaploid wheats can be used to introduce new genetic diversity into the bread wheat gene pool. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Structure of <Emphasis Type="Italic">Lycopersicon pimpinellifolium</Emphasis> (Solanaceae) Populations Collected after the ENSO Event of 1997–1998

The greatest extent of genetic variation and outcrossing for Lycopersicon pimpinellifolium occurs in northern Peru. This is also the area most affected by EI Niño Southern Oscillation (ENSO). Using morphological and the molecular markers SSRs and AFLPs, we studied the genetic structure of L. pimpinellifolium populations collected after the ENSO event of 1997–1998. This was the most intense in the last century and caused a vast increase in the size of L. pimpinellifolium populations. Populations in the area surveyed were not regionally differentiated. We did not find any cline or eco-geographic association for genetic diversity, and positive correlations between genetic and geographic distances were found only at very short distances. Flooding and water streams caused by ENSO might have facilitated a periodical seed migration from distant areas. Gene flow between populations could then occur, facilitated by the increase in the population sizes of plants and pollinators and by the high levels of stigmatic exsertion. Results revealed a significant lack of heterozygotes in comparison with those expected in a panmictic population without consanguinity. A high degree of endogamy was found in all populations. In this context, endogamy can be explained by the occurrence of crosses between relatives rather than by autogamy. In an area intensely disturbed by ENSO, we found a population that had not been reported by earlier collectors in this region. This yellow-fruited population remained morphologically and molecularly differentiated from all L. pimpinellifolium and L. esculentum populations analyzed.     

Molecular Analysis of Olive Cultivars in the Molise Region of Italy

The Italian region of Molise is characterised by a remarkable variety of microenvironments, where some olive cultivars have settled in the course of many centuries. The study of the varieties cultivated in Molise, and of their relationships with varieties of close regions, is very important in order to clarify the entity of the native olive germplasm, well adapted to the local conditions, and to characterise the oil with regional origin. Eighteen cultivars from Molise have been examined using AFLP markers. They were compared with other cultivars, widely cultivated in Italy and France, in order to evaluate their similarities and to test some hypotheses on their origin and spreading among different areas of cultivation. Numerous varieties showed a high similarity and one case of synonymy (Frantoio-Paesana Bianca) was observed. The results provide useful information in order to distinguish the native germplasm and evaluate the consistency of the olive heritage of the region.     

Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry

A linkage mapping approach was used to identify quantitative trait loci (QTL) associated with day-neutrality in the commercial strawberry, Fragaria  ×  ananassa (Duch ex Rozier). Amplified Fragment Length Polymorphism (AFLP) markers were used to build a genetic map with a population of 127 lines developed by crossing the day-neutral (DN) 'Tribute' with the short-day (SD) 'Honeoye'. The population was genotyped with AFLP markers and 429 single dose restriction fragments (SDRF) were placed on a consensus map of 1541 cM with 43 linkage groups. Individuals from the mapping population were observed for their flowering habit throughout the growing season in Michigan (MI), Minnesota (MN), Maryland (MD), Oregon (OR) and California (CA). Eight QTL were found that were either location specific or shared among locations. None of these QTL explained >36% of the phenotypic variation, indicating that the inheritance of day-neutrality is likely a polygenic trait.     

Use of microsatellite loci and AFLP markers to verify gynogenesis and clonal lines in Nile tilapia Oreochromis niloticus L.

To develop an effective system for parentage analysis in gynogenetic and clonal progeny of Nile tilapia, Oreochromis niloticus L., polymorphic microsatellite loci and amplified fragment length polymorphisms (AFLPs) were investigated in several gynogenetic families and clonal lines. Six microsatellite loci were screened in two meiotic gynogenetic families to look for loci with high gene–centromere recombination rates, which can be used to discriminate meiotic from mitotic gynogenetics. Microsatellite loci UNH189 and UNH211 showed 96.7% and 92.0% heterozygosity, respectively, in these families, while other loci showed lower recombination frequencies. Scoring both UNH189 and UNH211 would give a very low probability of an individual meiotic gynogenetic being homozygous for both loci. Multiplex polymerase chain reaction of microsatellite loci was used to verify parentage in four families of mitotic gynogenetics and five fully inbred clonal lines. The genotype of each clonal line should serve as a unique identifier. Twelve AFLP primers were also investigated and 26 diagnostic AFLP bands were identified to follow inheritance in mitotic gynogenetic individuals. Amplified fragment length polymorphisms were found to be effective for this purpose but microsatellites were more appropriate since they are co‐dominant, while AFLPs are dominant markers. A multiplex of the microsatellite loci used in this study would be useful for general parental assignment as well as for the analysis of the products of chromosome set manipulations.     

分子标记法和形态学特征对杏仁栽培种及野生种基因型的遗传关系构建的辨别

应用23个形态学特征,19个扩增片段长度多态性(AFLP)引物组合,80个随机扩增多态DNA(RAPD)引物和32个简单序列重复(SSR)引物对,比较三种分子标记法在29个杏仁栽培种和3个野生种遗传关系构建中的信息景和效率.根据预期杂合度的评价,与AFLPs和RAPDs相比,SSRs具有较高水平的多态性和较大的信息量.AFLPs预期朵合度值最低,但其辨别效率值最高,因为AFLPs能揭示每个反应中的大量条带,导致各种类型的多样性指数均较高.三种分子标记法对杏仁基因型的辨别效率均较高,只是SSRs无法辨别‘Monagha'和‘Sefied'杏仁基因型.三种分子标记法基因型相似性相关系数统计上显著,但SSR数据要低于RAPDs和AFLPs的值.尽管三种分子标记法树形图拓扑结构存在一些差异,但相似性水平均较高.SSRs、RAPDs和AFLPs的系统树图及其综合数据都能依据地理散布反映大多数栽培种的关系.AMOVA检测到每个地理组中栽培种和野生种的变异.辅助程序分析表明,实验所应用的标记物数量足以保证基因相似性估计的可靠性和标记法间的比较是有意义的.