Assessment of the uniformity of wheat and tomato varieties at DNA microsatellite loci

By analysing a number (20–38) of individuals from selected varieties of wheat and tomato, we have been able to assess intra-varietal uniformity at certain micro satellite (simple sequence repeat, SSR) loci. In total, 45 varieties of wheat were analysed at between 7–9 different SSR loci, and 10 varieties of tomato were analysed at six loci. The results showed that there was variation both between varieties and between microsatellites in the degree of non-uniformity observed, and it was possible to identify a number of different probable sources of non-uniformity. Twenty-four of the wheat varieties and nine of the tomato varieties were sufficiently uniform to meet the standards currently applied for distinctness, uniformity and stability (DUS) testing using phenotypic characteristics. The implications for the potential future use of SSRs in DUS testing are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular analysis of the barley cv. 'Valticky' and its X-ray-derived semidwarf-mutant 'Diamant'

The outstanding semidwarf spring barley cultivar ‘Diamant’ was derived from the cv.‘Valticky’ by X‐ray mutagenesis. More than 120 European spring barley varieties trace back to ‘Diamant’. This variety and nine German spring barley cultivars having ‘Diamant’ in their pedigree, as well as four cultivars not related to ‘Diamant’, were analysed by amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) in order to identify genomic regions associated with traits derived from ‘Diamant’. The total number of SSRs tested was 122, of which 88 were polymorphic taking all varieties into account, with 51 for ‘Valticky’ and ‘Diamant’, i.e. 42.8%. A varying level of polymorphism was detected on individual chromosomes (11.1–78.6%). In addition, AFLP revealed a high level of polymorphism. Out of the total number of 1591 bands, 670 were polymorphic for all varieties studied with 182 for ‘Valticky’ and ‘Diamant’, i.e. 11.4%. Based on SSR and AFLP data UPGMA cluster analysis was carried out, but no grouping according to the relatedness with ‘Diamant’ or ‘Valticky’, respectively, was found. It is concluded from these results that the mutagenic effect leading to the development of ‘Diamant’ out of ‘Valticky’ affected many genetic loci and is thus larger than expected.     

Significant effect of accidental pollinations on the progeny of low setting Prunus interspecific crosses

The incidence of fortuitous pollination on interspecific hybridizations of the plum rootstock Myrobalan with the apricot cultivars ‘Moniquí’ and ‘Moniquí Borde’ was assessed in this work. Progeny was originated through hand pollination of emasculated flowers of three Myrobalan clones, without bagging, in 1998 and 1999. Fruit set was low and variable among years (1.8–8.0%), but higher than the level of accidental pollination measured with emasculated and non-pollinated flowers (1.2%). Molecular characterization of the progeny was performed with three SSR markers showing that only 28% of the seedlings, obtained by in vitro germination and culture of immature embryos, were hybrids. This represents a lower percentage than expected, and is explained here by the low viability of hybrid embryos and seedlings. The use of molecular markers is discussed in terms of a convenient method for an early identification of putative hybrids in breeding programs with low setting crosses, where the proportion of non-hybrids is magnified.     

Morphological and molecular diversity of Nordic oat through one hundred years of breeding

Summary Genetic diversity in microsatellites and development of agronomical characters in Nordic oat cultivars (Avena sativa) from the 20th century, ranging from landraces to new cultivars, were studied. A clear development in agronomical characters has taken place in this period: Straw length has been reduced, harvest index has increased and heading date has declined. The persistent oat breeding effort in the northern part of the region was indicated by the data, since cultivars from this region showed higher harvest index. Also adaptation to shorter summers was apparent in cultivars from the most northern part of the area. When comparing cultivars released after 1940 to the landraces, the loss of diversity revealed for the agronomical characters was also indicated by the molecular data. This indicates that a more general loss of diversity has taken place in the period, possibly due to random factors during the breeding process (bottleneck effect). The reduction in diversity revealed by recent cultivars at an agronomical as well as a molecular level emphasises the importance of implementing a conservation strategy for older material in order to secure genetic diversity for future oat breeding efforts.     

Conservation genetic assessment of the paleback darter,Etheostoma pallididorsum,a narrowly distributed endemic in the Ouachita Highlands,Arkansas, USA

1. The paleback darter, Etheostoma pallididorsum, is considered imperilled and has recently been petitioned for listing under the Endangered Species Act. Previous allozyme-based studies found evidence of a small effective population size, warranting conservation concern. The objective of this study was to assess the population dynamics and the phylogeographical history of the paleback darter, using a multilocus microsatellite approach and mitochondrial DNA.
2. The predictions of this study were that: paleback darter populations will exhibit low genetic diversity and minimal gene flow; population structure will correspond to the river systems from which the samples are derived; reservoir dams impounding the reaches between the Caddo and Ouachita rivers would serve as effective barriers to gene flow; and the Caddo and Ouachita rivers are reciprocally monophyletic.
3. Microsatellite DNA loci revealed significant structure among sampled localities (global F_st = 0.17, P < 0.001), with evidence of two distinct populations representing the Caddo and Ouachita rivers. However, Bayesian phylogeographical analyses resulted in three distinct clades: Caddo River, Ouachita River, and Mazarn Creek. Divergence from the most recent ancestor shared among the river drainages was estimated at 60 Kya. Population genetic diversity was relatively low (H_e = 0.65; mean alleles per locus, A = 6.26), but was comparable with the population genetic diversity found in the close relatives slackwater darter, Etheostoma boschungi (H_e = 0.65; A = 6.74), and Tuscumbia darter, Etheostoma tuscumbia (H_e = 0.57; A = 5.53).
4. These results have conservation implications for paleback darter populations and can be informative for other headwater specialist species. Like other headwater species with population structuring and relatively low genetic diversity, the persistence of paleback darter populations is likely to be tied to the persistence and connectivity of local breeding and non-breeding habitat. These results do not raise conservation concern for a population decline; however, the restricted distribution and endemic status of the species still renders paleback darter populations vulnerable to extirpation or extinction.

     

基于新开发微卫星标记评价番红砗磲两个野生群体的遗传多样性及近缘种通用性检测

采用磁珠富集和PCR筛选相结合的方法,得到番红砗磲的19个多态性微卫星标记。利用新开发微卫星标记对西沙群岛2个野生群体的遗传多样性进行比较分析,七连屿海域野生群体和永兴岛海域野生群体的平均观测等位基因数(Na)分别为11.105、11.895,平均有效等位基因数(Ne)分别为6.274、6.173,平均期望杂合度(He)分别为0.776、0.788,平均多态性信息含量分别为0.730、0.744,发现2个野生群体的遗传多样性都处于高度多态水平,说明其有效群体大小仍然保持在较高水平。Bonferroni校正后,在2个群体中各有4个位点偏离Hardy-Weinberg平衡。另外分析了这些引物在近缘种中的通用性情况,发现鳞砗磲中有7对微卫星引物具有通用性,6对具有多态性;无鳞砗磲中有3对微卫星引物具有通用性,1对具有多态性;诺瓦砗磲中有5对微卫星引物具有通用性,5对具有多态性;长砗磲中有9对微卫星引物具有通用性,8对具有多态性;砗蚝中有2对引物具有通用性,2对具有多态性。     

黄鳍棘鲷家系亲缘关系鉴定

为了建立黄鳍棘鲷微卫星亲子鉴定技术,利用荧光引物和自动测序技术检测了自主开发的12对微卫星分子标记在505尾黄鳍棘鲷个体中的遗传多态性,并构建了亲子鉴定技术。结果显示,该研究中筛选的12个微卫星标记共检测到119个等位基因,平均等位基因数(N_a)为9.91,平均观测杂合度(H_o)为0.651,平均期望杂合度(H_e)为0.661,平均多态性信息含量(PIC)为0.621,具有丰富的多态性。此外,运用Cervus 3.0软件对已知系谱信息的112尾黄鳍棘鲷亲本和393尾子代个体进行模拟分析,结果显示,当双亲未知且置信度为95%时,12个标记的累积排除概率达99.58%;当微卫星标记数量为8时,累积排除概率达到99.1%。因此确定AL49、AL37、AL01、AL20、AL14、AL18、AL15和AL51共8个多态性较高的微卫星标记为黄鳍棘鲷微卫星亲子鉴定的核心体系。在双亲性别未知的情况下,其双亲的累积排除率为99.1%。根据黄鳍棘鲷子代的实际基因分型数据,实际鉴定率为89.31%。该研究构建的微卫星标记组合能为黄鳍棘鲷不同...     

Evaluating spawning performance among captive Florida pompano Trachinotus carolinus broodstock using microsatellite‐based parentage assignment

Florida pompano has been identified as a promising candidate for commercial‐scale aquaculture production, but to date, little information is available regarding captive broodstock spawning characteristics. Genetic markers were tested for their power in monitoring mating outcomes and potential in analysing heritability of rapid growth trait in Trachinotus carolinus. A total of 20 unrelated adults (10 females and 10 males) were chosen for a hormone‐induced mass spawning event. The 515 fastest growing and 485 slowest growing fish of the total 4852 offspring were considered a selected progeny stock, and fish were collected at 45 days post hatch based on their growth traits. Parentage analyses based on the 20 breeders and 1,000 selected progeny were performed using a total of nine microsatellite markers, a 100% assignment rate was achieved, and a four‐marker set was the minimum number for the parentage assignment. The effective breeding number for the selected progeny was 11 (six females and five males), among which three females and two males were predominant contributors with the total contribution of 95.8% and 94.7% respectively. The proportion of fast‐growing offspring from broodfish and each mating cross (sire/dam) was used for detecting whether variation in growth of the offspring was related to parental stocks. Results showed that three adults and their mated combination exhibited the greatest fast‐growing offspring proportion (69.73% and 55.95%). This research provided new information regarding spawning performance and parental contribution during mass spawning events; both important first steps towards developing improved management strategies for captive Florida pompano broodstock.     

Potato cultivar identification using simple sequence repeats markers (SSR)

Summary Identification of potato cultivars is currently based on phenotypic characters. Crop inspections are needed at different stages and the increasing number of cultivars means the process is becoming more and more complex. Molecular markers are a possible complementary tool to identify potato cultivars and to rapidly check the identity of seeds lots. In this study 286 potato cultivars produced in France were characterized by Polymerase Chain Reaction (PCR) using Simple Sequence Repeats (SSR) markers. Sequential amplifications with 4 to 5 of the chosen SSR markers enabled complete discrimination between all the cultivars. The patterns were registered in a database and the procedure is now used routinely in France.     

Population structure of Phytophthora infestans collected on potato and tomato in Italy

Late blight caused by the oomycete Phytophthora infestans is a disease of potato and tomato of worldwide relevance and is widespread throughout Europe and the Mediterranean region. While pathogen populations in northern Europe have been sampled and characterized for many years, the genetic structure of populations from southern Europe, including Italy, has been less studied. Between 2018 and 2019, we collected 91 samples of P. infestans from potato and tomato crops in Italy, Algeria, and Tunisia on FTA cards and genotyped them using 12-plex microsatellites. These samples were compared to genotypes of P. infestans previously collected within the framework of the EuroBlight network and from published sources. Four clonal lineages were identified: 13_A2 (Blue 13), 2_A1, 23_A1, and 36_A2. Two other isolates collected could not be matched to any currently known clonal lineage. The 13_A2 and 36_A2 lineages were found exclusively in southern Italy and Algeria, while 2_A1 was only found in Algeria. This is the first report of the 36_A2 lineage in Italy. Two isolates from Solanum nigrum were 13_A2, suggesting this weed host could be a reservoir of inoculum. The 23_A1 lineage was found widely on infected tomato crops in Italy and is the same as the lineage US-23 that is widespread in North America. Differences in genotypes across the country suggests that there may be different sources of introduction into Italy, possibly via infected seed tubers from other countries in Europe, tubers for consumption from North Africa, or tomatoes.