Genetic diversity within commercial populations of watercress (Rorippa nasturtium-aquaticum), and between allied Brassicaceae inferred from RAPD-PCR

Commercial productivity of watercress (Rorippa nasturtium-aquaticum) can be adversely affected by the pathogenic crook-root fungus, Spongospora subterranea f.sp. nasturti, and watercress viruses. As there are no effective control measures for these diseases, attempts have been made to breed varieties resistant to the crook-root pathogen. This work has been hindered by a lack of knowledge of the genetic base of commercial watercress, and the genetic distance between watercress and allied Brassicaceae which have been identified as candidates for hybridisation programmes. We measured the diversity within these two groups using the RAPD-PCR fingerprinting technique and analysed the data by both distance methods and principal co-ordinate analysis. Little genetic diversity was found within commercial watercress populations. However, watercress formed a unique cluster genetically distinct from other Rorippa species, but equidistant to Cardamine species. It was placed closer to Barbarea verna. This revised version was published online in August 2006 with corrections to the Cover Date.     

Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.)

The use of bulked leaf samples from individual plants for amplified fragment length polymorphism (AFLP) analysis was evaluated as a tool for assessment of genetic diversity in white clover (Trifolium repens L.). Bulking of leaf samples produced slightly simpler AFLP profiles compared to the combined profiles of individual plants from the same cultivar. Approximately 90% of bands which were present in individual plants were present in bulked samples of the same cultivar. The majority of those absent were rare bands, shared by less than 25% of individual plants. Replicate bulk samples gave almost identical banding patterns, demonstrating the robustness of the bulked AFLP technique. Cluster analysis of AFLP data derived from individual plants resulted in a phenogram similar to that produced from data derived from bulked samples of the same plants. AFLP analysis of bulked samples detected significant amounts of genetic variability among 52 cultivars and accessions with genetic similarity values ranging from 0.42 to 0.92. However, cluster analysis of AFLP data only partially reflected the geographic origin of cultivars and accessions and was not congruent with cluster analysis based on variation for morphophysiological characters. Bulked AFLP analysis provides a powerful tool for rapid assessment of genetic variability in white clover and may also be used for cultivar identification. This revised version was published online in August 2006 with corrections to the Cover Date.     

Differentiation of the high molecular weight glutenin subunit D t x 2.1 of Aegilops tauschii indicated by partial sequences of its encoding gene and SSR markers

The devastating late blight pathogen Phytophthora infestans infects foliage as well as tubers of potato. To date, resistance breeding has often focused on foliage blight resistance, but tuber blight resistance is becoming more and more important in cultivated potatoes. In this study, a reliable tuber assay for resistance assessment was developed and foliage and tuber blight resistance (R) was compared in four mapping populations. In the RH4X-103 population, tuber blight resistance inherited independently from foliage blight resistance. Three specific R genes against P. infestans were segregating. The Rpi-abpt and R3a genes function as foliage-specific R genes, whereas the R1 gene acts on both foliage and tuber. In the segregating populations SHRH and RH94-076, tuber and foliage blight resistance correlated significantly, which suggests that resistance in foliage and tuber is conferred by the same gene (could be R3b) and quantitative trait loci (QTL), respectively. In the CE population neither tuber nor foliage resistance was observed.     

Significance of host complexity and diversity for race-specific leaf-rust resistance in self-fertile synthetic rye populations

Leaf rust (Puccinia recondita Rob. ex. Des.) is the most frequently occurring leaf disease in German winter rye (Secale cereale L.). To test the usefulness of race‐specific resistance genes, the effects of increased host diversity and complexity by producing two‐ and four‐line synthetics from inbred lines carrying different resistance genes were analysed. Thirty‐three synthetics along with two full‐sib families and one hybrid variety were tested in 17 environments in Germany under natural infections. For comparison, the parent lines of the synthetics were evaluated in 11 environments. Only two synthetics and the full‐sib families were resistant across all environments. Observed resistance levels of the synthetics were highly correlated (r = 0.83, P = 0.01) with those predicted from the parental values. Host complexity had a minor effect in two‐line synthetics only. In conclusion, the effectiveness of race‐specific leaf‐rust resistances among environments, and increasing the host complexity and diversity does not lead to a higher resistance level than that expected from the resistances of the parents.     

Molecular diversity in Indian sugarcane cultivars as revealed by randomly amplified DNA polymorphisms

Genetic diversity in 28 prominent Indian sugarcane varieties cultivated under a wide range of agroclimatic conditions, was studied using 25 RAPD markers. The mean genetic distance among the 28 varieties was only 29.31%, implying that a large part of the genome is similar among the varieties. This probably arises from the lack of parental diversity, with few clones which are themselves related, contributing to the parentage of these varieties. The parentage of the varieties did not contribute significantly to the clustering pattern. Varieties belonging to the same parentage were grouped under different clusters while varieties from different parentages were grouped under the same cluster. The tropical and subtropical identities of the varieties also did not contribute to the clustering pattern as individual clusters included varieties from both tropics and subtropics. This shows that genetically similar varieties are present in both the regions. Among the varieties, Co 7717 was found to be totally distinct and divergent from rest of the varieties. The study reveals the limited genetic base of the current Indian commercial varieties and the need to diversify the genetic base by using new sources from the germplasm. This revised version was published online in August 2006 with corrections to the Cover Date.     

Use of PCR-based methodologies for the determination of DNA diversity between Saccharum varieties

Summary In this study, two PCR-based methodologies were evaluated for potential use in the determination of DNA diversity between 20 commercial sugarcane hybrids and 6 outgroup varieties of S. spontaneum, S. officinarum and hybrids from early in the genealogy. The first method involved PCR amplification of sugarcane DNA in the presence of random, decamer primers (RAPDs), while the second protocol utilized specific microsatellite and telomere sequences as primers. A total of 41 RAPD primers (356 loci) were screened across the varieties of which 15 (160 loci) were used in the calculation of DNA diversity (expressed% similarity). This varied from 61 to 95%, with most of the commercial varieties showing more than 80% similarity in their DNA. The RAPD data indicated that there had been a gradual decline in DNA diversity (84% reduction) from the early inter-specific crosses to the commercial hybrids, probably as a result of backcrossing and in-breeding strategies used in the previous 5 to 6 generations of sugarcane breeding. The microsatellite and telomere data produced a much greater range in DNA similarity values (25–91%), probably due to the fact that these primers detect highly variable regions of the genome. It is suggested that these specific primers would not be suitable for determination of DNA diversity, but could be used more effectively in the development of a methodology for routine, rapid identification of sugarcane varieties.     

利用DNA分子标志鉴别台湾茶树品种及评估种原之遗传歧异性

为评估台湾茶树种原之遗传歧异性。本研究由100条ISSR引子申筛选出12条可产生多型性条带明显的引子．这些引子共可产生67个的多型性条带。依据每一种原之分子标志数据进行UPGMA法分群分析结果。可将台湾133个茶树种原区分成六大群，包括油茶群、赤芽山茶群、野生茶树群、大叶变种与小叶变种混合群、大叶、小叶及大叶、小叶杂交种混合群及小叶变种群。而主成分向量分析的结果与利用群聚分析得到的亲缘关系树形固结果相符合。台湾茶树种原高比例的遗传歧异度是由台湾的野生茶树所贡献．部分重要栽培种间的相似性仍极高。为了探讨制茶过程封分子级品种鉴定之影响及DNA分子标志应用于咸茶品种鉴定之可行性，本研究分析不同发酵程度的茶类。在制茶过程申封DNA质量之影响。试验结果显示高温杀菁过程严重造成咸茶DNA的降解。利用各种类别咸茶与新鲜茶叶（封照）所抽取之DNA样品进行PCR扩增反应．结果发现分子量小于1,000bp的ISSR DNA条带表现较稳定。     

Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond,and its relationships with agronomic traits

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.     

黄秋葵种质资源遗传多样性及相关性分析

为有效地利用黄秋葵种质资源,给新品种选育提供理论依据,以60份黄秋葵种质资源为试验材料,对31个植物学特征和生物学特性指标进行了遗传多样性分析和相关性分析。结果表明:(1)黄秋葵植物学特征间存在明显相关性,茎色、茎表面、叶色、果色呈同一对应关系。叶姿越直立的,其叶型多为浅裂叶或全叶,花冠中等偏小,种子形状多是圆形;反之,叶姿下垂的,叶型多为深裂叶,花冠较大,种子多为扁圆形、肾形。(2)黄秋葵的生物学特性多样性丰富,存在广泛变异,其变异系数排序为:种子产量(72.51%)果数(43.84%)叶柄长(40.84%)果长(36.95%)第1朵花开花天数(28.22%)叶片长度(22.69%)叶片宽度(21.28%)分枝数(21.05%)株高(20.99%)开花天数(18.14%)出苗天数(16.96%)生育天数(8.97%)花瓣数(2.57%)。(3)黄秋葵生物学特性间存在明显相关性,黄秋葵种子产量与叶柄长度、果数、叶片长度、叶片宽度、开花天数达极显著正相关,相关系数分别为0.53、0.49、0.46、0.39、0.37。开展黄秋葵种质遗传多样性的研究对黄秋葵种质的鉴定、评价及利用有着重要的意义。     

Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP,ISSR and SSR markers

Molecular markers provide novel tools to differentiate between the various grades of Basmati rice, maintain fair-trade practices and to determine its relationship with other rice groups in Oryza sativa. We have evaluated the genetic diversity and patterns of relationships among the 18 rice genotypes representative of the traditional Basmati, cross-bred Basmati and non-Basmati (indica and japonica) rice varieties using AFLP, ISSR and SSR markers. All the three marker systems generated higher levels of polymorphism and could distinguish between all the 18 rice cultivars. The minimum number of assay-units per system needed to distinguish between all the cultivars was one for AFLP, two for ISSR and five for SSR. A total of 171 (110 polymorphic), 240 (188 polymorphic) and 160 (159 polymorphic) bands were detected using five primer combinations of AFLP, 25 UBC ISSR primers and 30 well distributed, mapped SSR markers, respectively. The salient features of AFLP, ISSR and SSR marker data analyzed using clustering algorithms, principal component analysis, Mantel test and AMOVA analysis are as given below: (i) the two traditional Basmati rice varieties were genetically distinct from indica and japonica rice varieties and invariably formed a separate cluster, (ii) the six Basmati varieties developed from various indica × Basmati rice crosses and backcrosses were grouped variably depending upon the marker system employed; CSR30 and Super being more closer to traditional Basmati followed by HKR228, Kasturi, Pusa Basmati 1 and Sabarmati, (iii) AFLP, ISSR and SSR marker data-sets showed moderate levels of positive correlation (Mantel test, r = 0.42–0.50), and (iv) the partitioning of the variance among and within rice groups (traditional Basmati, cross-bred Basmati, indica and japonica) using AMOVA showed greater variation among than within groups using SSR data-set, while reverse was true for both ISSR and AFLP data-sets. The study emphasizes the need for using a combination of different marker systems for a comprehensive genetic analysis of Basmati rice germplasm. The high-level polymorphism generated by SSR, ISSR and AFLP assays described in this study shall provide novel markers to differentiate between traditional Basmati rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.The first two authors have equal contribution