Genetic relationships of gladiolus cultivars inferred from fluorescence based AFLP markers

Gladiolus is one of the important commercial flowers with a large number of cultivars. However, genetic relationships among its genotypes have not been reported. This study analyzed genetic relatedness of 54 gladiolus cultivars using amplified fragment length polymorphism (AFLP) markers. A total of 24 AFLP primer pairs with three samples were initially screened, from which 9 primer sets that showed clear scorable and highly polymorphic bands were selected for AFLP reactions. Fluorescence-labeled amplification products were subjected to electrophoresis and then analyzed using an automated sequencer. A dendrogram was constructed by the unweighted pair group method using the arithmetic average (UPGMA). The number of AFLP fragments generated per primer set ranged from 10 to 151 with fragment sizes varying from 50 to 450 bp. A total of 660 AFLP fragments were detected, of which 658 (99.70%) were polymorphic. All the primers except E-AGG/M-CTA displayed 100% polymorphism. All cultivars were clearly differentiated by their AFLP profiles. The AFLP data were compared with previously obtained RAPD data and combined to generate a common dendrogram. The first cluster was dominated with indigenously bred cultivars while the second was dominated with exotic cultivars. This shows that most of the exotic cultivars as well as indigenous cultivars are closely related with each other. However, two indigenous cultivars viz., Pusa Suhagin and Pusa Archana share genetic similarity with exotic cultivars. Among the genotypes selected for the investigation, Pusa Gunjan was identified as the most distinct genotype. The AFLP markers developed will help future Gladiolus cultivar identification, germplasm conservation and new cultivar development. The assessed genetic relationships among gladiolus cultivars may enhance the efficiency of breeding program by selecting desirable parents with reduced breeding cycle.     

Assessment of genetic relationships among 29 introduced and 49 local sweet cherry accessions in Turkey using AFLP and SSR markers

Summary

The characterisation of sweet cherry (Prunus avium L.) genetic resources in Turkey may help to increase their use in breeding programmes worldwide, as Turkey is the centre of origin of sweet cherry. Amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers were therefore used to analyse genetic diversity among a total of 78 local and introduced sweet cherry cultivars. Four AFLP primer combinations, and six SSR primer pairs for sweet cherry were used for genetic diversity analysis. A genetic similarity matrix was calculated using the combined data from AFLP and SSR analyses with simple matching coefficient. Genetic similarities among the sweet cherry genotypes studied were higher than 42%. No two accessions had an identical AFLP and SSR marker profile, indicating that all 78 genotypes were unique. An UPGMA dendrogram, based on the similarity matrix, revealed 18 separate Groups at or above the 70% similarity level. While some Groups consisted of both introduced and local genotypes, other Groups had only local genotypes. This result suggests that there was broad genetic diversity among the local Turkish sweet cherry genotypes, which was not present in the introduced sweet cherry accessions. The genetic variation present in local Turkish sweet cherry genotypes may be useful for future breeding programmes. We found that the use of both SSR and AFLP marker systems was effective for distinguishing between genetically-close sweet cherry genotypes. These marker systems can be used to complement pomological and morphological markers during the characterisation and identification of sweet cherry genotypes.     

Germplasm diversity and genetic relationships among walnut (Juglans regia L.) cultivars and Greek local selections revealed by Inter-Simple Sequence Repeat (ISSR) markers

Inter-Simple Sequence Repeat (ISSR) markers were used for the assessment of genetic diversity among walnut (Juglans regia L.) selections from Greek native populations in comparison to internationally cultivated walnut genotypes. Similarity coefficient values from 0.13 to 0.93 (with an average of 0.48) were found among the 56 accessions examined, which indicated the presence of a high degree of genetic variability. Most international cultivars were grouped together while most Greek native populations could not be placed into a distinct group. The Greek native population genotypes were found more diverse than the international cultivars. The mean similarity coefficient values for the former and latter were 0.44 and 0.56, respectively. In the cultivar group, two subgroups were distinguished; one consisted of genotypes involving ‘Payne’ and the other ‘Franquette’ in their pedigrees. Some cultivars and populations could not be grouped according to their pedigrees or collection area. Analysis of molecular variance (AMOVA) revealed that a larger part of the genetic variation exists among Greek walnut populations within a collection region (89%) than among the regions (11%). The pairwise regional PhiPT values indicated that the most geographically distant regions are the most genetically differentiated. The high variability existing in the Greek germplasm in combination with their valuable agro-morphological traits suggested that it would be beneficial to utilize this native germplasm pool in walnut breeding programs and germplasm management activities to maximize genetic diversity in cultivated walnut.     

广东果梅种质资源遗传多样性的AFLP分析

为了从DNA分子水平上探讨广东境内果梅种质资源遗传多样性状况,利用荧光标记AFLP技术,对采自广东境内的57份果梅种质进行研究,筛选出适于果梅AFLP分析的8对Mse Ⅰ和EcoR Ⅰ引物组合,这些引物可以将供试材料完全分开.利用8对引物组合对57份果梅种质进行总基因组DNA水平上的多态性检测,得到了清晰的多态性指纹图...     

Assessment of genetic diversity among mango (Mangifera indica L.) genotypes using RAPD markers

Knowledge about the extent of genetic diversity/relatedness in mango germplasm is vital for developing coherent strategies for future gains in productivity. The genetic diversity/relatedness among mango cultivars/genotypes developed in Pakistan has not been investigated previously. We have assessed the genetic diversity among 25 mango genotypes/cultivars using randomly amplified polymorphic DNA (RAPD). Sixty random ten-mer primers were surveyed, out of which 45 yielded amplicons in all the genotypes. Genetic similarity between genotypes/cultivars was in the range of 64–89% with an average of 74%. Similarly, the genetic relatedness among all variants derived from a mango cultivar Chaunsa was in the range of 81.18–88.63%. These coefficients were utilized to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA). The genotypes were grouped into three (A, B, C) clusters. Generally, genotypes originating from Pakistan were grouped in cluster ‘A’ while cluster ‘B’ primarily composed of southern India as well as Florida cultivars. Kensington Pride was the most distantly related genotype which grouped with Maya and Yakta, forming a distinct cluster ‘C’.     

不同需冷量桃品种营养生长和光合特性研究

为了探明温带地区低需冷量桃早期丰产性的生理机制,以不同需冷量桃植株为试材,对其在郑州地区下半年生长季节的光合特性进行了研究。结果表明,在相同的生长期,低需冷量桃表现出较中、长需冷量种质更高的营养产物积累。分析其营养生长的影响因子认为,光合叶面积与植株营养生长相关性不明显,单叶净光合日总量才是低需冷量种质营养旺盛积累的主要原因,而单叶净光合日总量是植株较低的暗呼吸速率、光补偿点和较高的10:00光合速率、水分利用效率的综合表现。低需冷量桃在温带地区的这些光合特性可能是由它固有的遗传基础和植株对温带地区环境调节共同作用的结果。     

Genetic divergence in seedling trees of Persian walnut (Juglans regia L.) for various metric nut and kernel characters in Himachal Pradesh

The nature and magnitude of genetic divergence was assessed using non-hierarchical Euclidean cluster analysis in 229 seedling trees of Persian walnut growing naturally in four districts of Himachal Pradesh for 15 nut and kernel characters. Minimum and maximum values of coefficients of variability were recorded for nut width and kernel weight, respectively. All genotypes were grouped into 16 different clusters. The clustering pattern of walnut genotypes belonging to the same location revealed their distribution in more than one cluster showing non-parallelism between geographic and genetic diversity. Genotypes of clusters 5 and 8 were highly diverse from each other. Mean nut weight and kernel weight were highest in clusters 8 and 14, respectively. The highest mean kernel percentage and minimum shell thickness were observed in cluster 13. The highest mean value for fat was recorded in cluster 9 whereas cluster 3 had the maximum value of protein.     

Genetic diversity in ecotypes of Tunisian date-palm (Phoenix dactylifera L.) assessed by AFLP markers

Summary

Amplified fragment length polymorphisms (AFLP) were used successfully to survey genetic diversity in 40 ecotypes of date-palm (Phoenix dactylifera L.) collected from oases in Tunisia. Six primer pairs were screened to assess their ability to detect polymorphism in this tree crop. As a result, a total of 428 AFLPs have been generated and used to estimate genetic distances which ranged from 0.07 – 0.63. A large, and typically continuous, range of genetic diversity characterises Tunisian date-palm germplasm. In addition, the UPGMA dendrogram derived from these data exhibited two clusterings of ecotypes independent of their geographic origin or the sex of the trees. These data corroborate the hypothesis of the origin of date-palm domestication being in Mesopotamia. Moreover, taking into account the high percentage of polymorphic bands, together with their resolving power (Rp), all the primer pairs tested contributed to the discrimination of date-palm genotypes, suggesting that the AFLP method is efficient in assessing genetic diversity in this crop. The data are discussed in relation to the use of AFLP molecular markers in the management and improvement of date-palm.     

Analysis of genetic diversity among some Persian walnut genotypes (Juglans regia L.) using morphological traits and SSRs markers

There is a high diversity among cultivated walnut trees in Iran due to its long time of seed propagation and vast area of cultivation. In this study some morphological characters as well as Simple Sequence Repeat (SSRs) markers were used to analyze the genetic diversity and relationships among 31 Iranian walnut genotypes along with four foreign cultivars. The nut weight ranged from 7.52 to 17.73 g, kernel weight from 4.00 to 9.83 g, and kernel percentage ratio from 38.78 to 67.05% among studied genotypes. In SSRs analysis, nine primer pairs were tested that produced 39 alleles ranging from 2 to 8, with a mean value of 5.10 allele per primer. The Iranian genotypes showed relatively high diversity both for their SSRs loci and morphological traits. Although the foreign cultivars (‘Serr’, ‘Vina’, ‘Franquette’ and ‘Lara’) clustered with each other, they also laid close and within the Iranian genotype. The results of the study provided us with valuable diversity among our genotypes which could be used for breeding studies and also showed the power of genetic markers for analysis and evaluation of this diversity.     

Fingerprinting of three typical macrosperma Italian lentil (Lens culinaris Medik.) landraces using fluorescence-based AFLP markers

Italian lentil landraces are principally cultivated for self or local consumption. Most of them are disappearing, particularly macrosperma types by being less required by the market. A pre-requisite for the conservation and the efficient use of genetic resources is the better understanding of the extent and the distribution of the existing genetic variation, useful for future breeding programmes. Our study was undertaken to analyse and quantify the genetic diversity within and among three macrosperma Italian lentil landraces (Onano, Altamura and Villalba), using fluorescent AFLP markers. AFLP markers generated information to differentiate among closely related genotypes and group within the same cluster individuals belonging to the same landrace. The total genetic diversity (H_T), the genetic diversity within population (H_S) and the extent of differentiation between populations (D_ST) were 0.198, 0.155 and 0.043, respectively. The fixation index (G_ST = 0.219) showed that about 78% of the observed total genetic variation can be attributed to within population differences and around 22% is due to differences among populations. The gene flow estimate (N_m = 1.774) and the mean genetic distance value (0.077) suggested narrow genetic base among the analysed populations, confirming the tendency of Italian lentil landraces to group together. The present study showed that fluorescence-based AFLP technique is a biotechnological tool that can provide significant insights for research in genetic diversity of lentil landraces and their subsequent conservation and utilization in breeding programs.     

云南芋种质资源遗传多样性的AFLP分析

 采用荧光标记引物的AFLP分子标记技术, 用筛选出的“3 + 2”引物组合, 对48份云南芋种进行遗传多样性分析, 3对引物共扩增出184个DNA位点, 平均每对引物可检测出56.3个多态性位点,多态性位点高达91.8% , 云南芋种质资源在DNA分子水平上表现出极为丰富的遗传多样性。聚类分析表明: 野生种质和栽培种质的亲缘关系较远, 栽培种质基于AFLP标记的分类结果与形态性状基本一致, 少数材料差异较大。     

Identification of parental species of the Alstroemeria cv. ‘Jubilee’ using AFLP marker technique

Twelve Alstroemeria species, two hybrids, one cv. ‘Jubilee’, an anther-cultured plant from cultivar ‘Jubilee,’ and Bomarea salsilla and Leontochir ovallei (the latter two were chosen as outgroup) were evaluated using the AFLP marker technique in order to identify putative parental genotypes of the Alstroemeria cv. ‘Jubilee’ and of known interspecific hybrids, and to estimate their genetic relationships within the genus Alstroemeria. A total of 297 AFLP markers were scored by using the primer combination (E + ACCA/M + CTAG). In order to discriminate all Alstroemeria genotypes, cluster analysis (UPGMA) and principal coordinates analysis were performed. The Alstroemeria cv. ‘Jubilee’, of which the parents are unknown, had genetic distance (GD) 0.54 from Alstroemeria exserens, GD 0.57 from Alstroemeria garaventae, GD 0.62 from Alstroemeria gayana, and GD 0.66 from Alstroemeria hookeri cumminghiana. Thus, these four species are considered as putative parental genotypes. An interspecific hybrid (Alstroemeria aurea × Alstroemeria inodora), showed the smallest genetic distance from A. aurea (GD 0.56) and A. inodora (GD 0.45). The Alstroemeria ligtu group was distantly allocated from other Chilean species. We conclude that the AFLP marker technique appears to be a satisfactory tool for identifying the parental genotypes of interspecific hybrids in Alstroemeria.     

利用AFLP标记辅助甘蓝显性雄性不育高代回交系选择

 以甘蓝显性雄性不育系DGMS79-399-3与优良品系02-12回交自交系为材料, 利用远红外荧光标记AFLP技术及Li-cor基因测序仪对回交自交系不同基因型(MsMs、Msms和msms) 材料进行AFLP连锁标记快速筛选, 从512对引物组合中筛选出17个差异标记。利用这些差异标记在02-12回交8代群体中进行检测, 其中11个为与显性核不育基因相连锁的AFLP标记, 覆盖21 cM; 另外6个标记为与显性核不育基因不连锁的遗传滞留连锁群, 跨越9 cM。通过分析选择了其中3个单株为理想的雄性不育株, 可用于进一步回交。     

Using bulked AFLP analysis to assess genetic diversity in Echinacea species

Echinacea is an allogamous genus, thus its cultivars or populations are genetically heterogeneous. Using amplified fragment length polymorphism (AFLP) to estimate the genetic diversity of Echinacea is generally limited by the large number of individual plants and the higher cost that need to be processed. In the present study, effectiveness of several sizes of DNA bulking (10, 15, 20, 25 and 30 individuals) with 20, 36 and 55 primer pairs was compared using AFLP in determining the genetic diversity of Echinacea species. The results indicated that the use of bulked DNA-based AFLP analysis by using the selected eight primer pairs was capable of detecting genetic diversity between the tested Echinacea species, provided that the potential presence of low frequency variants was ignored and a possible bias in the estimates of genetic similarity was accepted. The assessments showed that a bulk of 15 individuals could detect sufficient AFLP variations at most genomic sites. Additionally, 20 primer pairs could generate sufficient polymorphic fragments to achieve high resolving power of AFLP for the tested Echinacea species.     

红肉猕猴桃种质资源果实性状及AFLP 遗传多样性分析

 对中国红肉猕猴桃种质资源进行收集和调查,并对其进行果实性状变异分析和AFLP 遗传多 样性及遗传关系分析。结果表明,红肉猕猴桃野生资源主要分布于湖南省、湖北省、河南省、江西省、 四川省和陕西省等地,共采集到52 份野生资源和2 份品种资源（包括软枣猕猴桃红肉类型、中华猕猴桃 红肉类型和美味猕猴桃红肉类型）。红肉猕猴桃种质资源在果实性状和DNA 分子水平上都存在丰富的变 异和较高的遗传多样性水平,4 对AFLP 引物共扩增出259 个多态性位点,多态性位点百分率为90.56%, Nei’s 基因多样性和Shannon’s 信息指数分别为0.318 和0.477;资源间遗传相似性系数介于0.568 ~ 0.883 之间,平均为0.714。聚类分析和主坐标分析将54 份资源划分为4 个组,软枣猕猴桃红肉类型单独聚为 一类;中华猕猴桃和美味猕猴桃红肉类型亲缘关系较近且有按地理来源优先聚类的趋势。果实性状数据 和AFLP 数据之间具有极显著的相关性,二者可结合用于红肉猕猴桃资源评价和保护利用工作中。     

AFLP and SSR marker analysis of grape rootstocks in Indian grape germplasm

Twenty-one rootstock accessions were analyzed with seven grape microsatellite (SSR) primers and seven AFLP primer combinations. SSR primers detected 56 alleles across 21 genotypes and primer heterozygosity varied from 0.617 to 0.856. Similarly 252 AFLP bands were obtained with seven primer pairs. The average similarity index for different rootstocks was relatively low and ranged from 0.068 to 0.36 for AFLP data and from 0.13 to 0.36 for SSR data. A combination of three SSR primers was sufficient to distinguish 21 rootstocks. In cluster analysis majority of rootstocks belonging to same species grouped together. Although the dendrograms obtained with two marker systems were not identical, rootstocks belonging to same species or having common parents were grouped together in both the dendrograms.     

SRAP标记在五十份新疆人工栽培核桃种质资源的鉴定与应用

以新疆核桃主栽区收集的50份核桃种质资源为试材,采用序列相关扩增多态性(sequence-related amplified polymorphism,SRAP)标记技术分析其遗传多样性,以期为分布于新疆地区的核桃种质资源的保存、鉴定及综合开发利用提供参考依据。结果表明:从100对引物中筛选出16对扩增条带清晰、稳定性好的多态性SRAP引物组合,16对引物组合在50份供试种质中共扩增出178条带,多态性条带135条,多态位点百分率为75.84%。聚类分析及聚类锐度测试显示供试种质可分为10类,热图显示出不同引物对种质的区分情况,多元回归树显示不同引物中的26个扩增条带能够区分50份供试种质,其中M4/E4、M7/E5、M14/E4、M2/E11、M3/E4、M2/E4、M12/E13、M7/E1、M14/E13和M1/E3共10对引物组合是供试种质鉴定中重要的引物组合。同时R语言在统计分析中的应用,为今后核桃植物形态与遗传变异研究提供了新的数据分析方法。     

Amplified fragment length polymorphism (AFLP) markers for fingerprinting of Argyranthemum frutescens cultivars

Argyranthemum frutescens is a commercially important ornamental species with extensive breeding programmes in several countries. Since it is vegetatively propagated there is a great need for tools for identification of cultivars. Vegetatively propagated species require clean-up from diseases, often performed through meristem-tip cultures. Forty-three cultivars of A. frutescens propagated by meristem-tip culture and traditional cuttings were analyzed for genetic relatedness and possible somaclonal variation using AFLP. Five primer combinations resulted in a relatively high degree of polymorphism. Ten molecular markers generated by one primer combination could distinguish between all 43 cultivars. Differences in fingerprints between meristem-tip culture and cuttings from the same cultivars were found, but the proportion of fragments being specific for either tissue culture or cuttings was relatively low. Some cultivars that did not display somaclonal variation as judged by the AFLP-fingerprints may still be genetically unstable since some morphological variation was observed in the true to type test.