Genetic divergence among inbred lines in Cucurbita moschata from China

Knowledge of genetic divergence among inbred lines is essential for cross breeding. The objectives of this study were to (1) analyze the level and character of genetic diversity in C. moschata accessions, and (2) classify the genetic divergence among inbred lines in C. moschata to assist in selection of parent genotypes for genetic improvement. Twenty agronomic characters were investigated and rich diversities were demonstrated among 39 inbred lines of C. moschata from China. Various degree correlations among these characters made it possible to summarize the diversities of the twenty characters into 3 major principal components: leaf, fruit and flesh quality factor. Forty-one inbred lines of pumpkin were clustered into four groups based on principal component data, which is more distinct for classification that based on the original data of the 20 characters. However, parent inbred lines whose hybrids displayed significant heterosis in fruit weight, soluble solid and fruit shape were located in different clusters or sub-clusters based on standardized original data. It was suggested that genotypes in the same clusters may represent members of one heterotic group.     

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。     

Assessment of genetic diversity in common bean (Phaseolus vulgaris L.) germplasm using amplified fragment length polymorphism (AFLP)

AFLP technique was applied to assess genetic diversity among 44 common bean accessions that included 6 exotic accessions, 15 Indian land races and 23 released varieties. Eight AFLP primer pairs were used that produced 820 products of which 698 were polymorphic (85.12%). Wide variations were observed among all the accessions for the number of amplification products, percent polymorphism and average polymorphism information content (PIC). The Jaccard's similarity indices (J) based on the AFLP profiles were subjected to UPGMA cluster analysis. The dendrogram generated revealed seven major groups. Seventeen out of 23 released varieties were restricted to clusters VI and VII. The value of r = 0.934 in Mantel's test for cophenetic corrlelation applied to the cluster analysis indicated the high fitness of the accessions to a group. The germplasm used in the present study had narrow genetic base, although moderate to high genetic diversity was observed. The details of diversity analysis and the potential use of Indian common bean accessions in common bean breeding programme are provided in the present study.     

Genetic diversity of Dimocarpus longan in China revealed by AFLP markers and partial rbcL gene sequences

Amplified fragment length polymorphism (AFLP) and partial rbcL gene sequencing were used to investigate genetic diversity among various longan (Dimocarpus longan Lour) accessions as well as a presumed closely related species Dimocarpus confinis How et Ho and litchi (Litchi chinensis Sonn). No significantly shared AFLP fragment was found between the three species, indicating that D. confinis and litchi are very far in genetic distance from any longan accession studied. Partial rbcL sequences of 501 bp from the first coding site in these species were obtained, which revealed several substitutes. One such DNA base pair substitute resulted in an amino acid difference between longan and litchi. Furthermore, another 4 bp resulted in a two amino acid difference between longan and D. confinis, which was consistent with AFLP results and indicated that D. confinis should be excluded from the longan genus, Dimocarpus. Within the longan species, no DNA substitute was found. Using nine primer combinations, a total of 66 AFLP markers were obtained from 41 longan accessions. One non-Chinese longan accession ‘Miaoqiao’ was distinctly different from all other longan cultivars collected in China, indicating that more genetic resources of longan might be collected also from longan production regions outside of China. AFLP markers might be developed to identify longan cultivars as well as expedite progeny screening in breeding programs of this perennial fruit tree.     

野生毛花猕猴桃果实表型性状及SSR遗传多样性分析

以江西省武功山境内的70份野生毛花猕猴桃种质资源为试材,对其果实表型性状、SSR遗传多样性及其亲缘关系进行分析和评价。根据UPOV（国际植物新品种保护联盟）公布的猕猴桃属品种测定标准对供试材料的果实表型性状进行观测。参照猕猴桃遗传连锁图谱,选用分布于中华猕猴桃基因组中的70对SSR引物对供试材料进行多态性分析。结果表明,在70对引物中,21对引物成功扩增出多态性片段。随机采集的70份野生毛花猕猴桃种质资源中,其果实表型性状和DNA分子水平均存在丰富的遗传多样性。基于UPGMA聚类分析将供试的野生毛花猕猴桃资源分为果实圆形和椭圆形混合组、果实椭圆形组以及果实圆柱形组。21对多态性高的SSR引物共检测出127个等位变异位点,变异范围在2 ~ 12之间,平均每对SSR引物可检测到6.04个等位位点。遗传相似系数（GS）变异范围为0.5306 ~ 0.9252。GS值在0.65水平上UPGMA聚类分析可将供试的野生毛花猕猴桃种质资源划分成Ⅰ、Ⅱ和 Ⅲ 共3个组,这与果实表型性状分析的结果基本一致。这些遗传变异丰富的种质资源可为猕猴桃育种提供有价值的材料。     

Genetic diversity in Indian ash gourd (Benincasa hispida) accessions as revealed by quantitative traits and RAPD markers

In present study, an attempt has been made to assess the genetic diversity among 34 accessions of Benincasa hispida using quantitative traits and RAPD data. Variability was observed for characters like days to first female flower, fruit weight, equatorial and polar diameter. Cluster analysis based on quantitative traits revealed a high degree of diversity among the accessions. RAPD-based dendrogram showed dissimilarity values 0.64–0.943 suggesting that the accessions represent a genetically diverse population. A non-significant correlation was observed between the clustering based on quantitative traits and RAPD markers. But the accessions like IVAG-107 and IVAG-81 clearly separated from rest of the accessions based on the quantitative traits and as well as RAPD primers. Both the dendrogram revealed that the accessions from northeastern region of India are diverse from the accessions of other parts of India, as they cluster together in both the dendrogram. The information generated could be utilized in developing cultivars/hybrids for specific traits.     

黄瓜种质资源遗传多样性及其亲缘关系的AFLP分析

 采用AFLP分子标记技术，对中国黄瓜种质资源遗传多样性及其与外来种质的关系进行了分析， 结果表明8对AFLP引物在70份黄瓜种质中共扩增出425条带，多态性带的比例为66％。供试黄瓜种质的平 均期望杂合度为0．376，中国种质的平均期望杂合度为0．387，明显高于国外种质的n 291。西双版纳黄瓜和印度野生黄瓜具有一些栽培种质没有的特异位点，中国栽培种质的特异位点多于外来栽培种质，后者也有一些中国栽培种质没有的特异位点。聚类分析将70份种质分为三大组群，即西双版纳黄瓜(Cucumis sativus L.vaF．xishuangbannanesis Qi et Yuan)组群，e sativus var．hardwickii野生黄瓜组群和栽培黄瓜组群。西双版纳黄瓜与栽培黄瓜的距离最远，与野生黄瓜次之。按一定的遗传距离可以将中国和外来栽培种质分开。大多数 华南型和华北型种质归属于不同的亚组。这些结果有助于有目的地利用这些变异拓宽育种材料的遗传背景。     

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.     

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.     

Genetic diversity and population genetic structure of pomegranate (Punica granatum L.) in Iran using AFLP markers

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits. It is native to Iran and spread from Iran to other areas. In this study amplified fragment length polymorphism (AFLP) was used to detect intra- and inter-population genetic diversity of pomegranate. A group of 67 accessions belonged to 4 populations from Iran was studied using eight primer combinations. A total of 221 scorable bands were amplified, of which, 118 (54.13%) were polymorphic. Resolving power (Rp) ranged from 5.70 to 9.21, and the average of polymorphism information content (PIC) per primer pair was 0.40. According to Nei's gene diversity and allelic statistics, Isfahan population had a highest genetic diversity (H = 0.3646, I = 0.5327, N_e = 1.6467). Coefficient of gene differentiation between populations (GST) was 0.124, indicated that mainly proportion of genetic variation (87.6%), was within populations and the remaining (12.4%) of the variation was among populations that, also supported by analysis of molecular variance (AMOVA). The gene flow (Nm) varied from 0.969 to 10.404 between pair-wise populations and was 3.504 among all of the populations. The Jaccard similarity coefficient between individuals ranged from 0.26 to 0.88. The UPGMA dendrogram clustered all 67 accessions into 6 groups. In some cases accessions from same region were grouped together but in most cases, there was gene exchange. To study the genetic relationships among populations, a principal coordinate analysis (PCoA) based on Nei's genetic distances was performed. Results of this study showed that AFLP marker can be a useful tool for investigating the genetic diversity of pomegranate genotypes.     

Association analysis of fruit traits in mulberry species (Morus L.)

Improvement of fruit traits is an important objective in current mulberry breeding programs. In this study, 93 mulberry accessions of diverse origin were genotyped using 15 ISSR markers to identify marker–trait associations with fruit traits. Fifteen ISSR primers generated a total of 104 amplification products, of which 94 were polymorphic, revealing 90.38% polymorphism; the mean PIC value was 0.2698. UPGMA cluster analysis showed clear genetic relationships between the 93 mulberry cultivars, and the major clusters were related to known pedigree relationships and their ecotype. The mean r² value for all intra-chromosomal loci pairs was 0.0210. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 24 marker–trait associations (p < 0.01) were identified using different ISSR markers. The results suggest that association mapping in mulberry is a viable alternative to quantitative trait loci mapping, and detection of associations between markers and mulberry fruit traits will also provide important information for marker-assisted breeding.     

Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers

Eighty-one accessions representing apricot germplasm in Tunisia were collected from different areas of cultivation and fingerprinted using amplified fragment length polymorphism (AFLP) and microsatellites (SSR) markers. A total of 339 polymorphic markers were revealed using 5 AFLP primers combinations and 24 SSR loci. AFLP and SSR markers expressed a high level of polymorphism allowing the distinction of the accessions with an efficiency coefficient of discrimination of 100% for AFLP and 97% for SSR markers. Genetic diversity structure was assessed with AFLPs and SSRs markers separately then with combined matrix data by the help of hierarchical clustering elaborated using Wards method based on Nei and Li (1979) distances. Comparison of the obtained dendrograms revealed a phylogeographic structure into two major groups with significant conservation between the observed subgroups in relation with the geographic origin of the accessions. The relative efficiency of the markers in determining the genetic relationships among apricot accessions has been assessed and a combination of AFLPs and SSRs markers was the most effective. In addition, Mantel test based on genetic distances indicated highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with Pearson correlation values of r = 0.873 and r = 0.692, respectively, revealing the higher efficiency of the combination of both molecular techniques (AFLP and SSR) to estimate the levels of genetic variability among apricot germplasm.     

Genetic variability in wild vs. cultivated Eruca vesicaria populations as assessed by morphological,agronomical and molecular analyses

In this study, the genetic diversity of 50 individuals of rocket, Eruca vesicaria, from five accessions, four of them wild type collected from different parts of Spain and one commercial, were evaluated using morphological, agronomical and inter simple sequence repeat DNA (ISSR) data. Molecular analysis was carried out using the ISSR technique with 20 primers. Out of these 20 primers, nine were polymorphic, producing a total of 395 DNA bands, 247 of which were polymorphic among the accessions. A dendrogram drawn on the basis of a similarity matrix using the UPGMA algorithm revealed that the 50 samples of rocket plants could be classified into three major clusters at a Nei's genetic distance of 0.36. The experiment shows that molecular markers such as ISSR are a good instrument for distinguishing and selecting rocket accessions to group different wild populations. In general, a high variation was observed for most of the 16 morphological and 6 agronomical traits showing significant differences. Some morphological traits such as leaf length, petiole length and lamina width explained 69.1% of the whole variation observed in the populations, and some agronomical traits such as leaf area, nitrate and chlorophyll contents accounted for 65.7%, but the clusters generated by means of agronomical and morphological variables were less evident than when ISSR markers used. Some accessions showed good qualities, such as small leaves, high chlorophyll content, late-flowering or low nitrate content. All these parameters, together with the high degree of genetic homogeneity found, could make the local accessions good candidates for a future breeding programme.     

Assessing Rosa persica genetic diversity using amplified fragment length polymorphisms analysis

The genetic diversity among 128 Iranian Rosa persica (R. persica) accessions in the different populations was analyzed. Amplified fragment length polymorphisms (AFLP) technique was used to produce 171 polymorphic fragments. The number of polymorphic loci ranged from 101 to 147 and the polymorphism information content (PIC) varied from 0.289 to 0.073, with an average of 0.16. This shows extreme variability and genetic diversity among the studied R. persica populations. An indirect estimate of the number of migrants per generation (Nm = 0.376) indicated that gene flow was relatively low among populations of the species. Cluster analysis using the UPGMA method grouped all accessions into six clusters. The results did not show relative agreement with the genotypes’ region of origin. Based on an analysis of molecular variance, 48% of the genetic variation of R. persica was within population and 52% was among populations. The present analysis revealed that Iranian R. persica genotypes are highly variable and genetically distinct from their origins. The apparent unique nature of the R. persica genotypes revealed by our results supports the case for the implementation of more intense characterization and conservation strategies, and provides useful information to address breeding programmes and germplasm resource management in Rosa spp.     

ISSR polymorphism in Indian wild orange (Citrus indica Tanaka,Rutaceae) and related wild species in North-east India

Inter simple sequence repeats (ISSR) polymorphism in Citrus indica Tanaka (Rutaceae), an endemic and threatened wild species, was examined along with three other closely related wild taxa (C. medica L., C. latipes (Swingle) Tanaka, and C. sp. ‘Memang athur’) by analyzing 53 representative accessions sampled from North-east India. Jaccard's similarity values among 53 accessions of Citrus ranged from 0.46 to 0.97 (average = 0.75). Genetic similarity values among all the 34 accessions of C. indica were found in the range of 0.82 to 0.97 with an average of 0.90. Heterozygosity (Ht = 0.123) and Shannon's information index (I = 0.188) values estimated for C. indica revealed significantly low level of genetic variation within the species. UPGMA dendrogram grouped all 53 accessions of Citrus into four major clusters: Cluster I – C. latipes; Cluster II – C. medica; Cluster III – ‘Memang athur’ and Cluster IV – C. indica. The dendrogram placed all the 34 accessions of C. indica in five sub-clusters under Cluster IV. The placement of C. indica accessions in various sub-clusters and groups in the dendrogram was based on molecular differentiation of individual accessions rather than their geographical origin. Very low genetic diversity and destruction of its natural habitat pose serious threat to C. indica even in the Citrus Gene Sanctuary in Nokrek Biosphere Reserve (NBR) in Meghalaya. Low genetic variability, heterozygosity and Shannon's information index in C. medica, C. latipes and ‘Memang athur’ are also concerns that need to be addressed for developing appropriate strategies to conserve the genetic diversity extant in these valuable genetic resources.     

Genetic characterization of asparagus doubled haploids collection and wild relatives

The genus Asparagus is very large consisting of around 150 species found as herbaceous perennials, tender woody shrubs and vines. The cultivated species (Asparagus officinalis L., diploid) is a highly prized vegetable, grown in different environments ranging from cool temperate zones to deserts, Mediterranean climates and tropical areas. As a consequence, Asparagus breeders have developed different cultivars that differ for their morpho-agronomic traits, habit and ploidic status (few triploid and tetraploid cultivars are used). Several breeding methods are used for developing cultivars, among which a well developed in vitro anther culture technique produces homozygous clones useful for F₁ hybrids constitution. A fluorescent based AFLP (amplified fragment length polymorphism) technique were applied with the aim to assess genetic diversity among a collection of 173 doubled haploid (DH) androgenetic clones, five Asparagus wild species and interspecific hybrids obtained among the cultivated species and two wild relatives. The average number of AFLP fragments generated per primer set was 105, varying in size from 50 to 550 bp. A total of 1054 AFLP fragments were detected, 20% of which were polymorphic. Genetic similarity based on DNA polymorphisms, showed that a few number of AFLP primer combinations are able to distinguish the cultivated DH clones from the wild species. Indeed, from one DH clone for each anther donors and the wild species were used to construct a dendrogram using Dice's coefficient and the unweighted pair group method with the arithmetic mean (UPGMA). Genetic distances among all DH clones were calculated using the C.S. Chord distance; and a neighbour-joining (NJ) consensus tree was constructed in order to support the breeder for parental genotype choice for asparagus hybrid constitution.     

萱草部分野生种和栽培品种亲缘关系的AFLP分析

 借助AFLP标记对35份萱草野生种和栽培品种进行亲缘关系研究, 结果表明, 7对引物组合对萱草共扩增出条带380条, 其中多态性条带357条, 平均多态性达到93.39% , 单对引物扩增条带19～85条, 平均每对引物组合扩增多态性条带51条。7对引物扩增出的多态性条带均超过90.0%。种质资源相似系数为0.3822～0.9656, 平均相似系数为0.7039。UPGMA聚类结果将供试材料分为3类, 即早花、中花和晚花类, 同一产地的品种基本能聚在一起。AFLP标记技术能较好地从分子水平揭示萱草种质资源的亲缘关系。     

Genetic diversity in fruiting-mei,apricot, plum and peach revealed by AFLP analysis

Summary

High-throughput amplified fragment length polymorphism (AFLP) analysis, employing a two-dye automated DNA sequencer, was used to genotype accessions of four important Prunus spp. fruit crops in China, fruiting-mei (P. mume), apricot (P. armeniaca), plum (P. salicina, and P. ussuriensis) and peach (P. persica). Nine primer pairs generated a total of 2,089 AFLP bands, of which 94.4% were polymorphic. Levels of polymorphism and the genetic relationships among the crops were studied.The fixation index (F_st) of the four different fruit trees ranged from 0.53 – 0.82, and the average genetic diversity (AGD) in these species ranged from 3.2% to 12.8%. These four stone fruit species could be clustered into four clear groups on a phylogenetic tree based on bootstrap analysis. Phylogenetically, fruiting-mei was shown to be closest to apricot and most distant from peach.