ArticlePDF Available

Abstract and Figures

Twenty four apricot genotypes with different geographic origins, maintained in the germplasm collections of Central Institute of Temperate Horticulture, Srinagar, India, were studied by means of RAPD markers. The aim of the study was to determine the genetic relationship amongst genetypes from different eco-geographical regions. Fourty three decamer primers were used in the study. All of them were polymorphic in the set of cultivars studied and allowed every genotype to be unambiguously distinguished. A dendrogram based on UPGMA analysis grouped the 24 genotypes into four main clusters with Jaccard's similarity coefficient ranging from 0.14 to 0.86 with an average of 0.40. RAPD markers have proved to be an efficient tool for fingerprinting of cultivars and conducting genetic-diversity studies in apricot.
Content may be subject to copyright.
A preview of the PDF is not available
... Different types of molecular markers have been used to study the diversity and genetic characterization of apricots and other Prunus germplasms such as Restriction fragment length polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR), Inter Simple Sequence Repeats (ISSR) and Sequence-related amplified polymorphism (SRAP) markers (Hormaza, 2002;Hurtado et al., 2002;Wünsch, 2009;Ai et al., 2011;Yilmaz et al., 2012;Chen et al., 2021). In Kashmir and Ladakh regions, very few studies on apricot genetic diversity have been conducted using molecular markers such as RAPD and ISSR (Kumar et al., 2009a(Kumar et al., , 2009bMishra, 2009;Mir et al., 2012). However, comprehensive genetic diversity analysis and genetic relationships among the apricot germplasm of Kashmir and Ladakh have not been taken up earlier. ...
... Moreover, details on the genetic relationship of the collected germplasm could be used in the identification of superior as well as parental genotypes to expand genetic material and to improve the apricot germplasm. The present study includes almost all of the genotypes from Kashmir and Ladakh regions with a more diverse group of genotypes than in earlier studies conducted by Kumar et al. (2009aKumar et al. ( , 2009bMishra, (2009);and Mir et al. (2012) using mostly RAPD and few ISSR markers. Therefore, this is the first report on genetic diversity analysis of such large apricot germplasm using microsatellite SSR markers. ...
... As apricot trees from the Ladakh region are the main source of most of the genotypes of the Kashmir region, a clear separation of Kashmir apricot genotypes from Ladakh apricot genotypes was not observed. Mir et al. (2012) using RAPD markers also reported the clustering of apricots of Kashmir and Ladakh regions in a common group. Moreover, from the dendrogram analysis, it was observed that there is not any genotype with different names used in different geographical locations of Kashmir or Ladakh region (Synonym) while as it was found that there are some genotypes with the same names (Homonyms) such as Boett Cher which is a common name to most of the sweet kernelled apricot found in different places of the Kashmir region. ...
Article
Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three ( K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.
... Several studies have been undertaken to study the genetic diversity of apricot germplasm using different molecular markers in the other parts of the world such as RAPD, AFLP, SSR, ISSR, and SRAP (Ercisli et al. 2009;Lamia et al. 2010;Yilmaz et al. 2012;Ai et al. 2011). However, in Jammu and Kashmir including Ladakh province, morphological tools have been mostly used to study the variability of apricot germplasm (Bhat et al. 2013;Malik et al. 2010;Girish et al. 2012;Abdul et al. 2016;Angmo et al. 2017;Kumar et al. 2015;Wani et al. 2017) and to the best of our knowledge, very limited work is available using molecular markers such as RAPD (Kumar et al. 2009a;Mir et al. 2012) and except for the study of Kumar et al. (2009b) from Ladakh region, no report is available on the evaluation of genetic diversity of apricot germplasm of Jammu and Kashmir using ISSR markers. Furthermore, these studies were often restricted by the limited number of accessions and specific locations. ...
Article
Full-text available
The collection and characterization of apricot germplasm is an important step for its utilization, conservation, and breeding programs. In the present study, the genetic diversity and population structure of 106 accessions of apricot including 82 indigenous and 24 exotic accessions collected from various geographical locations of Jammu and Kashmir, India were evaluated using 14 inter simple sequence repeat markers. The PCR amplification produced 365 loci of which 356 (97.53%) were polymorphic. The average number of alleles, effective number of alleles, expected heterozygosity, Shannon’s information index indicated high level of genetic diversity in the collected apricot accessions, and the polymorphism information content (0.82) revealed that these markers were highly polymorphic. The results of UPGMA dendrogram and model-based STRUCTURE analysis clearly divided the 106 apricot accessions into two main groups; one group included the 78 accessions of Kashmir province and the other included 28 accessions of Jammu province indicating the distinction of two genetic pools of apricot in the region. Nonetheless, PCoA also revealed a similar grouping of accessions except few exotic accessions that formed a small separate group. Moreover, analysis of molecular variance showed high genetic variation within the population (67%) and low among the population (33%). To our knowledge, this study represents the first comprehensive report on the ISSR based genetic diversity, relationship, and the structure of apricot accessions of Jammu and Kashmir. Further, the results of the present study will assist in efficient utilization, conservation, and MAS based breeding programs of apricot.
... Hence, targeting fragments in these classes is recommended for diversity analysis in case a large number of fragments are detected by a particular primer set. The average PIC value per primer (0.374) is comparable with that found by Mir et al. (2012) using RAPD markers in Prunus armeniaca (0.33) and Dalamu et al. (2012) using ISSR markers in Momordica charantia (0.40). For its ability to provide high PIC, the set of RAPD primers used was considered efficient and suitable for the analysis of Cymbopogon genome. ...
Article
Full-text available
Among monocots forming the grass family (Poaceae), Cymbopogon is one of the most important aromatic essential oil yielding genera. Genetic characterization is very important for proper utilization and improvement of the oil grasses. An improved random amplified polymorphic DNA (RAPD) analysis where touchdown polymerase chain reaction with prolonged RAMP time has been used to characterize the genetic variation in ten Indian elite cultivars of Cymbopogon aromatic grasses of essential oil trade types of Citronella, Palmarosa and Lemongrass. The total of 203 amplification products was scored using 23 RAPD primers, exhibiting an overall 92.61% polymorphism. Polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI) and resolving power (RP) averaged 0.374, 7.69, 2.92 and 5.15 per primer, respectively, showing the high efficiency and reliability of the markers used. Also, RAPDs of diagnostic and curatorial importance were discerned as ‘stand alone’ molecular descriptors for cultivar and species (biotype) identification. The order of the average value of Jaccard’s coefficient of similarity was found to be C. winterianus (0.890) > C. flexuosus (0.657) > C. martinii (0.425). The present study confirms the significance of the improved RAPD method in genetic characterization of Cymbopogon sp. and can be employed for efficient identification, conservation and utilization of germplasm resources for plant improvement through conventional as well as molecular breeding approaches.
... Shabir et al. (2012b) studied genetic variability in Inula racemosa using RAPD analysis. Mir et al. (2012) evaluated genetic diversity analysis by using RAPD markers in 24 apricot (Prunus armeniaca L.) genotypes with different geographic origins and revealed genetic relationships among these genotypes. Farooq (2013a) studied genetic diversity in different populations of Chenopodium album, Rumax dentatus and R. nepalensis by using RAPD markers. ...
Article
The present paper reviews research conducted on the cytogenetics of the plants of the Kashmir Himalaya. The review discloses that out of the total c.550 cytologically determined plants, there are c.190 genera and c.55 families of angiosperms. Among the cytologically determined species, c.50 species have been reported for the first time at global level along with varied chromosomal reports for c.110 species from the Kashmir Himalaya. The genus Jaeschkea has also been cytologically determined for the first time worldwide from the Kashmir Himalaya. The chromosome numbers in these species vary from 2n = 10 to 2n = 120 with frequency of 2n = 18 (13.73%), 2n = 16 (13.46%), 2n = 14 (7.96%) and 2n = 32 (7.41%). The reported base numbers of x = 7, x = 8, x = 9 are common ones. Most of the genera are polybasic, followed by monobasic and dibasics while tribasic taxa are least represented in the Kashmir Himalaya. New base numbers have been reported for Astragalus (x = 6), Cheiranthus (x = 6), Gypsophila (x = 13), Meconopsis (x = 7) and Saussurea (x = 18) from this region. In all, nearly 65% species are diploids and the rest (35%) are polyploids existing at various polyploid levels, with a preponderance of tetraploids. These plants depict significant level of intraspecific variability not only in chromosome numbers but also for meiotic behaviour and morphology. The knowledge of intraspecific variability of these species point out the existence of genetic diversities. Additionally, it has been observed that molecular marker studies are restricted to few plant species in the geographically diverse the Kashmir Himalaya. © 2016 Dipartimento di Biologia Evoluzionistica, Università di Firenze
... As the molecular markers are stable and environmentally independent, they are increasingly being preferred to phenotypic traits to detect genetic variation not only among populations but also between individuals within a population. A number of DNA marker systems such as simple sequence repeats (SSR) 21 , random amplified polymorphic DNA (RAPD) 5,7 , inter-simple sequence repeats (ISSR) 17,19 and amplified fragment length polymorphism (AFLP) 18 have been used to study the population genetics of different organisms including insects. The ISSR marker system was used to assess genetic diversity and differentiation among different commercially exploited populations of Samia cynthia ricini from North-Eastern states of India 2,12 . ...
Article
Full-text available
Philosamia ricini, the Indian eri silkworm, contributes significantly to the production of commercial silk and is widely distributed in the Brahmaputra valley of the North-Eastern India. Strains of P. ricini show wide variation in their phenotypic traits and are commercially exploited in these places because of their high silk yield potential. In this study, we have analyzed the partial mitochondrial 16S ribosomal RNA (16S rRNA) and partial cytochrome oxidase subunit I (CoxI) gene sequences to assess the genetic diversity among five different strains of P. ricini. Sequence analysis of mitochondrial 16S rRNA and mitochondrial CoxI genes showed variation among the strains. Except the Red cocoon variety, the sequence of the fragment of 16S rRNA gene was identical among White plain, White zebra, Blue plain and Blue zebra strains. Similarly, the sequence of the fragment of the CoxI gene grouped the strains into two distinct groups, (a) White plain and Red cocoon variety and (b) White zebra, Blue plain and Blue zebra strains. For the first time, the mitochondrial gene sequences of different strains of P. ricini have been studied.
Article
Full-text available
Thirteen papaya cultivars and lines were used to assess genetic diversity through dominant PCR based markers (16 RAPD and 12 ISSR primers). RAPD (random amplified polymorphic DNA) primers gave 58 polymorphic bands out of 126 with 47.19% polymorphism and ISSR (Inter simple sequence repeats) primers produced 49.80% polymorphism with 37 polymorphic bands out of 65 bands. Dendrogram showed clear grouping ancestrally related papaya cultivars. Principle coordinate analysis (PCoA) showed congruence with dendrogram pattern while bootstrap values at major nodes in both marker systems as well as in pooled data indicated robustness of cluster pattern in dendrogram construction. Analysis of molecular variance (AMOVA) indicated that highly significant genetic variability was obtained through both marker systems while cultivars showed noticeable variation in case of RAPD markers. Mantel's test between similarity and cophenetic coefficient matrices in different combination showed poor to very good correlation between matrices. This study indicates relation between papaya cultivars based on their ancestral relationship which can be utilized for conservation of important cultivars and development of future strategies for crop improvement programme.
Article
Full-text available
Almond [Prunus dulcis (Mill.) D.A. Webb, syn. P. amygdalus, Batsch; P. communis (l.) Archangell] represents a morphologically and physiologically variable group of populations that evolved primarily in central and southwest Asia. California cultivars have been developed from highly selected subgroups of these populations, while new breeding lines have incorporated germplasm from wild almond and closely related peach species. The genetic relatedness among 17 almond genotypes and 1 peach genotype was estimated using 37 RAPD markers. Genetic diversity within almond was found to be limited despite its need for obligate outcrossing. Three groupings of cultivar origins could be distinguished by RAPD analysis: bud-sport mutations, progeny from interbreeding of early California genotypes, and progeny from crosses to genotypes outside the California germplasm. A similarity index based on the proportion of shared fragments showed relatively high levels of 0.75 or greater within the almond germplasm. The level of similarity between almond and the peach was 0.424 supporting the value of peach germplasm to future almond genetic improvement.
Article
Full-text available
Apricot (Prunus armeniaca L.) culture is present in a wide range of areas and microclimates in Tunisia. Each of them contains several specific cultivars and shows a high level of morphological diversity. To characterize the related diversity, surveys were performed in the four main apricot cultivation areas, where 31 cultivars representing apricot landraces were sampled. DNA was extracted and amplified with five different EcoRI-MseI AFLP primer combinations. Autoradiographs revealed 203 polymorphic markers in a total of 295 detected fragments. A set of redundant marker patterns was identified and deleted from the binary data matrix, data analysis being performed on a total of 167 polymorphic markers. In a dendrogram calculated by the Ward clustering technique, two major groups were identified, separating nine cultivars from the other 22. Three subgroups have been revealed in each of the main groups. The groups and subgroups identified on the genetic basis are closely related to the geographic origin of the cultivars. Analysis of the actual repartition suggested at least the introduction of two independent gene funds in the northern and central prospected areas, followed by a local diversification and then a dissemination phase. Their interaction occurred at least in the two sites of Testour and Sbikha.
Article
Full-text available
This study was carried out to determine genetic relationships among 23 apricot cultivars from Turkey by using randomly amplified polymorphic DNA (RAPD) technology. Among the 40 decamer random primers were used for PCR reactions, 12 primers showed reproducible polymorphic patterns. These primers produced 121 bands, out of which 118 were polymorphic. UPGMA (Unweighted Pair Group Method using Arithmetic average) derived dendrogram, grouped the cultivars into one cluster and one outlier. The main cluster further divided into three subclusters. The highest dissimilarities found between Hacihaliloglu and Kabaasi cultivars (0.108). The variation detected among the closely related genotypes indicates the efficiency of RAPD markers over the morphological and isozyme markers for the identification and construction of genetic linkage maps.
Article
Full-text available
Linkage maps of the apricot accessions ‘Lito’ and ‘BO 81604311’ were constructed using a total of 185 simple sequence repeat (SSR) markers sampled from those isolated in peach, almond, apricot and cherry; 74 were derived from a new apricot genomic library enriched for AG/CT microsatellite repeats (UDAp series), and in total, 98 had never been mapped in Prunus before. Eight linkage groups putatively corresponding to the eight haploid apricot chromosomes were identified for each parent. The two maps were 504 and 620cM long, respectively, with 96 anchor markers showing a complete co-linearity between the two genomes. As few as three gaps larger than 15cM were present in ‘Lito’ and six in the male parent; the maps align well with all the available SSR-based Prunus maps through the many common anchor loci. Only occasionally inverted positions between adjacent markers were found, and this can be explained by the small size of cross populations analysed in these Prunus maps and in those reported in literature. The newly developed apricot SSRs will help saturating the existing Prunus maps and will extend the choice of markers in the development of genetic maps for new breeding populations.
Article
The genetic diversity of 84 varieties of European, Irano-Caucasian, Chinese, and Central Asian origin, hybrid cultivars, and some wild forms from the Dzungar-Zailij population of Prunus armeniaca L. were used as an object of investigation. A dendrogram reflecting the divergence of eco-geographical groups of apricots was built on the basis of isozyme (AAT, AMY, EST, LAP, PX, SOD, SKDH) and RAPD analyses. The distribution of the accessions in the dendrogram reflects the genetic heterogeneity within groups. We suggest that the cultivated apricot has been developed mainly from wild P. armeniaca. The introgression of closely related species played a large role in the domestication of apricots from the Chinese centre of origin. A narrow genetic basis of selection of the European apricots has also been inferred.
Article
Microsatellite and AFLP markers have been utilized to characterize six apricot cultivars and advanced selections. All of the cultivars tested could be clearly identified by SSR and AFLP markers. A total of twenty primer pairs flanking microsatellite loci were used. All the primers revealed polymorphisms among the cultivars tested. The high degree of polymorphisms of microsatellite markers allows a rapid efficient identification of apricot genotypes. A specific PCR marker developed for S-allele genotyping of sweet cherry as used to reveal possible variation among the tested apricots. Three of the apricots showed different S-alleles. The corresponding bands were sequenced and compared to those of sweet cherry. Apparently there is synteny between the genomes of apricot and sweet cherry.
Article
Eleven apple cultivars were differentiated using randomly amplified polymorphic DNA (RAPD) markers obtained by the polymerase chain reaction (PCR). The variability of the technique and of the origin of the DNA extract was analyzed. A set of bands consistent in their presence or absence was chosen to create a differentiating band pattern. A key is proposed by which one can differentiate apple cultivars using commercially available prime.
Article
Musa cultivars (bananas and plantains) are important crops in the humid tropics of Africa, America and Asia. This paper reports the extent of morphological variation of the Musa germplasm maintained in the gene-bank of the International Institute of Tropical Agriculture in southeastern Nigeria. Qualitative and quantitative descriptors were used to evaluate AA, BB, AB, AAA, AAB, AAAA, AAAB and AABB bananas, AAA and ABB cooking bananas, AAA beer bananas and AAB plantains and a few wild species. Univariate and principal component (PCA) analyses were performed to identify the most important descriptors to characterize and classify Musa germplasm collections. The most important qualitative morphological descriptors were persistence of male bud and hermaphrodite flowers, pigmentation in pseudostem, foliage, petiole and male flower, pseudostem blotching and waxiness, and leaf orientation. Furthermore, the most important quantitative morphological descriptors included pseudostem girth, height of tallest sucker, number of fruits and fruit sizes. These quantitative descriptors have a high heritability (>0.8), high repeatibility (>2.0) and low coefficient of variation (9–15%) with the exception of the height of the tallest sucker. The implications of the germplasm grouping revealed by PCA are briefly discussed in relation to the evolution of the triploid cultivars. This paper also proposes a new scientific nomenclature for the triploid Musa cultivars.
Article
A set of cultivars used as genitors in apricot breeding programs aimed at introducing sharka resistance were examined by AFLP molecular marker analysis. The markers obtained indicated that apricot cultivars resistant to sharka were related to the European cultivars, but they potentially share a common ancestor donor of sharka outside of the European group. Segregation of AFLP and RAPD markers has been tested in two progenies of two crosses, one between a resistant and a susceptible cultivar and one between two susceptible accessions. The heterozygozity of families obtained from crosses between resistant and susceptible cultivars is similar to those obtained from other self-incompatible Prunus species. On the other hand, heterozygosity of a progeny obtained from a cross between European susceptible cultivars was very low. The usefulness of the information provided by AFLPs for apricot breeding programs is discussed.