Mulberry (genus Morus) is an economically important plant used for sericulture, as it is the sole food plant for the domesticated silkworm, Bombyx mori. The genus Morus, which is widely distributed in Asia, Europe, North and South America, and Africa, is cultivated extensively in East, Central and South Asia for silk production. A few species of mulberry are also valued for their edible fruit (M. alba, M. indica and M. laevigata), timber (M. laevigata and M. serrata). Whereas it has been widely believed that mulberry species originated on the low slopes of the Himalayas bordering China and India, the study of Hou suggests a multicentered origin 1. Since the classification of the genus Morus is mainly based on morphological characteristics, considerable differences exist among systematists as to the number of species that exist in this genus 234567. So far, more than 150 species of mulberry have been cited in the Index Kewensis, but a majority of them have been treated either as synonyms or as varieties rather than species, and some have been transferred to allied genera. A study carried out by Koidzumi in 1917 3 recognised 24 species and one variety under the genus Morus based on the style length in female flowers and the nature of the stigma in male flowers. In contrast, more than 60 years later by analyzing the electrophoretic patterns of seven enzymes and sap proteins in 131 varieties of three mulberry species, M. bombycis, M. alba, and M. latifolia Hirano categorised them into seven varietal groups, and affinities among them 8. Because of environmental influence, phenotypic traits in many cases fail to serve as unambiguous markers for systematics and diversity analysis 9. Moreover, most of the putative mulberry species are dioecious and can cross-pollinate among themselves to produce fertile hybrids, suggesting that they have relatively close genetic relationships. Such a high degree of cross-species reproductive success is not encountered often in nature, and has thus created considerable doubt with regard to the species status of mulberry.

Molecular markers successfully developed during the last two decades have largely overcome the problems that are associated with phenotype-based classification. Initially, isozymes 101112 and Restriction Fragment Length Polymorphisms (RFLPs) 1314151617 served as reliable markers for genetic analyses in plants. But PCR based techniques developed in recent years such as Random Amplified Polymorphic DNA (RAPDs) 1819, Inter Simple Sequence Repeats (ISSR) 20, Amplified Fragment Length Polymorphisms (AFLPs) 21, and Simple Sequence Repeats (SSRs) 22, also called microsatellites, provide DNA markers that are dispersed throughout plant genomes 23 and are easier to reproduce and analyse. High levels of polymorphism and their co-dominant nature have made SSRs ideal markers for studying genetic diversity in plants 242526. However, the time and cost of identifying SSR motifs and designing primers for regions flanking SSRs have restricted the widespread use of microsatellites in plants 2728. ISSR markers, which show dominant inheritance, use SSR repeat-anchored primers and are being used as an alternate tool in diversity studies. ISSR markers are useful in detecting genetic polymorphisms among accessions by generating a large number of markers that target multiple microsatellite loci distributed across the genome. Further, they are simpler to use than the SSR technique as prior knowledge of the target sequences flanking the repeat regions is not required 20293031.

So far only a few attempts have been made to characterise the genetic diversity in mulberry by using molecular markers. These include AFLP based marker analysis 32, RAPD and DAMD profiles 33, ISSR based analysis 34, and genetic polymorphism estimation in mulberry hybrids using RAPDs 35. In the current study we report the use of RAPD and ISSR markers for assessing the genetic diversity and relationships among 12 cultivated and 3 wild mulberry species.

Mulberry is a perennial, heterogeneous outbreeding tree, the leaves of which are the exclusive food of the silk secreting insect, B. mori. Outbreeding in cultivated mulberry species is common and inter-species hybridization is often observed. Because of phenotypic plasticity, the occurrence of interspecific hybridization, mutation, and the absence of an unambiguous set of criteria for designating a true species, there is confusion in the systematic classification of mulberry. The present work evaluates the genetic diversity and relationships among fifteen mulberry species using RAPD and ISSR markers.

The wide variation in genetic distance among the different mulberry species revealed by both RAPD and ISSR techniques reflected a high level of polymorphism at the DNA level. Earlier studies by Sharma et al. using the AFLP technique 32 also showed a large genetic variation among different Morus genotypes. Such a high level of polymorphism, especially in cultivated mulberry, reflects the outcrossing nature of the species. Cluster analysis of RAPD and ISSR data using UPGMA revealed that the three wild species, namely, M. laevigata, M. serrata, and M. tiliaefolia, are genetically distant from the domesticated species studied here. The distinctness of the wild species as revealed by both RAPD and ISSR in the present study and that of Sharma et al. 32 can be attributed to their geographical isolation, which is in strong contrast to the outbreeding and high heterozygosity which have accompanied the long history of cultivation of domesticated mulberry species.

The ISSR profiles of mulberry generated by CA/TG repeat anchored primers showed that these repeats are abundant in the Morus genome. Vijayan and Chatterjee 34 also observed amplification of AC rich repeat based ISSR primers. However, this type of repeat is less abundant in plant genomes compared to other kinds of repeats 36, and the abundance of other classes of microsatellite repeats in the mulberry genome awaits to be demonstrated. The RAPD analysis revealed a close relationship between M. cathayana and M. rotundiloba, whereas these two species were found to be distinct in ISSR analysis. Such variation between RAPD and ISSR may be due to the fact that the PCR amplified profiles in the two marker assays originated from different repetitive and non-repetitive regions of the genomes, and the possibility that many co-migrating bands may be non-homologous, producing a background noise that could influence the results 3738. Similar to the RAPD analysis, the ISSR results showed no correlation to ploidy status or to the number of amplified products. For example, in the triploid species, M. laevigata and M. bombycis, 23 and 35 polymorphic products were observed, respectively, whereas the tetraploid species M. serrata revealed 20 ISSR products, and in the hexaploid, M. tiliaefolia, 25 products were amplified. These results are consistent with the earlier studies of RAPD patterns in Chrysanthemum by Wolf & Rijn 39, which show that the ploidy level of a plant does not appear to influence the number of fragments amplified per primer.

Classification of Morus based on phenotypic variations or isozyme patterns should be reconsidered in the context of molecular analyses by RAPD and ISSR as well as that of AFLP 32. Hirano 8 studied 131 varieties of cultivated mulberry morphologically classified as belonging to three species, viz., M. bombycis, M. alba, and M. latifolia. Examining isozymes and several sap proteins, he found no significant difference among these three species, prompting him to conclude that all three species are the same. However, our study as well as the AFLP study unambiguously place M. alba as a separate species distinct from the other two, which are likely to be independent species. Thus, RAPD and ISSR based molecular markers were able to distinguish differences between the species which were indistinguishable by isozyme based markers. Similarly, Koidzumi 34 considered that M. lhou, M. multicaulis, and M. latifolia are similar and belong to a single species. However, their wide separation in the present study contradicts this observation. Additional phylogenetic studies using chloroplast or mitochondrial gene sequences or appropriate nuclear gene sequences can help to evaluate the systematic positions of these species.

The present study reveals that PCR based fingerprinting techniques, RAPD and ISSR, are informative for estimating the extent of genetic diversity as well as to determine the pattern of genetic relationships between different species of Morus, with polymorphism levels sufficient to establish informative fingerprints with relatively fewer primer sets. The information obtained from the present study could be of practical use for mapping the mulberry genome as well as for classical breeding. The genetic similarity of wild mulberry with other cultivated species is low as indicated by the separation of these two groups in both RAPD and ISSR analyses. The informative primers identified in our studies will be useful in genetic analysis of mulberry accessions in germplasm holdings. The putative species-specific bands can be used as probes to ascertain whether they are in low or high copy numbers in the mulberry genome, and such specific bands may be used for genotype characterization and grouping germplasm accessions. Further, putative species-specific RAPD markers could be converted to sequence characterized amplification regions (SCARs) after sequencing and designing primer pairs to develop robust species specific markers. The study also provides a basis for mulberry breeders to make informed choices on selection of parental material based on genetic diversity to help overcome some of the problems usually associated with a tree crop improvement program.

AAK carried out RAPD and part of the ISSR work, GMN designed ISSR primers and carried out part of the ISSR work, GVN did DNA extraction and identified appropriate mulberry samples for the study, SK carried out data analysis and manuscript revision, TK carried out sample collection and JN conceived the study, and participated in its design, co-ordination and interpretation of the results.