title: Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species.
abstract: BACKGROUND
  Adoption of genomics based breeding has emerged as a promising approach for achieving comprehensive crop improvement. Such an approach is more relevant in the case of perennial species like mulberry. However, unavailability of genomic resources of co-dominant marker systems has been the major constraint for adopting molecular breeding to achieve genetic enhancement of Mulberry. The goal of this study was to develop and characterize a large number of locus specific genic and genomic SSR markers which can be effectively used for molecular characterization of mulberry species/genotypes.
  
  
  RESULTS
  We analyzed a total of 3485 DNA sequences including genomic and expressed sequences (ESTs) of mulberry (Morus alba L.) genome. We identified 358 sequences to develop appropriate microsatellite primer pairs representing 222 genomic and 136 EST regions. Primers amplifying locus specific regions of Dudia white (a genotype of Morus alba L), were identified and 137 genomic and 51 genic SSR markers were standardized. A two pronged strategy was adopted to assess the applicability of these SSR markers using mulberry species and genotypes along with a few closely related species belonging to the family Moraceae viz., Ficus, Fig and Jackfruit. While 100% of these markers amplified specific loci on the mulberry genome, 79% were transferable to other related species indicating the robustness of these markers and the potential they hold in analyzing the molecular and genetic diversity among mulberry germplasm as well as other related species. The inherent ability of these markers in detecting heterozygosity combined with a high average polymorphic information content (PIC) of 0.559 ranging between 0.076 and 0.943 clearly demonstrates their potential as genomic resources in diversity analysis. The dissimilarity coefficient determined based on Neighbor joining method, revealed that the markers were successful in segregating the mulberry species, genotypes and other related species into distinct clusters.
  
  
  CONCLUSIONS
  We report a total of 188 genomic and genic SSR markers in Morus alba L. A large proportion of these markers (164) were polymorphic both among mulberry species and genotypes. A substantial number of these markers (149) were also transferable to other related species like Ficus, Fig and Jackfruit. The extent of polymorphism revealed and the ability to detect heterozygosity among the cross pollinated mulberry species and genotypes render these markers an invaluable genomic resource that can be utilized in assessing molecular diversity as well as in QTL mapping and subsequently mulberry crop improvement through MAS.
authors.forename: Balachandran
authors.initials: B
authors.lastname: Mathithumilan
authors.forename: Niteen Narharirao
authors.initials: NN
authors.lastname: Kadam
authors.forename: Jyoti
authors.initials: J
authors.lastname: Biradar
authors.forename: Sowmya H
authors.initials: SH
authors.lastname: Reddy
authors.forename: Mahadeva
authors.initials: M
authors.lastname: Ankaiah
authors.forename: Madhura J
authors.initials: MJ
authors.lastname: Narayanan
authors.forename: Udayakumar
authors.initials: U
authors.lastname: Makarla
authors.forename: Paramjit
authors.initials: P
authors.lastname: Khurana
authors.affiliation: Department of Crop Physiology, University of Agricultural Sciences, Bangalore, India. msheshshayee@hotmail.com.
authors.forename: Sheshshayee Madavalam
authors.initials: SM
authors.lastname: Sreeman
mesh_terms: D020224:Expressed Sequence Tags; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D031625:Morus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny