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Sunnyvale, CA, United States

Krishnan R.R.,Central Host | Bindroo B.B.,Central Sericultural Research and Training Institute | Naik V.G.,Central Host
Plant Genetic Resources: Characterisation and Utilisation

Core collections are the integral part of biotechnology-aided modern-day crop improvement programmes and utilized for a variety of applications including conventional plant breeding, association mapping, resequencing, among others. Since their advent, determination of core collection size has been based on the size of the whole collection. In this study, we precisely estimated the size of the core collection based on the diversity of the whole collection using the Similarity Elimination method. For each of the elimination cycle, allele retention and pairwise and mean genetic distances were calculated and used as the criteria for the precise estimation of the core collection size. We sampled a coconut core collection with 266 entries by retaining the diversity of the whole collection. During the elimination process, accessions with very rare alleles were eliminated first when compared with those having rare and common alleles. Therefore, our results support the hypothesis that the less frequent alleles seldom contribute to the genetic distance when compared with common alleles. In conclusion, presize can be efficiently utilized in any crop for the precise estimation of core collection size. © 2014 NIAB. Source

Guruprasad,Central Host | Ramesh Krishnan R.,Central Host | Dandin S.B.,University of Horticultural science | Girish Naik V.,Central Host
Trees - Structure and Function

Key message: A strategy for effective utilization of RAPD marker data for sampling diverse entries was suggested and utilized for the development of mulberry core collection. Mulberry (Morus spp.) is a perennial tree cultivated mainly for its foliage in sericulture industry and also known for its edible fruits, fodder, and valued timber. In recent years, mulberry cultivation is confronted with several abiotic and biotic stresses due to inimical climatic factors and this has necessitated the genetic improvement of the crop. Core collection is an efficient way of harnessing the trait variation and novel genes available in a natural gene pool for the development of improved elite lines. In this study, we analyzed 850 mulberry accessions assembled from 23 countries with separate sets of polymorphic RAPD markers along with a limited number of ISSR, SSR, and phenotypic markers. A total of 75 accessions were duplicated in 20 clusters among five natural groups. The limitations of the RAPD marker system like problem in cross gel comparison were tackled by adopting a novel "Groupwise sampling" approach. A mulberry core collection with 100 diverse entries was selected using maximization method implemented in MSTRAT software. The mean Dice dissimilarity coefficient computed from marker data was 0.308 among core entries. Indigenous and exotic entries were not discriminated in cluster and principal component analysis supporting the spread of mulberry far from the place of origin. Accessions belonging to two wild mulberry species from Andaman Islands and Himalayan region formed separate clusters indicating the geographical, reproductive, and taxonomic distinction. The identified core collection will be available for researchers for intensive mining of desirable alleles in mulberry improvement as well as in genome resequencing program. © 2014 Springer-Verlag Berlin Heidelberg. Source

Ramesh Krishnan R.,Central Host | Sumathy R.,Central Sericultural Research and Training Institute | Bindroo B.B.,Central Host | Bindroo B.B.,Central Sericultural Research and Training Institute | Girish Naik V.,Central Host
Trees - Structure and Function

Key message: Simple sequence repeat motifs were mined from the genome and EST sequences ofMorus notabilisand archived in MulSatDB. Bioinformatics tools were integrated with the database for the analysis of genomic datasets.Abstract: Mulberry is a crop of economic importance in sericulture, which shapes the lives of millions of rural people among different Eurasian and Latin American countries. Limited availability of genomic resources has constrained the molecular breeding efforts in mulberry, a poorly studied crop. Microsatellite or simple sequence repeat (SSR) has revolutionized the plant breeding and is used in linkage mapping, association studies, diversity, and parentage analysis, etc. Recent availability of mulberry whole genome assembly provided an opportunity for the development of mulberry-specific DNA markers. In this study, we mined a total of 217,312 microsatellites from whole genome and 961 microsatellites from EST sequences of Morus notabilis. Mono-repeats were predominant among both whole genome and EST sequences. The SSR containing EST sequences were functionally annotated, and SSRs mined from whole genome were mapped on chromosomes of the phylogenetically related genus—Fragaria vesca, to aid the selection of markers based on the function and location. All the mined markers were archived in the mulberry microsatellite database (MulSatDB), and the markers can be retrieved based on different criteria like marker location, repeat kind, motif type and size. Primer3plus and CMap tools are integrated with the database to design primers for PCR amplification and to visualize markers on F. vesca chromosomes, respectively. A blast tool is also integrated to collate new markers with the database. MulSatDB is the first and complete destination for mulberry researchers to browse SSR markers, design primers, and locate markers on strawberry chromosomes. MulSatDB is freely accessible at http://btismysore.in/mulsatdb. © 2014, Springer-Verlag Berlin Heidelberg. Source

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