DNA fingerprinting in silkworm <i>Bombyx mori</i> using banded krait minor satellite DNA‐derived probe

Nagaraju, Javaregowda; Sharma, Abhay; Balakathiresan, Nagaraja S.; Rao, G. V.; Singh, Lalji

doi:10.1002/elps.11501601271

Cited by 16 publications

(13 citation statements)

References 15 publications

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“…Only in the SSR assay, the non‐diapausing strain, C. nichi , was found clustered with the diapausing strains. Similar results were also obtained by Nagaraju et al . (1995) and Sharma et al .…”

Section: Resultssupporting

confidence: 92%

“…The large number of PCR products observed in the ISSR‐PCR assay is not surprising since the B. mori genome is abundant with dinucleotide repeat motifs, particularly CA repeats (Reddy et al ., 1999b) and ISSR primers are designed to anchor such microsatellite motifs to amplify the genomic sequences lying between them. Many of the anonymous multilocus RFLP probes used in the present study are probably derived from genomic regions containing transposable elements or minisatellite‐like sequences which account for several thousand copies per haploid genome of the silkworm (Nagaraju et al ., 1995; Robertson & Asplund, 1996). Although most ISSR loci are dominant, rather than codominant, ISSR‐PCR markers offer several advantages over RFLPs for genotyping, the major one being the rapid production of a large number of markers in a cost‐effective manner.…”

Section: Discussionmentioning

confidence: 99%

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Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori

et al. 2001

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The utility of multilocus RFLPs and three PCR-based techniques, Random Ampli®ed Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat-PCR (ISSR-PCR) and simple sequence repeats (SSRs) for genetic characterization was examined using 13 diverse silkworm strains. All four approaches successfully discriminated the 13 silkworm varieties but diered in the amount of polymorphism detected. The usefulness of each system was examined in terms of number of loci revealed (eective multiplex ratio, EMR) and the amount of polymorphism detected (diversity index, DI). For example, the six multilocus RFLP probes produced 180 products of which 97% were polymorphic; 15 SSR loci gave rise to an average of 8 alleles each, of which 86% were polymorphic. The ISSR-PCR produced 39 fragments of which 76.98% were polymorphic. The highest diversity index was observed for ISSR-PCR (0.957) and the lowest for RAPDs (0.744). The RAPD, ISSR-PCR and RFLP assays clearly separated the diapausing and non-diapausing silkworm varieties. These results are discussed in terms of choice of appropriate marker technology for dierent aspects of silkworm genome analysis.

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Section: Resultssupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori

et al. 2001

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“…Similarly, Moria and Sarupat which show similar characteristics and are distributed in the state of Assam, are also grouped together. These observations are in agreement with the earlier results obtained with RAPDs ( Nagaraja & Nagaraju, 1995), the Bkm probe ( Nagaraju et al ., 1995 ) and SSRs ( Reddy et al ., 1999 ). …”

Section: Discussionsupporting

confidence: 94%

“…If economically important traits are found to have close linkage with the DNA markers, the latter could also be used in marker‐assisted selection. Attempts have already been made to fingerprint the diverse silkworm genotypes and establish their genetic relationships using defective transposons ( Tamura et al ., 1993 ), RAPDs ( Nagaraja & Nagaraju, 1995), a Bkm‐derived probe ( Nagaraju et al ., 1995 ) and SSRs ( Reddy et al ., 1999 ). In the present study, we report the feasibility of using the ISSR‐PCR method to analyse the diverse genotypes of silkworm in order to augment marker resources for silkworm genetic analysis.…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization of the silkworm Bombyx mori by simple sequence repeat (SSR)-anchored PCR

1999

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Thirteen diverse strains of the silkworm Bombyx mori were analysed using the simple sequence repeat anchored polymerase chain reaction (SSR-anchored PCR) or Inter-SSR-PCR (ISSR-PCR). A set of four 5'-anchored and two 3'-anchored repeat primers amplified a total of 239 bands out of which 184 (77%) were polymorphic. The 5'-anchored primers revealed more distinct polymorphic markers than the 3'-anchored primers and the ISSR-PCR method showed greater variability than RAPDs. The strain-specific pattern was shown to be inherited and segregated in a Mendelian fashion. A dendrogram constructed using the UPGMA method revealed two distinct groups, one comprising nondiapausing and one comprising diapausing strains. These results suggest that the ISSR-PCR method is potentially useful for genetic fingerprinting of silkworm genotypes and as a mapping tool in the silkworm.

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“…The closest nearest neighbor strains were found to be KA and NB 1 , NB 18 and NB 4 D 2 , Pure Mysore and Nistari, and Moria and Sarupat. These results are in close agreement with the previously reported RAPD (Nagaraja and Nagaraju 1995), a Bkm-2(8) probe (containing 66 copies of GATA repeats interspersed with TA repeats, Nagaraju et al 1995) and ISSR (Reddy et al 1999) based dendrograms. The microsatellite-based analysis reflected the geographical, pedigree, and morphological relations of the strains used in the study.…”

Section: Genetic Distances Analysissupporting

confidence: 92%

Microsatellites in the silkworm, <i>Bombyx mori</i>: Abundance, polymorphism, and strain characterization

Reddy¹,

Abraham²,

Nagaraju³

1999

Génome

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Abstract:We have isolated and characterized microsatellites (simple sequence repeat (SSR) loci) from the silkworm genome. The screening of a partial genomic library by the conventional hybridization method led to the isolation of 28 microsatellites harbouring clones. The abundance of (CA) n repeats in the silkworm genome was akin to those reported in the other organisms such as honey bee, pig, and human, but the (CT) n repeat motif is less common compared to bumble bee and honey bee genomes. Detailed analysis of 13 diverse silkworm strains with a representative of 15 microsatellite loci revealed a number of alleles ranging from 3 to 17 with heterozygosity values of 0.66-0.90. Along with strain-specific microsatellite markers, diapause and non-diapause strain-specific alleles were also identified. The repeat length did not show any relationship with the degree of polymorphism in the present study. The co-dominant inheritance of microsatellite markers was demonstrated in F 1 offspring. A list of primer sequences that tag each locus is provided. The availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in silkworm.Key words: microsatellites, simple sequence repeats, polymorphisms, silkworm strains, Bombyx mori.Résumé : Les auteurs ont isolé et caractérisé des microsatellites/SSR chez le vers à soie. Le criblage d'une banque génomique partielle par hybridation conventionnelle a permis d'isoler 28 clones contenant un microsatellite. L'abondance des microsatellites de type (CA) n dans le génome du vers à soie était semblable à ce qui a été rapporté précédemment chez d'autres espèces telles que l'abeille, le porc et l'humain tandis que les séquences (CT) n étaient moins abondantes que chez le bourdon et l'abeille. Une analyse détaillée de 13 souches de vers à soie avec 15 microsatellites représentatifs a révélé entre 3 et 17 allèles et des valeurs d'hétérozygotie variant entre 0,66 et 0,90. En plus de marqueurs spécifiques de certaines souches, des allèles spécifiques aux souches à diapause et sans diapause ont été identifiés. Le nombre de répétitions du motif de base n'était pas lié au degré de polymorphisme dans cette étude. La codominance des microsatellites a été démontrée dans des progénitures F 1 . Une liste des amorces spécifiques à chaque locus est fournie. La disponibilité de marqueurs microsatellites permettra vraisemblablement d'accroître la puissance et la résolution des analyses génomiques chez le vers à soie.

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DNA fingerprinting in silkworm Bombyx mori using banded krait minor satellite DNA‐derived probe

Cited by 16 publications

References 15 publications

Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori

Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori

Genetic characterization of the silkworm Bombyx mori by simple sequence repeat (SSR)-anchored PCR

Microsatellites in the silkworm, <i>Bombyx mori</i>: Abundance, polymorphism, and strain characterization

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