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Development of Novel Simple Sequence Repeat Markers in Bitter Gourd (Momordica charantia L.) Through Enriched Genomic Libraries and Their Utilization in Analysis of Genetic Diversity and Cross-Species Transferability

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Abstract

Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.

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Acknowledgments

This work was supported by NBPGR’s institutional project on development of genomic tools for enhanced utilization of horticultural crops and a DBT project on marker development in bitter gourd.

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Authors and Affiliations

  1. Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India

    Swati Saxena, Sunil Archak & Ambika B. Gaikwad

  2. Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India

    Archana Singh

  3. Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 110012, India

    Tushar K. Behera

  4. National Bureau of Plant Genetic Resources, Thrissur, 680656, Kerela, India

    Joseph K. John

  5. Rajiv Gandhi Biotechnology Centre, RTM Nagpur University, Nagpur, 440001, Maharashtra, India

    Sudhir U. Meshram

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  1. Swati Saxena
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Saxena, S., Singh, A., Archak, S. et al. Development of Novel Simple Sequence Repeat Markers in Bitter Gourd (Momordica charantia L.) Through Enriched Genomic Libraries and Their Utilization in Analysis of Genetic Diversity and Cross-Species Transferability. Appl Biochem Biotechnol 175, 93–118 (2015). https://doi.org/10.1007/s12010-014-1249-8

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