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Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane

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Abstract

Key message

Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane.

Abstract

Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3′UTRs than 5′UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.

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Acknowledgments

This work was carried out at the National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi in the project on “Development and use of molecular markers for mapping genes for red rot resistance and sugar traits in sugarcane” funded by the Department of Biotechnology (DBT), Government of India.

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  1. Swarup K. Parida

    Present address: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India

  2. Sanjay Kalia

    Present address: Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, 110003, India

  3. Awadhesh Pandit

    Present address: National Centre for Biological Sciences, Bengaluru, 560065, Karnataka , India

  4. Trilochan Mohapatra

    Present address: Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India

Authors and Affiliations

  1. National Research Centre on Plant Biotechnology, New Delhi, 110012, India

    Swarup K. Parida, Sanjay Kalia, Awadhesh Pandit, Kishor Gaikwad, Nagendra K. Singh & Trilochan Mohapatra

  2. Utkal University, Vanivihar, Bhubaneswar, Odisha, 751004, India

    Preetam Nayak

  3. U.P. Council of Sugarcane Research, Shahjahanpur, Uttar Pradesh, 242001, India

    Ram Kushal Singh

  4. Department of Biotechnology, Jamia Hamdard University, New Delhi, 110062, India

    Prem Shankar Srivastava

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  1. Swarup K. Parida
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  2. Sanjay Kalia
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  3. Awadhesh Pandit
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  4. Preetam Nayak
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  7. Prem Shankar Srivastava
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  8. Nagendra K. Singh
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  9. Trilochan Mohapatra
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Correspondence to Trilochan Mohapatra.

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Communicated by N. Sreenivasulu.

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Parida, S.K., Kalia, S., Pandit, A. et al. Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. Plant Cell Rep 35, 1629–1653 (2016). https://doi.org/10.1007/s00299-016-1978-y

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  • DOI: https://doi.org/10.1007/s00299-016-1978-y

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