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Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.)

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Abstract

Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements’ (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimers pipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.

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Abbreviations

TE:

Transposable element

RJ:

Repeat junctions

LTR:

Long terminal repeat

RJM:

Repeat junction marker

RJJM:

Repeat junction–junction marker

ISBP:

Insertion-site-based polymorphism junctions

RBIP:

Retrotransposon based insertion polymorphism

IRAP:

Inter-retrotransposon-amplified polymorphism

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Acknowledgements

The authors gratefully acknowledged the support and encouragement of the leadership of Dr. Makarand Phadke, Dr. Ajit Sapre and Dr. Santanu Dasgupta at the Reliance Industries Limited in carrying out the research work.

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Authors and Affiliations

  1. Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India

    Vijay Yepuri, Saakshi Jalali, Nagesh Kancharla & S. Arockiasamy

  2. AgriGenome Labs Private Limited, Hyderabad, 500078, India

    V. B. Reddy

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  1. Vijay Yepuri
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  2. Saakshi Jalali
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  4. V. B. Reddy
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Contributions

Conceptualization, VY, SA; Data curation, SJ; Formal analysis, SJ, VY; Supervision, SA; Writing original draft: VY, SJ; Writing: review and editing, VY, SJ, NK and SA; VBR, Contributed in whole genome sequence of Jatropha.

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Correspondence to S. Arockiasamy.

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11033_2020_5579_MOESM1_ESM.jpg

Supplementary file2 (JPG 89 kb) Supplementary Fig. 1 Types of repeat junctions identified in this study. Red colour represents repeat junctions. Orange and green represent different types of TE. Black colour represents unique gene or unknown sequence (adopted from Frank et al. 2010)

11033_2020_5579_MOESM2_ESM.jpg

Supplementary file3 (JPG 175 kb) Supplementary Fig. 2 Primer designing strategies for different TE junctions. Green, orange and pink colour represent different types of transposable element (TE) sequences. Red colour represents repeat junctions. Black colour represents unique gene or unknown sequence. The arrow marked with F1 and F2 are forward primers and R1 and R2 as reverse primer for each type of junctions (Adopted from Frank et al. 2010)

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Supplementary file1 (DOCX 25 kb)

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Yepuri, V., Jalali, S., Kancharla, N. et al. Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.). Mol Biol Rep 47, 5091–5099 (2020). https://doi.org/10.1007/s11033-020-05579-0

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