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Genes 2019, 10(1), 69; https://doi.org/10.3390/genes10010069

De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance

1
Reliance Technology Group, Reliance Industries Limited, Navi Mumbai 400701, India
2
AgriGenome Labs Private Limited, Hyderabad 500078, India
*
Author to whom correspondence should be addressed.
Received: 24 October 2018 / Revised: 3 December 2018 / Accepted: 7 December 2018 / Published: 21 January 2019
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

Jatropha curcas is an important perennial, drought tolerant plant that has been identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of J. curcas generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for Jatropha Mosaic Virus (JMV) resistance. In this study, we generated scaffolds of 265.7 Mbp in length, which correspond to 84.8% of the gene space, using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Additionally, 96.4% of predicted protein-coding genes were captured in RNA sequencing data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide simple sequence repeat (SSR) markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 207 polymorphic SSR markers were employed to construct a genetic linkage map for JMV resistance, using an interspecific F2 mapping population involving susceptible J. curcas and resistant Jatropha integerrima as parents. Quantitative trait locus (QTL) analysis led to the identification of three minor QTLs for JMV resistance, and the same has been validated in an alternate F2 mapping population. These validated QTLs were utilized in marker-assisted breeding for JMV resistance. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha, and serves as source for the development of agronomically improved virus-resistant and oil-producing lines. View Full-Text
Keywords: oil seed; biofuel; Euphorbiaceae; genome sequencing; transcriptomics; hybrid sequencing; simple sequence repeats; linkage map; geminivirus oil seed; biofuel; Euphorbiaceae; genome sequencing; transcriptomics; hybrid sequencing; simple sequence repeats; linkage map; geminivirus
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Kancharla, N.; Jalali, S.; Narasimham, J.V.; Nair, V.; Yepuri, V.; Thakkar, B.; Reddy, V.; Kuriakose, B.; Madan, N.; S, A. De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance. Genes 2019, 10, 69.

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