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

• Main Authors: Nagesh Kancharla, Saakshi Jalali, J. V. Narasimham, Vinod Nair, Vijay Yepuri, Bijal Thakkar, VB Reddy, Boney Kuriakose, Neeta Madan, Arockiasamy S
• Format: Article
• Language: English
• Published: MDPI AG 2019-01-01
• Series: Genes
• Subjects: oil seed; biofuel; Euphorbiaceae; genome sequencing; transcriptomics; hybrid sequencing; simple sequence repeats; linkage map; geminivirus
• Online Access: https://www.mdpi.com/2073-4425/10/1/69

<i>Jatropha curcas</i> 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 <i>J. curcas</i> generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for <i>Jatropha</i> 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 <i>J. curcas</i> and resistant <i>Jatropha integerrima</i> 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 <i>Jatropha</i>. This reference genome assembly gives an insight into the understanding of the complex genetic structure of <i>Jatropha</i>, and serves as source for the development of agronomically improved virus-resistant and oil-producing lines.