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

Nagesh Kancharla,J Narasimham,Neeta Madan,Boney Kuriakose,Bijal Thakkar,Vb Reddy,Saakshi Jalali,Arockiasamy S,Vinod Nair,Vijay Yepuri

doi:10.3390/genes10010069

Nagesh Kancharla, J Narasimham + Show 8 more

Open Access

https://doi.org/10.3390/genes10010069

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Journal: Genes	Publication Date: Jan 21, 2019
Citations: 20	License type: CC BY 4.0

Affiliation: Reliance Industries (India), SciGenom Labs (India)

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.

Highlights

Jatropha curcas L. belongs to the Euphorbiaceae family, which has species producing vegetable oils, medicinal, pesticidal industrial chemicals, and various other biologically active compounds [1]
The genome analyses presented in this study provides a rich resource of genetic information for advanced J. curcas breeding and genetic improvement programs
We considered three categories of plants for this study which includes oil-producing plants (Brassica napus, Brassica rapa, Arachis hypogaea, Helianthus annuus, and Ricinus communis), oil-producing algae (Botryococcus braunii, Chlamydomonas reinhardtii, Monoraphidium neglectum, and Nannochloropsis gaditana) and model plant species (Oryza sativa, Zea mays, Medicago truncatula, and Arabidopsis thaliana)

Summary

Introduction

Jatropha curcas L. belongs to the Euphorbiaceae family, which has species producing vegetable oils, medicinal, pesticidal industrial chemicals, and various other biologically active compounds [1]. This plant is a shrub which can grow in regions of low to moderate rainfall, and attain a height of 20 feet or more [2]. The shrub is well known for the production of non-edible oil-bearing seeds, and it is preferred for biodiesel production over other food crops It is cultivated on a smaller scale in Australia, South Africa, India, Brazil, Fiji, Honduras, Panama, El Salvador, Jamaica, Puerto Rico, and other parts of Caribbean [3].

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