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Genotyping by sequencing-based linkage map construction and identification of quantitative trait loci for yield-related traits and oil content in Jatropha (Jatropha curcas L.)

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Abstract

Background

Jatropha (Jatropha curcas L.) has been considered as a potential bioenergy crop and its genetic improvement is essential for higher seed yield and oil content which has been hampered due to lack of desirable molecular markers.

Methods and results

An F2 population was created using an intraspecific cross involving a Central American line RJCA9 and an Asiatic species RJCS-9 to develop a dense genetic map and for Quantitative trait loci (QTL) identification. The genotyping-by-sequencing (GBS) approach was used to genotype the mapping population of 136 F2 individuals along with the two parental lines for classification of the genotypes based on single nucleotide polymorphism (SNPs). NextSeq 2500 sequencing technology provided a total of 517.23 million clean reads, with an average of ~ 3.8 million reads per sample. We analysed 411 SNP markers and developed 11 linkage groups. The total length of the genetic map was 4092.3 cM with an average marker interval of 10.04 cM. We have identified a total of 83 QTLs for various yield and oil content governing traits. The percentage of phenotypic variation (PV) was found to be in the range of 8.81 to 65.31%, and a QTL showed the maximum PV of 65.3% for a total seed number on the 6th linkage group (LG).

Conclusions

The QTLs detected in this study for various phenotypic traits will lay down the path for marker-assisted breeding in the future and cloning of genes that are responsible for phenotypic variation.

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Data availability

GBS sequence data have been deposited in Gen-Bank with SRA data: PRJNA759411 and Submission ID: SUB10228265, also provided in results section.

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Acknowledgements

We thank Dr.Ajit Sapre, R&D, Group President at the Reliance Industries Ltd, for the encouragement and support for this work and Mr. Janyavula V. Narasimham and Dr.Makarand Phadke for their guidance all through this study. We thank Dr.Santanu Dasgupta, Senior vice president for providing guidance, support and for reviewing the paper. We also thank Genotypic Pvt. Ltd, Bangalore for carrying out the sequencing of the Jatropha genome.

Funding

We thank Reliance Industries Limited for funding this research. This research did not receive any specific grant from external funding agencies in the public, commercial, or not-for-profit sectors.

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SA and VY conceptualized the idea, designed experiments, wrote and edited the manuscript. VY conducted experiments and analysed all data. SJ did bioinformatics analysis, VY developed mapping population and did phenotyping. VM estimated total oil content. SP performed statistical analyses. SJ and NK reviewed the manuscript. SA supervised the entire study.

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Correspondence to S. Arockiasamy.

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Yepuri, V., Jalali, S., Mudunuri, V. et al. Genotyping by sequencing-based linkage map construction and identification of quantitative trait loci for yield-related traits and oil content in Jatropha (Jatropha curcas L.). Mol Biol Rep 49, 4293–4306 (2022). https://doi.org/10.1007/s11033-022-07264-w

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