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Identification of candidate genes JcARF19 and JcIAA9 associated with seed size traits in Jatropha

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Abstract

Jatropha curcas is a new promising bioenergy crop due to the high oil content in its seeds that can be converted into biodiesel. Seed size, a major determinant of Jatropha oil yield, is a target trait for Jatropha breeding. Due to the vital roles of phytohormone auxin in controlling seed and fruit development, we screened key genes in auxin pathway including ARF and IAA families and downstream effectors to identify candidate genes controlling seed size in Jatropha. As a result, JcARF19 was mapped in the major quantitative trait locus (QTL) region and significantly associated with seed length. By using expression QTL (eQTL) analysis to link variants with functional candidate genes, we provided evidences that seed traits were affected by the interaction of JcARF19 and JcIAA9. ARF19 and IAA9, involved in auxin signal transduction, were conserved in higher plants. These data including the single-nucleotide polymorphisms (SNPs) in the two genes could lead to utilization of the genes by integrating favored alleles into elite varieties through marker-assisted selection.

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Abbreviations

ANOVA:

Analysis of variance

ARF:

Auxin response factor

bp:

Base pair

kbp:

Kilobase pair

LG:

Linkage group

MAS:

Marker-assisted selection

PCR:

Polymerase chain reaction

QTL:

Quantitative trait locus

SE:

Standard error

SNP:

Single-nucleotide polymorphism

SSR:

Simple sequence repeat

RT:

Reverse transcriptase

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Acknowledgments

The work is part of the project “Genetic Improvement of Jatropha” initiated and coordinated by Professor Nam-Hai Chua, Rockefeller University, USA. We thank Dr. Frederic Berger, Yan Hong, Chengxin Yi, Zhongchao Yin, Jing Li, and Mr. Xuezhi Ouyang (Temasek Life Sciences Laboratory, Singapore) for providing materials and valuable technical assistance on this work. This work was supported by the Temasek Life Sciences Laboratory, JOil(S) Pte, and Strategic Priority Research Programof the Chinese Academy of Sciences Grant No. XDB11040300. CMW is supported by a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD, 010809001), the Fundamental Research Funds for the Central Universities (KYRC201208, KYZ201202-6), and “Shuangchuang” projects, Jiangsu Province, China. JY and YWS were supported by Strategic Priority Research Programof the Chinese Academy of Sciences Grant No. XDB11040300. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Conflict of interest

The authors have declared that no competing interests exist.

Author information

Authors and Affiliations

  1. Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore

    Jian Ye, Peng Liu, Jing Qu, Yanwei Sun, Fei Sun, Yulin Jiang, Genhua Yue & Chunming Wang

  2. Department of Psychiatry, Carve college of Medicine, University of Iowa, Iowa City, IA, 52242, USA

    Chengsong Zhu

  3. Biomass Energy Research Institute, Neijiang Academy of Agricultural Sciences, Sichuan, China

    Xianghua Wang

  4. State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China

    Jian Ye

  5. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China

    Chunming Wang

Authors
  1. Jian Ye
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  2. Peng Liu
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  3. Chengsong Zhu
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  4. Jing Qu
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  5. Xianghua Wang
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  6. Yanwei Sun
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  7. Fei Sun
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  8. Yulin Jiang
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  9. Genhua Yue
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  10. Chunming Wang
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Corresponding authors

Correspondence to Genhua Yue or Chunming Wang.

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Authors’ contribution

JY and CMW conceived the experiments. CMW, PL, XHW and FS collected genotype and phenotype data. CSZ, YWS and JQ analyzed the data. JY and CMW analyzed the data and wrote the manuscript. GHY supervised the project on Jatropha molecular breeding and revised the manuscript. All authors read and approved the final manuscript.

Jian Ye and Peng Liu contributed equally to this work.

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Ye, J., Liu, P., Zhu, C. et al. Identification of candidate genes JcARF19 and JcIAA9 associated with seed size traits in Jatropha. Funct Integr Genomics 14, 757–766 (2014). https://doi.org/10.1007/s10142-014-0400-5

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  • DOI: https://doi.org/10.1007/s10142-014-0400-5

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