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New insights into domestication of carrot from root transcriptome analyses
Jun Rong1, Youri Lammers, Jared L Strasburg
1Plant Ecology and Phytochemistry, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden 2300RA, The Netherlands. rong_jun@hotmail.com.
BMC Genomics
|October 15, 2014
Summary
Carrot domestication involved selection and gene flow from wild relatives, leading to reduced genetic diversity in western cultivars but retaining significant diversity. Regulatory gene expression changes were key to developing desirable traits.
Area of Science:
- Plant genetics
- Crop domestication
- Evolutionary biology
Background:
- Understanding crop domestication provides insights into rapid evolution and agricultural improvement.
- Carrot domestication processes and genes under selection were investigated using transcriptome analysis.
Purpose of the Study:
- To elucidate the evolutionary history and genetic underpinnings of carrot domestication.
- To identify genes and regulatory mechanisms influencing cultivated carrot traits.
Main Methods:
- Sequencing of root transcriptomes from cultivated and wild carrots.
- Optimization of single nucleotide polymorphism (SNP) discovery and genotyping.
- Phylogenetic analysis and population genetic statistics (e.g., Fst).
- Differential gene expression analysis between cultivated and wild carrot roots.
Main Results:
- Identified 11,369 SNPs, with 622 validated and genotyped across diverse carrot populations.
- Phylogenetic analysis suggested eastern carrots may originate from Western Asia, with western carrots selected from eastern types.
- Significant reduction in genetic diversity in western cultivars, offset by gene flow from wild carrots.
- Differential gene expression observed, including up-regulation of water-channel and carotenoid-binding protein genes, and silencing of allergen genes in cultivars.
Conclusions:
- Western carrots likely originated from eastern carrots, with domestication involving selection and introgression from wild Daucus carota subspecies.
- Domestication led to reduced genetic diversity in western cultivars, but substantial diversity is retained.
- Regulatory changes in gene expression, rather than just sequence variation, appear crucial for carrot domestication and the development of key traits.
