New insights into domestication of carrot from root transcriptome analyses

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• 作者：Jun Rong (1) (2)
  Youri Lammers (1)
  Jared L Strasburg (3)
  Natasha S Schidlo (1)
  Yavuz Ariyurek (4)
  Tom J de Jong (1)
  Peter GL Klinkhamer (1)
  Marinus JM Smulders (5)
  Klaas Vrieling (1)
  
  1. Plant Ecology and Phytochemistry ; Institute of Biology Leiden ; Leiden University ; PO Box 9505 ; Leiden ; 2300 ; RA ; The Netherlands
  2. Center for Watershed Ecology ; Institute of Life Science and Key Laboratory of Poyang Lake Environment and Resource Utilization ; Ministry of Education ; Nanchang University ; Nanchang ; 330031 ; China
  3. Department of Biology ; University of Minnesota-Duluth ; Duluth ; USA
  4. Leiden Genome Technology Center ; Human and Clinical Genetics ; Leiden University Medical Center ; Postzone S4-P ; PO Box 9600 ; Leiden ; 2300 ; RC ; The Netherlands
  5. Plant Research International ; Wageningen UR ; PO Box 16 ; Wageningen ; 6700 ; AA ; The Netherlands
  
• 关键词：Crop and wild relative ; Daucus carota ; Domestication gene ; Gene expression difference ; High ; throughput sequencing ; Single nucleotide polymorphism ; Root transcriptome
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,174 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. Results The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication. Conclusions Western carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.