New insights into domestication of carrot from root transcriptome analyses

Abstract

BackgroundUnderstanding 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.ResultsThe 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.ConclusionsWestern 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-895) contains supplementary material, which is available to authorized users.

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

“…In contrast, western cultivars clearly separated from wild and eastern cultivated carrots, and some inbred lines (I3 and I4) have a purified genetic pattern shared with western cultivated accessions, reflecting the intensive breeding practiced in western regions. Nucleotide diversity (π) 25 estimates showed that wild carrots have a slightly higher level of genetic diversity than cultivated carrots (Supplementary Table 18), indicating the occurrence of a limited domestication bottleneck, consistent with previous findings 3,26 . When D. carota subspecies, which have morphological characteristics contributing to their sexual isolation relative to carrot 27 , were excluded from diversity estimates, this observation was more evident from comparative analysis (wild, π = 9.5 × 10 −4 versus cultivated, π = 8.6 × 10 −4 ).…”

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

“…Future work will benefit from extra samples from neighboring countries of the central Asia geographic region. Rong et al [26] also used SNPs and samples of wild carrots from different geographic origins except central Asia, and their Bayesian tree showed that wild carrots from western Asia are the closest relatives to eastern cultivated carrots.…”

“…Arbizu et al [36], using 94 nuclear orthologs, also reported that accessions of D. carota from Portugal, Spain and Morocco were placed in an individual sub-clade with 100% bootstrap support. Rong et al [26] marked one group of their Bayesian tree containing subspecies of D. carota as “Mediterranean, southern Europe”. Within this group, there is a sub-clade consisting of samples from Portugal and Spain labeled subsp.…”

“…Similar results were obtained by Bradeen et al [25] with AFLPs and inter-simple sequence repeats (ISSR) and they concluded wild carrots had no substructure. Rong et al [26] obtained a Daucus phylogeny using SNPs and found the subspecies of D. carota to be intermixed. Later, Lee and Park [27] mentioned D. sahariensis , D. syrticus and D. gracilis are probably the closest relatives to D. carota .…”

High-throughput sequencing in medicinal plant transcriptome studies

“…The processes of carrot domestication were demonstrated, and genes under selection were identified based on transcriptome analyses (Rong et al, 2014). The processes of carrot domestication were demonstrated, and genes under selection were identified based on transcriptome analyses (Rong et al, 2014).…”