New insights into domestication of carrot from root transcriptome analyses

Abstract

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.

Figure 1

Cultivated and wild carrot roots used for the transcriptome sequencing in the study.

Figure 2

Illustration of the domestication model. The effective population size of wild carrot (N _W) is constant. Carrot domestication started T _B + T generations ago. The size of domestication bottleneck is N _B and the duration of the bottleneck is T _B. Afterwards, the effective population size of cultivated carrot increased exponentially. After T generations, cultivated carrot has a present population size of N _C. During the past T generations, gene flow occurred between cultivated and wild carrots. The migration rate from cultivated to wild carrot is m _WC and that from wild to cultivated carrot is m _CW.

Figure 3

Phylogenetic tree of carrot. Phylogenetic analysis was based on the combined datasets of 622-SNP and 89-SNP. Different Daucus species were used as outgroup to D. carota. Numbers at the nodes indicate posterior probabilities (%). Sample names beginning with “W” are wild species and those with “C” are cultivars; the middle name of each sample indicates species name (for outgroup) or subspecies name of wild species, or root type/accession name of cultivars; the sampling country is indicated at the end. For more details of the samples see Table 1 and Additional file 1: Table S1. Group 1–5 were designed to represent the main phylogeographic structure of the tree. Note that the grouping is somewhat arbitrary because there is no distinct boundary between groups, for instance a few wild carrots are within the Group 4 of Eastern Cultivars.

Figure 4

Genetic structure of carrot. Genetic structure of cultivated and wild carrots was inferred using Structure 2.3.4 based on the 622-SNP dataset. The clusters of K = 3 were shown for the highest Ln likelihood. Vertical bars represent different cultivated and wild carrots. The label of each sample is given above each bar. Those beginning with “C” are cultivars and with “W” are wild species; the middle name of each sample indicates root type/accession name of cultivars or subspecies name of wild Daucus carota subspecies; the sampling country is indicated at the end. For details of each carrot sample see Table 1 and Additional file 1: Table S1. The length of each colored segment in a bar represents the relative proportion of the Bayesian assignment to each cluster. Group 1–5 indicated below the bars are according to Figure 3.

Figure 5

Histogram of gene expression difference. Gene expression difference between cultivated and wild carrots of a contig was calculated as (mean coverage of cultivated carrots - mean coverage of wild carrots) / (mean coverage of cultivated and wild carrots).