Abstract
Carrot is one of the most important vegetables worldwide, owing to its capability to develop fleshy, highly nutritious storage roots. It was domesticated ca. 1,100 years ago in Central Asia. No systematic knowledge about the molecular mechanisms involved in the domestication syndrome in carrot are available, however, the ability to form a storage root is undoubtedly the essential transition from the wild Daucus carota to the cultivated carrot. Here, we expand on the results of a previous study which identified a polymorphism showing a significant signature for selection upon domestication. We mapped the region under selection to the distal portion of the long arm of carrot chromosome 2, confirmed that it had been selected, as reflected in both the lower nucleotide diversity in the cultivated gene pool, as compared to the wild (πw/πc = 7.4 vs. 1.06 for the whole genome), and the high FST (0.52 vs. 0.12 for the whole genome). We delimited the region to ca. 37 kb in length and identified a candidate domestication syndrome gene carrying three non-synonymous single nucleotide polymorphisms and one indel systematically differentiating the wild and the cultivated accessions. This gene, DcAHLc1, belongs to the AT-hook motif nuclear localized (AHL) family of plant regulatory genes which are involved in the regulation of organ development, including root tissue patterning. AHL genes work through direct interactions with other AHL family proteins and a range of other proteins that require intercellular protein movement. Based on QTL data on root thickening we speculate that DcAHLc1 might be involved in the development of the carrot storage root, as the localization of the gene overlapped with one of the QTLs. According to haplotype information we propose that the ‘cultivated’ variant of DcAHLc1 has been selected from wild Central Asian carrot populations upon domestication and it is highly predominant in the western cultivated carrot gene pool. However, some primitive eastern landraces and the derived B7262 purple inbred line still carry the ‘wild’ variant, reflecting a likely complexity of the genetic determination of the formation of carrot storage roots.
Highlights
Carrot is one of the most important root vegetable crops grown worldwide on ca. 1.2 million hectares (FAOSTAT, 2013)
The πw/πc peaked around 41,858,000–41,866,000, where 7-fold decrease in nucleotide diversity was observed in the cultivated group, confirming the previously reported selective sweep around the cult polymorphism (Grzebelus et al, 2014)
A set of traits differentiating the cultivated form from its wild progenitor, conferring adaptation to a cultivated environment and to consumer needs, can be defined. They are collectively called the domestication syndrome (Gepts, 2014). These traits have been under continuous selection in the course of the domestication process, resulting in local decrease of variability caused by selective sweeps in genomic regions overlapping with domestication syndrome genes in cultivated populations, as compared to their wild counterparts
Summary
Carrot is one of the most important root vegetable crops grown worldwide on ca. 1.2 million hectares (FAOSTAT, 2013). As a storage root similar to modern carrots, it has been grown in those regions since the 10th century (Mackevic, 1932; Zagorodskikh, 1939). The first domesticated carrots produced purple or yellow roots (Banga, 1963), while orange carrots did not appear in Europe before the 15th century (Banga, 1957a,b; Stolarczyk and Janick, 2011). Recent molecular studies have provided answers to questions concerning carrot evolution and domestication and confirmed that domesticated carrots were derived from wild populations of Central Asian D. carota (Iorizzo et al, 2013). It was clearly shown that the cultivated germplasm could be divided into two distinct groups: the eastern and the western gene pools (Baranski et al, 2012; Iorizzo et al, 2013; Grzebelus et al, 2014), in agreement with an earlier hypothesis on carrot evolution by Small (1978), based on morphological observations
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