Functional Gene Polymorphism to Reveal Species History: The Case of the CRTISO Gene in Cultivated Carrots

Abstract

BackgroundCarrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO) has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history.Methodology/Principal FindingsIn this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group), and another one mainly from Europe (Western group). The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots.ConclusionThe carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia material remains unclear.

Carotenoid Content and Root Color of Cultivated Carrot: A Candidate-Gene Association Study Using an Original Broad Unstructured Population

“…Polymorphic sequences for IPI, PDS, LCYE, LCYB1, CHXE, ZEP and CRTISO genes were obtained from previous works [ 33 , 35 ].…”

“…Primers were designed based on publicly available databases ( S1 Table ). PCR reactions, cycling conditions and sequencing protocol were identical as in [ 35 ]. All sequences were aligned by using Geneious software and haplotypes were inferred with DnaSP.…”

“…Indeed, false positives can be detected when phenotypic traits are correlated with underlying population structure at non causal loci [ 32 ]. Daucus carota L. genetic resources are known to be structured into two distinct genetic groups [ 33 – 35 ] according to their geographical origin. Moreover carotenoid content pattern is closely linked to these genetic groups: cultivars with high lycopene content belong mostly to one genetic group.…”

Carotenoid Presence Is Associated with the Or Gene in Domesticated Carrot

“…This is the first report of genome-wide LD in carrot. LD decay rates appear slower in domesticated samples around regions putatively under selection, such as the Y region (Iorizzo et al 2016) and the cult region (Macko-Podgorni et al 2017), as well as several carotenoid biosynthesis genes (Clotault et al 2010;Soufflet-Freslon et al 2013).…”

Carotene Hydroxylase Activity Determines the Levels of Both α-Carotene and Total Carotenoids in Orange Carrots

“…This color spectrum is mostly determined by the abundance of carotenoids, with the exception of purple carrots, which also accumulate anthocyanins (Simon et al, 2008;Montilla et al, 2011). The earliest cultivated carrots were yellow or purple and emerged in the Afghanistan region before the 900s, while orange and white cultivars were bred in the 16th century (Banga, 1957;Soufflet-Freslon et al, 2013). Despite significant progress in the identification of genetic markers associated with root color in recent years, knowledge of the molecular basis of diverse color phenotypes is sparse (Santos and Simon, 2006;Just et al, 2009;Fuentes et al, 2012;Rodriguez-Concepcion and Stange, 2013).…”