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

Abstract

Accumulated in large amounts in carrot, carotenoids are an important product quality attribute and therefore a major breeding trait. However, the knowledge of carotenoid accumulation genetic control in this root vegetable is still limited. In order to identify the genetic variants linked to this character, we performed an association mapping study with a candidate gene approach. We developed an original unstructured population with a broad genetic basis to avoid the pitfall of false positive detection due to population stratification. We genotyped 109 SNPs located in 17 candidate genes – mostly carotenoid biosynthesis genes – on 380 individuals, and tested the association with carotenoid contents and color components. Total carotenoids and β-carotene contents were significantly associated with genes zeaxanthin epoxydase (ZEP), phytoene desaturase (PDS) and carotenoid isomerase (CRTISO) while α-carotene was associated with CRTISO and plastid terminal oxidase (PTOX) genes. Color components were associated most significantly with ZEP. Our results suggest the involvement of the couple PDS/PTOX and ZEP in carotenoid accumulation, as the result of the metabolic and catabolic activities respectively. This study brings new insights in the understanding of the carotenoid pathway in non-photosynthetic organs.

Fine Mapping, Transcriptome Analysis, and Marker Development forY2, the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carotaL.)

“…Previous studies in carrot have mapped QTL for carotenoid accumulation with AFLP markers ( Santos and Simon 2002 ), and/or have utilized candidate genes from the MEP and carotenoid biosynthetic pathways to identify the genetic control of β-carotene accumulation ( Just et al 2007 , 2009 ; Jourdan et al 2015 ; Iorizzo et al 2016 ). However, this is the first study to use a whole-genome approach along with a transcriptome analysis to better understand the regulation of high β-carotene accumulation.…”

“…Several carrot studies have found associations between carotenoid content and carotenoid biosynthetic genes, including a study by Arango et al (2014) , which identified a Carotene Hydroxylase ( CYP97A3 ) homolog that contributed to increased carotenoid content due to increased amounts of α-carotene. Further, a candidate gene association analysis by Jourdan et al (2015) suggested total carotenoid and β-carotene quantities were significantly associated with the genes Zeaxanthin Epoxidase ( ZEP ), Phytoene Desaturase ( PDS ), and Carotenoid Isomerase ( CRTISO ). To verify whether these genes underlie the Y 2 locus, a whole-genome integrative approach was used.…”

ZEAXANTHIN EPOXIDASE Activity Potentiates Carotenoid Degradation in Maturing Seed

“…Quantitative trait locus (QTL) analyses have demonstrated that significant levels of natural variation for seed carotenoid traits exist in several plant species (Wong et al, 2004;Abbo et al, 2005;Fernandez et al, 2008;Blanco et al, 2011;Kandianis et al, 2013), but these intervals typically contain hundreds or thousands of genes; as a result, few causal loci underlying QTLs have been defined (Pozniak et al, 2007;Chandler et al, 2013;Gonzalez-Jorge et al, 2013). Significant natural variation for seed carotenoids also is present in diversity panels of maize (Zea mays), wheat (Triticum aestivum), Citrus spp., chickpea (Cicer arietinum), carrot (Daucus carota), pea (Pisum sativum), cassava (Manihot esculenta), and Arabidopsis (Abbo et al, 2010;Arango et al, 2010;Welsch et al, 2010;Yan et al, 2010;Blanco et al, 2011;Cook et al, 2012;Gonzalez-Jorge et al, 2013;Kandianis et al, 2013;Owens et al, 2014;Jourdan et al, 2015;Suwarno et al, 2015). Advances in high-throughput phenotyping and genotyping are allowing some of the genes underlying this natural variation to be identified through genome-wide association studies (GWAS; Harjes et al, 2008;Zhou et al, 2012;Gonzalez-Jorge et al, 2013;Owens et al, 2014;Wen et al, 2014;Sonah et al, 2015).…”

Advances in metabolomic applications in plant genetics and breeding.

“…Golden Rice was further enhanced by introducing a different phytoene synthase gene and increasing b-carotene accumulation another ten-fold [142]. Combined quantitative genetic and metabolomic approaches have recently identified several QTLs associated with b-carotene accumulation and/or carotenoid composition in maize [143], potato [144], carrot [145] and tomato [146], as well as candidate genes that could provide useful targets in carotenoid (e.g. b-carotene and lycopene) biofortification efforts.…”