title: Identification of alleles of carotenoid pathway genes important for zeaxanthin accumulation in potato tubers.
abstract: We have investigated the genetics and molecular biology of orange flesh colour in potato (Solanum tuberosum L.). To this end the natural diversity in three genes of the carotenoid pathway was assessed by SNP analyses. Association analysis was performed between SNP haplotypes and flesh colour phenotypes in diploid and tetraploid potato genotypes. We observed that among eleven beta-carotene hydroxylase 2 (Chy2) alleles only one dominant allele has a major effect, changing white into yellow flesh colour. In contrast, none of the lycopene epsilon cyclase (Lcye) alleles seemed to have a large effect on flesh colour. Analysis of zeaxanthin epoxidase (Zep) alleles showed that all (diploid) genotypes with orange tuber flesh were homozygous for one specific Zep allele. This Zep allele showed a reduced level of expression. The complete genomic sequence of the recessive Zep allele, including the promoter, was determined, and compared with the sequence of other Zep alleles. The most striking difference was the presence of a non-LTR retrotransposon sequence in intron 1 of the recessive Zep allele, which was absent in all other Zep alleles investigated. We hypothesise that the presence of this large sequence in intron 1 caused the lower expression level, resulting in reduced Zep activity and accumulation of zeaxanthin. Only genotypes combining presence of the dominant Chy2 allele with homozygosity for the recessive Zep allele produced orange-fleshed tubers that accumulated large amounts of zeaxanthin.
authors.affiliation: Laboratory of Plant Breeding, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands. Anne-marie.Wolters@wur.nl
authors.forename: Anne-Marie A
authors.initials: AM
authors.lastname: Wolters
authors.forename: Jan G A M L
authors.initials: JG
authors.lastname: Uitdewilligen
authors.forename: Bjorn A
authors.initials: BA
authors.lastname: Kloosterman
authors.forename: Ronald C B
authors.initials: RC
authors.lastname: Hutten
authors.forename: Richard G F
authors.initials: RG
authors.lastname: Visser
authors.forename: Herman J
authors.initials: HJ
authors.lastname: van Eck
mesh_terms: D000483:Alleles; D053898:Biosynthetic Pathways; D002338:Carotenoids / Q000096:biosynthesis*; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D019753:Intramolecular Lyases / Q000235:genetics / Q000378:metabolism; D006899:Mixed Function Oxygenases / Q000235:genetics / Q000378:metabolism; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D035281:Plant Tubers / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D011198:Solanum tuberosum / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D024341:Xanthophylls / Q000378:metabolism*; D065146:Zeaxanthins
chemical_list: D010940:Plant Proteins; D024341:Xanthophylls; D065146:Zeaxanthins; D002338:Carotenoids; D006899:Mixed Function Oxygenases; D010088:Oxidoreductases; C097153:zeaxanthin epoxidase; C079232:beta-carotene hydroxylase; D019753:Intramolecular Lyases; C070925:lycopene cyclase-isomerase