title: Sequence diversity in coding regions of candidate genes in the glycoalkaloid biosynthetic pathway of wild potato species.
abstract: Natural variation in five candidate genes of the steroidal glycoalkaloid (SGA) metabolic pathway and whole-genome single nucleotide polymorphism (SNP) genotyping were studied in six wild [Solanum chacoense (chc 80-1), S. commersonii, S. demissum, S. sparsipilum, S. spegazzinii, S. stoloniferum] and cultivated S. tuberosum Group Phureja (phu DH) potato species with contrasting levels of SGAs. Amplicons were sequenced for five candidate genes: 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 and 2 (HMG1, HMG2) and 2.3-squalene epoxidase (SQE) of primary metabolism, and solanidine galactosyltransferase (SGT1), and glucosyltransferase (SGT2) of secondary metabolism. SNPs (n = 337) producing 354 variations were detected within 3.7 kb of sequenced DNA. More polymorphisms were found in introns than exons and in genes of secondary compared to primary metabolism. Although no significant deviation from neutrality was found, dN/dS ratios < 1 and negative values of Tajima's D test suggested purifying selection and genetic hitchhiking in the gene fragments. In addition, patterns of dN/dS ratios across the SGA pathway suggested constraint by natural selection. Comparison of nucleotide diversity estimates and dN/dS ratios showed stronger selective constraints for genes of primary rather than secondary metabolism. SNPs (n = 24) with an exclusive genotype for either phu DH (low SGA) or chc 80-1 (high SGA) were identified for HMG2, SQE, SGT1 and SGT2. The SolCAP 8303 Illumina Potato SNP chip genotyping revealed eight informative SNPs on six pseudochromosomes, with homozygous and heterozygous genotypes that discriminated high, intermediate and low levels of SGA accumulation. These results can be used to evaluate SGA accumulation in segregating or association mapping populations.
authors.affiliation: Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
authors.forename: Norma C
authors.initials: NC
authors.lastname: Manrique-Carpintero
authors.forename: James G
authors.initials: JG
authors.lastname: Tokuhisa
authors.forename: Idit
authors.initials: I
authors.lastname: Ginzberg
authors.forename: Jason A
authors.initials: JA
authors.lastname: Holliday
authors.forename: Richard E
authors.initials: RE
authors.lastname: Veilleux
mesh_terms: D000470:Alkaloids / Q000096:biosynthesis* / Q000235:genetics; D000483:Alleles; D005700:Galactosyltransferases / Q000235:genetics; D018745:Genome, Plant; D005838:Genotype; D005964:Glucosyltransferases / Q000737:chemistry / Q000235:genetics; D024243:HMGB1 Protein / Q000235:genetics; D024261:HMGB2 Protein / Q000235:genetics; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000235:genetics*; D050603:Squalene Monooxygenase / Q000235:genetics
chemical_list: D000470:Alkaloids; D024243:HMGB1 Protein; D024261:HMGB2 Protein; D050603:Squalene Monooxygenase; D005700:Galactosyltransferases; D005964:Glucosyltransferases; C077995:solanidine glucosyltransferase
keywords: Infinium 8303 Potato Array; Solanum; dN/dS ratio; nucleotide diversity