Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species

dc.contributor.authorManrique-Carpintero, Norma C.en
dc.contributor.authorTokuhisa, James G.en
dc.contributor.authorGinzberg, Iditen
dc.contributor.authorHolliday, Jason A.en
dc.contributor.authorVeilleux, Richard E.en
dc.contributor.departmentForest Resources and Environmental Conservationen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.description.abstractNatural 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 galactosyl-transferase (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.en
dc.description.notesWe thank Suzanne Piovano for technical assistance, Maichel Miguel Aguayo Bustos for programming help, Jonathan Stallings of the Laboratory for Interdisciplinary Statistical Analysis LISA for statistical consultation, and Alexandre P. Marand for protein modeling. This research was supported by Research Grant No. IS-4134-08 R from BARD, The United States-Israel Binational Agricultural Research and Development Fund.en
dc.description.sponsorshipBARD, The United States-Israel Binational Agricultural Research and Development FundUS-Israel Binational Science Foundation [IS-4134-08 R]en
dc.publisherGenetics Society of Americaen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.subjectnucleotide diversityen
dc.subjectdN/dS ratioen
dc.subjectInfinium 8303 Potato Arrayen
dc.titleSequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Speciesen
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
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