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

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

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...

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Main Authors: Manrique-Carpintero, Norma C., Tokuhisa, James G., Ginzberg, Idit, Holliday, Jason A., Veilleux, Richard E.
Format: Online
Language:English
Published: Genetics Society of America 2013
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755908/
id pubmed-3755908
recordtype oai_dc
spelling pubmed-37559082013-09-01 Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species Manrique-Carpintero, Norma C. Tokuhisa, James G. Ginzberg, Idit Holliday, Jason A. Veilleux, Richard E. Investigations 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. Genetics Society of America 2013-09-01 /pmc/articles/PMC3755908/ /pubmed/23853090 http://dx.doi.org/10.1534/g3.113.007146 Text en Copyright © 2013 Manrique-Carpintero et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Manrique-Carpintero, Norma C.
Tokuhisa, James G.
Ginzberg, Idit
Holliday, Jason A.
Veilleux, Richard E.
spellingShingle Manrique-Carpintero, Norma C.
Tokuhisa, James G.
Ginzberg, Idit
Holliday, Jason A.
Veilleux, Richard E.
Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species
author_facet Manrique-Carpintero, Norma C.
Tokuhisa, James G.
Ginzberg, Idit
Holliday, Jason A.
Veilleux, Richard E.
author_sort Manrique-Carpintero, Norma C.
title Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species
title_short Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species
title_full Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species
title_fullStr Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species
title_full_unstemmed Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species
title_sort sequence diversity in coding regions of candidate genes in the glycoalkaloid biosynthetic pathway of wild potato species
description 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.
publisher Genetics Society of America
publishDate 2013
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755908/
_version_ 1612006483646480384

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