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

机译：野生马铃薯物种糖基生物碱生物合成途径中候选基因编码区的序列多样性

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摘要

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.

机译：在六种野生[Solanum chacoense（chc 80-1），S。commersonii，S。demissum，S]中研究了甾体生物碱（SGA）代谢途径的五个候选基因的自然变异和全基因组单核苷酸多态性（SNP）基因型。 [Sparsipilum，S。spegazzinii，S。stoloniferum]和栽培的S. tuberosum Group Phureja（phu DH）马铃薯物种具有相对的SGA水平。对五个候选基因的扩增子进行了测序：主要代谢的3-羟基-3-甲基戊二酰辅酶A还原酶1和2（HMG1，HMG2）和2.3-角鲨烯环氧酶（SQE），茄碱半乳糖基转移酶（SGT1）和葡萄糖基转移酶（SGT2）次生代谢。在3.7 kb的测序DNA中检测到产生354个变异的SNP（n = 337）。与初级代谢相比，在内含子中发现的多态性比外显子多，在次级基因中发现的多态性更高。尽管没有发现与中性的显着差异，但dN / dS比<1和Tajima D试验的负值表明纯化了基因片段中的选择和遗传搭便车。此外，整个SGA途径的dN / dS比模式提示自然选择会产生限制。核苷酸多样性估计值和dN / dS比值的比较显示，对一级代谢而非二级代谢的基因有更强的选择性约束。鉴定了 HMG2 ， SQE ， SGT1 和 SGT2 。 SolCAP 8303 Illumina马铃薯SNP芯片的基因分型显示了六个假染色体上的八个信息性SNP，其纯合型和杂合型基因型可区分SGA积累的高，中和低水平。这些结果可用于评估SGA在分离或关联作图群体中的积累。 展开▼

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期刊名称 G3: GenesGenomesGenetics

作者
Norma C. Manrique-Carpintero; James G. Tokuhisa; Idit Ginzberg; Jason A. Holliday; Richard E. Veilleux;
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年(卷),期 2013(3),9

年度 2013

页码 1467–1479

总页数 13

原文格式 PDF

正文语种

中图分类遗传学;

关键词
nucleotide diversity dN/dS ratio Solanum Infinium 8303 Potato Array;

机译：核苷酸多样性;dN / dS比;茄属植物;Infinium 8303马铃薯阵列;

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专利

1. Sequence Diversity in Coding Regions of Candidate Genes in the Glycoalkaloid Biosynthetic Pathway of Wild Potato Species [J] . Norma C. Manrique-Carpintero, James G. Tokuhisa, Idit Ginzberg, G3: Genes, Genomes, Genetics . 2013,第9期

机译：野生马铃薯物种糖基生物碱合成途径中候选基因编码区的序列多样性

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4. AFLP analysis of genetic diversity in wild species of malus [C] . Proceeding of International Apple Symposium 2002 null . 2002

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5. uses of a nucleic acid, a unit of expression, and the sequence of nucleic acid, nucleic acid, unit of expression, methods for altering or inducing transcription and gene expression rates in microorganisms compared to wild type, for prepare biosynthetic products, lysine, methionine, and threonine, expression cassette, expression vector, genetically modified microorganism, and expression unit [P] . 外国专利： BRPI0417770A . 2007-04-17

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

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