Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
G3 (Bethesda). 2013 Sep 4;3(9):1467-79. doi: 10.1534/g3.113.007146.
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.
对六个野生马铃薯物种（包括 chc80-1、S. commersonii、S. demissum、S. sparsipilum、S. spegazzinii 和 S. stoloniferum）和一个栽培马铃薯品种（phuDH）进行了类固醇糖苷生物碱（SGA）代谢途径的五个候选基因和全基因组单核苷酸多态性（SNP）基因分型的自然变异研究，这些物种的 SGA 含量存在差异。对五个候选基因的扩增子进行了测序：初级代谢的 3-羟基-3-甲基戊二酰辅酶 A 还原酶 1 和 2（HMG1、HMG2）和 2,3-鲨烯环氧化酶（SQE），以及次级代谢的茄碱半乳糖基转移酶（SGT1）和葡萄糖基转移酶（SGT2）。在所测序的 DNA 3.7kb 范围内共检测到 337 个 SNP，产生了 354 种变异。与外显子相比，内含子中发现的多态性更多，与初级代谢相比，次级代谢中的基因也更多。虽然没有发现明显的偏离中性，但 dN/dS 比值<1，Tajima 的 D 检验的负值表明，在基因片段中存在纯化选择和遗传连锁。此外，SGA 途径的 dN/dS 比值模式表明，自然选择对其存在限制。核苷酸多样性估计值和 dN/dS 比值的比较表明，初级代谢基因比次级代谢基因受到更强的选择限制。在 HMG2、SQE、SGT1 和 SGT2 基因中，鉴定出了 phuDH（低 SGA）或 chc80-1（高 SGA）专有的 SNP 基因型。使用 SolCAP 8303 Illumina 马铃薯 SNP 芯片对六个假染色体上的 24 个 SNP 进行基因分型，发现了 8 个有信息的 SNP，这些 SNP 的基因型可以区分高、中、低水平的 SGA 积累。这些结果可用于评估分离或关联作图群体中 SGA 的积累情况。
