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.

Genome-Wide HMG Family Investigation and Its Role in Glycoalkaloid Accumulation in Wild Tuber-Bearing Solanum commersonii

“…The remaining sequences were named HMG3, HMG4 and HMG5, using progressive numbering. It is noteworthy that StHMG5 has been previously annotated as StHMG2 [26,48]. However, our data rule out any orthologous relationship between StHMG5 and AtHMG2.…”

“…Previous papers on tobacco demonstrated that the constitutive expression of HMG resulted in phytosterol overproduction, indicating a major role of HMG in the upregulation of sterol abundance [53,54]. Carpintero et al [26] and Ginzberg et al [51] provided evidence that StHMG1 and StHMG2 were the primary metabolism genes directly involved in SGA biosynthesis, and that overexpression of StHMG1 in potato plants increased SGA content in the leaves. No papers have been published on the role of their orthologs in wild potato species, a strategic source of stress resistances and tuber quality traits.…”

“…Furthermore, it is the first wild potato whose genome sequence has been released [23], paving the way to different studies aimed to gain insights into genomic evolution at the sequence level from the wild to the cultivated form [24,25]. S. commersonii possesses a diverse mixture of glycoalkaloids, such as dehydrotomatine, dehydrodemissine and dehydrocommersonine, which are among the most poisonous compounds against different potato pests [26]. In this species, Vazquez et al [27] also reported the presence of demissine, commersonine and a-tomatine.…”

Development and application of a 20K SNP array in potato

“…Three more QTLs Sga3.1, Sga5.1 and Sga11.1 were identified at genomic positions, where no obvious candidate genes have been identified. Although Sga3.1 was only identified by GWAS and Sga5.1 only in one mapping population SH ´ RH, the QTL Sga11.1 was discovered by GWAS and validated in the SH × RH population, and co-localizes with QTLs identified in an earlier study (Manrique-Carpintero et al 2013). On the other hand the associated SolCAP SNPs identified by Manrique-Carpintero et al (2013) could not be reproduced in our study.…”

“…Previous mapping studies identified several QTLs for SGA accumulation in potato. While most studies measure SGA levels in potato leaves (Manrique-Carpintero et al 2013;Manrique-Carpintero et al 2014;Medina et al 2002;Ronning et al 1999;Sagredo et al 2006;Sagredo et al 2011;Yencho et al 1998), a few have also been conducted on SGA accumulation in tubers (Mariot et al 2016;Sørensen et al 2008;Valcarcel et al 2014). The majority of these mapping studies involved hybrids with wild species like S. sparsipilum (Sørensen et al 2008) S. berthaulthii (Yencho et al 1998), S. phureja (Medina et al 2002), S. commersonii (Carputo et al 2003) and S. chacoense (Manrique-Carpintero et al 2014;Medina et al 2002;Ronning et al 1999;Sagredo et al 2006;Sagredo et al 2011).…”