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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.

SUBMITTER: Manrique-Carpintero NC

PROVIDER: S-EPMC3755908 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Sequence diversity in coding regions of candidate genes in the glycoalkaloid biosynthetic pathway of wild potato species.

Manrique-Carpintero Norma C NC Tokuhisa James G JG Ginzberg Idit I Holliday Jason A JA Veilleux Richard E RE

G3 (Bethesda, Md.) 20130904 9

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 ...[more]

PMID: 23853090

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Project description:Late blight, caused by the oomycete Phytophthora infestans, is the most devastating disease in potato-producing regions of the world. Cultivation of resistant varieties is the most effective and environmentally friendly way to control potato late blight disease, and identification of germplasms with late blight resistance and clarification their genetic relationship would promote the development of the resistant varieties. In this study, a diverse population of 189 genotypes with potential late blight resistance, consisting of 20 wild species and cultivated Solanum tuberosum Andigenum group and Chilotanum group, was screened for the presence of late blight resistance by performing challenge inoculation with four Phytophthora infestans isolates including one 13_A2 isolate, CN152. Ten elite resources with broad-spectrum resistance and 127 with isolate-specific resistance against P. infestans were identified. To improve the available gene pool for future potato breeding programs, the population was genotyped using 30 simple sequence repeat (SSR) markers covering the entire potato genome. A total of 173 alleles were detected with an average of 5.77 alleles per locus. Structure analysis discriminated the 189 potato genotypes into five populations based on taxonomic classification and genetic origin with some deviations. There was no obvious clustering by country of origin, ploidy level, EBN (endosperm balance number) value, or nuclear clade. Analysis of molecular variance showed 10.08% genetic variation existed among populations. The genetic differentiation (Fst) ranged from 0.0937 to 0.1764, and the nucleotide diversity (π) was 0.2269 across populations with the range from 0.1942 to 0.2489. Further genotyping of 20K SNP array confirmed the classification of SSRs and could uncover the genetic relationships of Solanum germplasms. Our results indicate that there exits abundant genetic variation in wild and cultivated potato germplasms, while the cultivated S. tuberosum Chilotanum group has lower genetic diversity. The phenotypic and genetic information obtained in this study provide a useful guide for hybrid combination and resistance introgression from wild gene pool into cultivated species for cultivar improvement, as well as for germplasm conservation efforts and resistance gene mining.

Project description:BackgroundGlycoalkaloids are bioactive compounds that contribute to the defence response of plants against herbivore attack and during pathogenesis. Solanaceous plants, including cultivated and wild potato species, are sources of steroidal glycoalkaloids. Solanum plants differ in the content and composition of glycoalkaloids in organs. In wild and cultivated potato species, more than 50 steroidal glycoalkaloids were recognized. Steroidal glycoalkaloids are recognized as potential allelopathic/phytotoxic compounds that may modify the growth of target plants. There are limited data on the impact of the composition of glycoalkaloids on their phytotoxic potential.ResultsThe presence of α-solasonine and α-solamargine in potato leaf extracts corresponded to the high phytotoxic potential of the extracts. Among the differentially expressed genes between potato leaf bulks with high and low phytotoxic potential, the most upregulated transcripts in sample of high phytotoxic potential were anthocyanin 5-aromatic acyltransferase-like and subtilisin-like protease SBT1.7-transcript variant X2. The most downregulated genes were carbonic anhydrase chloroplastic-like and miraculin-like. An analysis of differentially expressed proteins revealed that the most abundant group of proteins were those related to stress and defence, including glucan endo-1,3-beta-glucosidase acidic isoform, whose expression level was 47.96× higher in potato leaf extract with low phytotoxic.ConclusionsThe phytotoxic potential of potato leaf extract possessing low glycoalkaloid content is determined by the specific composition of these compounds in leaf extract, where α-solasonine and α-solamargine may play significant roles. Differentially expressed gene and protein profiles did not correspond to the glycoalkaloid biosynthesis pathway in the expression of phytotoxic potential. We cannot exclude the possibility that the phytotoxic potential is influenced by other compounds that act antagonistically or may diminish the glycoalkaloids effect.

Dataset Information

Sequence diversity in coding regions of candidate genes in the glycoalkaloid biosynthetic pathway of wild potato species.

Publications

Sequence diversity in coding regions of candidate genes in the glycoalkaloid biosynthetic pathway of wild potato species.

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