Mapping of genes associated with leptine content of tetraploid potato

Allelic variation in the autotetraploid potato: genes involved in starch and steroidal glycoalkaloid metabolism as a case study

BACKGROUND

Tuber starch and steroidal glycoalkaloid (SGA)-related traits have been consistently prioritized in potato breeding, while allelic variation pattern of genes that underlie these traits is less explored.

RESULTS

Here, we focused on the genes involved in two important metabolic pathways in the potato: starch metabolism and SGA biosynthesis. We identified 119 genes consisting of 81 involved in starch metabolism and 38 in the biosynthesis of steroidal glycoalkaloids, and discovered 96,166 allelic variants among 2,169 gene haplotypes in six autotetraploid potato genomes. Comparative analyses revealed an uneven distribution of allelic variants among gene haplotypes and that the vast majority of deleterious mutations in these genes are retained in heterozygous state in the autotetraploid potato genomes. Leveraging full-length cDNA sequencing data, we find that approximately 70% of haplotypes of the 119 genes are transcribable. Population genetic analyses identify starch and SGA biosynthetic genes that are potentially conserved or diverged between potato varieties with varying starch or SGA content.

CONCLUSIONS

These results deepen the understanding of haplotypic diversity within functionally important genes in autotetraploid genomes and may facilitate functional characterization of genes or haplotypes contributing to traits related to starch and SGA in potato.

GWAS in tetraploid potato: identification and validation of SNP markers associated with glycoalkaloid content

Genome-wide association studies (GWAS) are a useful tool to unravel the genetic architecture of complex traits, but the results can be difficult to interpret. Population structure, genetic heterogeneity, and rare alleles easily result in false positive or false negative associations. This paper describes the analysis of a GWAS panel combined with three bi-parental mapping populations to validate GWAS results, using phenotypic data for steroidal glycoalkaloid (SGA) accumulation and the ratio (SGR) between the two major glycoalkaloids α-solanine and α-chaconine in potato tubers. SGAs are secondary metabolites in the Solanaceae family, functional as a defence against various pests and pathogens and in high quantities toxic for humans. With GWAS, we identified five quantitative trait loci (QTL) of which Sga1.1, Sgr8.1, and Sga11.1 were validated, but not Sga3.1 and Sgr7.1. In the bi-parental populations, Sga5.1 and Sga7.1 were mapped, but these were not identified with GWAS. The QTLs Sga1.1, Sga7.1, Sgr7.1, and Sgr8.1 co-localize with genes GAME9, GAME 6/GAME 11, SGT1, and SGT2, respectively. For other genes involved in SGA synthesis, no QTLs were identified. The results of this study illustrate a number of pitfalls in GWAS of which population structure seems the most important. We also show that introgression breeding for disease resistance has introduced new haplotypes to the gene pool involved in higher SGA levels in certain pedigrees. Finally, we show that high SGA levels remain unpredictable in potato but that α-solanine/α-chaconine ratio has a predictable outcome with specific SGT1 and SGT2 haplotypes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01344-2.

Mapping Solanum chacoense mediated Colorado potato beetle (Leptinotarsa decemlineata) resistance in a self-compatible F2 diploid population

A major QTL on chromosome 2 associated with leptine biosynthesis and Colorado potato beetle resistance was identified in a diploid S. chacoense F₂ population using linkage mapping and bulk-segregant analysis. We examined the genetic features underlying leptine glycoalkaloid mediated Colorado potato beetle (Leptinotarsa decemlineata) host plant resistance in a diploid F₂ mapping population of 233 individuals derived from Solanum chacoense lines USDA8380-1 and M6. The presence of foliar leptine glycoalkaloids in this population segregated as a single dominant gene and displayed continuous distribution of accumulated quantity in those individuals producing the compound. Using biparental linkage mapping, a major overlapping QTL region with partial dominance effects was identified on chromosome 2 explaining 49.3% and 34.1% of the variance in Colorado potato beetle field resistance and leptine accumulation, respectively. Association of this putative resistance region on chromosome 2 was further studied in an expanded F₂ population in a subsequent field season. Loci significantly associated with leptine synthesis colocalized to chromosome 2. Significant correlation between increased leptine content and decreased Colorado potato beetle defoliation suggests a single QTL on chromosome 2. Additionally, a minor QTL with overdominance effects explaining 6.2% associated with Colorado potato beetle resistance donated by susceptible parent M6 was identified on chromosome 7. Bulk segregant whole genome sequencing of the same F₂ population detected QTL associated with Colorado potato beetle resistance on chromosomes 2, 4, 6, 7, and 12. Weighted gene co-expression network analysis of parental lines and resistant and susceptible F₂ individuals identified a tetratricopeptide repeat containing protein with a putative regulatory function and a previously uncharacterized acetyltransferase within the QTL region on chromosome 2, possibly under the control of a regulatory Tap46 subunit within the minor QTL on chromosome 12.

Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases

The genus Solanum comprises three food crops (potato, tomato, and eggplant), which are consumed on daily basis worldwide and also producers of notorious anti-nutritional steroidal glycoalkaloids (SGAs). Hydroxylated SGAs (i.e. leptinines) serve as precursors for leptines that act as defenses against Colorado Potato Beetle (Leptinotarsa decemlineata Say), an important pest of potato worldwide. However, SGA hydroxylating enzymes remain unknown. Here, we discover that 2-OXOGLUTARATE-DEPENDENT-DIOXYGENASE (2-ODD) enzymes catalyze SGA-hydroxylation across various Solanum species. In contrast to cultivated potato, Solanum chacoense, a widespread wild potato species, has evolved a 2-ODD enzyme leading to the formation of leptinines. Furthermore, we find a related 2-ODD in tomato that catalyzes the hydroxylation of the bitter α-tomatine to hydroxytomatine, the first committed step in the chemical shift towards downstream ripening-associated non-bitter SGAs (e.g. esculeoside A). This 2-ODD enzyme prevents bitterness in ripe tomato fruit consumed today which otherwise would remain unpleasant in taste and more toxic.

Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.

Allelic variation in genes contributing to glycoalkaloid biosynthesis in a diploid interspecific population of potato

Variation for allelic state within genes of both primary and secondary metabolism influences the quantity and quality of steroidal glycoalkaloids produced in potato leaves. Genetic factors associated with the biosynthesis and accumulation of steroidal glycoalkaloids (SGAs) in potato were addressed by a candidate gene approach and whole genome single nucleotide polymorphism (SNP) genotyping. Allelic sequences spanning coding regions of four candidate genes [3-hydroxy-3-methylglutaryl coenzyme A reductase 2 (HMG2); 2,3-squalene epoxidase; solanidine galactosyltransferase; and solanidine glucosyltransferase (SGT2)] were obtained from two potato species differing in SGA composition: Solanum chacoense (chc 80-1) and Solanum tuberosum group Phureja (phu DH). An F2 population was genotyped and foliar SGAs quantified. The concentrations of α-solanine, α-chaconine, leptine I, leptine II and total SGAs varied broadly among F2 individuals. F2 plants with chc 80-1 alleles for HMG2 or SGT2 accumulated significantly greater leptines and total SGAs compared to plants with phu DH alleles. Plants with chc 80-1 alleles at both loci expressed the greatest levels of total SGAs, α-solanine and α-chaconine. A significant positive correlation was found between α-solanine and α-chaconine accumulation as well as between leptine I and leptine II. A whole genome SNP genotyping analysis of an F2 subsample verified the importance of chc 80-1 alleles at HMG2 and SGT2 for SGA synthesis and accumulation and suggested additional candidate genes including some previously associated with SGA production. Loci on five and seven potato pseudochromosomes were associated with synthesis and accumulation of SGAs, respectively. Two loci, on pseudochromosomes 1 and 6, explained phenotypic segregation of α-solanine and α-chaconine synthesis. Knowledge of the genetic factors influencing SGA production in potato may assist breeding for pest resistance.

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 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.

Steroidal glycoalkaloids in Solanum chacoense

Potato (Solanum tuberosum L.), a domesticated species that is the fourth most important world agricultural commodity, requires significant management to minimize the effects of herbivore and pathogen damage on crop yield. A wild relative, Solanum chacoense Bitt., has been of interest to plant breeders because it produces an abundance of novel steroidal glycoalkaloid compounds, leptines and leptinines, which are particularly effective deterrents of herbivory by the Colorado potato beetle (Leptinotarsa decemlineata Say). Biochemical approaches were used in this study to investigate the formation and accumulation of SGAs in S. chacoense. SGA contents were determined in various organs at different stages of organ maturity during a time course of plant development. Leptines and leptinines were the main contributors to the increased levels in SGA concentration measured in the aerial versus the subterranean organs of S. chacoense accession 8380-1. Leptines were not detected in aboveground stolons until the stage where shoots had formed mature chlorophyllous leaves. To gain insights into SGA biosynthesis, the abundance of SGAs and steady-state transcripts of genes coding for enzymes of the central terpene and SGA-specific pathways in various plant organs at anthesis were compared. For two genes of primary terpene metabolism, transcript and SGA abundances were correlated, although with some discrepancies. For genes associated with SGA biosynthesis, transcripts were not detected in some tissues containing SGAs; however these transcripts were detected in the progenitor tissues, indicating the possibility that under our standard growth conditions, SGA biosynthesis is largely limited to highly proliferative tissues such as shoot, root and floral meristems.

Linkage analysis of a rare alkaloid present in a tetraploid potato with Solanum chacoense background

The potato genotype ND4382-19 has Solanum chacoense Bitt. in its genetic background. Foliar alkaloid analysis of it and its progeny ND5873 (ND4382-19 × Chipeta) by gas chromatography-mass spectrometry (GC-MS) showed that, in addition to the expected alkaloids (solanidine, leptinidine, and acetyl-leptinidine), there was an aglycone of another rare alkaloid. Its molecular mass and some of the m/z fragment ions were similar to leptinidine, but the major fragment ion was the m/z 150 peak of solanidine. This fragmentation pattern suggested that this alkaloid is a solanidine-based compound with mass equal to leptinidine. Leptinidine differs from solanidine by an extra -OH group, but the GC-MS fragmentation pattern of the rare compound indicated hydroxylation at a different position than the C-23 of leptinidine. The exact chemical structure is still unknown, and further analysis, such as NMR will be necessary to determine the structure. Segregation analysis of ND5873 (ND4382-19 × Chipeta) showed that presence of this rare compound segregated in a 1:1 ratio, indicating that a single gene controlled its synthesis and/or accumulation in foliar tissue. Analysis with AFLP and microsatellite markers indicated that the locus-controlling presence of this alkaloid resided on potato chromosome I, with the nearest flanking AFLP markers 0.6 and 9.4 cM apart. This rare alkaloid was present in the foliage and not detected in potato tubers. Its presence in leaves did not affect resistance/susceptibility to Colorado potato beetle.

QTL mapping of internal heat necrosis in tetraploid potato

Internal heat necrosis (IHN) is a physiological disorder of potato tubers. We developed a linkage map of tetraploid potato using AFLP and SSR markers, and mapped QTL for mean severity and percent incidence of IHN. Phenotypic data indicated that the distribution of IHN is skewed toward resistance. Late foliage maturity was slightly but significantly correlated with increased IHN symptoms. The linkage map for 'Atlantic', the IHN-susceptible parent, covered 1034.4 cM and included 13 linkage groups, and the map for B1829-5, the IHN-resistant parent, covered 940.2 cM and contained 14 linkage groups. QTL for increased resistance to IHN were located on chromosomes IV, V, and groups VII and X of 'Atlantic', and on group VII of B1829-5 in at least 2 of 3 years. The QTL explained between 4.5 and 29.4% of the variation for mean severity, and from 3.7 to 14.5% of the variation for percent incidence. Most QTL detected were dominant, and associated with decreased IHN symptoms. One SSR and 13 AFLP markers that were linked to IHN were tested in a second population. One AFLP marker was associated with decreased symptoms in both populations. The SSR marker was not associated with IHN in the second population, but was closely linked in repulsion to another marker that was associated with IHN, and had the same (negative) effect on the trait as the SSR marker did in the first population. The correlation between maturity and IHN may be partially explained by the presence of markers on chromosome V that are linked to both traits. This research represents the first molecular genetic research of IHN in potato.

A QTL that confers resistance to Colorado potato beetle (Leptinotarsa decemlineata [Say]) in tetraploid potato populations segregating for leptine

Genetic resistance to Colorado potato beetle (Leptinotarsa decemlineata [Say]) from Solanum chacoense has been incorporated in the tetraploid potato selection, ND4382-19, which is highly resistant and contains moderate level of foliar leptines. We recently reported using ND4382-19 progeny, population ND5873 (ND4382-19 x Chipeta), to map two genes that segregated as complementary epistatic genes that allow accumulation of leptinidine (Lep) and acetyl-leptinidine (AL) on chromosomes 2 and 8, respectively. We describe here the characterization of a second half-sib population NDG116 (ND4382-19 x N142-72). In this population, solasodine from parent N142-72, which has Solanum berthaultii in its background, was predominant over solanidine-based alkaloids. Concentrations of solanidine, leptinidine, and acetyl-leptinidine were 15-, 5-, and 14-fold lower than in the ND5873 population. Nevertheless, Lep and AL mapped to the same locations on chromosomes 2 and 8 of parent ND4382-19, respectively. The two populations were evaluated for resistance to Leptinotarsa in field assays, and by detached leaf assay for population NDG116. In both families, QTL analysis identified a major QTL from ND4382-19 on the distal end of chromosome 2, close to the Lep locus. The contribution of this QTL to resistance ranged from 11 to 34% for ND5873 at four field sites. Contribution to resistance from the linkage group that contains the gene AL for the accumulation of leptine was not detected. In family NDG116, the same chromosome 2 QTL was detected for field and detached leaf assays, explaining 26 and 12% of the variance for defoliation and larval development, respectively. These data may indicate another resistance mechanism besides leptine in the Leptinotarsa resistance observed in these populations.

LC-MS analysis of solanidane glycoalkaloid diversity among tubers of four wild potato species and three cultivars (Solanum tuberosum)

Secondary metabolites in potato tubers include both phytonutrients and plant defense compounds. The extent these small molecules vary among different potato genotypes is not well characterized. LC-MS analysis of tuber extracts from seven potato genotypes showed that one large source of small molecule variation is the glycoalkaloids. Glycoalkaloids are involved in the resistance of potatoes to pathogens and pests, but they also have implications for human health and nutrition. This study focused on glycoalkaloids with solanidane or solanidane-like aglycones, of which over 50 were tentatively identified, many of which appeared to be novel glycoalkaloids. Results suggested the variety of glycoalkaloids in potatoes is considerably greater than previously thought. Dissecting the role of these many glycoalkaloids in human health or pest and pathogen resistance will be a formidable undertaking.

A major QTL and an SSR marker associated with glycoalkaloid content in potato tubers from Solanum tuberosum x S. sparsipilum located on chromosome I

New potato (Solanum tuberosum) varieties are required to contain low levels of the toxic glycoalkaloids and a potential approach to obtain this is through marker-assisted selection (MAS). Before applying MAS it is necessary to map quantitative trait loci (QTLs) for glycoalkaloid content in potato tubers and identify markers that link tightly to this trait. In this study, tubers of a dihaploid BC(1) population, originating from a cross between 90-HAF-01 (S. tuberosum(1)) and 90-HAG-15 (S. tuberosum(2) x S. sparsipilum), were evaluated for content of alpha-solanine and alpha-chaconine (total glycoalkaloid, TGA) after field trials. In addition, tubers were assayed for TGA content after exposure to light. A detailed analysis of segregation patterns indicated that a major QTL is responsible for the TGA content in tubers of this potato population. One highly significant QTL was mapped to chromosome I of the HAG and the HAF parent. Quantitative trait loci for glycoalkaloid production in foliage of different Solanum species have previously been mapped to this chromosome. In the present research, QTLs for alpha-solanine and alpha-chaconine content were mapped to the same location as for TGA content. Similar results were observed for tubers exposed to light. The simple sequence repeat marker STM5136 was closely linked to the identified QTL.