Diploid Potato Population Research Articles

Effect of Cytoplasm Types T and D on Quantitative Trait Loci for Chip Color and Proline Content in Potato Tubers in a Diploid Potato Population

Effect of Cytoplasm Types T and D on Quantitative Trait Loci for Chip Color and Proline Content in Potato Tubers in a Diploid Potato Population

Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato.

The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic characteristics of a diploid F2 potato population derived from the cross of two highly homozygous inbred lines. We investigate 20,382 traits generated from multi-omics dataset and identify 25,770 quantitative trait loci (QTLs). Coupled with gene expression data, we construct a systems-genetics network for gene discovery in potatoes. Importantly, we explore the genetic basis of heterosis in this population, especially for yield and male fertility heterosis. We find that positive heterotic effects of yield-related QTLs and negative heterotic effects of metabolite QTLs (mQTLs) contribute to yield heterosis. Additionally, we identify a PME gene with a dominance heterotic effect that plays an important role in male fertility heterosis. This study provides genetic resources for the potato community and will facilitate the application of heterosis in diploid potato breeding.

High-Density Linkage Map Constructed from a Skim Sequenced Diploid Potato Population Reveals Transmission Distortion and QTLs for Tuber Yield and Pollen Shed

The reinvention of potato, from a tetraploid clonal crop into a diploid seed-based hybrid crop, requires insight in the mutational load, recombination landscape, and the genetic basis of fertility. Genomics-based breeding and QTL discovery rely on efficient genotyping strategies such as skim sequencing, to gather genotypic information. The application of skim sequencing to full-sib population of non-inbred parents remains challenging. Here, we report on an R implementation of the OutcrossSeq pipeline for diploids. We applied this pipeline to a large diploid skim sequenced potato population. We used the resulting bin-markers for the construction of high-density parent specific linkage maps, highlighting variation in parental recombination rate and structural variations. We subsequently explored transmission ratio distortion and non-independent assortment of alleles, indicative of large-effect deleterious mutations. Finally, we identified QTLs for seedling tuber yield in pots and pollen shed. This study showcases the range of genetic analyses, from marker inference, identification of transmission ratio distortion, and linkage map construction to QTL mapping, resulting in new insights that contribute to breeding diploid potato.

Glycoalkaloid Composition and Flavonoid Content as Driving Forces of Phytotoxicity in Diploid Potato.

Despite their advantages, biotechnological and omic techniques have not been applied often to characterize phytotoxicity in depth. Here, we show the distribution of phytotoxicity and glycoalkaloid content in a diploid potato population and try to clarify the source of variability of phytotoxicity among plants whose leaf extracts have a high glycoalkaloid content against the test plant species, mustard. Six glycoalkaloids were recognized in the potato leaf extracts: solasonine, solamargine, α-solanine, α-chaconine, leptinine I, and leptine II. The glycoalkaloid profiles of the progeny of the group with high phytotoxicity differed from those of the progeny of the group with low phytotoxicity, which stimulated mustard growth. RNA sequencing analysis revealed that the upregulated flavonol synthase/flavonone 3-hydroxylase-like gene was expressed in the progeny of the low phytotoxicity group, stimulating plant growth. We concluded that the metabolic shift among potato progeny may be a source of different physiological responses in mustard. The composition of glycoalkaloids, rather than the total glycoalkaloid content itself, in potato leaf extracts, may be a driving force of phytotoxicity. We suggest that, in addition to glycoalkaloids, other metabolites may shape phytotoxicity, and we assume that these metabolites may be flavonoids.

QTL analysis of tuber shape in a diploid potato population.

Tuber shape is one of the most important traits for potato breeding. Since poor or irregular shape increases the difficulty of handling and processing, researching the inheritance of potato tuber shape for potato breeding is highly important. To efficiently identify QTL for tuber shape, a diploid potato population (PM7) was generated by self-pollinated M6 (S. chacoense). A QTL TScha6 for tuber shape was identified by the QTL-seq approach at 50.91-59.93 Mb on chromosome 6 in the potato DM reference genome. To confirm TScha6, four SSR and twenty CAPS markers around the QTL were developed and the TScha6 was narrowed down to an interval of ~ 1.85 Mb. The CAPS marker C6-58.27_665 linked to TScha6 was then used to screen 86 potato cultivars and advanced breeding lines. The tuber length/width (LW) ratio was significantly correlated with the presence/absence of C6-58.27_665, and the correlation coefficient was r = 0.55 (p < 0.01). These results showed that C6-58.27_665 could be applied in marker-assisted selection (MAS) for tuber shape breeding in the future. Our research sets the important stage for the future cloning of the tuber shape gene and utilities of the marker in the breeding program.

Germplasm Release: True Potato Seed (TPS) from a Late Blight Resistant, Long-day Adapted Diploid Potato Population that is Segregating for Early Blight Resistance

Germplasm Release: True Potato Seed (TPS) from a Late Blight Resistant, Long-day Adapted Diploid Potato Population that is Segregating for Early Blight Resistance

Allelic variants of a potato HEAT SHOCK COGNATE 70 gene confer improved tuber yield under a wide range of environmental conditions.

Previously, we developed and applied a glasshouse screen for potato tuber yield under heat stress and identified a candidate gene (HSc70) for heat tolerance by genetic analysis of a diploid potato population. Specific allelic variants were expressed at high levels on exposure to moderately elevated temperature due to variations in gene promoter sequence. In this study, we aimed to confirm the results from the glasshouse screen in field trials conducted over several seasons and locations including those in Kenya, Malawi and the UK. We extend our understanding of the HSc70gene and demonstrate that expression level of HSc70 correlates with tolerance to heat stress in a wide range of wild potato relatives. The physiological basis of the protective effect of HSc70 was explored and we show that genotypes carrying the highly expressed HSc70 A2 allele are protected against photooxidative damage to PSII induced by abiotic stresses. Overall, we show the potential of HSc70 alleles for breeding resilient potato genotypes for multiple environments.

The World’s First Diploid Recombinant Inbred Potato Population

CSA NewsVolume 66, Issue 11 p. 6-11 FEATURES The World’s First Diploid Recombinant Inbred Potato Population DJ McCauley, DJ McCauleySearch for more papers by this author DJ McCauley, DJ McCauleySearch for more papers by this author First published: 04 October 2021 https://doi.org/10.1002/csan.20602Citations: 1Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Video Short The World’s First Diploid Recombinant Inbred Potato Population by McCauley Volume66, Issue11November 2021Pages 6-11 RelatedInformation

Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population

Tuber dormancy and sprouting are commercially important potato traits as long-term tuber storage is necessary to ensure year-round availability. Premature dormancy release and sprout growth in tubers during storage can result in a significant deterioration in product quality. In addition, the main chemical sprout suppressant chlorpropham has been withdrawn in Europe, necessitating alternative approaches for controlling sprouting. Breeding potato cultivars with longer dormancy and slower sprout growth is a desirable goal, although this must be tempered by the needs of the seed potato industry, where dormancy break and sprout vigour are required for rapid emergence. We have performed a detailed genetic analysis of tuber sprout growth using a diploid potato population derived from two highly heterozygous parents. A dual approach employing conventional QTL analysis allied to a combined bulk-segregant analysis (BSA) using a novel potato whole-exome capture (WEC) platform was evaluated. Tubers were assessed for sprout growth in storage at six time-points over two consecutive growing seasons. Genetic analysis revealed the presence of main QTL on five chromosomes, several of which were consistent across two growing seasons. In addition, phenotypic bulks displaying extreme sprout growth phenotypes were subjected to WEC sequencing for performing BSA. The combined BSA and WEC approach corroborated QTL locations and served to narrow the associated genomic regions, while also identifying new QTL for further investigation. Overall, our findings reveal a very complex genetic architecture for tuber sprouting and sprout growth, which has implications both for potato and other root, bulb and tuber crops where long-term storage is essential.

Mapping Solanum berthaultii-based Late Blight (Phytophthora infestans) Resistance in a Diploid Population

Late blight, caused by the oomycete Phytophthora infestans (Mont) de Bary, is the most important disease of cultivated potato (Solanum tuberosum L.). An efficient long-term strategy for controlling late blight infection involves integration of host plant resistance to disease management programs. In this study, a diploid potato population segregating for late blight resistance was generated from an interspecific cross (MSX902) between S. tuberosum x S. chacoense hybrid (84SD22) and a late blight resistant Solanum berthaultii hybrid (Ber83). A total of 129 progeny and two parents were tested for foliar resistance against the US-23 P. infestans genotype using detached-leaf bioassays and inoculated field trials (2014 and 2015). Distribution of foliar late blight resistance and susceptibility was bimodal in both types of phenotype evaluation, suggesting a major R-gene may be associated with the resistance. A major QTL for late blight resistance on chromosome 10 was detected using both detached leaf bioassay and field trial data. The SNP marker solcap_snp_c1_15219 (26.5 cM) was at the peak of the QTL. Additionally, a minor QTL on chromosomes 5 was linked to SNPs solcap_snp_c1_3793. These SNP markers closely linked to the late blight resistance QTL can be used for marker-assisted breeding.

EQTL mapping of the 12S globulin cruciferin gene PGCRURSE5 as a novel candidate associated with starch content in potato tubers

Tuber starch content (TSC) is a very important trait in potato (Solanum tuberosum L.). This study is the first to use expression quantitative trait loci (eQTL) mapping of transcript-derived markers for TSC in potato. Thirty-four differentially expressed genes were selected by comparing the RNA-seq data of contrasting bulked segregants. For the 11 candidate genes, we determined their relative expression levels across the segregating diploid potato population using RT-qPCR. We detected 36 eQTL as candidate genes distributed on all twelve potato chromosomes, and nine of them overlapped with QTL for TSC. Peaks for two eQTL, eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of the large subunit of ADP-glucose pyrophosphorylase (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5), respectively. The eQTL peaks for AGPaseS-a and PGRCRURSE5 explained 41.0 and 28.3% of the phenotypic variation at the transcript level. We showed the association of the DNA markers for AGPaseS-a and PGRCRURSE5 with QTL for TSC, and significant correlation between the expression level of PGRCRURSE5 and TSC. We did not observe a significant correlation between the expression level of AGPaseS-a and TSC. We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers.

Identification of QTLs Associated with Nitrogen Use Efficiency and Related Traits in a Diploid Potato Population

Developing N use efficient potato varieties requires exploring the genetic basis of nitrogen use efficiency (NUE) and associated agronomic and physiological traits. In order to identify QTLs for NUE and NUE-related traits, and to determine the relationships between the traits and QTLs in potato, a diploid potato mapping population (CxE) was evaluated in the field in Ethiopia under low and high N fertilizer levels. QTL detection was performed using interval mapping and multiple QTL mapping (MQM). A total of 52 putative QTLs were identified for ten traits, of which 28 QTLs were detected under low N availability while the remaining 24 QTLs were detected under high N conditions. Several QTLs were location and N level specific, suggesting the presence of QTL x environment interaction. A region on linkage group V (21-38 cM) accumulated the largest number of QTLs. This region coincides with the earliness locus encoded by the CDF1 gene, suggesting that earliness has a profound influence on NUE. A putative second QTL region on linkage group V located 20 cM from the earliness locus (38-56 cM) and a region on linkage group IV (60-72 cM) might be useful other regions to focus on, for NUE improvement in potato. To verify the stability of the identified QTLs and to use these for the detection of possible candidate genes, further multi-environment trials with larger population size may be required.

Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja

Key MessageNovel major gene resistance against Potato virus Y in diploid populations of Solanum tuberosum Groups Phureja and Tuberosum was biologically and genetically characterised. Named Ry(o)phu, it mapped to chromosome 9.A new source of genetic resistance derived from Solanum tuberosum Group Phureja against Potato virus Y (PVY) was identified and genetically characterised in three diploid biparental potato populations. Segregation data for two populations (05H1 and 08H1) suggested the presence of a single dominant gene for resistance to PVY which, following DaRT analysis of the 08H1 cross, was mapped to chromosome 9. More detailed genetic analysis of resistance utilised a well-characterised SNP-linkage map for the 06H1 population, together with newly generated marker data. In these plants, which have both S. tuberosum Group Phureja and S. tuberosum Group Tuberosum in their pedigree, the resistance was shown to map to chromosome 9 at a locus not previously associated with PVY resistance, although there is evidence for at least one other genetic factor controlling PVY infection. The resistance factor location on chromosome 9 (named as Ry(o)phu) suggests a potential role of NB-LRR genes in this resistance. Phenotypic analysis using a GUS-tagged virus revealed that a small amount of PVY replication occurred in occasional groups of epidermal cells in inoculated leaves of resistant plants, without inducing any visible hypersensitive response. However, the virus did not enter the vascular system and systemic spread was completely prevented.

QTL mapping for microtuber ABA content in a diploid potato population

Abstract Abscisic acid (ABA) is known to impact many areas of plant growth and development and is also assumed to facilitate plant stress regulation. ABA is also involved in the rapid suberization of wounds and is the essential dormancy release regulator. The direct application of DNA markers to plant populations enables the use of mapping to help determine the regulation of a quantitatively inherited trait isolated in a population. QTLs represent a chromosomal region that is linked to a marker gene and that significantly affects the quantitative trait under review. In the present study, we investigated the ABA content after harvest and after sprouting in a diploid population. The most noticeable QTLs related to ABA were found on chromosomes I and IV, and these QTLs fully explained 6.5% and 7% of the entire phenotypic variance, respectively. The acquired information advances our understanding of the inheritance of traits applicable for variety development.

Novel gene Sen2 conferring broad-spectrum resistance to Synchytrium endobioticum mapped to potato chromosome XI

Key message Sen2gene for potato wart resistance, located on chromosome XI in a locus distinct fromSen1, provides resistance against eight wart pathotypes, including the virulent ones important in Europe.Synchytrium endobioticum causes potato wart disease imposing severe losses in potato production, and as a quarantine pathogen in many countries, it results in lost trade markets and land for potato cultivation. The resistance to S. endobioticum pathotype 1(D1) is widespread in potato cultivars but new virulent pathotypes appear and the problem re-emerges. To characterize and map a new gene for resistance to potato wart, we used diploid F1 potato population from a cross of potato clone resistant to S. endobioticum pathotype 1(D1) and virulent pathotypes: 2(G1), 6(O1), 8(F1), 18(T1), 2(Ch1), 3(M1) and 39(P1) with a potato clone resistant to pathotype 1(D1) only. The 176 progeny clones were tested for resistance to eight wart pathotypes with a modified Glynne–Lemmerzahl method. Bimodal distributions and co-segregation of resistance in the population show that a single resistance gene, Sen2, underlies the resistance to eight pathotypes. Resistance to pathotype 1(D1) was additionally conferred by the locus Sen1 inherited from both parents. Sen2 was mapped to chromosome XI using DArTseq markers. The genetic and physical distances between Sen1 and Sen2 loci were indirectly estimated at 63 cM and 32 Mbp, respectively. We developed PCR markers co-segregating with the Sen2 locus that can be applied in marker-assisted selection of potatoes resistant to eight important pathotypes of S. endobioticum. Wide spectrum of the Sen2 resistance may be an indication of durability which can be enhanced by the pyramiding of the Sen2 and Sen1 loci as in 61 clones selected within this study.

Additive and epistatic QTLs underlying the dormancy in a diploid potato population across seven environments

Abstract Tuber dormancy is important for potato tuber quality and is a typical quantitative trait. Understanding the genetic basis of potato tuber dormancy is essential for controlling the potato tuber dormancy length. In order to analyze the quantitative trait, a diploid potato population EB with a genetic background derived from S. tuberosum, S. berthaultii, S. phureja, S. vernei, etc, was used for QTL analyses. With tubers of population EB harvested from seven environments, six QTLs with additive effects and four other QTLs involved in epistatic interactions were uncovered. These QTLs might partially demonstrate the gene regulatory network of tuber dormancy in potato. The fine mapping and map-based cloning of these QTLs, especially DorE4.6 and DorB5.3 with major additive effects across seven environments, will further the understanding of the genetic mechanism of potato tuber dormancy. The molecular markers linked to the stable QTLs, DorE4.6 and DorB5.3, provided good assistant marker candidates for pyramid breeding aiming at the potato cultivar with a desirable dormancy length.

Genetic Loci Conferring Reducing Sugar Accumulation and Conversion of Cold-Stored Potato Tubers Revealed by QTL Analysis in a Diploid Population.

Cold-induced sweetening (CIS) caused by reducing sugar (RS) accumulation during storage in low temperature in potato tubers is a critical factor influencing the quality of fried potato products. The reconditioning (REC) by arising storage temperature is a common measure to lower down RS. However, both CIS and REC are genotype-dependent and the genetic basis remains uncertain. In the present study, with a diploid potato population with broad genetic background, four reproducible QTL of CIS and two of REC were resolved on chromosomes 5, 6, and 7 of the CIS-sensitive parent and chromosomes 5 and 11 of the CIS-resistant parent, respectively, implying that these two traits may be genetically independent. This hypothesis was also supported by the colocalization of two functional genes, a starch synthesis gene AGPS2 mapped in QTL CIS_E_07-1 and a starch hydrolysis gene GWD colocated with QTL REC_B_05-1. The cumulative effects of identified QTL were proved to contribute largely and stably to CIS and REC and confirmed with a natural population composed of a range of cultivars and breeding lines. The present research identified reproducible QTL for CIS and REC of potato in diverse conditions and elucidated for the first time their cumulative genetic effects, which provides theoretical bases and applicable means for tuber quality improvement.

Genetical genomics of quality related traits in potato tubers using proteomics

BackgroundRecent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D–gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins.ResultsWe subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed.ConclusionsFrom this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.

Engineering heat tolerance in potato by temperature-dependent expression of a specific allele of HEAT-SHOCK COGNATE 70.

SummaryFor many commercial potato cultivars, tuber yield is optimal at average daytime temperatures in the range of 14–22 °C. Further rises in ambient temperature can reduce or completely inhibit potato tuber production, with damaging consequences for both producer and consumer. The aim of this study was to use a genetic screen based on a model tuberization assay to identify quantitative trait loci (QTL) associated with enhanced tuber yield. A candidate gene encoding HSc70 was identified within one of the three QTL intervals associated with elevated yield in a Phureja–Tuberosum hybrid diploid potato population (06H1). A particular HSc70 allelic variant was linked to elevated yield in the 06H1 progeny. Expression of this allelic variant was much higher than other alleles, particularly on exposure to moderately elevated temperature. Transient expression of this allele in Nicotiana benthamiana resulted in significantly enhanced tolerance to elevated temperature. An TA repeat element was present in the promoter of this allele, but not in other HSc70 alleles identified in the population. Expression of the HSc70 allelic variant under its native promoter in the potato cultivar Desiree resulted in enhanced HSc70 expression at elevated temperature. This was reflected in greater tolerance to heat stress as determined by improved yield under moderately elevated temperature in a model nodal cutting tuberization system and in plants grown from stem cuttings. Our results identify HSc70 expression level as a significant factor influencing yield stability under moderately elevated temperature and identify specific allelic variants of HSc70 for the induction of thermotolerance via conventional introgression or molecular breeding approaches.

Self-Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single-Nucleotide Polymorphism Array.

Within a population of F hybrids between two genotypes ( L. Group Phureja DM 1-3 516 R44 [DM] and L. Group Tuberosum RH89-039-16 [RH]) used in the potato genome sequencing project, we observed fruit set after self-pollination on many plants. Examination of pollen tube growth in self-fertile and self-unfruitful F plants after controlled self-pollinations revealed no difference in the ability of pollen tubes to reach the ovary. To identify genomic regions linked with self-fertility, we genotyped the F population using a genome-wide single-nucleotide polymorphism (SNP) array. Polymorphic and robust SNPs were analyzed to identify allelic states segregating with the self-fertile phenotype. All 88 highly significant SNPs occurred on chromosome 12. Seeds obtained after self-pollination of self-fertile individuals were used to advance the population for four generations. Genotyping 46 self-fruitful and 46 self-unfruitful S plants on the Infinium 8303 Potato SNP array revealed eight SNPs segregating with self-fertility on chromosomes 4, 9, 11, and 12. Three times more heterozygosity than expected was found in the S generation. Estimates of heterozygosity were influenced by copy number variation (CNV) in the potato genome leading to spurious heterozygous genotyping calls. Some spurious heterozygosity could be removed by application of a CNV filter developed from alignment of additional monoploid potato genomic sequence to the DM reference genome. The genes responsible for fruit set in self-fertile plants in the F generation were restricted to chromosome 12, whereas new genomic regions contributed to the ability of S plants to set fruit after self-pollination.