1
|
Aalborg T, Sverrisdóttir E, Kristensen HT, Nielsen KL. The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato. FRONTIERS IN PLANT SCIENCE 2024; 15:1340189. [PMID: 38525152 PMCID: PMC10957621 DOI: 10.3389/fpls.2024.1340189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.
Collapse
Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | | |
Collapse
|
2
|
Massa AN, Manrique-Carpintero NC, Coombs J, Haynes KG, Bethke PC, Brandt TL, Gupta SK, Yencho GC, Novy RG, Douches DS. Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato. BMC Genet 2018; 19:87. [PMID: 30241465 PMCID: PMC6150958 DOI: 10.1186/s12863-018-0672-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 01/16/2023] Open
Abstract
Background Genome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance. Results In this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with ‘Premier Russet’ contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.). Conclusions Linkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control. Electronic supplementary material The online version of this article (10.1186/s12863-018-0672-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alicia N Massa
- USDA, Agricultural Research Service, National Peanut Research Laboratory, 1011 Forrester DR., SE, Dawson, GA, 39842, USA.
| | - Norma C Manrique-Carpintero
- Plant, Soil and Microbial Sciences Department, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA
| | - Joseph Coombs
- Plant, Soil and Microbial Sciences Department, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA
| | - Kathleen G Haynes
- USDA, Agricultural Research Service, 10300 Baltimore Ave, Beltsville, MD, 20705-1249, USA
| | - Paul C Bethke
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA
| | | | - Sanjay K Gupta
- Department of Soil, Water, and Climate, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - G Craig Yencho
- Department of Horticulture, North Carolina State University, 214 Kilgore Hall, Raleigh, NC, 27695, USA
| | - Richard G Novy
- USDA Agricultural Research Service, Small Grains and Potato Germplasm Research Unit, 1693 S 2700 W, Aberdeen, ID, 83210, USA
| | - David S Douches
- Plant, Soil and Microbial Sciences Department, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA.
| |
Collapse
|
3
|
Duarte-Delgado D, Juyó D, Gebhardt C, Sarmiento F, Mosquera-Vásquez T. Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja. BMC Genet 2017; 18:23. [PMID: 28279167 PMCID: PMC5345157 DOI: 10.1186/s12863-017-0489-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/03/2017] [Indexed: 11/22/2022] Open
Abstract
Background Potato frying color is an agronomic trait influenced by the sugar content of tubers. The candidate gene approach was employed to elucidate the molecular basis of this trait in Solanum tuberosum Group Phureja, which is mainly diploid and represents an important genetic resource for potato breeding. The objective of this research was to identify novel genetic variants related with frying quality in loci with key functions in carbohydrate metabolism, with the purpose of discovering genetic variability useful in breeding programs. Therefore, an association analysis was implemented with 109 SNP markers identified in ten candidate genes. Results The analyses revealed four associations in the locus InvGE coding for an apoplastic invertase and one association in the locus SssI coding for a soluble starch synthase. The SNPs SssI-C45711901T and InvGE-C2475454T were associated with sucrose content and frying color, respectively, and were not found previously in tetraploid genotypes. The rare haplotype InvGE-A2475187C2475295A2475344 was associated with higher fructose contents. Our study allowed a more detailed analysis of the sequence variation of exon 3 from InvGE, which was not possible in previous studies because of the high frequency of insertion-deletion polymorphisms in tetraploid potatoes. Conclusion The association mapping strategy using a candidate gene approach in Group Phureja allowed the identification of novel SNP markers in InvGE and SssI associated with frying color and the tuber sugar content measured by High Performance Liquid Chromatography (HPLC). These novel associations might be useful in potato breeding programs for improving quality traits and to increase crop genetic variability. The results suggest that some genes involved in the natural variation of tuber sugar content and frying color are conserved in both Phureja and tetraploid germplasm. Nevertheless, the associated variants in both types of germplasm were present in different regions of these genes. This study contributes to the understanding of the genetic architecture of tuber sugar contents and frying color at harvest in Group Phureja. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0489-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Diana Duarte-Delgado
- Faculty of Agricultural Sciences, Agronomy Department, National University of Colombia, Bogotá, Colombia.,Present address: INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Deissy Juyó
- Faculty of Agricultural Sciences, Agronomy Department, National University of Colombia, Bogotá, Colombia
| | - Christiane Gebhardt
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Felipe Sarmiento
- Faculty of Sciences, Biology Department, National University of Colombia, Bogotá, Colombia
| | - Teresa Mosquera-Vásquez
- Faculty of Agricultural Sciences, Agronomy Department, National University of Colombia, Bogotá, Colombia.
| |
Collapse
|
4
|
Leskow CC, Kamenetzky L, Dominguez PG, Díaz Zirpolo JA, Obata T, Costa H, Martí M, Taboga O, Keurentjes J, Sulpice R, Ishihara H, Stitt M, Fernie AR, Carrari F. Allelic differences in a vacuolar invertase affect Arabidopsis growth at early plant development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4091-103. [PMID: 27194734 DOI: 10.1093/jxb/erw185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Improving carbon fixation in order to enhance crop yield is a major goal in plant sciences. By quantitative trait locus (QTL) mapping, it has been demonstrated that a vacuolar invertase (vac-Inv) plays a key role in determining the radical length in Arabidopsis. In this model, variation in vac-Inv activity was detected in a near isogenic line (NIL) population derived from a cross between two divergent accessions: Landsberg erecta (Ler) and Cape Verde Island (CVI), with the CVI allele conferring both higher Inv activity and longer radicles. The aim of the current work is to understand the mechanism(s) underlying this QTL by analyzing structural and functional differences of vac-Inv from both accessions. Relative transcript abundance analyzed by quantitative real-time PCR (qRT-PCR) showed similar expression patterns in both accessions; however, DNA sequence analyses revealed several polymorphisms that lead to changes in the corresponding protein sequence. Moreover, activity assays revealed higher vac-Inv activity in genotypes carrying the CVI allele than in those carrying the Ler allele. Analyses of purified recombinant proteins showed a similar K m for both alleles and a slightly higher V max for that of Ler. Treatment of plant extracts with foaming to release possible interacting Inv inhibitory protein(s) led to a large increase in activity for the Ler allele, but no changes for genotypes carrying the CVI allele. qRT-PCR analyses of two vac-Inv inhibitors in seedlings from parental and NIL genotypes revealed different expression patterns. Taken together, these results demonstrate that the vac-Inv QTL affects root biomass accumulation and also carbon partitioning through a differential regulation of vac-Inv inhibitors at the mRNA level.
Collapse
Affiliation(s)
- Carla Coluccio Leskow
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1712WAA Castelar, Argentina
| | - Laura Kamenetzky
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1712WAA Castelar, Argentina
| | - Pia Guadalupe Dominguez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1712WAA Castelar, Argentina
| | - José Antonio Díaz Zirpolo
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1712WAA Castelar, Argentina
| | - Toshihiro Obata
- Max Planck Institute for Molecular Plant Physiology, Wissenschafts Park Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Hernán Costa
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, (6700) Luján, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina
| | - Oscar Taboga
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1712WAA Castelar, Argentina
| | | | - Ronan Sulpice
- Max Planck Institute for Molecular Plant Physiology, Wissenschafts Park Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Hirofumi Ishihara
- Max Planck Institute for Molecular Plant Physiology, Wissenschafts Park Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Wissenschafts Park Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair Robert Fernie
- Max Planck Institute for Molecular Plant Physiology, Wissenschafts Park Golm, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1712WAA Castelar, Argentina
| |
Collapse
|
5
|
Schreiber L, Nader-Nieto AC, Schönhals EM, Walkemeier B, Gebhardt C. SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.). G3 (BETHESDA, MD.) 2014; 4:1797-811. [PMID: 25081979 PMCID: PMC4199688 DOI: 10.1534/g3.114.012377] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/17/2014] [Indexed: 01/17/2023]
Abstract
Starch accumulation and breakdown are vital processes in plant storage organs such as seeds, roots, and tubers. In tubers of potato (Solanum tuberosum L.) a small fraction of starch is converted into the reducing sugars glucose and fructose. Reducing sugars accumulate in response to cold temperatures. Even small quantities of reducing sugars affect negatively the quality of processed products such as chips and French fries. Tuber starch and sugar content are inversely correlated complex traits that are controlled by multiple genetic and environmental factors. Based on in silico annotation of the potato genome sequence, 123 loci are involved in starch-sugar interconversion, approximately half of which have been previously cloned and characterized. By means of candidate gene association mapping, we identified single-nucleotide polymorphisms (SNPs) in eight genes known to have key functions in starch-sugar interconversion, which were diagnostic for increased tuber starch and/or decreased sugar content and vice versa. Most positive or negative effects of SNPs on tuber-reducing sugar content were reproducible in two different collections of potato cultivars. The diagnostic SNP markers are useful for breeding applications. An allele of the plastidic starch phosphorylase PHO1a associated with increased tuber starch content was cloned as full-length cDNA and characterized. The PHO1a-HA allele has several amino acid changes, one of which is unique among all known starch/glycogen phosphorylases. This mutation might cause reduced enzyme activity due to impaired formation of the active dimers, thereby limiting starch breakdown.
Collapse
Affiliation(s)
- Lena Schreiber
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Anna Camila Nader-Nieto
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Elske Maria Schönhals
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Birgit Walkemeier
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Christiane Gebhardt
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| |
Collapse
|
6
|
Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Walkemeier B, Rotter B, Gebhardt C. Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. FRONTIERS IN PLANT SCIENCE 2013; 4:423. [PMID: 24294214 PMCID: PMC3827546 DOI: 10.3389/fpls.2013.00423] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/05/2013] [Indexed: 05/23/2023]
Abstract
Resistance to pathogens is essential for survival of wild and cultivated plants. Pathogen susceptibility causes major losses of crop yield and quality. Durable field resistance combined with high yield and other superior agronomic characters are therefore, important objectives in every crop breeding program. Precision and efficacy of resistance breeding can be enhanced by molecular diagnostic tools, which result from knowledge of the molecular basis of resistance and susceptibility. Breeding uses resistance conferred by single R genes and polygenic quantitative resistance. The latter is partial but considered more durable. Molecular mechanisms of plant pathogen interactions are elucidated mainly in experimental systems involving single R genes, whereas most genes important for quantitative resistance in crops like potato are unknown. Quantitative resistance of potato to Phytophthora infestans causing late blight is often compromised by late plant maturity, a negative agronomic character. Our objective was to identify candidate genes for quantitative resistance to late blight not compromised by late plant maturity. We used diagnostic DNA-markers to select plants with different field levels of maturity corrected resistance (MCR) to late blight and compared their leaf transcriptomes before and after infection with P. infestans using SuperSAGE (serial analysis of gene expression) technology and next generation sequencing. We identified 2034 transcripts up or down regulated upon infection, including a homolog of the kiwi fruit allergen kiwellin. 806 transcripts showed differential expression between groups of genotypes with contrasting MCR levels. The observed expression patterns suggest that MCR is in part controlled by differential transcript levels in uninfected plants. Functional annotation suggests that, besides biotic and abiotic stress responses, general cellular processes such as photosynthesis, protein biosynthesis, and degradation play a role in MCR.
Collapse
Affiliation(s)
- Astrid M. Draffehn
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Li Li
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Jia Ding
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jens Lübeck
- Saka-Pflanzenzucht GmbH & Co. KGWindeby, Germany
| | | | - Meki S. Muktar
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Birgit Walkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Christiane Gebhardt
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| |
Collapse
|