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Sharma SK, McLean K, Hedley PE, Dale F, Daniels S, Bryan GJ. Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:180. [PMID: 38980417 PMCID: PMC11233353 DOI: 10.1007/s00122-024-04651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/10/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.
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Affiliation(s)
- Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Karen McLean
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Finlay Dale
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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2
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Zhu X, Chen A, Butler NM, Zeng Z, Xin H, Wang L, Lv Z, Eshel D, Douches DS, Jiang J. Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato. THE PLANT CELL 2024; 36:1985-1999. [PMID: 38374801 PMCID: PMC11062429 DOI: 10.1093/plcell/koae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024]
Abstract
Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene (VInv) and cause reducing sugar accumulation. This process, referred to as "cold-induced sweetening," is a major postharvest problem for the potato industry. We discovered that the cold-induced expression of VInv is controlled by a 200 bp enhancer, VInvIn2En, located in its second intron. We identified several DNA motifs in VInvIn2En that bind transcription factors involved in the plant cold stress response. Mutation of these DNA motifs abolished VInvIn2En function as a transcriptional enhancer. We developed VInvIn2En deletion lines in both diploid and tetraploid potato using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. VInv transcription in cold-stored tubers was significantly reduced in the deletion lines. Interestingly, the VInvIn2En sequence is highly conserved among distantly related Solanum species, including tomato (Solanum lycopersicum) and other non-tuber-bearing species. We conclude that the VInv gene and the VInvIn2En enhancer have adopted distinct roles in the cold stress response in tubers of tuber-bearing Solanum species.
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Affiliation(s)
- Xiaobiao Zhu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Airu Chen
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Nathaniel M Butler
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Madison, WI 53706, USA
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan Province, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu 610101, Sichuan Province, China
| | - Haoyang Xin
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lixia Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Zhaoyan Lv
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Dani Eshel
- Department of Postharvest Science, The Volcani Institute, ARO, Rishon LeZion 50250, Israel
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
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3
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Visse-Mansiaux M, Shumbe L, Brostaux Y, Ballmer T, Smit I, Dupuis B, Vanderschuren H. Identification of potato varieties suitable for cold storage and reconditioning: A safer alternative to anti-sprouting chemicals for potato sprouting control. Food Res Int 2024; 184:114249. [PMID: 38609227 DOI: 10.1016/j.foodres.2024.114249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/14/2024]
Abstract
Low temperature storage as an alternative to anti-sprouting chemicals in potato storage may induce reducing sugars (RS) accumulation (i.e. glucose and fructose) in potato tubers. This phenomenon is called "cold induced sweetening" (CIS) and occurs in certain varieties. CIS leads to a decrease in the organoleptic qualities and darkening of processed potato and the accumulation of toxic molecules such as acrylamide. To identify potato varieties suitable for storage at low temperatures, we screened six commercial processing varieties: Lady Claire (LC), Verdi, Kiebitz (KB), Pirol, Agria and Markies for their CIS characteristics and sprout-forming potential after storage at 4 °C and 8 °C. Our findings reveal that 4 °C storage allows for efficient sprout reduction in all six tested varieties for up to 4.5 months of storage. Three CIS-resistant varieties, namely Verdi, Lady Claire and Kiebitz, were identified as able to be stored for up to four months at 4 °C with limited increase in glucose content. Conversely, Pirol, Agria and Markies showed an increase in glucose content with a decrease in storage temperature and can be considered as CIS-susceptible varieties. After processing into crisps, the CIS-susceptible varieties displayed poor crisp color quality (brown to black color crisps) after storage for two months at 4 °C compared to the storage at 8 °C, whereas the CIS-resistant varieties had good crisp color quality (pale yellow color crisps) after storage at both 4 and 8 °C. Interestingly, the trends of total RS and/or glucose content in the CIS-resistant and in the CIS-susceptible varieties were correlated with the trends in Vacuolar Invertase (VInv) gene expression for most varieties, as well as with the trends in acrylamide content after processing. In addition, reconditioning of Markies variety after storage at 4 °C by gradually increasing the temperature to 15 °C resulted in a significant decrease of VInv transcript levels (reduction of 80 %), acrylamide content (reduction of 75 %) and glucose content when compared to a storage at 4 °C without reconditioning. Those results demonstrate that the reconditioning technique is a key factor for a sustainable potato storage and for improving the quality of processed potatoes.
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Affiliation(s)
- Margot Visse-Mansiaux
- Agroscope, Swiss Confederation's Center for Agricultural Research, Plant-Production Systems, Cultivation Techniques and Varieties in Arable Farming, Route de Duillier 50, 1260 Nyon, Switzerland; Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Leonard Shumbe
- Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Yves Brostaux
- Applied Statistics, Computer Science and Modeling Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Theodor Ballmer
- Agroscope, Swiss Confederation's Center for Agricultural Research, Plant-Production Systems, Cultivation Techniques and Varieties in Arable Farming, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Inga Smit
- Max Rubner-Institut (MRI), Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Cereals, Detmold, Germany.
| | - Brice Dupuis
- Agroscope, Swiss Confederation's Center for Agricultural Research, Plant-Production Systems, Cultivation Techniques and Varieties in Arable Farming, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Hervé Vanderschuren
- Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Tropical Crop Improvement Laboratory, Biosystems Department, KU Leuven, 3001 Heverlee, Belgium.
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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.
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Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Angelin-Bonnet O, Thomson S, Vignes M, Biggs PJ, Monaghan K, Bloomer R, Wright K, Baldwin S. Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes. BMC PLANT BIOLOGY 2023; 23:238. [PMID: 37147582 PMCID: PMC10161554 DOI: 10.1186/s12870-023-04255-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. RESULTS When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. CONCLUSION This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.
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Affiliation(s)
- Olivia Angelin-Bonnet
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, 4442, New Zealand.
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Matthieu Vignes
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, 4412, New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, 4412, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, 4412, New Zealand
| | - Katrina Monaghan
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Rebecca Bloomer
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Kathryn Wright
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
| | - Samantha Baldwin
- The New Zealand Institute for Plant and Food Research Limited, Christchurch, 8140, New Zealand
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Kulakova A, Efremov G, Shchennikova A, Kochieva E. Dependence of the content of starch and reducing sugars on the level of expression of the genes of β-amylases StBAM1 and StBAM9 and the amylase inhibitor StAI during long-term low-temperature storage of potato tubers. Vavilovskii Zhurnal Genet Selektsii 2022; 26:507-514. [PMID: 36313822 PMCID: PMC9556308 DOI: 10.18699/vjgb-22-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 11/06/2022] Open
Abstract
Solanum tuberosum L. is the most important non-grain starch crop with a potential yield of 38-48 t/ha and a starch content of 13.2-18.7 %. Potato tubers are stored at a low temperature (2-4 °C) in a state of physiological dormancy. A disadvantage of this type of storage is the degradation of starch and the accumulation of reducing sugars (cold-induced sweetening), including due to an increase in the activity of β-amylases that hydrolyze starch to maltose. In this study, a comparative analysis of the β-amylase (StBAM1, StBAM9) and amylase inhibitor (StAI ) gene expression, as well as starch and reducing sugar content in tubers during long-term low-temperature storage (September, February, April) was performed using potato cultivars Nadezhda, Barin, Krasavchik, Severnoe siyanie and Utro. The β-amylase genes, StBAM9 and one of the two StBAM1 homologs (with the highest degree of homology with AtBAM1), were selected based on phylogenetic analysis data. Evaluation of the expression of these genes and the amylase inhibitor gene showed a tendency to decrease in transcription for all analyzed cultivars. The starch content also significantly decreased during tuber storage. The amount of reducing sugars increased in the September-April period, while in February-April, their content did not change (Krasavchik), decreased (Barin, Severnoe siyanie) or continued to grow (Utro, Nadezhda). It can be assumed that the gene activity of StBAM1 and StBAM9 correlates with the amount of starch (positively) and monosaccharides (negatively). The level of StAI expression, in turn, may be directly dependent on the level of StBAM1 expression. At the same time, there is no relationship between the degree of cultivar predisposition to cold-induced sweetening and the expression profile of the StBAM1, StBAM9, and StAI genes.
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Affiliation(s)
- A.V. Kulakova
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
| | - G.I. Efremov
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
| | - A.V. Shchennikova
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
| | - E.Z. Kochieva
- Institute of Bioengineering, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia
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Recent Advances in Molecular Improvement for Potato Tuber Traits. Int J Mol Sci 2022; 23:ijms23179982. [PMID: 36077378 PMCID: PMC9456189 DOI: 10.3390/ijms23179982] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Potato is an important crop due to its nutritional value and high yield potential. Improving the quality and quantity of tubers remains one of the most important breeding objectives. Genetic mapping helps to identify suitable markers for use in the molecular breeding, and combined with transgenic approaches provides an efficient way for gaining desirable traits. The advanced plant breeding tools and molecular techniques, e.g., TALENS, CRISPR-Cas9, RNAi, and cisgenesis, have been successfully used to improve the yield and nutritional value of potatoes in an increasing world population scenario. The emerging methods like genome editing tools can avoid incorporating transgene to keep the food more secure. Multiple success cases have been documented in genome editing literature. Recent advances in potato breeding and transgenic approaches to improve tuber quality and quantity have been summarized in this review.
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Szajko K, Sołtys-Kalina D, Heidorn-Czarna M, Smyda-Dajmund P, Wasilewicz-Flis I, Jańska H, Marczewski W. Transcriptomic and proteomic data provide new insights into cold-treated potato tubers with T- and D-type cytoplasm. PLANTA 2022; 255:97. [PMID: 35380306 PMCID: PMC8983635 DOI: 10.1007/s00425-022-03879-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Tuber-omics in potato with the T- and D-types of cytoplasm showed different sets of differentially expressed genes and proteins in response to cold storage. For the first time, we report differences in gene and protein expression in potato (Solanum tuberosum L.) tubers possessing the T- or D-type cytoplasm. Two F1 diploid reciprocal populations, referred to as T and D, were used. The pooling strategy was applied for detection of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in tubers consisting of extreme chip colour after cold storage. RNA and protein bulks were constructed from contrasting phenotypes. We recognized 48 and 15 DEGs for the T and D progenies, respectively. DEPs were identified in the amyloplast and mitochondrial fractions. In the T-type cytoplasm, only 2 amyloplast-associated and 5 mitochondria-associated DEPs were detected. Of 37 mitochondria-associated DEPs in the D-type cytoplasm, there were 36 downregulated DEPs in the dark chip colour bulks. These findings suggest that T- and D-type of cytoplasm might influence sugar accumulation in cold-stored potato tubers in different ways. We showed that the mt/nucDNA ratio was higher in D-possessing tubers after cold storage than in T progeny. For the D-type cytoplasm, the pt/nucDNA ratio was higher for tubers characterized by dark chip colour than for those with light chip colour. Our findings suggest that T- and D-type cytoplasm might influence sugar accumulation in cold-stored potato tubers in different ways.
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Affiliation(s)
- Katarzyna Szajko
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | | | - Paulina Smyda-Dajmund
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Hanna Jańska
- Faculty of Biotechnology, University of Wroclaw, 50-383, Wrocław, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
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Lindqvist-Kreuze H, De Boeck B, Unger P, Gemenet D, Li X, Pan Z, Sui Q, Qin J, Woldegjorgis G, Negash K, Seid I, Hirut B, Gastelo M, De Vega J, Bonierbale M. Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation. G3-GENES GENOMES GENETICS 2021; 11:6342414. [PMID: 34549785 PMCID: PMC8527470 DOI: 10.1093/g3journal/jkab251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 06/29/2021] [Indexed: 11/18/2022]
Abstract
The identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the clonal and polyploid nature of the crop and the rapid evolution of the pathogen. A diversity panel of tetraploid potato germplasm bred for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and evaluated for late blight resistance in three countries where the International Potato Center (CIP) has established breeding work. Health-indexed, in vitro plants of 380 clones and varieties were distributed from CIP headquarters and tuber seed was produced centrally in Peru, China, and Ethiopia. Phenotypes were recorded following field exposure to local isolates of Phytophthora infestans. QTL explaining resistance in four experiments conducted across the three countries were identified in chromosome IX, and environment-specific QTL were found in chromosomes III, V, and X. Different genetic models were evaluated for prediction ability to identify best performing germplasm in each and all environments. The best prediction ability (0.868) was identified with the genomic best linear unbiased predictors (GBLUPs) when using the diploid marker data and QTL-linked markers as fixed effects. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT, and B3-LTVR populations. The results show that many of the advanced clones bred in Peru for high levels of late blight resistance maintain their resistance in Ethiopia and China, suggesting that the centralized selection strategy has been largely successful.
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Affiliation(s)
| | | | - Paula Unger
- International Potato Center, CIP, Lima 15024, Peru
| | | | - Xianping Li
- ndustrial Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), 2238 Beijing Road, Kunming, Yunnan 650205, P.R. China
| | - Zhechao Pan
- ndustrial Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), 2238 Beijing Road, Kunming, Yunnan 650205, P.R. China
| | - Qinjun Sui
- ndustrial Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), 2238 Beijing Road, Kunming, Yunnan 650205, P.R. China
| | | | - Gebremedhin Woldegjorgis
- Ethiopian Institute of Agricultural Research, (EIAR), Holetta Agricultural research Center. P.O. Box 31, West Showa Zone, Oromia Region, Ethiopia
| | - Kassaye Negash
- Ethiopian Institute of Agricultural Research, (EIAR), Holetta Agricultural research Center. P.O. Box 31, West Showa Zone, Oromia Region, Ethiopia
| | - Ibrahim Seid
- Ethiopian Institute of Agricultural Research, (EIAR), Holetta Agricultural research Center. P.O. Box 31, West Showa Zone, Oromia Region, Ethiopia
| | - Betaw Hirut
- CIP Ethiopia, c/o ILRI Ethiopia P.O. Box 5689, Addis Ababa, Ethiopia
| | | | - Jose De Vega
- Earlham Institute (EI), Norwich Research Park, Norwich NR4 7UZ, UK
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Tosetti R, Waters A, Chope G, Cools K, Alamar M, McWilliam S, Thompson A, Terry L. New insights into the effects of ethylene on ABA catabolism, sweetening and dormancy in stored potato tubers. POSTHARVEST BIOLOGY AND TECHNOLOGY 2021; 173:111420. [PMID: 33658745 PMCID: PMC7814342 DOI: 10.1016/j.postharvbio.2020.111420] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Continuous ethylene supplementation suppresses postharvest sprouting, but it can increase reducing sugars, limiting its use as an alternative to chlorpropham for processing potatoes. To elucidate the mechanisms involved, tubers were treated after curing with or without the ethylene binding inhibitor 1-methylcyclopropene (1-MCP at 1 μL L-1 for 24 h), and then stored in air or air supplemented with continuous ethylene (10 μL L-1). Across three consecutive seasons, changes in tuber physiology were assessed alongside transcriptomic and metabolomic analysis. Exogenous ethylene alone consistently induced a respiratory rise and the accumulation of undesirable reducing sugars. The transient respiratory peak was preceded by the strong upregulation of two genes encoding 1-aminocyclopropane-1-carboxylate oxidase (ACO), typical of wound and stress induced ethylene production. Profiles of parenchymatic tissue highlighted that ethylene triggered abscisic acid (ABA) catabolism, evidenced by a steep fall in ABA levels and a transient rise in the catabolite phaseic acid, accompanied by upregulation of transcripts encoding an ABA 8'-hydroxylase. Moreover, analysis of non-structural carbohydrate-related genes revealed that ethylene strongly downregulated the expression of the Kunitz-type invertase inhibitor, already known to be involved in cold-induced sweetening. All these ethylene-induced effects were negated by 1-MCP with one notable exception: 1-MCP enhanced the sprout suppressing effect of ethylene whilst preventing ethylene-induced sweetening. This study supports the conclusions that: i) tubers adapt to ethylene by regulating conserved pathways (e.g. ABA catabolism); ii) ethylene-induced sweetening acts independently from sprout suppression, and is similar to cold-induced sugar accumulation.
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Affiliation(s)
- R. Tosetti
- Plant Science Laboratory, Cranfield University, Cranfield, MK43 0AL, UK
| | - A. Waters
- PepsiCo Inc., 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - G.A. Chope
- PepsiCo International Limited, Beaumont Park, 4 Leycroft Road, Leicester, LE4 1ET, UK
| | - K. Cools
- Postharvest BioScience Consultant, Binfield, Berkshire, RG42 5LG, UK
| | - M.C. Alamar
- Plant Science Laboratory, Cranfield University, Cranfield, MK43 0AL, UK
| | - S. McWilliam
- PepsiCo International Limited, Beaumont Park, 4 Leycroft Road, Leicester, LE4 1ET, UK
| | - A.J. Thompson
- Plant Science Laboratory, Cranfield University, Cranfield, MK43 0AL, UK
| | - L.A. Terry
- Plant Science Laboratory, Cranfield University, Cranfield, MK43 0AL, UK
- Corresponding author.
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11
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Saidi A, Hajibarat Z. Application of Next Generation Sequencing, GWAS, RNA seq, WGRS, for genetic improvement of potato (Solanum tuberosum L.) under drought stress. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Wen F, Ye F, Xiao Z, Liao L, Li T, Jia M, Liu X, Wu X. Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon. BMC Genomics 2020; 21:53. [PMID: 31948407 PMCID: PMC6966850 DOI: 10.1186/s12864-020-6475-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/09/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Ca2+ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca2+ sensors, which could directly translate Ca2+ signals into downstream phosphorylation signals. Considering the importance of CDPKs as Ca2+ effectors for regulation of plant stress tolerance and few studies on Brachypodium distachyon were available, it was of interest for us to isolate CDPKs from B. distachyon. RESULTS A systemic analysis of 30 CDPK family genes in B. distachyon was performed. Results showed that all BdCDPK family members contained conserved catalytic Ser/Thr protein kinase domain, autoinhibitory domain, and EF-hand domain, and a variable N-terminal domain, could be divided into four subgroup (I-IV), based upon sequence homology. Most BdCDPKs had four EF-hands, in which EF2 and EF4 revealed high variability and strong divergence from EF-hand in AtCDPKs. Synteny results indicated that large number of syntenic relationship events existed between rice and B. distachyon, implying their high conservation. Expression profiles indicated that most of BdCDPK genes were involved in phytohormones signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. Moreover, the co-expression network implied that BdCDPKs might be both the activator and the repressor involved in WRKY transcription factors or MAPK cascade genes mediated stress response processes, base on their complex regulatory network. CONCLUSIONS BdCDPKs might play multiple function in WRKY or MAPK mediated abiotic stresses response and phytohormone signaling transduction in B. distachyon. Our genomics analysis of BdCDPKs could provide fundamental information for further investigation the functions of CDPKs in integrating Ca2+ signalling pathways in response to environments stresses in B. distachyon.
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Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Feng Ye
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhulong Xiao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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13
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Tai HH, Lagüe M, Thomson S, Aurousseau F, Neilson J, Murphy A, Bizimungu B, Davidson C, Deveaux V, Bègue Y, Wang HY, Xiong X, Jacobs JME. Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:163-176. [PMID: 31756603 DOI: 10.1016/j.plaphy.2019.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 05/19/2023]
Abstract
Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2-4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.
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Affiliation(s)
- Helen H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada.
| | - Martin Lagüe
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - Frédérique Aurousseau
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Jonathan Neilson
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Agnes Murphy
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Benoit Bizimungu
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Charlotte Davidson
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, P. O. Box 20280, 850 Lincoln Rd, Fredericton, N. B, E3B 4Z7, Canada
| | - Virginie Deveaux
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Yves Bègue
- Sipre-Responsable Scientifique Création Variétale, Station de Recherche du Comité Nord, 76110, Bretteville du Grand Caux, France
| | - Hui Ying Wang
- College of Horticulture and Landscape, Hunan Agriculture Univ, Hunan, Changsha, 410128, China
| | - Xingyao Xiong
- College of Horticulture and Landscape, Hunan Agriculture Univ, Hunan, Changsha, 410128, China
| | - Jeanne M E Jacobs
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, New Zealand
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14
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Sharma SK, MacKenzie K, McLean K, Dale F, Daniels S, Bryan GJ. Linkage Disequilibrium and Evaluation of Genome-Wide Association Mapping Models in Tetraploid Potato. G3 (BETHESDA, MD.) 2018; 8:3185-3202. [PMID: 30082329 PMCID: PMC6169395 DOI: 10.1534/g3.118.200377] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022]
Abstract
Genome-wide association studies (GWAS) have become a powerful tool for analyzing complex traits in crop plants. The current study evaluates the efficacy of various GWAS models and methods for elucidating population structure in potato. The presence of significant population structure can lead to detection of spurious marker-trait associations, as well as mask true ones. While appropriate statistical models are needed to detect true marker-trait associations, in most published potato GWAS, a 'one model fits all traits' approach has been adopted. We have examined various GWAS models on a large association panel comprising diverse tetraploid potato cultivars and breeding lines, genotyped with single nucleotide polymorphism (SNP) markers. Phenotypic data were generated for 20 quantitative traits assessed in different environments. Best Linear Unbiased Estimates (BLUEs) for these traits were obtained for use in assessing GWAS models. Goodness of fit of GWAS models, derived using different combinations of kinship and population structure for all traits, was evaluated using Quantile-Quantile (Q-Q) plots and genomic control inflation factors (λGC). Kinship was found to play a major role in correcting population confounding effects and results advocate a 'trait-specific' fit of different GWAS models. A survey of genome-wide linkage disequilibrium (LD), one of the critical factors affecting GWAS, is also presented and our findings are compared to other recent studies in potato. The genetic material used here, and the outputs of this study represent a novel resource for genetic analysis in potato.
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Affiliation(s)
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland (BioSS), Dundee DD2 5DA, UK
| | | | - Finlay Dale
- The James Hutton Institute, Dundee DD2 5DA, UK
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15
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Ahmed S, Zhou X, Pang Y, Jin L, Bao J. Improving Starch‐Related Traits in Potato Crops: Achievements and Future Challenges. STARCH-STARKE 2018. [DOI: 10.1002/star.201700113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sulaiman Ahmed
- Institute of Nuclear Agricultural ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHuajiachi CampusHangzhou310029China
| | - Xin Zhou
- Institute of Nuclear Agricultural ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHuajiachi CampusHangzhou310029China
| | - Yuehan Pang
- Institute of Nuclear Agricultural ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHuajiachi CampusHangzhou310029China
| | - Liping Jin
- Department of PotatoInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing100081China
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of AgricultureBeijing100081P.R. China
| | - Jinsong Bao
- Institute of Nuclear Agricultural ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHuajiachi CampusHangzhou310029China
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of AgricultureBeijing100081P.R. China
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16
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De Lepeleire J, Strobbe S, Verstraete J, Blancquaert D, Ambach L, Visser RGF, Stove C, Van Der Straeten D. Folate Biofortification of Potato by Tuber-Specific Expression of Four Folate Biosynthesis Genes. MOLECULAR PLANT 2018; 11:175-188. [PMID: 29277427 DOI: 10.1016/j.molp.2017.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/24/2023]
Abstract
Insufficient dietary intake of micronutrients, known as "hidden hunger", is a devastating global burden, affecting two billion people. Deficiency of folates (vitamin B9), which are known to play a central role in C1 metabolism, causes birth defects in at least a quarter million people annually. Biofortification to enhance the level of naturally occurring folates in crop plants, proves to be an efficient and cost-effective tool in fighting folate deficiency. Previously, introduction of folate biosynthesis genes GTPCHI and ADCS, proven to be a successful biofortification strategy in rice and tomato, turned out to be insufficient to adequately increase folate levels in potato tubers. Here, we provide a proof of concept that additional introduction of HPPK/DHPS and/or FPGS, downstream genes in mitochondrial folate biosynthesis, enables augmentation of folates to satisfactory levels (12-fold) and ensures folate stability upon long-term storage of tubers. In conclusion, this engineering strategy can serve as a model in the creation of folate-accumulating potato cultivars, readily applicable in potato-consuming populations suffering from folate deficiency.
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Affiliation(s)
- Jolien De Lepeleire
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Jana Verstraete
- Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Dieter Blancquaert
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Lars Ambach
- Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6700 Wageningen, the Netherlands
| | - Christophe Stove
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6700 Wageningen, the Netherlands
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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17
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Sverrisdóttir E, Byrne S, Sundmark EHR, Johnsen HØ, Kirk HG, Asp T, Janss L, Nielsen KL. Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2091-2108. [PMID: 28707250 PMCID: PMC5606954 DOI: 10.1007/s00122-017-2944-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/29/2017] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development. Chipping quality was evaluated as the colour of a potato chip after frying following cold induced sweetening. We used genotyping-by-sequencing to genotype 762 offspring, derived from a population generated from biparental crosses of 18 tetraploid parents. Additionally, 74 breeding clones were genotyped, representing a test panel for model validation. We generated genomic prediction models from 171,859 single-nucleotide polymorphisms to calculate genomic estimated breeding values. Cross-validated prediction correlations of 0.56 and 0.73 were obtained within the training population for starch content and chipping quality, respectively, while correlations were lower when predicting performance in the test panel, at 0.30-0.31 and 0.42-0.43, respectively. Predictions in the test panel were slightly improved when including representatives from the test panel in the training population but worsened when preceded by marker selection. Our results suggest that genomic prediction is feasible, however, the extremely high allelic diversity of tetraploid potato necessitates large training populations to efficiently capture the genetic diversity of elite potato germplasm and enable accurate prediction across the entire spectrum of elite potatoes. Nonetheless, our results demonstrate that GS is a promising breeding strategy for tetraploid potato.
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Affiliation(s)
- Elsa Sverrisdóttir
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - Stephen Byrne
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
- Crop Science Department, Teagasc, Oak Park, Carlow, Ireland
| | - Ea Høegh Riis Sundmark
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Heidi Øllegaard Johnsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | | | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Luc Janss
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark
| | - Kåre L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
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18
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Schönhals EM, Ding J, Ritter E, Paulo MJ, Cara N, Tacke E, Hofferbert HR, Lübeck J, Strahwald J, Gebhardt C. Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array. BMC Genomics 2017; 18:642. [PMID: 28830357 PMCID: PMC5567664 DOI: 10.1186/s12864-017-3979-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/01/2017] [Indexed: 02/08/2023] Open
Abstract
Background Tuber yield and starch content of the cultivated potato are complex traits of decisive importance for breeding improved varieties. Natural variation of tuber yield and starch content depends on the environment and on multiple, mostly unknown genetic factors. Dissection and molecular identification of the genes and their natural allelic variants controlling these complex traits will lead to the development of diagnostic DNA-based markers, by which precision and efficiency of selection can be increased (precision breeding). Results Three case-control populations were assembled from tetraploid potato cultivars based on maximizing the differences between high and low tuber yield (TY), starch content (TSC) and starch yield (TSY, arithmetic product of TY and TSC). The case-control populations were genotyped by restriction-site associated DNA sequencing (RADseq) and the 8.3 k SolCAP SNP genotyping array. The allele frequencies of single nucleotide polymorphisms (SNPs) were compared between cases and controls. RADseq identified, depending on data filtering criteria, between 6664 and 450 genes with one or more differential SNPs for one, two or all three traits. Differential SNPs in 275 genes were detected using the SolCAP array. A genome wide association study using the SolCAP array on an independent, unselected population identified SNPs associated with tuber starch content in 117 genes. Physical mapping of the genes containing differential or associated SNPs, and comparisons between the two genome wide genotyping methods and two different populations identified genome segments on all twelve potato chromosomes harboring one or more quantitative trait loci (QTL) for TY, TSC and TSY. Conclusions Several hundred genes control tuber yield and starch content in potato. They are unequally distributed on all potato chromosomes, forming clusters between 0.5–4 Mbp width. The largest fraction of these genes had unknown function, followed by genes with putative signalling and regulatory functions. The genetic control of tuber yield and starch content is interlinked. Most differential SNPs affecting both traits had antagonistic effects: The allele increasing TY decreased TSC and vice versa. Exceptions were 89 SNP alleles which had synergistic effects on TY, TSC and TSY. These and the corresponding genes are primary targets for developing diagnostic markers. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3979-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elske Maria Schönhals
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jia Ding
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Nicolás Cara
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Jens Lübeck
- SaKa-Pflanzenzucht GmbH & Co. KG, Windeby, Germany
| | | | - Christiane Gebhardt
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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19
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Álvarez MF, Angarita M, Delgado MC, García C, Jiménez-Gomez J, Gebhardt C, Mosquera T. Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja. FRONTIERS IN PLANT SCIENCE 2017; 8:1040. [PMID: 28674545 PMCID: PMC5475386 DOI: 10.3389/fpls.2017.01040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/30/2017] [Indexed: 05/16/2023]
Abstract
The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein (StTL15A) and a stem 28 kDa glycoprotein (StGP28). Key message: A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight.
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Affiliation(s)
- María F. Álvarez
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
- Rice Program International Centre for Tropical Agriculture (CIAT)Cali, Colombia
| | - Myrian Angarita
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
| | - María C. Delgado
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
| | - Celsa García
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
| | - José Jiménez-Gomez
- Department of Genetics and Plant Breeding, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Christiane Gebhardt
- Department of Genetics and Plant Breeding, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Teresa Mosquera
- Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaBogotá, Colombia
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20
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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.
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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.
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21
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Neilson J, Lagüe M, Thomson S, Aurousseau F, Murphy AM, Bizimungu B, Deveaux V, Bègue Y, Jacobs JME, Tai HH. Gene expression profiles predictive of cold-induced sweetening in potato. Funct Integr Genomics 2017; 17:459-476. [PMID: 28236275 DOI: 10.1007/s10142-017-0549-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/18/2017] [Accepted: 01/30/2017] [Indexed: 10/24/2022]
Abstract
Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS. A distance matrix for potato clones based on glucose levels after cold storage was constructed and compared to distance matrices constructed using RNA-seq gene expression data. Congruence between glucose and gene expression distance matrices was tested for each gene. Correlation between glucose and gene expression was also tested. Seventy-three genes were found that had significant p values in the congruence and correlation tests. Twelve genes from the list of 73 genes also had a high correlation between glucose and gene expression as measured by Nanostring nCounter. The gene annotations indicated functions in protein degradation, nematode resistance, auxin transport, and gibberellin response. These 12 genes were used to build models for prediction of CIS using multiple linear regression. Nine linear models were constructed that used different combinations of the 12 genes. An F-box protein, cellulose synthase, and a putative Lax auxin transporter gene were most frequently used. The findings of this study demonstrate the utility of gene expression profiles in predictive diagnostics for severity of CIS.
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Affiliation(s)
- Jonathan Neilson
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
| | - M Lagüe
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - S Thomson
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - F Aurousseau
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - A M Murphy
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - B Bizimungu
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - V Deveaux
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - Y Bègue
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - J M E Jacobs
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - H H Tai
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
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22
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Vos PG, Paulo MJ, Voorrips RE, Visser RGF, van Eck HJ, van Eeuwijk FA. Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:123-135. [PMID: 27699464 PMCID: PMC5214954 DOI: 10.1007/s00122-016-2798-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/26/2016] [Indexed: 05/20/2023]
Abstract
The number of SNPs required for QTL discovery is justified by the distance at which linkage disequilibrium has decayed. Simulations and real potato SNP data showed how to estimate and interpret LD decay. The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the desired numbers of SNPs on arrays. To study LD and LD decay in tetraploid potato, we simulated autotetraploid genotypes and used it to explore the dependence on: (1) the number of haplotypes in the population (the amount of genetic variation) and (2) the percentage of haplotype specific SNPs (hs-SNPs). Several estimators for short-range LD were explored, such as the average r 2, median r 2, and other percentiles of r 2 (80, 90, and 95 %). For LD decay, we looked at LD½,90, the distance at which the short-range LD is halved when using the 90 % percentile of r 2 at short range, as estimator for LD. Simulations showed that the performance of various estimators for LD decay strongly depended on the number of haplotypes, although the real value of LD decay was not influenced very much by this number. The estimator LD½,90 was chosen to evaluate LD decay in 537 tetraploid varieties. LD½,90 values were 1.5 Mb for varieties released before 1945 and 0.6 Mb in varieties released after 2005. LD½,90 values within three different subpopulations ranged from 0.7 to 0.9 Mb. LD½,90 was 2.5 Mb for introgressed regions, indicating large haplotype blocks. In pericentromeric heterochromatin, LD decay was negligible. This study demonstrates that several related factors influencing LD decay could be disentangled, that no universal approach can be suggested, and that the estimation of LD decay has to be performed with great care and knowledge of the sampled material.
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Affiliation(s)
- Peter G Vos
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - M João Paulo
- Biometris, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
| | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
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23
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Mosquera T, Alvarez MF, Jiménez-Gómez JM, Muktar MS, Paulo MJ, Steinemann S, Li J, Draffehn A, Hofmann A, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Walkemeier B, Gebhardt C. Targeted and Untargeted Approaches Unravel Novel Candidate Genes and Diagnostic SNPs for Quantitative Resistance of the Potato (Solanum tuberosum L.) to Phytophthora infestans Causing the Late Blight Disease. PLoS One 2016; 11:e0156254. [PMID: 27281327 PMCID: PMC4900573 DOI: 10.1371/journal.pone.0156254] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/08/2016] [Indexed: 11/18/2022] Open
Abstract
The oomycete Phytophthora infestans causes late blight of potato, which can completely destroy the crop. Therefore, for the past 160 years, late blight has been the most important potato disease worldwide. The identification of cultivars with high and durable field resistance to P. infestans is an objective of most potato breeding programs. This type of resistance is polygenic and therefore quantitative. Its evaluation requires multi-year and location trials. Furthermore, quantitative resistance to late blight correlates with late plant maturity, a negative agricultural trait. Knowledge of the molecular genetic basis of quantitative resistance to late blight not compromised by late maturity is very limited. It is however essential for developing diagnostic DNA markers that facilitate the efficient combination of superior resistance alleles in improved cultivars. We used association genetics in a population of 184 tetraploid potato cultivars in order to identify single nucleotide polymorphisms (SNPs) that are associated with maturity corrected resistance (MCR) to late blight. The population was genotyped for almost 9000 SNPs from three different sources. The first source was candidate genes specifically selected for their function in the jasmonate pathway. The second source was novel candidate genes selected based on comparative transcript profiling (RNA-Seq) of groups of genotypes with contrasting levels of quantitative resistance to P. infestans. The third source was the first generation 8.3k SolCAP SNP genotyping array available in potato for genome wide association studies (GWAS). Twenty seven SNPs from all three sources showed robust association with MCR. Some of those were located in genes that are strong candidates for directly controlling quantitative resistance, based on functional annotation. Most important were: a lipoxygenase (jasmonate pathway), a 3-hydroxy-3-methylglutaryl coenzyme A reductase (mevalonate pathway), a P450 protein (terpene biosynthesis), a transcription factor and a homolog of a major gene for resistance to P. infestans from the wild potato species Solanum venturii. The candidate gene approach and GWAS complemented each other as they identified different genes. The results of this study provide new insight in the molecular genetic basis of quantitative resistance in potato and a toolbox of diagnostic SNP markers for breeding applications.
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Affiliation(s)
- Teresa Mosquera
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Maria Fernanda Alvarez
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia
| | - José M. Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute Jean-Pierre Bourgin, INRA, AgroParis Tech, CNRS, Université Paris-Saclay, Versailles, France
| | - Meki Shehabu Muktar
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Sebastian Steinemann
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jinquan Li
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Astrid Draffehn
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea Hofmann
- Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jens Lübeck
- SaKa-Pflanzenzucht GmbH & Co. KG, 24340, Windeby, Germany
| | | | | | | | - Birgit Walkemeier
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christiane Gebhardt
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
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24
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Schönhals EM, Ortega F, Barandalla L, Aragones A, Ruiz de Galarreta JI, Liao JC, Sanetomo R, Walkemeier B, Tacke E, Ritter E, Gebhardt C. Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:767-785. [PMID: 26825382 PMCID: PMC4799268 DOI: 10.1007/s00122-016-2665-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 01/09/2016] [Indexed: 05/23/2023]
Abstract
SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.
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Affiliation(s)
- E M Schönhals
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | | | | | - J-C Liao
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - R Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - B Walkemeier
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - C Gebhardt
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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25
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Ali A, Ahmad Nasir I, Muzaffar A, Shahzad Iqbal M, Qayyum Rao A, Husnain T. Screening of Potato Germplasm Resistant Against Low Temperature Sweetening. J FOOD QUALITY 2016. [DOI: 10.1111/jfq.12196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Arfan Ali
- Centre of Excellence in Molecular Biology, University of the Punjab; Lahore Pakistan
- Institute of Molecular Biology and Biotechnology, The University of Lahore; Lahore Pakistan
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab; Lahore Pakistan
| | - Adnan Muzaffar
- Centre of Excellence in Molecular Biology, University of the Punjab; Lahore Pakistan
| | | | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab; Lahore Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab; Lahore Pakistan
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26
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Xin C, Hou R, Wu F, Zhao Y, Xiao H, Si W, Ali ME, Cai L, Guo J. Analysis of cytosine methylation status in potato by methylation-sensitive amplified polymorphisms under low-temperature stress. JOURNAL OF PLANT BIOLOGY 2015; 58:383-390. [DOI: 10.1007/s12374-015-0316-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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27
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Zivy M, Wienkoop S, Renaut J, Pinheiro C, Goulas E, Carpentier S. The quest for tolerant varieties: the importance of integrating "omics" techniques to phenotyping. FRONTIERS IN PLANT SCIENCE 2015; 6:448. [PMID: 26217344 PMCID: PMC4496562 DOI: 10.3389/fpls.2015.00448] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
The primary objective of crop breeding is to improve yield and/or harvest quality while minimizing inputs. Global climate change and the increase in world population are significant challenges for agriculture and call for further improvements to crops and the development of new tools for research. Significant progress has been made in the molecular and genetic analysis of model plants. However, is science generating false expectations? Are 'omic techniques generating valuable information that can be translated into the field? The exploration of crop biodiversity and the correlation of cellular responses to stress tolerance at the plant level is currently a challenge. This viewpoint reviews concisely the problems one encounters when working on a crop and provides an outline of possible workflows when initiating cellular phenotyping via "-omic" techniques (transcriptomics, proteomics, metabolomics).
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Affiliation(s)
- Michel Zivy
- Department Génétique Quantitative et Évolution, Le Moulon INRA, CNRS, AgroParisTech, Plateforme PAPPSO, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Jenny Renaut
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, Oeiras, Portugal
- Faculdade de Ciências e Tecnologia, New University of Lisbon, Caparica, Portugal
| | - Estelle Goulas
- Department of Sciences et Technologies, CNRS/Université Lille, Villeneuve d’Ascq, France
| | - Sebastien Carpentier
- Department of Biosystems, University of Leuven, Leuven, Belgium
- SYBIOMA, University of Leuven, Leuven, Belgium
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28
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Sanetomo R, Gebhardt C. Cytoplasmic genome types of European potatoes and their effects on complex agronomic traits. BMC PLANT BIOLOGY 2015; 15:162. [PMID: 26112802 PMCID: PMC4480903 DOI: 10.1186/s12870-015-0545-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/10/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND Various wild species germplasm has been used in European potato breeding since the first introduction of potato (Solanum tuberosum L.) to Europe. As the plant cytoplasmic genome including chloroplast and mitochondrial genomes is transmitted only through the maternal parent, cytoplasmic markers are useful tools in breeding programs to determine cytoplasmic genome types and to trace maternal ancestors. The potato cytoplasmic genome can be distinguished into six distinct types (M, P, A, W, T, and D). Male sterility was found in genotypes with S. demissum-derived D-type cytoplasm and S. stoloniferum-derived W/γ-type cytoplasm. These wild species were frequently used to incorporate superior pathogen resistance genes. As a result, the percentage of these two types is increasing unintentionally in the European germplasm pool. Other than cytoplasmic male sterility, little is known about effects of the cytoplasmic genome on complex agronomic traits in potato. RESULT The cytoplasm types of 1,217 European potato cultivars and breeding clones were determined with type specific DNA markers. Most frequent were T- (59.4 %), D- (27.4 %), and W- (12.2 %) type cytoplasm, while A- (0.7 %) and M-type cytoplasm (0.3 %) was rare and P-type cytoplasm was absent. When comparing varieties with breeding clones, the former showed a relatively higher frequency of T-type and lower frequency of D- and W-type cytoplasm. Correlation analysis of cytoplasm types and agronomic data showed that W/γ-type cytoplasm was correlated with increased tuber starch content and later plant maturity. Correlation with quantitative resistance to late blight was observed for D-type and M-type cytoplasm. Both cytoplasm types had a positive effect on resistance. CONCLUSION This study revealed and quantified the cytoplasmic diversity in the European potato germplasm pool. Knowledge of cytoplasm type is important for maintaining genetic diversity and managing the male sterility problem in breeding programs. This is the first comprehensive study to show correlations of distinct cytoplasmic genomes with complex agronomic traits in potato. Correlations particularly with tuber starch content and resistance to late blight provided new knowledge on cytoplasmic effects on these important traits, which can be exploited for genetic improvement of potato.
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Affiliation(s)
- Rena Sanetomo
- Obihiro University of Agriculture and Veterinary Medicine, Potato Germplasm Enhancement Laboratory, West 2-11, Inada, Obihiro, Hokkaido, 080-8555, Japan.
| | - Christiane Gebhardt
- Max-Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, Carl von Linné Weg 10, 50829, Cologne, Germany.
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Sołtys-Kalina D, Szajko K, Sierocka I, Śliwka J, Strzelczyk-Żyta D, Wasilewicz-Flis I, Jakuczun H, Szweykowska-Kulinska Z, Marczewski W. Novel candidate genes AuxRP and Hsp90 influence the chip color of potato tubers. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:224. [PMID: 26612975 PMCID: PMC4648990 DOI: 10.1007/s11032-015-0415-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/11/2015] [Indexed: 05/11/2023]
Abstract
Potato (Solanum tuberosum L.) tubers exhibit significant variation in reducing sugar content directly after harvest, cold storage and reconditioning. Here, we performed QTL analysis for chip color, which is strongly influenced by reducing sugar content, in a diploid potato mapping population. Two QTL on chromosomes I and VI were detected for chip color after harvest and reconditioning. Only one region on chromosome VI was linked with cold-induced sweetening. Using the RT-PCR technique, we showed differential expression of the auxin-regulated protein (AuxRP) gene. The AuxRP transcript was presented in light chip color parental clone DG 97-952 and the RNA progeny of the bulk sample consisting of light chip color phenotypes after cold storage. This amplicon was absent in dark chip parental clone DG 08-26/39 and the RNA bulk sample of dark chip progeny. Genetic variation of AuxRP explained up to 16.6 and 15.2 % of the phenotypic variance after harvest and 3 months of storage at 4 °C, respectively. Using an alternative approach, the RDA-cDNA method was used to recognize 25 gene sequences, of which 11 could be assigned to potato chromosome VI. One of these genes, Heat-shock protein 90 (Hsp90), demonstrated higher mRNA and protein expression in RT-qPCR and western blotting assays in the dark chip color progeny bulk sample compared with the light chip color progeny bulk sample. Our study, for the first time, suggests that the AuxRP and Hsp90 genes are novel candidate genes capable of influencing the chip color of potato tubers.
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Affiliation(s)
- Dorota Sołtys-Kalina
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Katarzyna Szajko
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Izabela Sierocka
- />Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Jadwiga Śliwka
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Danuta Strzelczyk-Żyta
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Iwona Wasilewicz-Flis
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Henryka Jakuczun
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Zofia Szweykowska-Kulinska
- />Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Waldemar Marczewski
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
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30
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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.
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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
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31
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D'hoop BB, Keizer PLC, Paulo MJ, Visser RGF, van Eeuwijk FA, van Eck HJ. Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:731-48. [PMID: 24408376 DOI: 10.1007/s00122-013-2254-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 12/13/2013] [Indexed: 05/23/2023]
Abstract
Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits. Two association mapping panels were analysed for marker-trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
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Affiliation(s)
- Björn B D'hoop
- Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
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