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Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Front Genet 2023; 14:1197206. [PMID: 37564870 PMCID: PMC10411547 DOI: 10.3389/fgene.2023.1197206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 08/12/2023] Open
Abstract
Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.
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Golubeva TS, Cherenko VA, Sinitsyna OI, Kochetov AV. Molecular and Genetic Aspects of Potato Response to Late Blight Infection. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422020053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Selga C, Reslow F, Pérez-Rodríguez P, Ortiz R. The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato. G3 (BETHESDA, MD.) 2022; 12:6407142. [PMID: 34849763 PMCID: PMC8728039 DOI: 10.1093/g3journal/jkab362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 12/02/2022]
Abstract
Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.
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Affiliation(s)
- Catja Selga
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma SE-23422, Sweden
- Corresponding author:
| | - Fredrik Reslow
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma SE-23422, Sweden
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma SE-23422, Sweden
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Frolova TS, Cherenko VA, Sinitsyna OI, Kochetov AV. [Genetic aspects of potato resistance to phytophthorosis]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:164-170. [PMID: 34901714 PMCID: PMC8627881 DOI: 10.18699/vj21.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/10/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022] Open
Abstract
Оомицет Рhytophthora infestans Mont. de Bary – основной патоген сельскохозяйственных культур
семейства Пасленовые, особенно картофеля (Solanum tuberosum). С учетом того, что картофель – четвертая культура в мире по масштабам выращивания, ежегодные потери от фитофтороза огромны. Исследования базовых
механизмов взаимодействия между картофелем и возбудителем фитофтороза не только расширяют фундаментальные знания в этой области, но и открывают новые возможности для влияния на эти взаимодействия с целью
повышения резистентности к патогену. Взаимодействие картофеля и возбудителя фитофтороза можно рассматривать с генетической точки зрения, причем интересны как ответ картофеля на процесс колонизации со стороны P. infestans, так и изменение активности генов у фитофторы при заражении растения. Можно исследовать
этот процесс через изменение профиля вторичных метаболитов хозяина и патогена. Помимо фундаментальных
исследований в этой области, не меньшее значение имеют и прикладные работы в виде создания новых препаратов для защиты картофеля. Представленный обзор кратко описывает основные этапы исследований устойчивости картофеля к фитофторозу, начиная с самых первых работ. Большое внимание уделяется ключевым
моментам по изменению профиля вторичных метаболитов (фитоалексинов). Отдельный раздел посвящен описанию как качественных, так количественных признаков устойчивости картофеля к возбудителю фитофтороза:
их вкладу в общую резистентность, картированию и возможности регуляции. Оба вида признаков важны для
селекции картофеля: качественная устойчивость за счет R-генов быстро преодолевается патогеном, в то время
как пирамидирование локусов количественных признаков способствует созданию высокоустойчивых сортов.
Новейшие подходы молекулярной биологии дают возможность изучать и транслятомные профили, что позволяет посмотреть на взаимодействие картофеля и возбудителя фитофтороза. Показано, что процесс колонизации
картофеля отражается не только на активности различных генов и профиле вторичных метаболитов, выявлены
также белки-маркеры ответа на заражение со стороны картофеля – это патоген-зависимые белки и пластидная
углекислая ангидраза. Маркерами заражения от P. infestans были белки грибной целлюлозо-синтазы и гаусторий-специфический мембранный белок. В данном обзоре приведена информация по наиболее актуальным комплексным исследованиям генетических механизмов устойчивости картофеля к фитофторозу.
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Affiliation(s)
- T S Frolova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V A Cherenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - O I Sinitsyna
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Totsky IV, Rozanova IV, Safonova AD, Batov AS, Gureeva YA, Khlestkina EK, Kochetov AV. Genotyping of potato samples from the GenAgro ICG SB RAS collection using DNA markers of genes conferring resistance to phytopathogens. Vavilovskii Zhurnal Genet Selektsii 2021; 25:677-686. [PMID: 34755022 PMCID: PMC8553976 DOI: 10.18699/vj21.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/19/2022] Open
Abstract
Wart (a disease caused by Synchytrium endobioticum) and golden cyst potato nematode (Globodera rostochiensis), which parasitize the roots of the host plant, cause signif icant damage to potato crop. Both of these disease factors are quarantined in the Russian Federation, and each registered variety is tested for resistance to their most common races and pathotypes. The main method of opposing such diseases is by the development of resistant varieties. An important step in this process is the selection of resistant genotypes from the population and the estimation of the resistance of hybrids obtained by crosses during the breeding process. Conducting a permanent phenotypic evaluation is associated with diff iculties, for example, it is not always possible to work with pathogens, and phenotypic evaluation is very costly and time consuming. However, the use of DNA markers linked to resistance genes can signif icantly speed up and reduce the cost of the breeding process. The aim of the study was to screen the GenAgro potato collection of ICG SB RAS using known diagnostic PCR markers linked to golden potato cyst nematode and wart resistance. Genotyping was carried out on 73 potato samples using three DNA markers 57R, CP113, Gro1-4 associated with nematode resistance and one marker, NL25, associated with wart resistance. The genotyping data were compared with the data on the resistance of the collection samples. Only the 57R marker had a high level of correlation (Spearman R = 0.722008, p = 0.000000, p < 0.05) between resistance and the presence of a diagnostic fragment. The diagnostic eff iciency of the 57R marker was 86.11 %. This marker can be successfully used for screening a collection, searching for resistant genotypes and marker-assisted selection. The other markers showed a low correlation between the presence of the DNA marker and resistance. The diagnostic eff iciency of the CP113 marker was only 44.44 %. Spearman's correlation coeff icient (Spearman R = -0.109218, p = 0.361104, p < 0.05) did not show signif icant correlation between resistance and the DNA marker. The diagnostic eff iciency of the NL25 marker was 61.11 %. No signif icant correlation was found between the NL25 marker and resistance (Spearman R = -0.017946, p = 0.881061, p < 0.05). The use of these markers for the search for resistant samples is not advisable.
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Affiliation(s)
- I V Totsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Rozanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A D Safonova
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Batov
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu A Gureeva
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E K Khlestkina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Yu WQ, Li P, Yan FC, Zheng GP, Liu WZ, Lin WX, Wang Y, Luo ZQ. Protein Elicitor EsxA Induces Resistance to Seedling Blight and PR Genes Differential Transcription in Rice. RICE (NEW YORK, N.Y.) 2021; 14:91. [PMID: 34735664 PMCID: PMC8568749 DOI: 10.1186/s12284-021-00532-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Protein elicitors can induce plant systemic resistance to pathogens. In an earlier study, we cloned an EsxA gene from the plant growth-promoting rhizobacterium Paenibacillus terrae NK3-4 and expressed it in Pichia pastoris. In addition to being important for the pathogenicity of animal pathogens, EsxA can also induce an immune response in animals. While, we found the exogenously expressed EsxA has the activity of elicitor, which can trigger hypersensitive response and reactive oxygen species burst in leaves as well as enhanced rice plant growth. The effects of EsxA on seedling blight (Fusarium oxysporum) resistance and gene transcription, including pathogenesis-related (PR) genes in rice were evaluated. The germination rate was 95.0% for seeds treated with EsxA and then inoculated with F. oxysporum, which was 2.8-times higher than that of F. oxysporum-infected control seeds that were not treated with EsxA (Con). The buds and roots of EsxA-treated seedlings were 2.4- and 15.9-times longer than those of Con seedlings. The plants and roots of seedlings dipped in an EsxA solution and then inoculated with F. oxysporum were longer than those of the Con seedlings. Theplant length, number of total roots, and number of white roots were respectively 23.2%, 1.74-times, and 7.42-times greater for the seedlings sprayed with EsxA and then inoculated with F. oxysporum than for the Con seedlings. The EsxA induction efficiency (spray treatment) on seedling blight resistance was 60.9%. The transcriptome analysis revealed 1137 and 239 rice genes with EsxA-induced up-regulated and down-regulated transcription levels, respectively. At 48 h after the EsxA treatment, the transcription of 611 and 160 genes was up-regulated and down-regulated, respectively, compared with the transcription levels for the untreated control at the same time-point. Many disease resistance-related PR genes had up-regulated transcription levels. The qPCR data were consistent with the transcriptome sequencing results. EsxA triggered rice ISR to seedling blight and gene differential transcription, including the up-regulated transcription of rice PR genes. These findings may be relevant for the use of EsxA as a protein elicitor to control plant diseases.
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Affiliation(s)
- Wen Qing Yu
- College of Life Sciences, Shangrao Normal University, Shanrao, 334001, Jiangxi, China
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, 150038, China
- Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Peng Li
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, 150038, China
| | - Feng Chao Yan
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, 150038, China
| | - Gui Ping Zheng
- Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Wen Zhi Liu
- College of Life Sciences, Shangrao Normal University, Shanrao, 334001, Jiangxi, China.
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, 150038, China.
| | - Wen Xi Lin
- College of Life Sciences, Shangrao Normal University, Shanrao, 334001, Jiangxi, China
| | - Yi Wang
- College of Life Sciences, Shangrao Normal University, Shanrao, 334001, Jiangxi, China
| | - Zhi Qing Luo
- College of Life Sciences, Shangrao Normal University, Shanrao, 334001, Jiangxi, China
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Zia MAB, Demirel U, Nadeem MA, Çaliskan ME. Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1003-1020. [PMID: 32377049 PMCID: PMC7196606 DOI: 10.1007/s12298-020-00785-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 02/01/2020] [Accepted: 02/21/2020] [Indexed: 05/22/2023]
Abstract
Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Niğde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.
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Affiliation(s)
- Muhammad Abu Bakar Zia
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
- College of Agriculture, Bolu Abant Izzet Baysal University, Bahadur Sub Campus Layyah, Pakistan
| | - Ufuk Demirel
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
| | - Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Science, Bahauddin Zakariya University, 14000 Bolu, Turkey
| | - Mehmet Emin Çaliskan
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
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Juyo Rojas DK, Soto Sedano JC, Ballvora A, Léon J, Mosquera Vásquez T. Novel organ-specific genetic factors for quantitative resistance to late blight in potato. PLoS One 2019; 14:e0213818. [PMID: 31310605 PMCID: PMC6634379 DOI: 10.1371/journal.pone.0213818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/23/2019] [Indexed: 01/25/2023] Open
Abstract
Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.
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Affiliation(s)
| | | | - Agim Ballvora
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias Agrarias, Bogotá, Colombia
- * E-mail:
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Font i Forcada C, Guajardo V, Chin-Wo SR, Moreno MÁ. Association Mapping Analysis for Fruit Quality Traits in Prunus persica Using SNP Markers. FRONTIERS IN PLANT SCIENCE 2019; 9:2005. [PMID: 30705685 PMCID: PMC6344403 DOI: 10.3389/fpls.2018.02005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 12/28/2018] [Indexed: 05/24/2023]
Abstract
The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from the peach genome sequence was used in this study. A set of 94 individuals from a peach germplasm collection was phenotyped and genotyped, including local Spanish and modern cultivars maintained at the Experimental Station of Aula Dei, Spain. Phenotypic evaluation based on agronomical, pomological and fruit quality traits was performed at least 3 years. A set of 4,558 out of a total of 8,144 SNPs markers developed by the Illumina Infinium BeadArray (v1.0) technology platform, covering the peach genome, were analyzed for population structure analysis and genome-wide association studies (GWAS). Population structure analysis identified two subpopulations, with admixture within them. While one subpopulation contains only modern cultivars, the other one is formed by local Spanish and several modern cultivars from international breeding programs. To test the marker trait associations between markers and phenotypic traits, four models comprising both general linear model (GLM) and mixed linear model (MLM) were selected. The MLM approach using co-ancestry values from population structure and kinship estimates (K model) identified a maximum of 347 significant associations between markers and traits. The associations found appeared to map within the interval where many candidate genes involved in different pathways are predicted in the peach genome. These results represent a promising situation for GWAS in the identification of SNP variants associated to fruit quality traits, potentially applicable in peach breeding programs.
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Juyo Rojas DK, Soto Sedano JC, Ballvora A, Léon J, Mosquera Vásquez T. Novel organ-specific genetic factors for quantitative resistance to late blight in potato. PLoS One 2019. [PMID: 31310605 DOI: 10.1101/567289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site-associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.
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Affiliation(s)
| | | | - Agim Ballvora
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation Plant Breeding, Katzenburgweg, Bonn, Germany
| | - Teresa Mosquera Vásquez
- Universidad Nacional de Colombia, sede Bogotá, Facultad de Ciencias Agrarias, Bogotá, Colombia
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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: 32] [Impact Index Per Article: 5.3] [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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Glander S, He F, Schmitz G, Witten A, Telschow A, de Meaux J. Assortment of Flowering Time and Immunity Alleles in Natural Arabidopsis thaliana Populations Suggests Immunity and Vegetative Lifespan Strategies Coevolve. Genome Biol Evol 2018; 10:2278-2291. [PMID: 30215800 PMCID: PMC6133262 DOI: 10.1093/gbe/evy124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/31/2022] Open
Abstract
The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host immunity, however, has seldom been documented. Optimal investment into immunity is expected to decrease with shortening lifespan, because a shorter life decreases the probability to encounter pathogens or enemies. Here, we document that in natural populations of Arabidopsis thaliana, the expression levels of immunity genes correlate positively with flowering time, which in annual species is a proxy for lifespan. Using a novel genetic strategy based on bulk-segregants, we partitioned flowering time-dependent from -independent immunity genes and could demonstrate that this positive covariation can be genetically separated. It is therefore not explained by the pleiotropic action of some major regulatory genes controlling both immunity and lifespan. Moreover, we find that immunity genes containing variants reported to impact fitness in natural field conditions are among the genes whose expression covaries most strongly with flowering time. Taken together, these analyses reveal that natural selection has likely assorted alleles promoting lower expression of immunity genes with alleles that decrease the duration of vegetative lifespan in A. thaliana and vice versa. This is the first study documenting a pattern of variation consistent with the impact that selection on flowering time is predicted to have on diversity in host immunity.
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Affiliation(s)
- Shirin Glander
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany
| | - Fei He
- Institute of Botany, University of Cologne, Germany
| | | | - Anika Witten
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany
| | - Arndt Telschow
- Institute for Evolution and Biodiversity, University of Münster, Germany
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Enciso-Rodriguez F, Douches D, Lopez-Cruz M, Coombs J, de Los Campos G. Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato ( Solanum tuberosum). G3 (BETHESDA, MD.) 2018; 8:2471-2481. [PMID: 29794167 PMCID: PMC6027896 DOI: 10.1534/g3.118.200273] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potato (Solanum tuberosum) is a staple food crop and is considered one of the main sources of carbohydrates worldwide. Late blight (Phytophthora infestans) and common scab (Streptomyces scabies) are two of the primary production constraints faced by potato farming. Previous studies have identified a few resistance genes for both late blight and common scab; however, these genes explain only a limited fraction of the heritability of these diseases. Genomic selection has been demonstrated to be an effective methodology for breeding value prediction in many major crops (e.g., maize and wheat). However, the technology has received little attention in potato breeding. We present the first genomic selection study involving late blight and common scab in tetraploid potato. Our data involves 4,110 (Single Nucleotide Polymorphisms, SNPs) and phenotypic field evaluations for late blight (n=1,763) and common scab (n=3,885) collected in seven and nine years, respectively. We report moderately high genomic heritability estimates (0.46 ± 0.04 and 0.45 ± 0.017, for late blight and common scab, respectively). The extent of genotype-by-year interaction was high for late blight and low for common scab. Our assessment of prediction accuracy demonstrates the applicability of genomic prediction for tetraploid potato breeding. For both traits, we found that more than 90% of the genetic variance could be captured with an additive model. For common scab, the highest prediction accuracy was achieved using an additive model. For late blight, small but statistically significant gains in prediction accuracy were achieved using a model that accounted for both additive and dominance effects. Using whole-genome regression models we identified SNPs located in previously reported hotspots regions for late blight, on genes associated with systemic disease resistance responses, and a new locus located in a WRKY transcription factor for common scab.
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Affiliation(s)
| | | | | | | | - Gustavo de Los Campos
- Department of Epidemiology & Biostatistics
- Department of Statistics & Probability
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, 48824
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Stich B, Van Inghelandt D. Prospects and Potential Uses of Genomic Prediction of Key Performance Traits in Tetraploid Potato. FRONTIERS IN PLANT SCIENCE 2018; 9:159. [PMID: 29563919 PMCID: PMC5845909 DOI: 10.3389/fpls.2018.00159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/29/2018] [Indexed: 05/20/2023]
Abstract
Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy. With genomic best linear unbiased prediction (GBLUP), BayesA, BayesCπ, and Bayesian LASSO, four different prediction methods were used for genomic prediction of relative area under disease progress curve after a Phytophthora infestans infection, plant maturity, maturity corrected resistance, tuber starch content, tuber starch yield (TSY), and tuber yield (TY) of 184 tetraploid potato clones or subsets thereof genotyped with the SolCAP 8.3k SNP array. The cross-validated prediction accuracies with GBLUP and the three Bayesian approaches for the six evaluated traits ranged from about 0.5 to about 0.8. For traits with a high expected genetic complexity, such as TSY and TY, we observed an 8% higher prediction accuracy using a model with additive and dominance effects compared with a model with additive effects only. Our results suggest that for oligogenic traits in general and when diagnostic markers are available in particular, the use of Bayesian methods for genomic prediction is highly recommended and that the diagnostic markers should be modeled as fixed effects. The evaluation of the relative performance of genomic prediction vs. phenotypic selection indicated that the former is superior, assuming cycle lengths and selection intensities that are possible to realize in commercial potato breeding programs.
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Affiliation(s)
- Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, Düsseldorf, Germany
| | - Delphine Van Inghelandt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
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15
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Identification and functional characterisation of an allene oxide synthase from grapevine (Vitis vinifera L. Sauvignon blanc). Mol Biol Rep 2018; 45:263-277. [DOI: 10.1007/s11033-018-4159-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/31/2018] [Indexed: 01/01/2023]
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16
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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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17
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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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18
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Rosyara UR, De Jong WS, Douches DS, Endelman JB. Software for Genome-Wide Association Studies in Autopolyploids and Its Application to Potato. THE PLANT GENOME 2016; 9. [PMID: 27898814 DOI: 10.3835/plantgenome2015.08.0073] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome-wide association studies (GWAS) are widely used in diploid species to study complex traits in diversity and breeding populations, but GWAS software tailored to autopolyploids is lacking. The objectives of this research were to (i) develop an R package for autopolyploids based on the + mixed model, (ii) validate the software with simulated data, and (iii) analyze a diversity panel of tetraploid potatoes. A unique feature of the R package, called GWASpoly, is its ability to model different types of polyploid gene action, including additive, simplex dominant, and duplex dominant. Using a simulated tetraploid population, we confirmed our hypothesis that statistical power is higher when the assumed gene action in the GWAS model matches the gene action at unobserved quantitative trait loci (QTL). Thirteen traits were analyzed in the Solanaceae Coordinated Agricultural Project (SolCAP) potato diversity panel and, consistent with previous studies, significant QTL for tuber shape and eye depth co-localized on chromosome 10. For the other traits, only marginally significant QTL were detected, most likely due to insufficient statistical power: for simulated traits with a heritability () of 0.3, the median genome-wide power was only 0.01. Our results indicate that both marker density and population size were limiting factors for GWAS with the SolCAP panel.
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19
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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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20
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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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21
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Huq A, Akter S, Nou IS, Kim HT, Jung YJ, Kang KK. Identification of functional SNPs in genes and their effects on plant phenotypes. ACTA ACUST UNITED AC 2016. [DOI: 10.5010/jpb.2016.43.1.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Amdadul Huq
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Shahina Akter
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Hoy Taek Kim
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Yu Jin Jung
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
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22
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Litholdo CG, Leal GA, Albuquerque PSB, Figueira A. Differential expression of jasmonate biosynthesis genes in cacao genotypes contrasting for resistance against Moniliophthora perniciosa. PLANT CELL REPORTS 2015; 34:1747-1759. [PMID: 26071948 DOI: 10.1007/s00299-015-1821-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/19/2015] [Accepted: 06/05/2015] [Indexed: 06/04/2023]
Abstract
The resistance mechanism of cacao against M. perniciosa is likely to be mediated by JA/ET-signaling pathways due to the preferential TcAOS and TcSAM induction in a resistant genotype. The basidiomycete Moniliophthora perniciosa causes a serious disease in cacao (Theobroma cacao L.), and the use of resistant varieties is the only sustainable long-term solution. Cacao resistance against M. perniciosa is characterized by pathogen growth inhibition with reduced colonization and an attenuation of disease symptoms, suggesting a regulation by jasmonate (JA)/ethylene (ET) signaling pathways. The hypothesis that genes involved in JA biosynthesis would be active in the interaction of T. cacao and M. perniciosa was tested here. The cacao JA-related genes were evaluated for their relative quantitative expression in susceptible and resistant genotypes upon the exogenous application of ET, methyl-jasmonate (MJ), and salicylic acid (SA), or after M. perniciosa inoculation. MJ treatment triggered changes in the expression of genes involved in JA biosynthesis, indicating that the mechanism of positive regulation by exogenous MJ application occurs in cacao. However, a higher induction of these genes was observed in the susceptible genotype. Further, a contrast in JA-related transcriptional expression was detected between susceptible and resistant plants under M. perniciosa infection, with the induction of the allene oxide synthase gene (TcAOS), which encodes a key enzyme in the JA biosynthesis pathway in the resistant genotype. Altogether, this work provides additional evidences that the JA-dependent signaling pathway is modulating the defense response against M. perniciosa in a cacao-resistant genotype.
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Affiliation(s)
- Celso G Litholdo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
- School of Biological Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Gildemberg A Leal
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
- Universidade Federal de Alagoas, Centro de Ciências Agrárias, BR 104, km 85 N, Rio Largo, AL, 57100-000, Brazil
| | - Paulo S B Albuquerque
- Comissão Executiva do Plano da Lavoura Cacaueira, ERJOH, BR 316 km 17, CP 46, Marituba, 67105-970, PA, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil.
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23
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Muktar MS, Lübeck J, Strahwald J, Gebhardt C. Selection and validation of potato candidate genes for maturity corrected resistance to Phytophthora infestans based on differential expression combined with SNP association and linkage mapping. Front Genet 2015; 6:294. [PMID: 26442110 PMCID: PMC4585299 DOI: 10.3389/fgene.2015.00294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/04/2015] [Indexed: 12/23/2022] Open
Abstract
Late blight of potato (Solanum tuberosum L.) caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most important bottlenecks of potato production worldwide. Cultivars with high levels of durable, race unspecific, quantitative resistance are part of a solution to this problem. However, breeding for quantitative resistance is hampered by the correlation between resistance and late plant maturity, which is an undesirable agricultural attribute. The objectives of our research are (i) the identification of genes that condition quantitative resistance to P. infestans not compromised by late plant maturity and (ii) the discovery of diagnostic single nucleotide polymorphism (SNP) markers to be used as molecular tools to increase efficiency and precision of resistance breeding. Twenty two novel candidate genes were selected based on comparative transcript profiling by SuperSAGE (serial analysis of gene expression) in groups of plants with contrasting levels of maturity corrected resistance (MCR). Reproducibility of differential expression was tested by quantitative real time PCR and allele specific pyrosequencing in four new sets of genotype pools with contrasting late blight resistance levels, at three infection time points and in three independent infection experiments. Reproducibility of expression patterns ranged from 28 to 97%. Association mapping in a panel of 184 tetraploid cultivars identified SNPs in five candidate genes that were associated with MCR. These SNPs can be used in marker-assisted resistance breeding. Linkage mapping in two half-sib families (n = 111) identified SNPs in three candidate genes that were linked with MCR. The differentially expressed genes that showed association and/or linkage with MCR putatively function in phytosterol synthesis, fatty acid synthesis, asparagine synthesis, chlorophyll synthesis, cell wall modification, and in the response to pathogen elicitors.
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Affiliation(s)
- Meki S Muktar
- Department for 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 for Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research Cologne, Germany
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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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Carpenter MA, Joyce NI, Genet RA, Cooper RD, Murray SR, Noble AD, Butler RC, Timmerman-Vaughan GM. Starch phosphorylation in potato tubers is influenced by allelic variation in the genes encoding glucan water dikinase, starch branching enzymes I and II, and starch synthase III. FRONTIERS IN PLANT SCIENCE 2015; 6:143. [PMID: 25806042 PMCID: PMC4354307 DOI: 10.3389/fpls.2015.00143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/23/2015] [Indexed: 05/23/2023]
Abstract
Starch phosphorylation is an important aspect of plant metabolism due to its role in starch degradation. Moreover, the degree of phosphorylation of starch determines its physicochemical properties and is therefore relevant for industrial uses of starch. Currently, starch is chemically phosphorylated to increase viscosity and paste stability. Potato cultivars with elevated starch phosphorylation would make this process unnecessary, thereby bestowing economic and environmental benefits. Starch phosphorylation is a complex trait which has been previously shown by antisense gene repression to be influenced by a number of genes including those involved in starch synthesis and degradation. We have used an association mapping approach to discover genetic markers associated with the degree of starch phosphorylation. A diverse collection of 193 potato lines was grown in replicated field trials, and the levels of starch phosphorylation at the C6 and C3 positions of the glucosyl residues were determined by mass spectrometry of hydrolyzed starch from tubers. In addition, the potato lines were genotyped by amplicon sequencing and microsatellite analysis, focusing on candidate genes known to be involved in starch synthesis. As potato is an autotetraploid, genotyping included determination of allele dosage. Significant associations (p < 0.001) were found with SNPs in the glucan water dikinase (GWD), starch branching enzyme I (SBEI) and the starch synthase III (SSIII) genes, and with a SSR allele in the SBEII gene. SNPs in the GWD gene were associated with C6 phosphorylation, whereas polymorphisms in the SBEI and SBEII genes were associated with both C6 and C3 phosphorylation and the SNP in the SSIII gene was associated with C3 phosphorylation. These allelic variants have potential as genetic markers for starch phosphorylation in potato.
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Affiliation(s)
| | - Nigel I. Joyce
- The New Zealand Institute for Plant and Food Research Ltd.Lincoln, New Zealand
| | - Russell A. Genet
- The New Zealand Institute for Plant and Food Research Ltd.Lincoln, New Zealand
| | - Rebecca D. Cooper
- The New Zealand Institute for Plant and Food Research Ltd.Auckland, New Zealand
| | - Sarah R. Murray
- The New Zealand Institute for Plant and Food Research Ltd.Lincoln, New Zealand
| | | | - Ruth C. Butler
- The New Zealand Institute for Plant and Food Research Ltd.Lincoln, New Zealand
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Font i Forcada C, Velasco L, Socias i Company R, Fernández i Martí Á. Association mapping for kernel phytosterol content in almond. FRONTIERS IN PLANT SCIENCE 2015; 6:530. [PMID: 26217374 PMCID: PMC4496553 DOI: 10.3389/fpls.2015.00530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/29/2015] [Indexed: 05/21/2023]
Abstract
Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.
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Affiliation(s)
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible, Consejo Superior Investigaciones CientíficasCórdoba, Spain
| | - Rafel Socias i Company
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de AragónZaragoza, Spain
| | - Ángel Fernández i Martí
- Genome Center, University of California, DavisDavis, CA, USA
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de AragónZaragoza, Spain
- *Correspondence: Ángel Fernández i Martí, Genome Center, University of California, 451 Health Sciences Dr., Davis, Davis, CA 95616, USA
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Vitte C, Fustier MA, Alix K, Tenaillon MI. The bright side of transposons in crop evolution. Brief Funct Genomics 2014; 13:276-95. [PMID: 24681749 DOI: 10.1093/bfgp/elu002] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The past decades have revealed an unexpected yet prominent role of so-called 'junk DNA' in the regulation of gene expression, thereby challenging our view of the mechanisms underlying phenotypic evolution. In particular, several mechanisms through which transposable elements (TEs) participate in functional genome diversity have been depicted, bringing to light the 'TEs bright side'. However, the relative contribution of those mechanisms and, more generally, the importance of TE-based polymorphisms on past and present phenotypic variation in crops species remain poorly understood. Here, we review current knowledge on both issues, and discuss how analyses of massively parallel sequencing data combined with statistical methodologies and functional validations will help unravelling the impact of TEs on crop evolution in a near future.
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Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Walkemeier B, Rotter B, Gebhardt C. Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. FRONTIERS IN PLANT SCIENCE 2013; 4:423. [PMID: 24294214 PMCID: PMC3827546 DOI: 10.3389/fpls.2013.00423] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/05/2013] [Indexed: 05/23/2023]
Abstract
Resistance to pathogens is essential for survival of wild and cultivated plants. Pathogen susceptibility causes major losses of crop yield and quality. Durable field resistance combined with high yield and other superior agronomic characters are therefore, important objectives in every crop breeding program. Precision and efficacy of resistance breeding can be enhanced by molecular diagnostic tools, which result from knowledge of the molecular basis of resistance and susceptibility. Breeding uses resistance conferred by single R genes and polygenic quantitative resistance. The latter is partial but considered more durable. Molecular mechanisms of plant pathogen interactions are elucidated mainly in experimental systems involving single R genes, whereas most genes important for quantitative resistance in crops like potato are unknown. Quantitative resistance of potato to Phytophthora infestans causing late blight is often compromised by late plant maturity, a negative agronomic character. Our objective was to identify candidate genes for quantitative resistance to late blight not compromised by late plant maturity. We used diagnostic DNA-markers to select plants with different field levels of maturity corrected resistance (MCR) to late blight and compared their leaf transcriptomes before and after infection with P. infestans using SuperSAGE (serial analysis of gene expression) technology and next generation sequencing. We identified 2034 transcripts up or down regulated upon infection, including a homolog of the kiwi fruit allergen kiwellin. 806 transcripts showed differential expression between groups of genotypes with contrasting MCR levels. The observed expression patterns suggest that MCR is in part controlled by differential transcript levels in uninfected plants. Functional annotation suggests that, besides biotic and abiotic stress responses, general cellular processes such as photosynthesis, protein biosynthesis, and degradation play a role in MCR.
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Affiliation(s)
- Astrid M. Draffehn
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Li Li
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Jia Ding
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jens Lübeck
- Saka-Pflanzenzucht GmbH & Co. KGWindeby, Germany
| | | | - Meki S. Muktar
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Birgit Walkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Christiane Gebhardt
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
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Fischer M, Schreiber L, Colby T, Kuckenberg M, Tacke E, Hofferbert HR, Schmidt J, Gebhardt C. Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping. BMC PLANT BIOLOGY 2013; 13:113. [PMID: 23919263 PMCID: PMC3750364 DOI: 10.1186/1471-2229-13-113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 08/02/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND Higher plants evolved various strategies to adapt to chilling conditions. Among other transcriptional and metabolic responses to cold temperatures plants accumulate a range of solutes including sugars. The accumulation of the reducing sugars glucose and fructose in mature potato tubers during exposure to cold temperatures is referred to as cold induced sweetening (CIS). The molecular basis of CIS in potato tubers is of interest not only in basic research on plant adaptation to environmental stress but also in applied research, since high amounts of reducing sugars affect negatively the quality of processed food products such as potato chips. CIS-tolerance varies considerably among potato cultivars. Our objective was to identify by an unbiased approach genes and cellular processes influencing natural variation of tuber sugar content before and during cold storage in potato cultivars used in breeding programs. We compared by two-dimensional polyacrylamide gel electrophoresis the tuber proteomes of cultivars highly diverse for CIS. DNA polymorphisms in genomic sequences encoding differentially expressed proteins were tested for association with tuber starch content, starch yield and processing quality. RESULTS Pronounced natural variation of CIS was detected in tubers of a population of 40 tetraploid potato cultivars. Significant differences in protein expression were detected between CIS-tolerant and CIS-sensitive cultivars before the onset as well as during cold storage. Identifiable differential proteins corresponded to protease inhibitors, patatins, heat shock proteins, lipoxygenase, phospholipase A1 and leucine aminopeptidase (Lap). Association mapping based on single nucleotide polymorphisms supported a role of Lap in the natural variation of the quantitative traits tuber starch and sugar content. CONCLUSIONS The combination of comparative proteomics and association genetics led to the discovery of novel candidate genes for influencing the natural variation of quantitative traits in potato tubers. One such gene was a leucine aminopeptidase not considered so far to play a role in starch sugar interconversion. Novel SNP's diagnostic for increased tuber starch content, starch yield and chip quality were identified, which are useful for selecting improved potato processing cultivars.
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Affiliation(s)
- Matthias Fischer
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | - Lena Schreiber
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Colby
- Max-Planck-Institute for Plant Breeding Research, Mass Spectrometry Group, Cologne, Germany
| | - Markus Kuckenberg
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | - Eckhard Tacke
- BIOPLANT, Biotechnologisches Forschungslabor GmbH, Cologne, Germany
| | | | - Jürgen Schmidt
- Max-Planck-Institute for Plant Breeding Research, Mass Spectrometry Group, Cologne, Germany
| | - Christiane Gebhardt
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
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30
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Fischer M, Schreiber L, Colby T, Kuckenberg M, Tacke E, Hofferbert HR, Schmidt J, Gebhardt C. Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping. BMC PLANT BIOLOGY 2013; 13:113. [PMID: 23919263 DOI: 10.1186/1471-222913-113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 08/02/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Higher plants evolved various strategies to adapt to chilling conditions. Among other transcriptional and metabolic responses to cold temperatures plants accumulate a range of solutes including sugars. The accumulation of the reducing sugars glucose and fructose in mature potato tubers during exposure to cold temperatures is referred to as cold induced sweetening (CIS). The molecular basis of CIS in potato tubers is of interest not only in basic research on plant adaptation to environmental stress but also in applied research, since high amounts of reducing sugars affect negatively the quality of processed food products such as potato chips. CIS-tolerance varies considerably among potato cultivars. Our objective was to identify by an unbiased approach genes and cellular processes influencing natural variation of tuber sugar content before and during cold storage in potato cultivars used in breeding programs. We compared by two-dimensional polyacrylamide gel electrophoresis the tuber proteomes of cultivars highly diverse for CIS. DNA polymorphisms in genomic sequences encoding differentially expressed proteins were tested for association with tuber starch content, starch yield and processing quality. RESULTS Pronounced natural variation of CIS was detected in tubers of a population of 40 tetraploid potato cultivars. Significant differences in protein expression were detected between CIS-tolerant and CIS-sensitive cultivars before the onset as well as during cold storage. Identifiable differential proteins corresponded to protease inhibitors, patatins, heat shock proteins, lipoxygenase, phospholipase A1 and leucine aminopeptidase (Lap). Association mapping based on single nucleotide polymorphisms supported a role of Lap in the natural variation of the quantitative traits tuber starch and sugar content. CONCLUSIONS The combination of comparative proteomics and association genetics led to the discovery of novel candidate genes for influencing the natural variation of quantitative traits in potato tubers. One such gene was a leucine aminopeptidase not considered so far to play a role in starch sugar interconversion. Novel SNP's diagnostic for increased tuber starch content, starch yield and chip quality were identified, which are useful for selecting improved potato processing cultivars.
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Affiliation(s)
- Matthias Fischer
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany.
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31
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Gebhardt C. Bridging the gap between genome analysis and precision breeding in potato. Trends Genet 2013; 29:248-56. [DOI: 10.1016/j.tig.2012.11.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/01/2012] [Accepted: 11/15/2012] [Indexed: 12/16/2022]
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Du J, Tian Z, Liu J, Vleeshouwers VGAA, Shi X, Xie C. Functional analysis of potato genes involved in quantitative resistance to Phytophthora infestans. Mol Biol Rep 2013; 40:957-67. [PMID: 23224656 DOI: 10.1007/s11033-012-2137-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 10/03/2012] [Indexed: 11/28/2022]
Abstract
The most significant threat to potato production worldwide is the late blight disease, which is caused by the oomycete pathogen Phytophthora infestans. Based on previous cDNA microarrays and cDNA-amplified fragment length polymorphism analysis, 63 candidate genes that are expected to contribute to developing a durable resistance to late blight were selected for further functional analysis. We performed virus-induced gene silencing (VIGS) to these candidate genes on both Nicotiana benthamiana and potato, subsequently inoculated detached leaves and assessed the resistance level. Ten genes decreased the resistance to P. infestans after VIGS treatment. Among those, a lipoxygenase (LOX; EC 1.13.11.12) and a suberization-associated anionic peroxidase affected the resistance in both N. benthamiana and potato. Our results identify genes that may play a role in quantitative resistance mechanisms to late blight.
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Affiliation(s)
- Juan Du
- Key Laboratory of Horticultural Plant Biology (Huazhong Agricultural University), Ministry of Education, National Center for Vegetable Improvement (Central China), Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
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Landgraf R, Schaarschmidt S, Hause B. Repeated leaf wounding alters the colonization of Medicago truncatula roots by beneficial and pathogenic microorganisms. PLANT, CELL & ENVIRONMENT 2012; 35:1344-57. [PMID: 22329418 DOI: 10.1111/j.1365-3040.2012.02495.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In nature, plants are subject to various stresses that are often accompanied by wounding of the aboveground tissues. As wounding affects plants locally and systemically, we investigated the impact of leaf wounding on interactions of Medicago truncatula with root-colonizing microorganisms, such as the arbuscular mycorrhizal (AM) fungus Glomus intraradices, the pathogenic oomycete Aphanomyces euteiches and the nitrogen-fixing bacterium Sinorhizobium meliloti. To obtain a long-lasting wound response, repeated wounding was performed and resulted in locally and systemically increased jasmonic acid (JA) levels accompanied by the expression of jasmonate-induced genes, among them the genes encoding allene oxide cyclase 1 (MtAOC1) and a putative cell wall-bound invertase (cwINV). After repeated wounding, colonization with the AM fungus was increased, suggesting a role of jasmonates as positive regulators of mycorrhization, whereas the interaction with the rhizobacterium was not affected. In contrast, wounded plants appeared to be less susceptible to pathogens which might be caused by JA-induced defence mechanisms. The effects of wounding on mycorrhization and pathogen infection could be partially mimicked by foliar application of JA. In addition to JA itself, the positive effect on mycorrhization might be mediated by systemically induced cwINV, which was previously shown to exhibit a regulatory function on interaction with AM fungi.
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Affiliation(s)
- Ramona Landgraf
- Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
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Fusari CM, Di Rienzo JA, Troglia C, Nishinakamasu V, Moreno MV, Maringolo C, Quiroz F, Álvarez D, Escande A, Hopp E, Heinz R, Lia VV, Paniego NB. Association mapping in sunflower for Sclerotinia Head Rot resistance. BMC PLANT BIOLOGY 2012; 12:93. [PMID: 22708963 PMCID: PMC3778846 DOI: 10.1186/1471-2229-12-93] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/21/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sclerotinia Head Rot (SHR) is one of the most damaging diseases of sunflower in Europe, Argentina, and USA, causing average yield reductions of 10 to 20 %, but leading to total production loss under favorable environmental conditions for the pathogen. Association Mapping (AM) is a promising choice for Quantitative Trait Locus (QTL) mapping, as it detects relationships between phenotypic variation and gene polymorphisms in existing germplasm without development of mapping populations. This article reports the identification of QTL for resistance to SHR based on candidate gene AM. RESULTS A collection of 94 sunflower inbred lines were tested for SHR under field conditions using assisted inoculation with the fungal pathogen Sclerotinia sclerotiorum. Given that no biological mechanisms or biochemical pathways have been clearly identified for SHR, 43 candidate genes were selected based on previous transcript profiling studies in sunflower and Brassica napus infected with S. sclerotiorum. Associations among SHR incidence and haplotype polymorphisms in 16 candidate genes were tested using Mixed Linear Models (MLM) that account for population structure and kinship relationships. This approach allowed detection of a significant association between the candidate gene HaRIC_B and SHR incidence (P < 0.01), accounting for a SHR incidence reduction of about 20 %. CONCLUSIONS These results suggest that AM will be useful in dissecting other complex traits in sunflower, thus providing a valuable tool to assist in crop breeding.
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Affiliation(s)
- Corina M Fusari
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
| | - Julio A Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Carolina Troglia
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Verónica Nishinakamasu
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
| | - María Valeria Moreno
- Estación Experimental Agropecuaria Manfredi, INTA, 5988, Manfredi, Córdoba, Argentina
| | - Carla Maringolo
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Facundo Quiroz
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Daniel Álvarez
- Estación Experimental Agropecuaria Manfredi, INTA, 5988, Manfredi, Córdoba, Argentina
| | - Alberto Escande
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Esteban Hopp
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruth Heinz
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
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Gyetvai G, Sønderkær M, Göbel U, Basekow R, Ballvora A, Imhoff M, Kersten B, Nielsen KL, Gebhardt C. The transcriptome of compatible and incompatible interactions of potato (Solanum tuberosum) with Phytophthora infestans revealed by DeepSAGE analysis. PLoS One 2012; 7:e31526. [PMID: 22328937 PMCID: PMC3273468 DOI: 10.1371/journal.pone.0031526] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/09/2012] [Indexed: 01/01/2023] Open
Abstract
Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). Understanding the molecular basis of resistance and susceptibility to late blight is therefore highly relevant for developing resistant cultivars, either by marker-assissted selection or by transgenic approaches. Specific P. infestans races having the Avr1 effector gene trigger a hypersensitive resistance response in potato plants carrying the R1 resistance gene (incompatible interaction) and cause disease in plants lacking R1 (compatible interaction). The transcriptomes of the compatible and incompatible interaction were captured by DeepSAGE analysis of 44 biological samples comprising five genotypes, differing only by the presence or absence of the R1 transgene, three infection time points and three biological replicates. 30,859 unique 21 base pair sequence tags were obtained, one third of which did not match any known potato transcript sequence. Two third of the tags were expressed at low frequency (<10 tag counts/million). 20,470 unitags matched to approximately twelve thousand potato transcribed genes. Tag frequencies were compared between compatible and incompatible interactions over the infection time course and between compatible and incompatible genotypes. Transcriptional changes were more numerous in compatible than in incompatible interactions. In contrast to incompatible interactions, transcriptional changes in the compatible interaction were observed predominantly for multigene families encoding defense response genes and genes functional in photosynthesis and CO(2) fixation. Numerous transcriptional differences were also observed between near isogenic genotypes prior to infection with P. infestans. Our DeepSAGE transcriptome analysis uncovered novel candidate genes for plant host pathogen interactions, examples of which are discussed with respect to possible function.
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Affiliation(s)
- Gabor Gyetvai
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mads Sønderkær
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Ulrike Göbel
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rico Basekow
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Agim Ballvora
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maren Imhoff
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Birgit Kersten
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Kåre-Lehman Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
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Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S. SNP markers and their impact on plant breeding. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:728398. [PMID: 23316221 PMCID: PMC3536327 DOI: 10.1155/2012/728398] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/14/2012] [Indexed: 05/19/2023]
Abstract
The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.
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Affiliation(s)
- Jafar Mammadov
- Department of Trait Genetics and Technologies, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
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Stich B, Gebhardt C. Detection of epistatic interactions in association mapping populations: an example from tetraploid potato. Heredity (Edinb) 2011; 107:537-47. [PMID: 21673745 PMCID: PMC3242626 DOI: 10.1038/hdy.2011.40] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/09/2022] Open
Abstract
Epistatic interactions among loci are expected to contribute substantially to variation of quantitative traits. The objectives of our research were to (i) compare a classical mixed-model approach with a combined mixed-model and analysis of variance approach for detecting epistatic interactions; (ii) examine using computer simulations the statistical power to detect additive-additive, additive-dominance and dominance-dominance epistatic interactions and (iii) detect epistatic interactions between candidate genes for resistance to leaf blight in a set of tetraploid potato clones. Our study was based on the genotypic and phenotypic data of 184 tetraploid potato cultivars as well as computer simulations. The number of significant (α* =1 × 10(-6)) epistatic interactions ranged for the three examined traits from 3 to 32. Our findings suggested that the combined mixed-model and analysis of variance approach leads in comparison with the classical mixed-model approach not to an increased rate of false-positives. The results of the computer simulations suggested that, if molecular markers are available that are in high LD (D'>0.9) with the trait-coding loci, the statistical power to detect epistatic interactions, which explain 5-10% of the phenotypic variance, was of a size that seems promising for their detection.
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Affiliation(s)
- B Stich
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, Köln, Germany.
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Ballvora A, Flath K, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Gebhardt C. Multiple alleles for resistance and susceptibility modulate the defense response in the interaction of tetraploid potato (Solanum tuberosum) with Synchytrium endobioticum pathotypes 1, 2, 6 and 18. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1281-92. [PMID: 21822548 PMCID: PMC3214262 DOI: 10.1007/s00122-011-1666-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 07/16/2011] [Indexed: 05/03/2023]
Abstract
The obligate biotrophic, soil-borne fungus Synchytrium endobioticum causes wart disease of potato (Solanum tuberosum), which is a serious problem for crop production in countries with moderate climates. S. endobioticum induces hypertrophic cell divisions in plant host tissues leading to the formation of tumor-like structures. Potato wart is a quarantine disease and chemical control is not possible. From 38 S. endobioticum pathotypes occurring in Europe, pathotypes 1, 2, 6 and 18 are the most relevant. Genetic resistance to wart is available but only few current potato varieties are resistant to all four pathotypes. The phenotypic evaluation of wart resistance is laborious, time-consuming and sometimes ambiguous, which makes breeding for resistance difficult. Molecular markers diagnostic for genes for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 would greatly facilitate the selection of new, resistant cultivars. Two tetraploid half-sib families (266 individuals) segregating for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 were produced by crossing a resistant genotype with two different susceptible ones. The families were scored for five different wart resistance phenotypes. The distribution of mean resistance scores was quantitative in both families. Resistance to pathotypes 2, 6 and 18 was correlated and independent from resistance to pathotype 1. DNA pools were constructed from the most resistant and most susceptible individuals and screened with genome wide simple sequence repeat (SSR), inverted simple sequence region (ISSR) and randomly amplified polymorphic DNA (RAPD) markers. Bulked segregant analysis identified three SSR markers that were linked to wart resistance loci (Sen). Sen1-XI on chromosome XI conferred partial resistance to pathotype 1, Sen18-IX on chromosome IX to pathotype 18 and Sen2/6/18-I on chromosome I to pathotypes 2,6 and 18. Additional genotyping with 191 single nucleotide polymorphism (SNP) markers confirmed the localization of the Sen loci. Thirty-three SNP markers linked to the Sen loci permitted the dissection of Sen alleles that increased or decreased resistance to wart. The alleles were inherited from both the resistant and susceptible parents.
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Affiliation(s)
- Agim Ballvora
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
- Present Address: INRES-Crop Genetics and Biotechnology, University of Bonn, Bonn, Germany
| | - Kerstin Flath
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Kleinmachnow, Germany
| | - Jens Lübeck
- SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany
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Urbany C, Colby T, Stich B, Schmidt L, Schmidt J, Gebhardt C. Analysis of Natural Variation of the Potato Tuber Proteome Reveals Novel Candidate Genes for Tuber Bruising. J Proteome Res 2011; 11:703-16. [DOI: 10.1021/pr2006186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claude Urbany
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Thomas Colby
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Benjamin Stich
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Lysann Schmidt
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Jürgen Schmidt
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Brazauskas G, Lenk I, Pedersen MG, Studer B, Lübberstedt T. Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:412-420. [PMID: 21889047 DOI: 10.1016/j.plantsci.2011.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/07/2011] [Accepted: 06/30/2011] [Indexed: 05/26/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars. The aim of this study was to assess the extent of linkage disequilibrium (LD) within European elite germplasm and to evaluate the appropriate methodology for genetic association mapping in perennial ryegrass. A high level of genetic diversity was observed in a set of 380 perennial ryegrass elite genotypes when genotyped with 40 SSRs and 2 STS markers. A Bayesian structure analysis identified two subpopulations, which were confirmed by principal coordinate analysis (PCoA). One subpopulation consisted mainly of genotypes originating from the UK, while germplasm mostly from Continental Europe was grouped into the second subpopulation. LD (r(2)) decay was rapid and occurred within 0.4cM across European varieties, when population structure was taken into consideration. However, an extended LD of up to 6.6cM was detected within the variety Aberdart. High genetic diversity and rapid LD decay provide means for high resolution association mapping in elite materials of perennial ryegrass. However, different strategies need to be applied depending on the material used. Genome-wide association study (GWAS) with several hundred markers can be applied within synthetic varieties to identify large (up to 10cM) genomic regions affecting trait variation. A combination of available and novel DNA markers is needed to achieve resolution required for GWAS in elite breeding materials. An even higher marker density of several million SNPs might be needed for GWAS in diverse ecotype collections, potentially resulting in quantitative trait polymorphism (QTP) identification.
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Affiliation(s)
- Gintaras Brazauskas
- Lithuanian Research Centre for Agriculture and Forestry, Institute of Agriculture, Instituto a. 1, Akademija, Kedainiai, Lithuania.
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Urbany C, Stich B, Schmidt L, Simon L, Berding H, Junghans H, Niehoff KH, Braun A, Tacke E, Hofferbert HR, Lübeck J, Strahwald J, Gebhardt C. Association genetics in Solanum tuberosum provides new insights into potato tuber bruising and enzymatic tissue discoloration. BMC Genomics 2011; 12:7. [PMID: 21208436 PMCID: PMC3023753 DOI: 10.1186/1471-2164-12-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 01/05/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most agronomic plant traits result from complex molecular networks involving multiple genes and from environmental factors. One such trait is the enzymatic discoloration of fruit and tuber tissues initiated by mechanical impact (bruising). Tuber susceptibility to bruising is a complex trait of the cultivated potato (Solanum tuberosum) that is crucial for crop quality. As phenotypic evaluation of bruising is cumbersome, the application of diagnostic molecular markers would empower the selection of low bruising potato varieties. The genetic factors and molecular networks underlying enzymatic tissue discoloration are sparsely known. Hitherto there is no association study dealing with tuber bruising and diagnostic markers for enzymatic discoloration are rare. RESULTS The natural genetic diversity for bruising susceptibility was evaluated in elite middle European potato germplasm in order to elucidate its molecular basis. Association genetics using a candidate gene approach identified allelic variants in genes that function in tuber bruising and enzymatic browning. Two hundred and five tetraploid potato varieties and breeding clones related by descent were evaluated for two years in six environments for tuber bruising susceptibility, specific gravity, yield, shape and plant maturity. Correlations were found between different traits. In total 362 polymorphic DNA fragments, derived from 33 candidate genes and 29 SSR loci, were scored in the population and tested for association with the traits using a mixed model approach, which takes into account population structure and kinship. Twenty one highly significant (p < 0.001) and robust marker-trait associations were identified. CONCLUSIONS The observed trait correlations and associated marker fragments provide new insight in the molecular basis of bruising susceptibility and its natural variation. The markers diagnostic for increased or decreased bruising susceptibility will facilitate the combination of superior alleles in breeding programs. In addition, this study presents novel candidates that might control enzymatic tissue discoloration and tuber bruising. Their validation and characterization will increase the knowledge about the underlying biological processes.
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Affiliation(s)
- Claude Urbany
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
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Odeny DA, Stich B, Gebhardt C. Physical organization of mixed protease inhibitor gene clusters, coordinated expression and association with resistance to late blight at the StKI locus on potato chromosome III. PLANT, CELL & ENVIRONMENT 2010; 33:2149-61. [PMID: 20716067 DOI: 10.1111/j.1365-3040.2010.02213.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Protease inhibitors (PIs) play a role in plant defence against pests and pathogens as well as in plant development. Potato (Solanum tuberosum) contains abundant levels of diverse PIs. Most potato Kunitz-type inhibitor (KTI) genes map to the StKI locus on potato chromosome III, which is linked to a quantitative trait locus (QTL) for resistance to Phytophthora infestans. To elucidate the physical organization of PIs at the StKI locus, we screened bacterial artificial chromosome (BAC) libraries with KTI probes. Ten different clones were selected, sequenced and annotated. Of 100 putative genes, 22 corresponded to five PI classes. Expression analysis by quantitative real-time PCR (qRT-PCR) using PI class-specific primers in different tissues of the tetraploid potato cultivars 'Nikita' and 'Baltica' revealed different transcript levels, depending on PI type and genotype. During the compatible interaction with a complex race of P. infestans, four PI classes showed coordinated expression over 3 d after infection, a strong decrease in infected leaves and a transient induction in systemic leaves. Basal transcript levels in non-infected leaves differed strongly between the two genotypes examined. Two microsatellite markers located within the PI gene cluster were associated with resistance to P. infestans in a population of potato varieties and breeding clones.
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Li L, Paulo MJ, van Eeuwijk F, Gebhardt C. Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1303-10. [PMID: 20603706 PMCID: PMC2955219 DOI: 10.1007/s00122-010-1389-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 06/14/2010] [Indexed: 05/18/2023]
Abstract
Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ≤ 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ≤ 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed.
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Affiliation(s)
- Li Li
- Department Plant Breeding and Genetics, MPI for Plant Breeding Research, Carl von Linné Weg 10, 50829 Cologne, Germany
| | - Maria-João Paulo
- Department Plant Breeding and Genetics, MPI for Plant Breeding Research, Carl von Linné Weg 10, 50829 Cologne, Germany
- Biometris, Wageningen University, 6700 AC Wageningen, The Netherlands
| | - Fred van Eeuwijk
- Biometris, Wageningen University, 6700 AC Wageningen, The Netherlands
| | - Christiane Gebhardt
- Department Plant Breeding and Genetics, MPI for Plant Breeding Research, Carl von Linné Weg 10, 50829 Cologne, Germany
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Herrmann D, Barre P, Santoni S, Julier B. Association of a CONSTANS-LIKE gene to flowering and height in autotetraploid alfalfa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:865-76. [PMID: 20473652 DOI: 10.1007/s00122-010-1356-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 04/28/2010] [Indexed: 05/18/2023]
Abstract
In alfalfa (Medicago sativa), an autotetraploid forage legume, stem length is a major component of forage yield, quality and competing ability. In this species, flowering date is not a breeding criterion. Association mapping based on a candidate gene approach has given good results in plants, including autotetraploid species for which genetic analyses are complex. The role of a CONSTANS-LIKE gene, identified as a candidate for stem elongation and flowering date in the model legume M. truncatula, was tested for association with the same traits in alfalfa. Four hundred genotypes from ten cultivars were evaluated for stem height and flowering date in two locations during 4 years. They were genotyped with simple sequence repeat markers and a low structuration was noticed. Primers were designed to amplify and sequence two regions of the alfalfa gene homologous to CONSTANS-LIKE. Single nucleotide polymorphisms (SNPs) were detected and their allelic dose in each genotype was scored. Linkage disequilibrium within CONSTANS-LIKE rapidly decreased as expected. Eight SNPs with a frequency above 10% were detected over 1,010 bp (one SNP every 126 bp on average) in the 400 genotypes. This number was lower than observed in a neutral gene (a SNP every 31 bp on average). Highly significant associations of three SNPs to flowering date and stem height were identified. Each SNP explained up to 4.2% of the genetic variance. Thus, as in the model species, the CONSTANS-LIKE gene was shown to be involved in flowering date and stem height in alfalfa.
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Affiliation(s)
- Doris Herrmann
- INRA, UR 4, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, BP 6, 86600, Lusignan, France
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Stich B, Melchinger AE. Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis. BMC Genomics 2009; 10:94. [PMID: 19250529 PMCID: PMC2676307 DOI: 10.1186/1471-2164-10-94] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 02/27/2009] [Indexed: 11/23/2022] Open
Abstract
Background In recent years, several attempts have been made in plant genetics to detect QTL by using association mapping methods. The objectives of this study were to (i) evaluate various methods for association mapping in five plant species and (ii) for three traits in each of the plant species compare the Topt, the restricted maximum likelihood (REML) estimate of the conditional probability that two genotypes carry at the same locus alleles that are identical in state but not identical by descent. In order to compare the association mapping methods based on scenarios with realistic estimates of population structure and familial relatedness, we analyzed phenotypic and genotypic data of rapeseed, potato, sugar beet, maize, and Arabidopsis. For the same reason, QTL effects were simulated on top of the observed phenotypic values when examining the adjusted power for QTL detection. Results The correlation between the Topt values identified using REML deviance profiles and profiles of the mean of squared difference between observed and expected P values was 0.83. Conclusion The mixed-model association mapping approaches using a kinship matrix, which was based on Topt, were more appropriate for association mapping than the recently proposed QK method with respect to the adherence to the nominal α level and the adjusted power for QTL detection. Furthermore, we showed that Topt differs considerably among the five plant species but only marginally among different traits.
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Affiliation(s)
- Benjamin Stich
- Department of Applied Genetics and Plant Breeding, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany.
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Stich B, Melchinger AE. Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis. BMC Genomics 2009. [PMID: 19250529 DOI: 10.1186/1471‐2164‐10‐94] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, several attempts have been made in plant genetics to detect QTL by using association mapping methods. The objectives of this study were to (i) evaluate various methods for association mapping in five plant species and (ii) for three traits in each of the plant species compare the Topt, the restricted maximum likelihood (REML) estimate of the conditional probability that two genotypes carry at the same locus alleles that are identical in state but not identical by descent. In order to compare the association mapping methods based on scenarios with realistic estimates of population structure and familial relatedness, we analyzed phenotypic and genotypic data of rapeseed, potato, sugar beet, maize, and Arabidopsis. For the same reason, QTL effects were simulated on top of the observed phenotypic values when examining the adjusted power for QTL detection. RESULTS The correlation between the Topt values identified using REML deviance profiles and profiles of the mean of squared difference between observed and expected P values was 0.83. CONCLUSION The mixed-model association mapping approaches using a kinship matrix, which was based on Topt, were more appropriate for association mapping than the recently proposed QK method with respect to the adherence to the nominal alpha level and the adjusted power for QTL detection. Furthermore, we showed that Topt differs considerably among the five plant species but only marginally among different traits.
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Affiliation(s)
- Benjamin Stich
- Department of Applied Genetics and Plant Breeding, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593, Stuttgart, Germany.
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