1
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Islam MAU, Nupur JA, Shafiq M, Ali Q, Sami A, Shahid MA. In silico and computational analysis of zinc finger motif-associated homeodomain (ZF-HD) family genes in chilli (Capsicum annuum L). BMC Genomics 2023; 24:603. [PMID: 37821819 PMCID: PMC10566081 DOI: 10.1186/s12864-023-09682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger-homeodomain (ZHD) proteins are mostly expressed in plants and are involved in proper growth and development and minimizing biotic and abiotic stress. A recent study identified and characterized the ZHD gene family in chilli (Capsicum annuum L.) to determine their probable molecular function. ZHD genes with various physicochemical characteristics were discovered on twelve chromosomes in chilli. We separated ZHD proteins into two major groups using sequence alignment and phylogenetic analysis. These groups differ in gene structure, motif distribution, and a conserved ZHD and micro-zinc finger ZF domain. The majority of the CaZHDs genes are preserved, early duplication occurred recently, and significant pure selection took place throughout evolution, according to evolutionary study. According to expression profiling, the genes were found to be equally expressed in tissues above the ground, contribute to plant growth and development and provide tolerance to biotic and abiotic stress. This in silico analysis, taken as a whole, hypothesized that these genes perform distinct roles in molecular and phytohormone signaling processes, which may serve as a foundation for subsequent research into the roles of these genes in other crops.
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Affiliation(s)
- Md Abir Ul Islam
- United Graduate School of Agricultural Science, Faculty of Biological Sciences, Gifu University, Yanagido, Gifu, 501-1193, Japan
| | - Juthy Abedin Nupur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Muhammad Shafiq
- Department of Horticulture, University of Panjab, Lahore, 54000, Pakistan.
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan.
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, P.O BOX. 54590, Lahore, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL, USA
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2
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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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3
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Slootweg E, Koropacka K, Roosien J, Dees R, Overmars H, Lankhorst RK, van Schaik C, Pomp R, Bouwman L, Helder J, Schots A, Bakker J, Smant G, Goverse A. Sequence Exchange between Homologous NB-LRR Genes Converts Virus Resistance into Nematode Resistance, and Vice Versa. PLANT PHYSIOLOGY 2017; 175:498-510. [PMID: 28747428 PMCID: PMC5580749 DOI: 10.1104/pp.17.00485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/20/2017] [Indexed: 05/24/2023]
Abstract
Plants have evolved a limited repertoire of NB-LRR disease resistance (R) genes to protect themselves against myriad pathogens. This limitation is thought to be counterbalanced by the rapid evolution of NB-LRR proteins, as only a few sequence changes have been shown to be sufficient to alter resistance specificities toward novel strains of a pathogen. However, little is known about the flexibility of NB-LRR R genes to switch resistance specificities between phylogenetically unrelated pathogens. To investigate this, we created domain swaps between the close homologs Gpa2 and Rx1, which confer resistance in potato (Solanum tuberosum) to the cyst nematode Globodera pallida and Potato virus X, respectively. The genetic fusion of the CC-NB-ARC of Gpa2 with the LRR of Rx1 (Gpa2CN/Rx1L) results in autoactivity, but lowering the protein levels restored its specific activation response, including extreme resistance to Potato virus X in potato shoots. The reciprocal chimera (Rx1CN/Gpa2L) shows a loss-of-function phenotype, but exchange of the first three LRRs of Gpa2 by the corresponding region of Rx1 was sufficient to regain a wild-type resistance response to G. pallida in the roots. These data demonstrate that exchanging the recognition moiety in the LRR is sufficient to convert extreme virus resistance in the leaves into mild nematode resistance in the roots, and vice versa. In addition, we show that the CC-NB-ARC can operate independently of the recognition specificities defined by the LRR domain, either aboveground or belowground. These data show the versatility of NB-LRR genes to generate resistance to unrelated pathogens with completely different lifestyles and routes of invasion.
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Affiliation(s)
- Erik Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Kamila Koropacka
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Jan Roosien
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Robert Dees
- Laboratory of Molecular Recognition and Antigen Technology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Rene Klein Lankhorst
- Plant Research International, Centre for Biosystems Genomics, 6708 PD Wageningen, The Netherlands
| | - Casper van Schaik
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Rikus Pomp
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Liesbeth Bouwman
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Arjen Schots
- Laboratory of Molecular Recognition and Antigen Technology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Jaap Bakker
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PD Wageningen, The Netherlands
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4
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Shen J, Li Z, Chen J, Song Z, Zhou Z, Shi Y. SHEsisPlus, a toolset for genetic studies on polyploid species. Sci Rep 2016; 6:24095. [PMID: 27048905 PMCID: PMC4822172 DOI: 10.1038/srep24095] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/17/2016] [Indexed: 11/09/2022] Open
Abstract
Currently, algorithms and softwares for genetic analysis of diploid organisms with bi-allelic markers are well-established, while those for polyploids are limited. Here, we present SHEsisPlus, the online algorithm toolset for both dichotomous and quantitative trait genetic analysis on polyploid species (compatible with haploids and diploids, too). SHEsisPlus is also optimized for handling multiple-allele datasets. It's free, open source and also designed to perform a range of analyses, including haplotype inference, linkage disequilibrium analysis, epistasis detection, Hardy-Weinberg equilibrium and single locus association tests. Meanwhile, we developed an accurate and efficient haplotype inference algorithm for polyploids and proposed an entropy-based algorithm to detect epistasis in the context of quantitative traits. A study of both simulated and real datasets showed that our haplotype inference algorithm was much faster and more accurate than existing ones. Our epistasis detection algorithm was the first try to apply information theory to characterizing the gene interactions in quantitative trait datasets. Results showed that its statistical power was significantly higher than conventional approaches. SHEsisPlus is freely available on the web at http://shesisplus.bio-x.cn/. Source code is freely available for download at https://github.com/celaoforever/SHEsisPlus.
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Affiliation(s)
- Jiawei Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.,School of Bio-medical Engineering, Shanghai Jiao Tong University, Shanghai 200230, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Zhijian Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Zhaowei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.,Shandong Provincial Key Laboratory of Metabolic Disease, the Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China.,Institute of Clinical Research, the Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.,School of Bio-medical Engineering, Shanghai Jiao Tong University, Shanghai 200230, P.R. China.,Shanghai Changning Mental Health Center, Shanghai 200042, P.R. China.,Department of Psychiatry, the First Teaching Hospital of Xinjiang Medical University, Urumqi 830054, P.R. China
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5
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Destefanis M, Nagy I, Rigney B, Bryan GJ, McLean K, Hein I, Griffin D, Milbourne D. A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages. BMC PLANT BIOLOGY 2015; 15:255. [PMID: 26496718 PMCID: PMC4619397 DOI: 10.1186/s12870-015-0645-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. RESULTS A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. CONCLUSIONS S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.
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Affiliation(s)
- Marialaura Destefanis
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
- Pesticides, Plant Health & Seed Testing Laboratories, Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare, Ireland.
| | - Istvan Nagy
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.
| | - Brian Rigney
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
| | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Karen McLean
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Denis Griffin
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
| | - Dan Milbourne
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
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6
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Wolters AMA, Caro M, Dong S, Finkers R, Gao J, Visser RGF, Wang X, Du Y, Bai Y. Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1987-97. [PMID: 26152571 PMCID: PMC4572051 DOI: 10.1007/s00122-015-2561-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/13/2015] [Indexed: 05/07/2023]
Abstract
A chromosomal inversion associated with the tomato Ty - 2 gene for TYLCV resistance is the cause of severe suppression of recombination in a tomato Ty - 2 introgression line. Among tomato and its wild relatives inversions are often observed, which result in suppression of recombination. Such inversions hamper the transfer of important traits from a related species to the crop by introgression breeding. Suppression of recombination was reported for the TYLCV resistance gene, Ty-2, which has been introgressed in cultivated tomato (Solanum lycopersicum) from the wild relative S. habrochaites accession B6013. Ty-2 was mapped to a 300-kb region on the long arm of chromosome 11. The suppression of recombination in the Ty-2 region could be caused by chromosomal rearrangements in S. habrochaites compared with S. lycopersicum. With the aim of visualizing the genome structure of the Ty-2 region, we compared the draft de novo assembly of S. habrochaites accession LYC4 with the sequence of cultivated tomato ('Heinz'). Furthermore, using populations derived from intraspecific crosses of S. habrochaites accessions, the order of markers in the Ty-2 region was studied. Results showed the presence of an inversion of approximately 200 kb in the Ty-2 region when comparing S. lycopersicum and S. habrochaites. By sequencing a BAC clone from the Ty-2 introgression line, one inversion breakpoint was identified. Finally, the obtained results are discussed with respect to introgression breeding and the importance of a priori de novo sequencing of the species involved.
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Affiliation(s)
- Anne-Marie A Wolters
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Myluska Caro
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Shufang Dong
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Richard Finkers
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Jianchang Gao
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Xiaoxuan Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Yongchen Du
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Yuling Bai
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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7
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de Boer JM, Datema E, Tang X, Borm TJA, Bakker EH, van Eck HJ, van Ham RCHJ, de Jong H, Visser RGF, Bachem CWB. Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin. BMC Genomics 2015; 16:374. [PMID: 25958312 PMCID: PMC4470070 DOI: 10.1186/s12864-015-1578-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/24/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned. RESULTS For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1-3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5. CONCLUSIONS Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Averis Seeds B.V., Valtherblokken Zuid 40, 7876 TC, Valthermond, The Netherlands.
| | - Erwin Datema
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Xiaomin Tang
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: Department of Biology, Colorado State University, Fort Collins, USA.
| | - Theo J A Borm
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Erin H Bakker
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Herman J van Eck
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Roeland C H J van Ham
- Wageningen University and Research Centre, Applied Bioinformatics, Plant Research International, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands. .,Current address: KeyGene N.V., P.O. Box 216, 6700, Wageningen, The Netherlands.
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Christian W B Bachem
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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8
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Aversano R, Contaldi F, Ercolano MR, Grosso V, Iorizzo M, Tatino F, Xumerle L, Dal Molin A, Avanzato C, Ferrarini A, Delledonne M, Sanseverino W, Cigliano RA, Capella-Gutierrez S, Gabaldón T, Frusciante L, Bradeen JM, Carputo D. The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives. THE PLANT CELL 2015; 27:954-68. [PMID: 25873387 PMCID: PMC4558694 DOI: 10.1105/tpc.114.135954] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/01/2015] [Indexed: 05/02/2023]
Abstract
Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Felice Contaldi
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | | | - Valentina Grosso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Massimo Iorizzo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Filippo Tatino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Luciano Xumerle
- Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy
| | - Alessandra Dal Molin
- Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy
| | - Carla Avanzato
- Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy
| | - Alberto Ferrarini
- Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy
| | - Massimo Delledonne
- Center of Functional Genomics, Department of Biotechnologies, University of Verona, 37134 Cà Vignal, Italy
| | | | | | - Salvador Capella-Gutierrez
- Center for Genomic Regulation, 08003 Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Toni Gabaldón
- Center for Genomic Regulation, 08003 Barcelona, Spain Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - James M Bradeen
- Department of Plant Pathology and Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, Saint Paul, Minnesota 55108
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
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9
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Abdollahi Mandoulakani B, Yaniv E, Kalendar R, Raats D, Bariana HS, Bihamta MR, Schulman AH. Development of IRAP- and REMAP-derived SCAR markers for marker-assisted selection of the stripe rust resistance gene Yr15 derived from wild emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:211-9. [PMID: 25388968 DOI: 10.1007/s00122-014-2422-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/27/2014] [Indexed: 05/08/2023]
Abstract
Yr15 provides broad resistance to stripe rust, an important wheat disease. REMAP- and IRAP-derived co-dominant SCAR markers were developed and localize Yr15 to a 1.2 cM interval. They are reliable across many cultivars. Stripe rust [Pucinia striiformis f.sp. tritici (Pst)] is one of the most important fungal diseases of wheat, found on all continents and in over 60 countries. Wild emmer wheat (Triticum dicoccoides), which is the tetraploid progenitor of durum wheat, is a valuable source of novel stripe rust resistance genes for wheat breeding. T. dicoccoides accession G25 carries Yr15 on chromosome 1BS. Yr15 confers resistance to virtually all tested Pst isolates; it is effective in durum and bread wheat introgressions and their derivatives. Retrotransposons generate polymorphic insertions, which can be scored as Mendelian markers using techniques such as REMAP and IRAP. Six REMAP- and IRAP-derived SCAR markers were mapped using 1,256 F2 plants derived from crosses of the susceptible T. durum accession D447 (DW1) with its resistant BC3F9 and BC3F10 (B9 and B10) near isogenic lines, which carried Yr15 introgressed from G25. The nearest markers segregated 0.1 cM proximally and 1.1 cM distally to Yr15. These markers were also mapped and validated at the same position in another 500 independent F2 plants derived from crosses of B9 and B10 with the susceptible cultivar Langdon (LDN). SC2700 and SC790, defining Yr15 on an interval of 1.2 cM, were found to be reliable and robust co-dominant markers in a wide range of wheat lines and cultivars with and without Yr15. These markers are useful tags in marker-assisted wheat breeding programs that aim to incorporate Yr15 into elite wheat lines and cultivars for durable and broad-spectrum resistance to stripe rust.
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Khan MA, Saravia D, Munive S, Lozano F, Farfan E, Eyzaguirre R, Bonierbale M. Multiple QTLs Linked to Agro-Morphological and Physiological Traits Related to Drought Tolerance in Potato. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:1286-1298. [PMID: 26339121 PMCID: PMC4551535 DOI: 10.1007/s11105-014-0824-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Dissection of the genetic architecture of adaptation and abiotic stress-related traits is highly desirable for developing drought-tolerant potatoes and enhancing the resilience of existing cultivars, particularly as agricultural production in rain-fed areas may be reduced by up to 50 % by 2020. The "DMDD" potato progeny was developed at International Potato Center (CIP) by crossing the sequenced double monoploid line DM and a diploid cultivar of the Solanum tuberosum diploid Andigenum Goniocalyx group. Recently, a high-density integrated genetic map based on single nucleotide polymorphism (SNP), diversity array technology (DArT), simple sequence repeats (SSRs), and amplified fragment length polymorphism (AFLP) markers was also made available for this population. Two trials were conducted, in greenhouse and field, for drought tolerance with two treatments each, well-watered and terminal drought, in which watering was suspended 60 days after planting. The DMDD population was evaluated for agro-morphological and physiological traits before and after initiation of stress, at multiple time points. Two dense parental genetic maps were constructed using published genotypic data, and quantitative trait locus (QTL) analysis identified 45 genomic regions associated with nine traits in well-watered and terminal drought treatments and 26 potentially associated with drought stress. In this study, the strong influence of environmental factors besides water shortage on the expression of traits and QTLs reflects the multigenic control of traits related to drought tolerance. This is the first study to our knowledge in potato identifying QTLs for drought-related traits in field and greenhouse trials, giving new insights into genetic architecture of drought-related traits. Many of the QTLs identified have the potential to be used in potato breeding programs for enhanced drought tolerance.
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Affiliation(s)
- M. Awais Khan
- International Potato Center, P.O. Box 1558, Lima 12, Peru
| | - David Saravia
- International Potato Center, P.O. Box 1558, Lima 12, Peru
| | - Susan Munive
- International Potato Center, P.O. Box 1558, Lima 12, Peru
| | - Flavio Lozano
- International Potato Center, P.O. Box 1558, Lima 12, Peru
| | - Evelyn Farfan
- International Potato Center, P.O. Box 1558, Lima 12, Peru
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11
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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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12
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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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13
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de Boer JM, Borm TJA, Jesse T, Brugmans B, Wiggers-Perebolte L, de Leeuw L, Tang X, Bryan GJ, Bakker J, van Eck HJ, Visser RGF. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome. BMC Genomics 2011; 12:594. [PMID: 22142254 PMCID: PMC3261212 DOI: 10.1186/1471-2164-12-594] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 12/05/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). RESULTS First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. CONCLUSIONS The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
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Affiliation(s)
- Jan M de Boer
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalstesteeg 1, 6708 PD Wageningen, The Netherlands.
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14
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Bakker E, Borm T, Prins P, van der Vossen E, Uenk G, Arens M, de Boer J, van Eck H, Muskens M, Vossen J, van der Linden G, van Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J, Goverse A. A genome-wide genetic map of NB-LRR disease resistance loci in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:493-508. [PMID: 21590328 PMCID: PMC3135832 DOI: 10.1007/s00122-011-1602-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 04/26/2011] [Indexed: 05/14/2023]
Abstract
Like all plants, potato has evolved a surveillance system consisting of a large array of genes encoding for immune receptors that confer resistance to pathogens and pests. The majority of these so-called resistance or R proteins belong to the super-family that harbour a nucleotide binding and a leucine-rich-repeat domain (NB-LRR). Here, sequence information of the conserved NB domain was used to investigate the genome-wide genetic distribution of the NB-LRR resistance gene loci in potato. We analysed the sequences of 288 unique BAC clones selected using filter hybridisation screening of a BAC library of the diploid potato clone RH89-039-16 (S. tuberosum ssp. tuberosum) and a physical map of this BAC library. This resulted in the identification of 738 partial and full-length NB-LRR sequences. Based on homology of these sequences with known resistance genes, 280 and 448 sequences were classified as TIR-NB-LRR (TNL) and CC-NB-LRR (CNL) sequences, respectively. Genetic mapping revealed the presence of 15 TNL and 32 CNL loci. Thirty-six are novel, while three TNL loci and eight CNL loci are syntenic with previously identified functional resistance genes. The genetic map was complemented with 68 universal CAPS markers and 82 disease resistance trait loci described in literature, providing an excellent template for genetic studies and applied research in potato.
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Affiliation(s)
- Erin Bakker
- Laboratory of Nematology, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, The Netherlands.
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15
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Genome sequence and analysis of the tuber crop potato. Nature 2011; 475:189-95. [PMID: 21743474 DOI: 10.1038/nature10158] [Citation(s) in RCA: 1182] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 05/03/2011] [Indexed: 02/03/2023]
Abstract
Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
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16
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Finkers-Tomczak A, Bakker E, de Boer J, van der Vossen E, Achenbach U, Golas T, Suryaningrat S, Smant G, Bakker J, Goverse A. Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:595-608. [PMID: 21049265 PMCID: PMC3026667 DOI: 10.1007/s00122-010-1472-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/30/2010] [Indexed: 05/04/2023]
Abstract
The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146-152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.
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17
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Draffehn AM, Meller S, Li L, Gebhardt C. Natural diversity of potato (Solanum tuberosum) invertases. BMC PLANT BIOLOGY 2010; 10:271. [PMID: 21143910 PMCID: PMC3012049 DOI: 10.1186/1471-2229-10-271] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 12/09/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Invertases are ubiquitous enzymes that irreversibly cleave sucrose into fructose and glucose. Plant invertases play important roles in carbohydrate metabolism, plant development, and biotic and abiotic stress responses. In potato (Solanum tuberosum), invertases are involved in 'cold-induced sweetening' of tubers, an adaptive response to cold stress, which negatively affects the quality of potato chips and French fries. Linkage and association studies have identified quantitative trait loci (QTL) for tuber sugar content and chip quality that colocalize with three independent potato invertase loci, which together encode five invertase genes. The role of natural allelic variation of these genes in controlling the variation of tuber sugar content in different genotypes is unknown. RESULTS For functional studies on natural variants of five potato invertase genes we cloned and sequenced 193 full-length cDNAs from six heterozygous individuals (three tetraploid and three diploid). Eleven, thirteen, ten, twelve and nine different cDNA alleles were obtained for the genes Pain-1, InvGE, InvGF, InvCD141 and InvCD111, respectively. Allelic cDNA sequences differed from each other by 4 to 9%, and most were genotype specific. Additional variation was identified by single nucleotide polymorphism (SNP) analysis in an association-mapping population of 219 tetraploid individuals. Haplotype modeling revealed two to three major haplotypes besides a larger number of minor frequency haplotypes. cDNA alleles associated with chip quality, tuber starch content and starch yield were identified. CONCLUSIONS Very high natural allelic variation was uncovered in a set of five potato invertase genes. This variability is a consequence of the cultivated potato's reproductive biology. Some of the structural variation found might underlie functional variation that influences important agronomic traits such as tuber sugar content. The associations found between specific invertase alleles and chip quality, tuber starch content and starch yield will facilitate the selection of superior potato genotypes in breeding programs.
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Affiliation(s)
- Astrid M Draffehn
- Max-Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Sebastian Meller
- Max-Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Li Li
- Max-Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Christiane Gebhardt
- Max-Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
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18
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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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19
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Achenbach UC, Tang X, Ballvora A, de Jong H, Gebhardt C. Comparison of the chromosome maps around a resistance hot spot on chromosome 5 of potato and tomato using BAC-FISH painting. Genome 2010; 53:103-10. [PMID: 20140028 DOI: 10.1139/g09-086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Potato chromosome 5 harbours numerous genes for important qualitative and quantitative traits, such as resistance to the root cyst nematode Globodera pallida and the late blight fungus, Phytophthora infestans. The genes make up part of a "hot spot" for resistances to various pathogens covering a genetic map length of 3 cM between markers GP21 and GP179. We established the physical size and position of this region on chromosome 5 in potato and tomato using fluorescence in situ hybridization (FISH) on pachytene chromosomes. Five potato bacterial artificial chromosome (BAC) clones with the genetically anchored markers GP21, R1-contig (proximal end), CosA, GP179, and StPto were selected, labeled with different fluorophores, and hybridized in a five-colour FISH experiment. Our results showed the location of the BAC clones in the middle of the long arm of chromosome 5 in both potato and tomato. Based on chromosome measurements, we estimate the physical size of the GP21-GP179 interval at 0.85 Mb and 1.2 Mb in potato and tomato, respectively. The GP21-GP179 interval is part of a genome segment known to have inverted map positions between potato and tomato.
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Affiliation(s)
- Ute C Achenbach
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, Köln, Germany
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20
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Biber A, Kaufmann H, Linde M, Spiller M, Terefe D, Debener T. Molecular markers from a BAC contig spanning the Rdr1 locus: a tool for marker-assisted selection in roses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:765-73. [PMID: 19911159 DOI: 10.1007/s00122-009-1197-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/17/2009] [Indexed: 05/03/2023]
Abstract
We constructed a BAC contig of about 300 kb spanning the Rdr1 locus for black spot resistance in Rosa multiflora hybrids, using a new BIBAC library from DNA of this species. From this contig, we developed broadly applicable simple sequence repeat (SSR) markers tightly linked to Rdr1, which are suitable for genetic analyses and marker-assisted selection in roses. As a source for the high molecular weight DNA, we chose the homozygous resistant R. multiflora hybrid 88/124-46. For the assembly of the BAC contig, we made use of molecular markers derived from a previously established R. rugosa contig. In order to increase the resolution for fine mapping, the size of the population was increased to 974 plants. The genomic region spanning Rdr1 is now genetically restricted to 0.2 cM, corresponding to a physical distance of about 300 kb. One single-stranded conformational polymorphism (SSCP) and one SSR marker cosegregate with the Rdr1-mediated black spot resistance, while one SSR and several cleaved amplified polymorphic sequence or SSCP markers are very tightly linked with one to three recombinants among the 974 plants. The benefits of the molecular markers developed from the R. multiflora contig for the genetic analysis of roses and the integration of rose genetic maps are discussed.
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Affiliation(s)
- Anja Biber
- Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Strasse 2, Hannover, Germany
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21
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Danan S, Chauvin JE, Caromel B, Moal JD, Pellé R, Lefebvre V. Major-effect QTLs for stem and foliage resistance to late blight in the wild potato relatives Solanum sparsipilum and S. spegazzinii are mapped to chromosome X. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:705-719. [PMID: 19533081 DOI: 10.1007/s00122-009-1081-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 05/21/2009] [Indexed: 05/27/2023]
Abstract
To find out new resistance sources to late blight in the wild germplasm for potato breeding, we examined the polygenic resistance of Solanum sparsipilum and S. spegazzinii by a quantitative trait locus (QTL) analysis. We performed stem and foliage tests under controlled conditions in two diploid mapping progenies. Four traits were selected for QTL detection. A total of 30 QTLs were mapped, with a large-effect QTL region on chromosome X detected in both potato relatives. The mapping of literature-derived markers highlighted colinearities with published late blight QTLs or R-genes. Results showed (a) the resistance potential of S. sparsipilum and S. spegazzinii for late blight control, and (b) the efficacy of the stem test as a complement to the foliage test to break down the complex late blight resistance into elementary components. The relationships of late blight resistance QTLs with R-genes and maturity QTLs are discussed.
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Affiliation(s)
- Sarah Danan
- INRA, UR 1052 GAFL Génétique et Amélioration des Fruits et Légumes, BP 94, 84140, Montfavet, France
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22
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Finkers-Tomczak A, Danan S, van Dijk T, Beyene A, Bouwman L, Overmars H, van Eck H, Goverse A, Bakker J, Bakker E. A high-resolution map of the Grp1 locus on chromosome V of potato harbouring broad-spectrum resistance to the cyst nematode species Globodera pallida and Globodera rostochiensis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:165-173. [PMID: 19363662 PMCID: PMC2690855 DOI: 10.1007/s00122-009-1026-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 03/20/2009] [Indexed: 05/27/2023]
Abstract
The Grp1 locus confers broad-spectrum resistance to the potato cyst nematode species Globodera pallida and Globodera rostochiensis and is located in the GP21-GP179 interval on the short arm of chromosome V of potato. A high-resolution map has been developed using the diploid mapping population RHAM026, comprising 1,536 genotypes. The flanking markers GP21 and GP179 have been used to screen the 1,536 genotypes for recombination events. Interval mapping of the resistances to G. pallida Pa2 and G. rostochiensis Ro5 resulted in two nearly identical LOD graphs with the highest LOD score just north of marker TG432. Detailed analysis of the 44 recombinant genotypes showed that G. pallida and G. rostochiensis resistance could not be separated and map to the same location between marker SPUD838 and TG432. It is suggested that the quantitative resistance to both nematode species at the Grp1 locus is mediated by one or more tightly linked R genes that might belong to the NBS-LRR class.
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Affiliation(s)
- Anna Finkers-Tomczak
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Sarah Danan
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
- INRA UR 1052 GAFL Génétique et Amélioration des Fruits et Légumes, BP94, 84140 Montfavet, France
| | - Thijs van Dijk
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Amelework Beyene
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Liesbeth Bouwman
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Herman van Eck
- Laboratory of Plant Breeding, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Jaap Bakker
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
| | - Erin Bakker
- Laboratory of Nematology, Plant Science Group, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
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The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of disease resistance in the Solanaceae. Genetics 2009; 182:1351-64. [PMID: 19474202 DOI: 10.1534/genetics.109.101022] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomics provides a powerful tool for the identification of genes that encode traits shared between crop plants and model organisms. Pathogen resistance conferred by plant R genes of the nucleotide-binding-leucine-rich-repeat (NB-LRR) class is one such trait with great agricultural importance that occupies a critical position in understanding fundamental processes of pathogen detection and coevolution. The proposed rapid rearrangement of R genes in genome evolution would make comparative approaches tenuous. Here, we test the hypothesis that orthology is predictive of R-gene genomic location in the Solanaceae using the pepper R gene Bs2. Homologs of Bs2 were compared in terms of sequence and gene and protein architecture. Comparative mapping demonstrated that Bs2 shared macrosynteny with R genes that best fit criteria determined to be its orthologs. Analysis of the genomic sequence encompassing solanaceous R genes revealed the magnitude of transposon insertions and local duplications that resulted in the expansion of the Bs2 intron to 27 kb and the frequently detected duplications of the 5'-end of R genes. However, these duplications did not impact protein expression or function in transient assays. Taken together, our results support a conservation of synteny for NB-LRR genes and further show that their distribution in the genome has been consistent with global rearrangements.
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Pajerowska-Mukhtar K, Stich B, Achenbach U, Ballvora A, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Ilarionova E, Bellin D, Walkemeier B, Basekow R, Kersten B, Gebhardt C. Single nucleotide polymorphisms in the allene oxide synthase 2 gene are associated with field resistance to late blight in populations of tetraploid potato cultivars. Genetics 2009; 181:1115-27. [PMID: 19139145 PMCID: PMC2651047 DOI: 10.1534/genetics.108.094268] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 01/08/2009] [Indexed: 11/18/2022] Open
Abstract
The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identification of natural gene variation underlying late blight resistance not compromised by late maturity will facilitate the selection of resistant cultivars and give new insight in the mechanisms controlling quantitative pathogen resistance. We tested 24 candidate loci for association with field resistance to late blight and plant maturity in a population of 184 tetraploid potato individuals. The individuals were genotyped for 230 single nucleotide polymorphisms (SNPs) and 166 microsatellite alleles. For association analysis we used a mixed model, taking into account population structure, kinship, allele substitution and interaction effects of the marker alleles at a locus with four allele doses. Nine SNPs were associated with maturity corrected resistance (P < 0.001), which collectively explained 50% of the genetic variance of this trait. A major association was found at the StAOS2 locus encoding allene oxide synthase 2, a key enzyme in the biosynthesis of jasmonates, plant hormones that function in defense signaling. This finding supports StAOS2 as being one of the factors controlling natural variation of pathogen resistance.
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Affiliation(s)
- Karolina Pajerowska-Mukhtar
- Max Planck Institute for Plant Breeding Research, Department for Plant Breeding and Genetics, Cologne, Germany
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25
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Hernández-Pinzón I, de Jesús E, Santiago N, Casacuberta JM. The frequent transcriptional readthrough of the tobacco Tnt1 retrotransposon and its possible implications for the control of resistance genes. J Mol Evol 2009; 68:269-78. [PMID: 19221683 DOI: 10.1007/s00239-009-9204-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/21/2008] [Accepted: 01/21/2009] [Indexed: 12/20/2022]
Abstract
Retrotransposons are a major component of eukaryote genomes, being especially abundant in plant genomes. They are frequently found inserted in gene-rich regions and have greatly contributed to the evolution of gene coding capacity and regulation. Retrotransposon insertions can influence the expression of neighboring genes in many ways, such as modifying their promoter or terminator sequences and altering their epigenetic control. Plant retrotransposons are highly regulated and their expression is usually associated with stress situations. While the control of transcription of some plant retrotransposons has been analyzed in some detail, little is known about the transcriptional termination of these elements. Here we show that the transcripts of the tobacco retrotransposon Tnt1 display a high variability of polyadenylation sites, only a fraction of them terminating at the major termination site. We also report on the ability of Tnt1 to extend its transcription into flanking genomic sequences and we analyze a particular case in which Tnt1 transcripts include sequences of an oppositely oriented resistance-like gene. The expression of this gene and the neighboring Tnt1 copy generate transcripts overlapping in more that 800 nucleotides, which could anneal and form dsRNAs and enter into silencing regulatory pathways. Resistance gene loci are usually composed of tandem arrays of resistance-like genes, a number of which contain mutations, including retrotransposon insertions, and are considered as to be pseudogenes. Given that plant retrotransposons are usually regulated by stress, the convergent expression of these resistance-like pseudogenes and the interleaving inducible retrotransposons may contribute to the control of plant responses to stress.
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Affiliation(s)
- Inmaculada Hernández-Pinzón
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB, Institut de Biología Molecular de Barcelona (IBMB-CSIC), Jordi Girona 18, 08034, Barcelona, Spain
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26
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Achenbach U, Paulo J, Ilarionova E, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Gebhardt C. Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:619-29. [PMID: 19020852 DOI: 10.1007/s00122-008-0925-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 10/24/2008] [Indexed: 05/18/2023]
Abstract
The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.
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Affiliation(s)
- Ute Achenbach
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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27
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Neigenfind J, Gyetvai G, Basekow R, Diehl S, Achenbach U, Gebhardt C, Selbig J, Kersten B. Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 2008; 9:356. [PMID: 18667059 PMCID: PMC2566320 DOI: 10.1186/1471-2164-9-356] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 07/30/2008] [Indexed: 12/13/2022] Open
Abstract
Background Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous. Results Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes. Conclusion Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at . The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.
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Affiliation(s)
- Jost Neigenfind
- Bioinformatics, GabiPD team, Max Planck Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany.
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Zhu W, Ouyang S, Iovene M, O'Brien K, Vuong H, Jiang J, Buell CR. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics 2008; 9:286. [PMID: 18554403 PMCID: PMC2442093 DOI: 10.1186/1471-2164-9-286] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 06/13/2008] [Indexed: 11/29/2022] Open
Abstract
Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to Solanum lycopersicon (tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported.
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Affiliation(s)
- Wei Zhu
- Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA.
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29
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Datema E, Mueller LA, Buels R, Giovannoni JJ, Visser RGF, Stiekema WJ, van Ham RCHJ. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC PLANT BIOLOGY 2008; 8:34. [PMID: 18405374 PMCID: PMC2324086 DOI: 10.1186/1471-2229-8-34] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 04/11/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Tomato (Solanum lycopersicon) and potato (S. tuberosum) are two economically important crop species, the genomes of which are currently being sequenced. This study presents a first genome-wide analysis of these two species, based on two large collections of BAC end sequences representing approximately 19% of the tomato genome and 10% of the potato genome. RESULTS The tomato genome has a higher repeat content than the potato genome, primarily due to a higher number of retrotransposon insertions in the tomato genome. On the other hand, simple sequence repeats are more abundant in potato than in tomato. The two genomes also differ in the frequency distribution of SSR motifs. Based on EST and protein alignments, potato appears to contain up to 6,400 more putative coding regions than tomato. Major gene families such as cytochrome P450 mono-oxygenases and serine-threonine protein kinases are significantly overrepresented in potato, compared to tomato. Moreover, the P450 superfamily appears to have expanded spectacularly in both species compared to Arabidopsis thaliana, suggesting an expanded network of secondary metabolic pathways in the Solanaceae. Both tomato and potato appear to have a low level of microsynteny with A. thaliana. A higher degree of synteny was observed with Populus trichocarpa, specifically in the region between 15.2 and 19.4 Mb on P. trichocarpa chromosome 10. CONCLUSION The findings in this paper present a first glimpse into the evolution of Solanaceous genomes, both within the family and relative to other plant species. When the complete genome sequences of these species become available, whole-genome comparisons and protein- or repeat-family specific studies may shed more light on the observations made here.
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Affiliation(s)
- Erwin Datema
- Applied Bioinformatics, Plant Research International, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, Transitorium, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Lukas A Mueller
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Robert Buels
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - James J Giovannoni
- United States Department of Agriculture and Boyce Thompson Institute for Plant, Research, Cornell University, Ithaca, New York 14853, USA
| | - Richard GF Visser
- Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Willem J Stiekema
- Laboratory of Bioinformatics, Wageningen University, Transitorium, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), PO Box 98, 6700 AB Wageningen, The Netherlands
| | - Roeland CHJ van Ham
- Applied Bioinformatics, Plant Research International, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, Transitorium, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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