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Yadava YK, Chaudhary P, Yadav S, Rizvi AH, Kumar T, Srivastava R, Soren KR, Bharadwaj C, Srinivasan R, Singh NK, Jain PK. Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2023; 13:17623. [PMID: 37848483 PMCID: PMC10582051 DOI: 10.1038/s41598-023-44990-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.
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Affiliation(s)
- Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Pooja Chaudhary
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Aqeel Hasan Rizvi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tapan Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rachna Srivastava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K R Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 208024, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - R Srinivasan
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India.
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Jiang X, Li D, Du H, Wang P, Guo L, Zhu G, Zhang C. Genomic features of meiotic crossovers in diploid potato. HORTICULTURE RESEARCH 2023; 10:uhad079. [PMID: 37323232 PMCID: PMC10261879 DOI: 10.1093/hr/uhad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Meiotic recombination plays an important role in genome evolution and crop improvement. Potato (Solanum tuberosum L.) is the most important tuber crop in the world, but research about meiotic recombination in potato is limited. Here, we resequenced 2163 F2 clones derived from five different genetic backgrounds and identified 41 945 meiotic crossovers. Some recombination suppression in euchromatin regions was associated with large structural variants. We also detected five shared crossover hotspots. The number of crossovers in each F2 individual from the accession Upotato 1 varied from 9 to 27, with an average of 15.5, 78.25% of which were mapped within 5 kb of their presumed location. We show that 57.1% of the crossovers occurred in gene regions, with poly-A/T, poly-AG, AT-rich, and CCN repeats enriched in the crossover intervals. The recombination rate is positively related with gene density, SNP density, Class II transposon, and negatively related with GC density, repeat sequence density and Class I transposon. This study deepens our understanding of meiotic crossovers in potato and provides useful information for diploid potato breeding.
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Affiliation(s)
- Xiuhan Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hui Du
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
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Guo ZH, Ma PF, Yang GQ, Hu JY, Liu YL, Xia EH, Zhong MC, Zhao L, Sun GL, Xu YX, Zhao YJ, Zhang YC, Zhang YX, Zhang XM, Zhou MY, Guo Y, Guo C, Liu JX, Ye XY, Chen YM, Yang Y, Han B, Lin CS, Lu Y, Li DZ. Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos. MOLECULAR PLANT 2019; 12:1353-1365. [PMID: 31145999 DOI: 10.1016/j.molp.2019.05.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 05/15/2023]
Abstract
Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.
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Affiliation(s)
- Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Qian Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jin-Yong Hu
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Mi-Cai Zhong
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gui-Ling Sun
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, Henan 475001, China
| | - Yu-Xing Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - You-Jie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Yi-Chi Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Xiao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Xue-Mei Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xia-Ying Ye
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yun-Mei Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yang Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Bin Han
- National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei.
| | - Ying Lu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Monden Y, Tahara M. Genetic linkage analysis using DNA markers in sweetpotato. BREEDING SCIENCE 2017; 67:41-51. [PMID: 28465667 PMCID: PMC5407921 DOI: 10.1270/jsbbs.16142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/03/2016] [Indexed: 05/23/2023]
Abstract
Sweetpotato is one of the most important food crop species in the world, with more than 104,000,000 tons produced each year, and the breeding of superior cultivars with agronomically important traits, such as improved disease resistance, yield, and nutrient richness, is necessary, especially in developing countries. However, as a result of the crop's complex genomic architecture, which results from its hexaploidy (2n = 6× = 90), high heterozygosity, huge genome, and outcrossing nature, the analysis of genetic linkage in sweetpotato has been challenging. In addition, the lack of whole genome sequences or gene annotations for cultivated hexaploids has interrupted the validation of mapped QTL regions and gene cloning. In spite of these technical difficulties, linkage map construction and QTL mapping analysis have been reported. This review summarizes the results of these linkage analyses, which used SSR, AFLP, and retrotransposon-based molecular markers, and describes future directions for the genetic analysis and marker-assisted breeding of this important but genetically complex crop species.
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Affiliation(s)
- Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University,
1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530,
Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University,
1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530,
Japan
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Dukić M, Berner D, Roesti M, Haag CR, Ebert D. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna. BMC Genet 2016; 17:137. [PMID: 27737627 PMCID: PMC5064971 DOI: 10.1186/s12863-016-0445-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. RESULTS A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. CONCLUSIONS Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.
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Affiliation(s)
- Marinela Dukić
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.
| | - Daniel Berner
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Marius Roesti
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.,Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive - CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, campus CNRS, 1919, route de Mende, 34293, Montpellier Cedex 5, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Muśee 10, 1700, Fribourg, Switzerland
| | - Dieter Ebert
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
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High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Sci Rep 2015; 5:17512. [PMID: 26631981 PMCID: PMC4668357 DOI: 10.1038/srep17512] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/30/2015] [Indexed: 12/18/2022] Open
Abstract
This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.
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Xiao B, Tan Y, Long N, Chen X, Tong Z, Dong Y, Li Y. SNP-based genetic linkage map of tobacco (Nicotiana tabacum L.) using next-generation RAD sequencing. ACTA ACUST UNITED AC 2015; 22:11. [PMID: 26473145 PMCID: PMC4607152 DOI: 10.1186/s40709-015-0034-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 09/18/2015] [Indexed: 12/30/2022]
Abstract
Background Tobacco (Nicotiana tabacum L.) is an important model system, which has been widely used in plant physiological studies and it is particularly useful as a bioreactor. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping and breeding. Restriction-site associated DNA sequencing (RAD-seq) is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis through linkage mapping. Results We constructed a RAD library using genomic DNA from a BC1 backcross population. Sequencing of 196 individuals was performed on an Illumina HiSeq 2500. Two linkage maps were constructed, one with a reference genome and another, termed as de novo identification of single nucleotide polymorphism (SNP) by RAD-seq, without a reference genome. Overall, 4138 and 2162 SNP markers with a total length of 1944.74 and 2000.9 cM were mapped to 24 linkage groups in the genetic maps based on reference genome and without reference, respectively. Conclusions Using two different SNP discovery methods based on next generation RAD sequencing technology, we have respectively mapped 2162 and 4318 SNPs in our backcross population. This study gives an excellent example for high density linkage map construction, irrespective of genome sequence availability, and provides saturated information for downstream genetic investigations such as quantitative trait locus analyses or genomic selection (e.g. bioreactor suitable cultivars). Electronic supplementary material The online version of this article (doi:10.1186/s40709-015-0034-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bingguang Xiao
- Yunnan Academy of Tobacco Agricultural Science, Yuantong Street No. 33, Kunming, 650021 Yunnan China
| | - Yuntao Tan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, JingMing South Road No. 727, Kunming, 650500 Yunnan China
| | - Ni Long
- Faculty of Life Science and Technology, Kunming University of Science and Technology, JingMing South Road No. 727, Kunming, 650500 Yunnan China
| | - Xuejun Chen
- Yunnan Academy of Tobacco Agricultural Science, Yuantong Street No. 33, Kunming, 650021 Yunnan China
| | - Zhijun Tong
- Yunnan Academy of Tobacco Agricultural Science, Yuantong Street No. 33, Kunming, 650021 Yunnan China
| | - Yang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, JingMing South Road No. 727, Kunming, 650500 Yunnan China
| | - Yongping Li
- Yunnan Academy of Tobacco Agricultural Science, Yuantong Street No. 33, Kunming, 650021 Yunnan China
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Wang F, Singh R, Genovesi AD, Wai CM, Huang X, Chandra A, Yu Q. Sequence-tagged high-density genetic maps of Zoysia japonicaprovide insights into genome evolution in Chloridoideae. THE PLANT JOURNAL 2015; 82:744-57. [PMID: 0 DOI: 10.1111/tpj.12842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 03/02/2015] [Accepted: 03/30/2015] [Indexed: 05/24/2023]
Affiliation(s)
- Fangfang Wang
- Texas A&M AgriLife Research Center at Dallas; Texas A&M University System; Dallas TX 75252 USA
| | - Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas; Texas A&M University System; Dallas TX 75252 USA
| | - Anthony D. Genovesi
- Texas A&M AgriLife Research Center at Dallas; Texas A&M University System; Dallas TX 75252 USA
| | - Ching Man Wai
- Department of Plant Biology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Fujian Agriculture and Forestry University; Fuzhou 350002 China
| | - Xiaoen Huang
- Texas A&M AgriLife Research Center at Dallas; Texas A&M University System; Dallas TX 75252 USA
| | - Ambika Chandra
- Texas A&M AgriLife Research Center at Dallas; Texas A&M University System; Dallas TX 75252 USA
- Department of Soil & Crop Sciences; Texas A&M University; College Station TX 77843 USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas; Texas A&M University System; Dallas TX 75252 USA
- Department of Plant Pathology and Microbiology; Texas A&M University; College Station TX 77843 USA
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Watanabe K. Potato genetics, genomics, and applications. BREEDING SCIENCE 2015; 65:53-68. [PMID: 25931980 PMCID: PMC4374564 DOI: 10.1270/jsbbs.65.53] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/17/2015] [Indexed: 05/20/2023]
Abstract
Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding.
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10
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Maphosa L, Langridge P, Taylor H, Parent B, Emebiri LC, Kuchel H, Reynolds MP, Chalmers KJ, Okada A, Edwards J, Mather DE. Genetic control of grain yield and grain physical characteristics in a bread wheat population grown under a range of environmental conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1607-24. [PMID: 24865506 DOI: 10.1007/s00122-014-2322-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 05/02/2014] [Indexed: 05/24/2023]
Abstract
Genetic analysis of the yield and physical quality of wheat revealed complex genetic control, including strong effects of photoperiod-sensitivity loci. Environmental conditions such as moisture deficit and high temperatures during the growing period affect the grain yield and grain characteristics of bread wheat (Triticum aestivum L.). The aim of this study was to map quantitative trait loci (QTL) for grain yield and grain quality traits using a Drysdale/Gladius bread wheat mapping population grown under a range of environmental conditions in Australia and Mexico. In general, yield and grain quality were reduced in environments exposed to drought and/or heat stress. Despite large effects of known photoperiod-sensitivity loci (Ppd-B1 and Ppd-D1) on crop development, grain yield and grain quality traits, it was possible to detect QTL elsewhere in the genome. Some of these QTL were detected consistently across environments. A locus on chromosome 6A (TaGW2) that is known to be associated with grain development was associated with grain width, thickness and roundness. The grain hardness (Ha) locus on chromosome 5D was associated with particle size index and flour extraction and a region on chromosome 3B was associated with grain width, thickness, thousand grain weight and yield. The genetic control of grain length appeared to be largely independent of the genetic control of the other grain dimensions. As expected, effects on grain yield were detected at loci that also affected yield components. Some QTL displayed QTL-by-environment interactions, with some having effects only in environments subject to water limitation and/or heat stress.
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Affiliation(s)
- Lancelot Maphosa
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
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11
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Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae). BMC Genomics 2013; 14:32. [PMID: 23324215 PMCID: PMC3583795 DOI: 10.1186/1471-2164-14-32] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 01/14/2013] [Indexed: 11/10/2022] Open
Abstract
Background The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD) sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus Gnathopogon (Cyprinidae) for comparative genomics with the zebrafish Danio rerio (a member of the same family as gudgeons) and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of Gnathopogon. Results We constructed the first genetic linkage map of Gnathopogon using a 198 F2 interspecific cross between two closely related species in Japan: river-dwelling Gnathopogon elongatus and lake-dwelling Gnathopogon caerulescens. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD). Synteny and collinearity were extensively conserved between Gnathopogon and zebrafish. Conclusions The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.
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Affiliation(s)
- Ryo Kakioka
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, 606-8502, Kyoto, Japan.
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A high density consensus map of rye (Secale cereale L.) based on DArT markers. PLoS One 2011; 6:e28495. [PMID: 22163026 PMCID: PMC3232230 DOI: 10.1371/journal.pone.0028495] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/09/2011] [Indexed: 12/02/2022] Open
Abstract
Background Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers. Methodology/Principal Findings Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers. Conclusions/Significance Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization.
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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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Li G, Huang S, Guo X, Li Y, Yang Y, Guo Z, Kuang H, Rietman H, Bergervoet M, Vleeshouwers VGGA, van der Vossen EAG, Qu D, Visser RGF, Jacobsen E, Vossen JH. Cloning and characterization of r3b; members of the r3 superfamily of late blight resistance genes show sequence and functional divergence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1132-42. [PMID: 21649512 DOI: 10.1094/mpmi-11-10-0276] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Massive resistance (R) gene stacking is considered to be one of the most promising approaches to provide durable resistance to potato late blight for both conventional and genetically modified breeding strategies. The R3 complex locus on chromosome XI in potato is an example of natural R gene stacking, because it contains two closely linked R genes (R3a and R3b) with distinct resistance specificities to Phytophthora infestans. Here, we report about the positional cloning of R3b. Both transient and stable transformations of susceptible tobacco and potato plants showed that R3b conferred full resistance to incompatible P. infestans isolates. R3b encodes a coiled-coil nucleotide-binding site leucine-rich repeat protein and exhibits 82% nucleotide identity with R3a located in the same R3 cluster. The R3b gene specifically recognizes Avr3b, a newly identified avirulence factor from P. infestans. R3b does not recognize Avr3a, the corresponding avirulence gene for R3a, showing that, despite their high sequence similarity, R3b and R3a have clearly distinct recognition specificities. In addition to the Rpi-mcd1/Rpi-blb3 locus on chromosome IV, the R3 locus on chromosome XI is the second example of an R-gene cluster with multiple genes recognizing different races of P. infestans.
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Affiliation(s)
- Guangcun Li
- key Laboratory of Corp Genetic Improvement and Biotechnology, Shandong Province, Shandong Academy of Agricultural Sciences, Jinan 250100, P.R. China
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15
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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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16
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Danan S, Veyrieras JB, Lefebvre V. Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC PLANT BIOLOGY 2011; 11:16. [PMID: 21247437 PMCID: PMC3037844 DOI: 10.1186/1471-2229-11-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 01/19/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits. RESULTS Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes. CONCLUSIONS Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database.
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Affiliation(s)
- Sarah Danan
- Institut National de la Recherche Agronomique (INRA), UR 1052 Génétique et Amélioration des Fruits et Légumes (GAFL), BP94, 84140 Montfavet, France
| | - Jean-Baptiste Veyrieras
- Institut National de la Recherche Agronomique (INRA-UPS-INA PG-CNRS), UMR 320 Génétique Végétale, Ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Véronique Lefebvre
- Institut National de la Recherche Agronomique (INRA), UR 1052 Génétique et Amélioration des Fruits et Légumes (GAFL), BP94, 84140 Montfavet, France
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17
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Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley. Mol Genet Genomics 2010; 284:319-31. [DOI: 10.1007/s00438-010-0570-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 08/13/2010] [Indexed: 11/26/2022]
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Multilocus tetrasomic linkage analysis using hidden Markov chain model. Proc Natl Acad Sci U S A 2010; 107:4270-4. [PMID: 20142473 DOI: 10.1073/pnas.0908477107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically important species are autopolyploids, with autotetraploidy being a typical example. These species undergo much more complicated chromosomal segregation and recombination at meiosis than diploids. In addition, there is evidence of polyploidy-induced and highly dynamic changes in the structure of the genome. These polysomic characteristics indicate the inappropriateness of the theory and methods of linkage analysis in diploids for use in these species and a gap in the theory and methodology of tetraploid map construction. This paper presents a theoretical model and statistical framework for multilocus linkage analysis in autotetraploids for use with dominant and/or codominant DNA molecular markers. The theory and methods incorporate the essential features of allele segregation and recombination under tetrasomic inheritance and the major challenges in statistical modeling and marker data analysis. We validated the method and explored its statistical properties by intensive simulation study and demonstrated its utility by analysis of AFLP and SSR marker data from an outbred autotetraploid potato population.
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McIntyre CL, Mathews KL, Rattey A, Chapman SC, Drenth J, Ghaderi M, Reynolds M, Shorter R. Molecular detection of genomic regions associated with grain yield and yield-related components in an elite bread wheat cross evaluated under irrigated and rainfed conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:527-41. [PMID: 19865806 DOI: 10.1007/s00122-009-1173-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 09/27/2009] [Indexed: 05/20/2023]
Abstract
Grain yield and grain weight of wheat are often decreased by water-limitation in the north-eastern cropping belt of Australia. Based on knowledge that CIMMYT lines are well-adapted in this region, a recombinant inbred line (RIL) population between two elite CIMMYT bread wheats (Seri M82 and Babax) was evaluated under water-limited environments. Fourteen productivity traits were evaluated in 192 progeny in up to eight trials. For three aggregations of the environments (all, high yield or low yield), multiple quantitative trait loci (QTL) were detected, each explaining <15% of variation. Co-location of multiple trait QTL was greatest on linkage groups 1B-a, 1D-b, 4A-a, 4D-a, 6A-a, 6B-a, 7A-a and an unassigned linkage group. Two putative QTL (LOD > 3) from Seri (6D-b and UA-d) increased grain yield and co-located with a suggestive (2 < LOD < 3) and a putative QTL for increased stem carbohydrate content (WSC), respectively; the latter QTL also co-located with a putative anthesis QTL for earlier flowering. Both QTL were detected only in high yield (>4t ha(-1)) environments. A third increased grain yield QTL (7A-a) from Babax co-located with QTL for increased grain number. Six putative QTL increased grain weight and co-located with QTL for harvest index, grains per spike and spike number. Three putative QTL for increased grains per spike co-located with strong QTL for earlier flowering, increased grain weight and fewer spikes. A group of progeny that exceeded the mean grain yield and grain weight of commercial checks had an increased frequency of QTL for high WSC, large grain size, increased harvest index and greater height, but fewer stems, when compared to low yielding (20% less), low grain weight progeny. These findings were consistent with agronomic analyses of the germplasm and demonstrate that there should be opportunities to independently manipulate grain number and grain size which is typically difficult due to strong negative correlations.
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Affiliation(s)
- C Lynne McIntyre
- CSIRO Plant Industry, 306 Carmody Rd, St Lucia, QLD 4067, Australia.
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20
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Pel MA, Foster SJ, Park TH, Rietman H, van Arkel G, Jones JDG, Van Eck HJ, Jacobsen E, Visser RGF, Van der Vossen EAG. Mapping and cloning of late blight resistance genes from Solanum venturii using an interspecific candidate gene approach. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:601-15. [PMID: 19348577 DOI: 10.1094/mpmi-22-5-0601] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of potato. Resistance (R) genes from the wild species Solanum demissum have been used by breeders to generate late-blight-resistant cultivars but resistance was soon overcome by the pathogen. A more recent screening of a large number of wild species has led to the identification of novel sources of resistance, many of which are currently being characterized further. Here, we report on the cloning of dominant Rpi genes from S. venturii. Rpi-vnt1.1 and Rpi-vnt1.3 were mapped to chromosome 9 using nucleotide binding site (NBS) profiling. Subsequently, a Tm-2(2)-based allele mining strategy was used to clone both genes. Rpi-vnt1.1 and Rpi-vnt1.3 belong to the coiled-coil NBS leucine-rich repeat (LRR) class of plant R genes and encode predicted peptides of 891 and 905 amino acids (aa), respectively, which share 75% amino acid identity with the Tomato mosaic virus resistance protein Tm-2(2) from tomato. Compared with Rpi-vnt1.1, Rpi-vnt1.3 harbors a 14-aa insertion in the N-terminal region of the protein and two different amino acids in the LRR domain. Despite these differences, Rpi-vnt1.1 and Rpi-vnt1.3 genes have the same resistance spectrum.
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Affiliation(s)
- Mathieu A Pel
- Wageningen UR Plant Breeding, Wageningen, The Netherlands
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21
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Mace ES, Rami JF, Bouchet S, Klein PE, Klein RR, Kilian A, Wenzl P, Xia L, Halloran K, Jordan DR. A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers. BMC PLANT BIOLOGY 2009; 9:13. [PMID: 19171067 PMCID: PMC2671505 DOI: 10.1186/1471-2229-9-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 01/26/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. RESULTS The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci (1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. CONCLUSION The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.
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Affiliation(s)
- Emma S Mace
- The Department of Primary Industries & Fisheries, Queensland (DPI&F), Hermitage Research Station, Warwick, QLD 4370, Australia
| | - Jean-Francois Rami
- CIRAD UMR DAP, TA A-96/03, Av Agropolis, 34398 Montpellier CEDEX 5, France
| | - Sophie Bouchet
- CIRAD UMR DAP, TA A-96/03, Av Agropolis, 34398 Montpellier CEDEX 5, France
| | - Patricia E Klein
- Department of Horticulture and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843-2123, USA
| | - Robert R Klein
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Andrzej Kilian
- Diversity Arrays Technology P/L, PO Box 7141, Yarralumla ACT 2600, Australia
| | - Peter Wenzl
- Diversity Arrays Technology P/L, PO Box 7141, Yarralumla ACT 2600, Australia
| | - Ling Xia
- Diversity Arrays Technology P/L, PO Box 7141, Yarralumla ACT 2600, Australia
| | - Kirsten Halloran
- The Department of Primary Industries & Fisheries, Queensland (DPI&F), Hermitage Research Station, Warwick, QLD 4370, Australia
| | - David R Jordan
- The Department of Primary Industries & Fisheries, Queensland (DPI&F), Hermitage Research Station, Warwick, QLD 4370, Australia
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Mathews KL, Malosetti M, Chapman S, McIntyre L, Reynolds M, Shorter R, van Eeuwijk F. Multi-environment QTL mixed models for drought stress adaptation in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1077-91. [PMID: 18696042 DOI: 10.1007/s00122-008-0846-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Accepted: 07/09/2008] [Indexed: 05/18/2023]
Abstract
Many quantitative trait loci (QTL) detection methods ignore QTL-by-environment interaction (QEI) and are limited in accommodation of error and environment-specific variance. This paper outlines a mixed model approach using a recombinant inbred spring wheat population grown in six drought stress trials. Genotype estimates for yield, anthesis date and height were calculated using the best design and spatial effects model for each trial. Parsimonious factor analytic models best captured the variance-covariance structure, including genetic correlations, among environments. The 1RS.1BL rye chromosome translocation (from one parent) which decreased progeny yield by 13.8 g m(-2) was explicitly included in the QTL model. Simple interval mapping (SIM) was used in a genome-wide scan for significant QTL, where QTL effects were fitted as fixed environment-specific effects. All significant environment-specific QTL were subsequently included in a multi-QTL model and evaluated for main and QEI effects with non-significant QEI effects being dropped. QTL effects (either consistent or environment-specific) included eight yield, four anthesis, and six height QTL. One yield QTL co-located (or was linked) to an anthesis QTL, while another co-located with a height QTL. In the final multi-QTL model, only one QTL for yield (6 g m(-2)) was consistent across environments (no QEI), while the remaining QTL had significant QEI effects (average size per environment of 5.1 g m(-2)). Compared to single trial analyses, the described framework allowed explicit modelling and detection of QEI effects and incorporation of additional classification information about genotypes.
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Affiliation(s)
- Ky L Mathews
- CSIRO Plant Industry, Queensland Biosciences Precinct, 306 Carmody Rd, St Lucia, QLD 4067, Australia
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23
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Brugmans B, Wouters D, van Os H, Hutten R, van der Linden G, Visser RGF, van Eck HJ, van der Vossen EAG. Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1379-88. [PMID: 18806994 DOI: 10.1007/s00122-008-0871-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Accepted: 08/15/2008] [Indexed: 05/04/2023]
Abstract
NBS profiling is a method for the identification of resistance gene analog (RGA) derived fragments. Here we report the use of NBS profiling for the genome wide mapping of RGA loci in potato. NBS profiling analyses on a minimal set of F1 genotypes of the diploid mapping population previously used to generate the ultra dense (UHD) genetic map of potato, allowed us to efficiently map polymorphic RGA fragments relative to 10,000 existing AFLP markers. In total, 34 RGA loci were mapped, of which only 13 contained RGA sequences homologous to RGAs genetically positioned at approximately similar positions in potato or tomato. The remaining RGA loci mapped either at approximate chromosomal regions previously shown to contain RGAs in potato or tomato without sharing homology to these RGAs, or mapped at positions not yet identified as RGA-containing regions. In addition to markers representing RGAs with unknown functions, segregating markers were detected that were closely linked to four functional R genes that segregate in the UHD mapping population. To explore the potential of NBS profiling in RGA transcription analyses, RNA isolated from different tissues was used as template for NBS profiling. Of all the fragments amplified approximately 15% showed putative intensity or absent/present differences between different tissues suggesting putative tissue specific RGA or R gene transcription. Putative absent/present differences between individuals were also found. In addition to being a powerful tool for generating candidate gene markers linked to R gene loci, NBS profiling, when applied to cDNA, can be instrumental in identifying those members of an R gene cluster that are transcribed, and thus putatively functional.
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Affiliation(s)
- Bart Brugmans
- Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
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van Berloo R, Zhu A, Ursem R, Verbakel H, Gort G, van Eeuwijk FA. Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:89-101. [PMID: 18389208 PMCID: PMC2413108 DOI: 10.1007/s00122-008-0755-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 03/14/2008] [Indexed: 05/18/2023]
Abstract
Within the Dutch genomics initiative the "Centre for Biosystems Genomics" (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies.
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Affiliation(s)
- Ralph van Berloo
- Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
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Ritter E, Ruiz de Galarreta JI, van Eck HJ, Sánchez I. Construction of a potato transcriptome map based on the cDNA-AFLP technique. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:1003-1013. [PMID: 18317719 DOI: 10.1007/s00122-008-0731-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 02/09/2008] [Indexed: 05/26/2023]
Abstract
The cDNA-AFLP technique can be used to monitor differential gene expression, but also for linkage mapping. Extending previous works, we have now constructed an integrated linkage map of the potato transcriptome based on the said technique that has a length of around 800 cM and contains nearly 700 transcriptome derived fragments (TDFs). At the same time, most of these markers are anchored to the bins of a highly saturated reference map in potato, combining in this way the information provided by different marker types. Moreover, we detected and confirmed an elevated degree of allelic fragments with this marker type, which was present in nearly half of all primer combinations and involved around 20% of all fragments. These properties were particularly useful to establish anchor points for integrating the individual parental linkage maps. Comparative expression profiling in different plant materials revealed that only a few additional TDFs were obtained which were specific for mature leaves or tubers compared to the TDFs present in whole in vitro plants. Since TDF markers are derived from coding regions, they generally also represent sequences with a biological function. In four case studies, co-migrating TDFs in different Solanum wild species always represented potential alleles based on elevated homologies among them. Two resistance gene homologs were identified by analysing TDFs, which were co-located with known QTLs.
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Affiliation(s)
- E Ritter
- NEIKER, The Basque Institute of Agricultural Research and Development, PO Box 46, E01080 Vitoria, Spain
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26
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Barchi L, Bonnet J, Boudet C, Signoret P, Nagy I, Lanteri S, Palloix A, Lefebvre V. A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping. Genome 2007; 50:51-60. [PMID: 17546071 DOI: 10.1139/g06-140] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) was constructed from a population of 297 recombinant inbred lines. The parents were the large-fruited inbred cultivar 'Yolo Wonder' and the hot pepper line 'Criollo de Morelos 334', which is heavily used as a source of resistance to a number of diseases. A set of 587 markers (507 amplified fragment length polymorphisms, 40 simple sequence repeats, 19 restriction fragment length polymorphisms, 17 sequence-specific amplified polymorphisms, and 4 sequence tagged sites) were used to generate the map; of these, 489 were assembled into 49 linkage groups (LGs), including 14 LGs with 10 to 60 markers per LG and 35 with 2 to 9 markers per LG. The framework map covered 1857 cM with an average intermarker distance of 5.71 cM. Twenty-three LGs, composed of 69% of the markers and covering 1553 cM, were assigned to 1 of the 12 haploid pepper chromosomes, leaving 26 LGs (304 cM) unassigned. The chromosome framework map built with 250 markers led to a high level of mapping confidence and an average intermarker distance of 6.54 cM. By applying MapPop software, it was possible to select smaller subsets of 141 or 93 most informative individuals with a view to reducing the time and cost of further mapping and phenotyping. To define the smallest number of individuals sufficient for assigning any new marker to a chromosome, subsets from 12 to 45 individuals and a set of 13 markers distributed over all 12 chromosomes were screened. In most cases, the markers were correctly assigned to their expected chromosome, but the accuracy of the map position decreased as the number of individuals was reduced.
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Affiliation(s)
- Lorenzo Barchi
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, BP94, Montfavet F-84140, France
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Park TH, Kim JB, Hutten RCB, van Eck HJ, Jacobsen E, Visser RGF. Genetic positioning of centromeres using half-tetrad analysis in a 4x-2x cross population of potato. Genetics 2007; 176:85-94. [PMID: 17339217 PMCID: PMC1893073 DOI: 10.1534/genetics.107.070870] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Accepted: 02/23/2007] [Indexed: 11/18/2022] Open
Abstract
From biological and genetic standpoints, centromeres play an important role in the delivery of the chromosome complement to the daughter cells at cell division. The positions of the centromeres of potato were determined by half-tetrad analysis in a 4x-2x population where the male parent produced 2n pollen by first-division restitution (FDR). The genetic linkage groups and locations of 95 male parent-derived amplified fragment length polymorphism markers could be determined by comparing their position on a 2x-2x highly saturated linkage map of potato. Ten centromere positions were identified by 100% heterozygosity transmitted from the 2n heterozygous gametes of the paternal parent into the tetraploid offspring. The position of these centromeric marker loci was in accordance with those predicted by the saturated 2x-2x map using the level of marker clustering as a criterion. Two remaining centromere positions could be determined by extrapolation. The frequent observation of transmission of 100% heterozygosity proves that the meiotic restitution mechanism is exclusively based on FDR. Additional investigations on the position of recombination events of three chromosomes with sufficient numbers of markers showed that only one crossover occurred per chromosome arm, proving strong interference of recombination between centromere and telomere.
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Affiliation(s)
- Tae-Ho Park
- Laboratory of Plant Breeding, Wageningen University, The Netherlands
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28
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Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A. A high density barley microsatellite consensus map with 775 SSR loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1091-103. [PMID: 17345060 DOI: 10.1007/s00122-007-0503-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 01/07/2007] [Indexed: 05/14/2023]
Abstract
A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.
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Affiliation(s)
- R K Varshney
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
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29
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Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJD, Graner A, Niks RE. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:487-500. [PMID: 17115126 DOI: 10.1007/s00122-006-0448-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 10/25/2006] [Indexed: 05/12/2023]
Abstract
A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin.
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Affiliation(s)
- T C Marcel
- Laboratory of Plant Breeding, Graduate school for Experimental Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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30
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Bradshaw JE, Hackett CA, Lowe R, McLean K, Stewart HE, Tierney I, Vilaro MDR, Bryan GJ. Detection of a quantitative trait locus for both foliage and tuber resistance to late blight [Phytophthora infestans (Mont.) de Bary] on chromosome 4 of a dihaploid potato clone (Solanum tuberosum subsp. tuberosum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:943-51. [PMID: 16845519 DOI: 10.1007/s00122-006-0353-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 06/21/2006] [Indexed: 05/10/2023]
Abstract
Linkage analysis, Kruskal-Wallis analysis, interval mapping and graphical genotyping were performed on a potato diploid backcross family comprising 120 clones segregating for resistance to late blight. A hybrid between the Solanum tuberosum dihaploid clone PDH247 and the long-day-adapted S. phureja clone DB226(70) had been crossed to DB226(70) to produce the backcross family. Eighteen AFLP primer combinations provided 186 and 123 informative maternal and paternal markers respectively, with 63 markers in common to both parents. Eleven microsatellite (SSR) markers proved useful for identifying chromosomes. Linkage maps of both backcross parents were constructed. The results of a Kruskal-Wallis analysis, interval mapping and graphical genotyping were all consistent with a QTL or QTLs for blight resistance between two AFLP markers 30 cM apart on chromosome 4, which was identified by a microsatellite marker. The simplest explanation of the results is a single QTL with an allele from the dihaploid parent conferring resistance to race 1, 4 of P. infestans in the foliage in the glasshouse and to race 1, 2, 3, 4, 6, 7 in the foliage in the field and in tubers from glasshouse raised plants. The QTL was of large effect, and explained 78 and 51% of the variation in phenotypic scores for foliage blight in the glasshouse and field respectively, as well as 27% of the variation in tuber blight. Graphical genotyping and the differences in blight scores between the parental clones showed that all of the foliage blight resistance is accounted for by chromosome 4, whereas undetected QTLs for tuber resistance probably exist on other chromosomes. Graphical genotyping also explained the lack of precision in mapping the QTL(s) in terms of lack of appropriate recombinant chromosomes.
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Affiliation(s)
- John E Bradshaw
- Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
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31
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Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 2006. [PMID: 16904008 DOI: 10.1186/1471‐2164‐7‐206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. RESULTS The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. CONCLUSION Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.
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Affiliation(s)
- Peter Wenzl
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia.
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32
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Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 2006; 7:206. [PMID: 16904008 PMCID: PMC1564146 DOI: 10.1186/1471-2164-7-206] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 08/12/2006] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. RESULTS The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. CONCLUSION Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.
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Affiliation(s)
- Peter Wenzl
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Haobing Li
- School of Agricultural Science, University of Tasmania, PO Box 252-54, Hobart TAS 7001, Australia
| | - Jason Carling
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agricultural Research, PO Box 46, Kings Meadows TAS 7249, Australia
| | - Harsh Raman
- NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
| | - Edie Paul
- GeneFlow Inc., 14582 Olde Kent Rd., Centreville VA 20120, USA
| | - Phillippa Hearnden
- School of Agriculture, Food and Wine, Plant Genomics Centre, The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
| | - Christina Maier
- Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman WA 99164-6420, USA
| | - Ling Xia
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Vanessa Caig
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Jaroslava Ovesná
- Research Institute of Crop Production, Drnovská 507, 161 06 Prague 6, Czech Republic
| | - Mehmet Cakir
- Molecular Plant Breeding CRC, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
| | - David Poulsen
- Department of Primary Industries & Fisheries, Plant Science, MS 508 Warwick, QLD 4370, Australia
| | - Junping Wang
- NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
| | - Rosy Raman
- NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Ken J Chalmers
- School of Agriculture, Food and Wine, Plant Genomics Centre, The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
| | - Andris Kleinhofs
- Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman WA 99164-6420, USA
| | - Eric Huttner
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
| | - Andrzej Kilian
- Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
- DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
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Mullins E, Milbourne D, Petti C, Doyle-Prestwich BM, Meade C. Potato in the age of biotechnology. TRENDS IN PLANT SCIENCE 2006; 11:254-60. [PMID: 16621672 DOI: 10.1016/j.tplants.2006.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 02/22/2006] [Accepted: 03/23/2006] [Indexed: 05/08/2023]
Abstract
Biotechnology-based tools are now widely used to enhance and expand the traditional remit of potato in food production. By modifying its functionality, the capacity of the potato to produce, for example, therapeutic or industrial compounds is now a reality, and its ability to resist disease can also be radically improved. Two developments have been crucial to expanding the role of potato: the recent advances in the fields of structural and functional potato genomics and the ability to integrate genes of interest into the potato genome. In this review we discuss how both developments have diversified the remit of this crop.
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Affiliation(s)
- Ewen Mullins
- Plant Biotechnology Unit, Teagasc Crops Research Centre, Oakpark, Carlow, Ireland.
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34
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Lanteri S, Acquadro A, Comino C, Mauro R, Mauromicale G, Portis E. A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1532-42. [PMID: 16565844 DOI: 10.1007/s00122-006-0256-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 03/01/2006] [Indexed: 05/07/2023]
Abstract
We present the first genetic maps of globe artichoke (Cynara cardunculus var. scolymus L. 2n=2x=34), constructed with a two-way pseudo-testcross strategy. A F1 mapping population of 94 individuals was generated between a late-maturing, non-spiny type and an early-maturing spiny type. The 30 AFLP, 13 M-AFLP and 9 S-SAP primer combinations chosen identified, respectively, 352, 38 and 41 polymorphic markers. Of 32 microsatellite primer pairs tested, 12 identified heterozygous loci in one or other parent, and 7 were fully informative as they segregated in both parents. The female parent map comprised 204 loci, spread over 18 linkage groups and spanned 1330.5 cM with a mean marker density of 6.5 cM. The equivalent figures for the male parent map were 180 loci, 17 linkage groups, 1239.4 and 6.9 cM. About 3% of the AFLP and AFLP-derived markers displayed segregation distortion with a P value below 0.01, and were not used for map construction. All the SSR loci were included in the linkage analysis, although one locus did show some segregation distortion. The presence of 78 markers in common to both maps allowed the alignment of 16 linkage groups. The maps generated provide a firm basis for the mapping of agriculturally relevant traits, which will then open the way for the application of a marker-assisted selection breeding strategy in this species.
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Affiliation(s)
- S Lanteri
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Turin, via L. da Vinci 44, 10095 Grugliasco (Turin), Italy
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Hagenblad J, Bechsgaard J, Charlesworth D. Linkage disequilibrium between incompatibility locus region genes in the plant Arabidopsis lyrata. Genetics 2006; 173:1057-73. [PMID: 16582433 PMCID: PMC1526524 DOI: 10.1534/genetics.106.055780] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied diversity in Arabidopsis lyrata of sequences orthologous to the ARK3 gene of A. thaliana. Our main goal was to test for recombination in the S-locus region. In A. thaliana, the single-copy ARK3 gene is closely linked to the non-functional copies of the self-incompatibility loci, and the ortholog in A. lyrata (a self-incompatible species) is in the homologous genome region and is known as Aly8. It is thus of interest to test whether Aly8 sequence diversity is elevated due to close linkage to the highly polymorphic incompatibility locus, as is theoretically predicted. However, Aly8 is not a single-copy gene, and the presence of paralogs could also lead to the appearance of elevated diversity. We established a typing approach based on different lengths of Aly8 PCR products and show that most A. lyrata haplotypes have a single copy, but some have two gene copies, both closely linked to the incompatibility locus, one being a pseudogene. We determined the phase of multiple haplotypes in families of plants from Icelandic and other populations. Different Aly8 sequence types are associated with different SRK alleles, while haplotypes with the same SRK sequences tend to have the same Aly8 sequence. There is evidence of some exchange of sequences between different Aly8 sequences, making it difficult to determine which ones are allelic or to estimate the diversity. However, the homogeneity of the Aly8 sequences of each S-haplotype suggests that recombination between the loci has been very infrequent over the evolutionary history of these populations. Overall, the results suggest that recombination rarely occurs in the interval between the S-loci and Aly8 and that linkage to the S-loci can probably account for the observed high Aly8 diversity.
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Affiliation(s)
- Jenny Hagenblad
- Institute of Evolutionary Biology, University of Edinburgh, UK
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36
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van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JNAMR, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ. Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 2006; 173:1075-87. [PMID: 16582432 PMCID: PMC1526527 DOI: 10.1534/genetics.106.055871] [Citation(s) in RCA: 205] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).
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Affiliation(s)
- Hans van Os
- Laboratory of Plant Breeding, Wageningen University, The Netherlands
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37
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Bradshaw JE, Bryan GJ, Lees AK, McLean K, Solomon-Blackburn RM. Mapping the R10 and R11 genes for resistance to late blight (Phytophthora infestans) present in the potato (Solanum tuberosum) R-gene differentials of black. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:744-51. [PMID: 16395567 DOI: 10.1007/s00122-005-0179-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 11/30/2005] [Indexed: 05/06/2023]
Abstract
The R10 and R11 late blight differentials of Black (tetraploid clones 3681ad1 and 5008ab6) were crossed with the susceptible potato (Solanum tuberosum) cultivar Maris Piper and the progeny were assessed for blight resistance in a whole plant glasshouse test using race 1,2,3,4,6,7 of Phytophthora infestans. The disease scores for the R10 population displayed a continuous distribution whereas the progeny in the R11 population could be categorised as resistant or susceptible. A bulk segregant analysis using amplified fragment length polymorphism assays was done on the ten most resistant and ten most susceptible progeny in each population and two closely linked markers were found to be associated with resistance. R11 mapped to 8.5 cM from marker PAG/MAAG_172.3 and R10 mapped as a quantitative trait locus in which marker PAC/MATC_264.1 explained 56.9% of the variation in disease scores. The results were consistent with R10 and R11 being allelic versions of genes at the R3 locus on chromosome 11. The implications are discussed for mapping R-genes which fail to give complete immunity to a pathogen.
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Affiliation(s)
- John E Bradshaw
- Scottish Crop Research Institute, Invergowrie, DD2 5DA, Dundee, UK.
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38
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Luo ZW, Zhang Z, Leach L, Zhang RM, Bradshaw JE, Kearsey MJ. Constructing genetic linkage maps under a tetrasomic model. Genetics 2006; 172:2635-45. [PMID: 16415363 PMCID: PMC1456397 DOI: 10.1534/genetics.105.052449] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.
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Affiliation(s)
- Z W Luo
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom.
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39
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Brugmans B, Hutten RGB, Rookmaker ANO, Visser RGF, van Eck HJ. Exploitation of a marker dense linkage map of potato for positional cloning of a wart disease resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:269-77. [PMID: 16261329 DOI: 10.1007/s00122-005-0125-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 10/20/2004] [Indexed: 05/05/2023]
Abstract
A marker-saturated linkage map of potato was used to genetically map a locus involved in the resistance against wart disease Synchytrium endobioticum race 1. The locus mapped on the long arm of chromosome 4 and is named Sen1-4 in contrast to a Sen1 locus on chromosome 11. The AFLP markers from the Sen1-4 interval enabled the isolation of BAC clones from an 11 genome equivalent BAC library. This was achieved via fingerprinting of BAC pools with the AFLP primer pairs that resemble the genetic marker loci. With non-selective AFLP primers, fingerprints of individual BAC clones were generated to analyse the overlap between BAC clones using FPC. This resulted in a complete contig and a minimal tiling path of 14 BAC clones enclosing the Sen1-4 locus. The BAC contig has a genetic length of approximately 6 cM and a physical length of approximately 1 Mb. Our results demonstrate that map-based cloning of Sen1-4 can be pursued on the basis of a strategy of marker saturation alone. Genetic resolution achieved by screening large numbers of offspring for recombination events may not be required. Together with the construction of the BAC contig, a physical map with the position of the markers is accomplished in one step. This provides proof of concept for the utility of the marker saturation that is offered by the ultra dense AFLP map of potato for gene cloning.
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Affiliation(s)
- Bart Brugmans
- Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
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40
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Van Os H, Stam P, Visser RGF, Van Eck HJ. RECORD: a novel method for ordering loci on a genetic linkage map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 112:30-40. [PMID: 16228189 DOI: 10.1007/s00122-005-0097-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 08/20/2005] [Indexed: 05/04/2023]
Abstract
A new method, REcombination Counting and ORDering (RECORD) is presented for the ordering of loci on genetic linkage maps. The method minimizes the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local reshuffling. Since the criterion we propose does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. A simulation study was performed to compare the performance of RECORD and JoinMap. RECORD is much faster and less sensitive to missing observations and scoring errors, since the optimisation criterion is less dependent on the position of the erroneous markers. In particular, RECORD performs better in regions of the map with high marker density. The implications of high marker densities on linkage map construction are discussed.
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Affiliation(s)
- Hans Van Os
- Laboratory of Plant Breeding, Wageningen University, 386, 6700 AJ Wageningen, The Netherlands
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41
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Van Os H, Stam P, Visser RGF, Van Eck HJ. RECORD: a novel method for ordering loci on a genetic linkage map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 112:30-40. [PMID: 16228189 DOI: 10.1007/s00122-005-0152-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 08/20/2005] [Indexed: 05/24/2023]
Abstract
A new method, REcombination Counting and ORDering (RECORD) is presented for the ordering of loci on genetic linkage maps. The method minimizes the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local reshuffling. Since the criterion we propose does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. A simulation study was performed to compare the performance of RECORD and JoinMap. RECORD is much faster and less sensitive to missing observations and scoring errors, since the optimisation criterion is less dependent on the position of the erroneous markers. In particular, RECORD performs better in regions of the map with high marker density. The implications of high marker densities on linkage map construction are discussed.
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Affiliation(s)
- Hans Van Os
- Laboratory of Plant Breeding, Wageningen University, 386, 6700 AJ Wageningen, The Netherlands
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42
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van Os H, Stam P, Visser RGF, van Eck HJ. SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 112:187-94. [PMID: 16258753 DOI: 10.1007/s00122-005-0124-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 10/28/2004] [Indexed: 05/05/2023]
Abstract
High-density genetic linkage maps can be used for purposes such as fine-scale targeted gene cloning and anchoring of physical maps. However, their construction is significantly complicated by even relatively small amounts of scoring errors. Currently available software is not able to solve the ordering ambiguities in marker clusters, which inhibits the application of high-density maps. A statistical method named SMOOTH was developed to remove genotyping errors from genetic linkage data during the mapping process. The program SMOOTH calculates the difference between the observed and predicted values of data points based on data points of neighbouring loci in a given marker order. Highly improbable data points are removed by the program in an iterative process with a mapping algorithm that recalculates the map after cleaning. SMOOTH has been tested with simulated data and experimental mapping data from potato. The simulations prove that this method is able to detect a high amount of scoring errors and demonstrates that the program enables mapping software to successfully construct a very accurate high-density map. In potato the application of the program resulted in a reliable placement of nearly 1,000 markers in one linkage group.
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Affiliation(s)
- Hans van Os
- Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
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43
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Smith JJ, Kump DK, Walker JA, Parichy DM, Voss SR. A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. Genetics 2005; 171:1161-71. [PMID: 16079226 PMCID: PMC1456819 DOI: 10.1534/genetics.105.046433] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Accepted: 07/26/2005] [Indexed: 11/18/2022] Open
Abstract
Expressed sequence tag (EST) markers were developed for Ambystoma tigrinum tigrinum (Eastern tiger salamander) and for A. mexicanum (Mexican axolotl) to generate the first comprehensive linkage map for these model amphibians. We identified 14 large linkage groups (125.5-836.7 cM) that presumably correspond to the 14 haploid chromosomes in the Ambystoma genome. The extent of genome coverage for these linkage groups is apparently high because the total map size (5251 cM) falls within the range of theoretical estimates and is consistent with independent empirical estimates. Unlike most vertebrate species, linkage map size in Ambystoma is not strongly correlated with chromosome arm number. Presumably, the large physical genome size ( approximately 30 Gbp) is a major determinant of map size in Ambystoma. To demonstrate the utility of this resource, we mapped the position of two historically significant A. mexicanum mutants, white and melanoid, and also met, a quantitative trait locus (QTL) that contributes to variation in metamorphic timing. This new collection of EST-based PCR markers will better enable the Ambystoma system by facilitating development of new molecular probes, and the linkage map will allow comparative studies of this important vertebrate group.
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Affiliation(s)
- J J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA.
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44
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Caromel B, Mugniéry D, Kerlan MC, Andrzejewski S, Palloix A, Ellissèche D, Rousselle-Bourgeois F, Lefebvre V. Resistance quantitative trait loci originating from Solanum sparsipilum act independently on the sex ratio of Globodera pallida and together for developing a necrotic reaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:1186-94. [PMID: 16353553 DOI: 10.1094/mpmi-18-1186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant resistance to nematodes is related to the ability of the host to reduce the development of nematode juveniles into females. Resistance to the potato cyst nematode (PCN) Globodera pallida, originating from the wild species Solanum sparsipilum, was dissected by a quantitative trait loci (QTL) approach. Two QTL explained 89% of the phenotypic variation. The QTL GpaV(s)spl on chromosome V displayed the major effect on the cyst number (coefficient of determination [R2] = 76.6%). It restricted G. pallida development to 16.2% of juveniles, 81.5% of males, and 2.3% of females. The QTL GpaXI(s)spl on chromosome XI displayed a lower effect on the cyst number (R2 = 12.7%). It restricted G. pallida development to 13.8% of juveniles, 35.4% of males, and 50.8% of females. Clones carrying both QTL restricted the nematode development to 58.1% juveniles, 41.1% of males, and 0.8% of females. We demonstrated that potato clones carrying both QTL showed a strong necrotic reaction in roots infected by nematodes, while no such reaction was observed in clones carrying a single QTL. This result underlines the importance to introgress together GpaV(s)spl and GpaXI(s)spl into potato cultivars, in order to reduce the density of this quarantine pest in soil and to decrease the risk of selecting overcoming G. pallida subpopulations.
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Affiliation(s)
- Bernard Caromel
- Institut National de la Recherche Agronomique, UGAFL, Unité de Génétique et d'Amélioration des Fruits et Légumes, Domaine Saint Maurice, Montfavet, France.
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45
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Song YS, Hepting L, Schweizer G, Hartl L, Wenzel G, Schwarzfischer A. Mapping of extreme resistance to PVY (Ry (sto)) on chromosome XII using anther-culture-derived primary dihaploid potato lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:879-87. [PMID: 16044270 DOI: 10.1007/s00122-005-0010-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Accepted: 05/31/2005] [Indexed: 05/03/2023]
Abstract
The inheritance of extreme resistance to PVY (Ry (sto)) by a single dominant locus was confirmed by obtaining a 1:1 segregation ratio in a virus inoculation test with 28 resistant (Ryry) to 29 susceptible (ryry) anther culture-derived dihaploid lines (2n=2x=24) from cv. "Assia" (2n=4x=48) having extreme resistance derived from Solanum stoloniferum in simplex constitution (Ryryryry). Twelve Ry (sto) markers selected in AFLP assays using bulked segregant analysis were applied to 106 tested potato cultivars from Germany, The Netherlands and Poland and 19 potato cultivars were identified by these markers as extremely resistant to PVY in alignment with phenotypic data. The locus for extreme resistance (Ry (sto)) to PVY was mapped on chromosome XII co-segregating with the SSR marker STM 0003. The utility of anther-culture derived dihaploid potatoes for genetic marker development was demonstrated. Marker transferability from diploids to tetraploids provides an optimistic potential for marker-assisted selection in potato breeding programs.
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Affiliation(s)
- Ye-Su Song
- Bayerische Landesanstalt für Landwirtschaft, Institut für Pflanzenbau und Pflanzenzüchtung, Am Gereuth 8, 85354 Freising, Germany
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46
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Huang S, van der Vossen EAG, Kuang H, Vleeshouwers VGAA, Zhang N, Borm TJA, van Eck HJ, Baker B, Jacobsen E, Visser RGF. Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:251-61. [PMID: 15807786 DOI: 10.1111/j.1365-313x.2005.02365.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Comparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race-specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co-evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown.
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Affiliation(s)
- Sanwen Huang
- Laboratory of Plant Breeding, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
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47
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Bradshaw JE, Pande B, Bryan GJ, Hackett CA, McLean K, Stewart HE, Waugh R. Interval mapping of quantitative trait loci for resistance to late blight [Phytophthora infestans (Mont.) de Bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). Genetics 2005; 168:983-95. [PMID: 15514069 PMCID: PMC1448831 DOI: 10.1534/genetics.104.030056] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interval mapping of quantitative trait loci (QTL) for resistance to late blight, height, and maturity was performed on a tetraploid full-sib family of potato comprising 227 clones from a cross between a susceptible parent, 12601ab1, and a resistant cultivar, Stirling, which were of similar height and main crop maturity. Thirty-eight AFLP primer combinations provided 585 informative markers, and 23 SSRs proved useful for identifying linkage groups (LGs). A simplex QTL allele was found on LGV of Stirling close to marker STM3179, which was associated with early maturity, short plants, and susceptibility to blight and explained 54.7, 26.5, 26.3, and 17.5% of the variation for maturity, height, tuber blight, and foliage blight. When the residuals from the regressions of foliage and tuber blight on maturity were analyzed, there was no significant effect of a QTL on LGV, but a duplex QTL allele for resistance was found on LGIV of Stirling, which explained 30.7 and 13.6% of the variation for foliage and tuber blight on an additive model. Partial dominance for resistance explained even more of the variation, up to 37.2% for foliage blight. A major gene for blight resistance in Stirling was also mapped to LGXI.
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Affiliation(s)
- John E Bradshaw
- Genome Dynamics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom.
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48
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Visker MHPW, Heilersig HJB, Kodde LP, Van de Weg WE, Voorrips RE, Struik PC, Colon LT. Genetic linkage of QTLs for late blight resistance and foliage maturity type in six related potato progenies. EUPHYTICA 2005. [PMID: 0 DOI: 10.1007/s10681-005-3444-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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49
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Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A. Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci U S A 2004; 101:9915-20. [PMID: 15192146 PMCID: PMC470773 DOI: 10.1073/pnas.0401076101] [Citation(s) in RCA: 286] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2004] [Indexed: 11/18/2022] Open
Abstract
Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised approximately 385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics.
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Affiliation(s)
- Peter Wenzl
- Center for the Application of Molecular Biology to International Agriculture, G.P.O. Box 3200, Canberra, ACT 2601, Australia
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