51
|
Yang H, Jian J, Li X, Renshaw D, Clements J, Sweetingham MW, Tan C, Li C. Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius). BMC Genomics 2015; 16:660. [PMID: 26329386 PMCID: PMC4557927 DOI: 10.1186/s12864-015-1878-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/24/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. RESULTS Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. CONCLUSIONS We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.
Collapse
Affiliation(s)
- Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Jianbo Jian
- Beijing Genome Institute - Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Xuan Li
- Beijing Genome Institute - Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel Renshaw
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Jonathan Clements
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Mark W Sweetingham
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Cong Tan
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia.
| | - Chengdao Li
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia.
| |
Collapse
|
52
|
Zang W, Eckstein PE, Colin M, Voth D, Himmelbach A, Beier S, Stein N, Scoles GJ, Beattie AD. Fine mapping and identification of a candidate gene for the barley Un8 true loose smut resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1343-1357. [PMID: 25877520 DOI: 10.1007/s00122-015-2510-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 03/27/2015] [Indexed: 06/04/2023]
Abstract
The candidate gene for the barley Un8 true loose smut resistance gene encodes a deduced protein containing two tandem protein kinase domains. In North America, durable resistance against all known isolates of barley true loose smut, caused by the basidiomycete pathogen Ustilago nuda (Jens.) Rostr. (U. nuda), is under the control of the Un8 resistance gene. Previous genetic studies mapped Un8 to the long arm of chromosome 5 (1HL). Here, a population of 4625 lines segregating for Un8 was used to delimit the Un8 gene to a 0.108 cM interval on chromosome arm 1HL, and assign it to fingerprinted contig 546 of the barley physical map. The minimal tilling path was identified for the Un8 locus using two flanking markers and consisted of two overlapping bacterial artificial chromosomes. One gene located close to a marker co-segregating with Un8 showed high sequence identity to a disease resistance gene containing two kinase domains. Sequence of the candidate gene from the parents of the segregating population, and in an additional 19 barley lines representing a broader spectrum of diversity, showed there was no intron in alleles present in either resistant or susceptible lines, and fifteen amino acid variations unique to the deduced protein sequence in resistant lines differentiated it from the deduced protein sequences in susceptible lines. Some of these variations were present within putative functional domains which may cause a loss of function in the deduced protein sequences within susceptible lines.
Collapse
Affiliation(s)
- Wen Zang
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
53
|
Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M. BARLEX - the Barley Draft Genome Explorer. MOLECULAR PLANT 2015; 8:964-6. [PMID: 25804976 DOI: 10.1016/j.molp.2015.03.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/11/2015] [Accepted: 03/18/2015] [Indexed: 05/03/2023]
Affiliation(s)
- Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany.
| |
Collapse
|
54
|
Dawson IK, Russell J, Powell W, Steffenson B, Thomas WTB, Waugh R. Barley: a translational model for adaptation to climate change. THE NEW PHYTOLOGIST 2015; 206:913-931. [PMID: 25605349 DOI: 10.1111/nph.13266] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.
Collapse
Affiliation(s)
- Ian K Dawson
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Joanne Russell
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Wayne Powell
- CGIAR Consortium Office, Montpellier Cedex 5, France
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - William T B Thomas
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, College of Life Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
| |
Collapse
|
55
|
Ui H, Sameri M, Pourkheirandish M, Chang MC, Shimada H, Stein N, Komatsuda T, Handa H. High-resolution genetic mapping and physical map construction for the fertility restorer Rfm1 locus in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:283-90. [PMID: 25412992 DOI: 10.1007/s00122-014-2428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/08/2014] [Indexed: 05/11/2023]
Abstract
High-resolution genetic linkage mapping and BAC physical mapping narrowed the fertility restorer locus Rfm1 in barley to a sub-centimorgan genetic interval and a 208-kb physical interval. Rfm1 restores the fertility of msm1 and msm2 male-sterile cytoplasms in barley. The fertility restoration gene is located on the short arm of chromosome 6H (6HS), and we pursued a positional cloning of this gene. Starting from a previous result that has delimited Rfm1 within a 10.8 cM region on 6HS, we developed novel CAPS and SSR markers tightly linked to the gene in barley using the sequence information from the syntenic region of rice and barley genome assemblies. Next, we performed fine mapping of the Rfm1 locus. To isolate recombinants, we surveyed 3,638 F2 plants derived from a cross between the CMS strain and the Rf strain with adjacent markers (NAS2090 and NAS1080). This analysis identified 175 recombinant plants from the F2 population to build a high-resolution map with nine markers tightly linked to the Rfm1 locus. Rfm1 was located within the 0.14 cM region delimited by two markers (NAS9113 and NAS9200). Using these flanking markers as well as marker cosegregating with Rfm1 (NAS9133), we screened the BAC libraries of the cultivar Morex, an rfm1 carrier. We isolated 11 BAC clones and constructed a BAC physical map using their fingerprints. Finally, we delimited the Rfm1 locus encompassing the rfm1 allele on a 208-kb contig composed of three minimally overlapping BAC clones. This precise localization of the Rfm1 locus in the barley genome is expected to greatly accelerate the future map-based cloning of the Rfm1 gene by sequence analysis and its genetic transformation for the complementation of cytoplasmic male-sterile plants.
Collapse
Affiliation(s)
- Hajime Ui
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2, Kan-non-dai, Tsukuba, 305-8602, Japan
| | | | | | | | | | | | | | | |
Collapse
|
56
|
Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
Collapse
Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
57
|
Esch M, Chen J, Colmsee C, Klapperstück M, Grafahrend-Belau E, Scholz U, Lange M. LAILAPS: the plant science search engine. PLANT & CELL PHYSIOLOGY 2015; 56:e8. [PMID: 25480116 PMCID: PMC4301746 DOI: 10.1093/pcp/pcu185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing >13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS's functionality and capabilities by comparing this system's performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley.
Collapse
Affiliation(s)
- Maria Esch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Jinbo Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Matthias Klapperstück
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Eva Grafahrend-Belau
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, D-06466 Stadt Seeland, Germany
| |
Collapse
|
58
|
Gao F, Wen W, Liu J, Rasheed A, Yin G, Xia X, Wu X, He Z. Genome-Wide Linkage Mapping of QTL for Yield Components, Plant Height and Yield-Related Physiological Traits in the Chinese Wheat Cross Zhou 8425B/Chinese Spring. FRONTIERS IN PLANT SCIENCE 2015; 6:1099. [PMID: 26734019 PMCID: PMC4683206 DOI: 10.3389/fpls.2015.01099] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/22/2015] [Indexed: 05/18/2023]
Abstract
Identification of genes for yield components, plant height (PH), and yield-related physiological traits and tightly linked molecular markers is of great importance in marker-assisted selection (MAS) in wheat breeding. In the present study, 246 F8 RILs derived from the cross of Zhou 8425B/Chinese Spring were genotyped using the high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay. Field trials were conducted at Zhengzhou and Zhoukou of Henan Province, during the 2012-2013 and 2013-2014 cropping season under irrigated conditions, providing data for four environments. Analysis of variance (ANOVA) of agronomic and physiological traits revealed significant differences (P < 0.01) among RILs, environments, and RILs × environments interactions. Broad-sense heritabilities of all traits including thousand kernel weight (TKW), PH, spike length (SL), kernel number per spike (KNS), spike number/m(2) (SN), normalized difference in vegetation index at anthesis (NDVI-A) and at 10 days post-anthesis (NDVI-10), SPAD value of chlorophyll content at anthesis (Chl-A) and at 10 days post-anthesis (Chl-10) ranged between 0.65 and 0.94. A linkage map spanning 3609.4 cM was constructed using 5636 polymorphic SNP markers, with an average chromosome length of 171.9 cM and marker density of 0.64 cM/marker. A total of 866 SNP markers were newly mapped to the hexaploid wheat linkage map. Eighty-six QTL for yield components, PH, and yield-related physiological traits were detected on 18 chromosomes except 1D, 5D, and 6D, explaining 2.3-33.2% of the phenotypic variance. Ten stable QTL were identified across four environments, viz. QTKW.caas-6A.1, QTKW.caas-7AL, QKNS.caas-4AL, QSN.caas-1AL.1, QPH.caas-4BS.2, QPH.caas-4DS.1, QSL.caas-4AS, QSL.caas-4AL.1, QChl-A.caas-5AL, and QChl-10.caas-5BL. Meanwhile, 10 QTL-rich regions were found on chromosome 1BS, 2AL (2), 3AL, 4AL (2), 4BS, 4DS, 5BL, and 7AL exhibiting pleiotropic effects. These QTL or QTL clusters are tightly linked to SNP markers, with genetic distances to the closest SNPs ranging from 0 to 1.5 cM, and could serve as target regions for fine mapping, candidate gene discovery, and MAS in wheat breeding.
Collapse
Affiliation(s)
- Fengmei Gao
- Key Laboratory of Soybean Biology, Soybean Research Institute, Ministry of Education, Northeast Agricultural UniversityHarbin, China
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- Keshan Sub-Academy, Heilongjiang Academy of Agricultural SciencesKeshan, China
| | - Weie Wen
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Awais Rasheed
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o Chinese Academy of Agricultural SciencesBeijing, China
| | - Guihong Yin
- Zhoukou Academy of Agricultural SciencesZhoukou, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xiaoxia Wu
- Key Laboratory of Soybean Biology, Soybean Research Institute, Ministry of Education, Northeast Agricultural UniversityHarbin, China
- *Correspondence: Xiaoxia Wu
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o Chinese Academy of Agricultural SciencesBeijing, China
- Zhonghu He
| |
Collapse
|
59
|
Wei Q, Wang Y, Qin X, Zhang Y, Zhang Z, Wang J, Li J, Lou Q, Chen J. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing. BMC Genomics 2014; 15:1158. [PMID: 25534138 PMCID: PMC4367881 DOI: 10.1186/1471-2164-15-1158] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/11/2014] [Indexed: 11/29/2022] Open
Abstract
Background Cucumber, Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide. However, the narrow genetic base in cucumber makes it difficult for constructing high-density genetic maps. The development of massively parallel genotyping methods and next-generation sequencing (NGS) technologies provides an excellent opportunity for developing single nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of horticultural traits. Specific-length amplified fragment sequencing (SLAF-seq) is a recent marker development technology that allows large-scale SNP discovery and genotyping at a reasonable cost. In this study, we constructed a high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs. Results An F2 population of 148 individuals was developed from an intra-varietal cross between CC3 and NC76. Genomic DNAs extracted from two parents and 148 F2 individuals were subjected to high-throughput sequencing and SLAF library construction. A total of 10.76 Gb raw data and 75,024,043 pair-end reads were generated to develop 52,684 high-quality SLAFs, out of which 5,044 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 1,800 SNPs was constructed for cucumber spanning 890.79 cM. The average distance between adjacent markers was 0.50 cM. 183 scaffolds were anchored to the SNP-based genetic map covering 46% (168.9 Mb) of the cucumber genome (367 Mb). Nine QTLs for fruit length and weight were detected, a QTL designated fl3.2 explained 44.60% of the phenotypic variance. Alignment of the SNP markers to draft genome scaffolds revealed two mis-assembled scaffolds that were validated by fluorescence in situ hybridization (FISH). Conclusions We report herein the development of evenly dispersed SNPs across cucumber genome, and for the first time an SNP-based saturated linkage map. This 1,800-locus map would likely facilitate genetic mapping of complex QTL loci controlling fruit yield, and the orientation of draft genome scaffolds. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1158) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No,1, Nanjing 210095, China.
| | | |
Collapse
|
60
|
Nussbaumer T, Kugler KG, Schweiger W, Bader KC, Gundlach H, Spannagl M, Poursarebani N, Pfeifer M, Mayer KFX. chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes. BMC PLANT BIOLOGY 2014; 14:348. [PMID: 25491094 PMCID: PMC4266971 DOI: 10.1186/s12870-014-0348-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/24/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner. DESCRIPTION We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering. CONCLUSIONS This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.
Collapse
Affiliation(s)
- Thomas Nussbaumer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Karl G Kugler
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Wolfgang Schweiger
- />Institute for Biotechnology in Plant Production, IFA-Tulln, University of
Natural Resources and Life Sciences, A-3430 Tulln, Austria
| | - Kai C Bader
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Heidrun Gundlach
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Manuel Spannagl
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Naser Poursarebani
- />Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Matthias Pfeifer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Klaus FX Mayer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| |
Collapse
|
61
|
Wendler N, Mascher M, Nöh C, Himmelbach A, Scholz U, Ruge-Wehling B, Stein N. Unlocking the secondary gene-pool of barley with next-generation sequencing. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1122-31. [PMID: 25040223 DOI: 10.1111/pbi.12219] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 05/18/2023]
Abstract
Crop wild relatives (CWR) provide an important source of allelic diversity for any given crop plant species for counteracting the erosion of genetic diversity caused by domestication and elite breeding bottlenecks. Hordeum bulbosum L. is representing the secondary gene pool of the genus Hordeum. It has been used as a source of genetic introgressions for improving elite barley germplasm (Hordeum vulgare L.). However, genetic introgressions from H. bulbosum have yet not been broadly applied, due to a lack of suitable molecular tools for locating, characterizing, and decreasing by recombination and marker-assisted backcrossing the size of introgressed segments. We applied next-generation sequencing (NGS) based strategies for unlocking genetic diversity of three diploid introgression lines of cultivated barley containing chromosomal segments of its close relative H. bulbosum. Firstly, exome capture-based (re)-sequencing revealed large numbers of single nucleotide polymorphisms (SNPs) enabling the precise allocation of H. bulbosum introgressions. This SNP resource was further exploited by designing a custom multiplex SNP genotyping assay. Secondly, two-enzyme-based genotyping-by-sequencing (GBS) was employed to allocate the introgressed H. bulbosum segments and to genotype a mapping population. Both methods provided fast and reliable detection and mapping of the introgressed segments and enabled the identification of recombinant plants. Thus, the utilization of H. bulbosum as a resource of natural genetic diversity in barley crop improvement will be greatly facilitated by these tools in the future.
Collapse
Affiliation(s)
- Neele Wendler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | | | | | | | | |
Collapse
|
62
|
Mascher M, Stein N. Genetic anchoring of whole-genome shotgun assemblies. Front Genet 2014; 5:208. [PMID: 25071835 PMCID: PMC4083584 DOI: 10.3389/fgene.2014.00208] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
The recent advances in sequencing throughput and genome assembly algorithms have established whole-genome shotgun (WGS) assemblies as the cornerstone of the genomic infrastructure for many species. WGS assemblies can be constructed with comparative ease and give a comprehensive representation of the gene space even of large and complex genomes. One major obstacle in utilizing WGS assemblies for important research applications such as gene isolation or comparative genomics has been the lack of chromosomal positioning and contextualization of short sequence contigs. Assigning chromosomal locations to sequence contigs required the construction and integration of genome-wide physical maps and dense genetic linkage maps as well as synteny to model species. Recently, methods to rapidly construct ultra-dense linkage maps encompassing millions of genetic markers from WGS sequencing data of segregating populations have made possible the direct assignment of genetic positions to short sequence contigs. Here, we review recent developments in the integration of WGS assemblies and sequence-based linkage maps, discuss challenges for further improvement of the methodology and outline possible applications building on genetically anchored WGS assemblies.
Collapse
Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland Germany
| |
Collapse
|
63
|
Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014; 15:R78. [PMID: 24917130 PMCID: PMC4073093 DOI: 10.1186/gb-2014-15-6-r78] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/10/2014] [Indexed: 01/02/2023] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
Collapse
|
64
|
Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014. [PMID: 24917130 DOI: 10.1186/gb‐2014‐15‐6‐r78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
Collapse
|
65
|
Braumann I, Stein N, Hansson M. Reduced chlorophyll biosynthesis in heterozygous barley magnesium chelatase mutants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 78:10-4. [PMID: 24607574 DOI: 10.1016/j.plaphy.2014.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/05/2014] [Indexed: 05/20/2023]
Abstract
Chlorophyll biosynthesis is initiated by magnesium chelatase, an enzyme composed of three proteins, which catalyzes the insertion of Mg2+ into protoporphyrin IX to produce Mg-protoporphyrin IX. In barley (Hordeum vulgare L.) the three proteins are encoded by Xantha-f, Xantha-g and Xantha-h. Two of the gene products, XanH and XanG, belong to the structurally conserved family of AAA+ proteins (ATPases associated with various cellular activities) and form a complex involving six subunits of each protein. The complex functions as an ATP-fueled motor of the magnesium chelatase that uses XanF as substrate, which is the catalytic subunit responsible for the insertion of Mg2+ into protoporphyrin IX. Previous studies have shown that semi-dominant Xantha-h mutations result in non-functional XanH subunits that participate in the formation of inactive AAA complexes. In the present study, we identify severe mutations in the barley mutants xantha-h.38, -h.56 and -h.57. A truncated form of the protein is seen in xantha-h.38, whereas no XanH is detected in xantha-h.56 and -h.57. Heterozygous mutants show a reduction in chlorophyll content by 14-18% suggesting a slight semi-dominance of xantha-h.38, -h.56 and -h.57, which otherwise have been regarded as recessive mutations.
Collapse
Affiliation(s)
- Ilka Braumann
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT Gatersleben, Germany
| | - Mats Hansson
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark.
| |
Collapse
|