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Saade S, Kutlu B, Draba V, Förster K, Schumann E, Tester M, Pillen K, Maurer A. A donor-specific QTL, exhibiting allelic variation for leaf sheath hairiness in a nested association mapping population, is located on barley chromosome 4H. PLoS One 2017; 12:e0189446. [PMID: 29216333 PMCID: PMC5720540 DOI: 10.1371/journal.pone.0189446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/25/2017] [Indexed: 12/02/2022] Open
Abstract
Leaf sheath hairiness is a morphological trait associated with various advantages, including tolerance to both abiotic and biotic stresses, thereby increasing yield. Understanding the genetic basis of this trait in barley can therefore improve the agronomic performance of this economically important crop. We scored leaf sheath hairiness in a two-year field trial in 1,420 BC1S3 lines from the wild barley nested association mapping (NAM) population HEB-25. Leaf sheath hairiness segregated in six out of 25 families with the reference parent Barke being glabrous. We detected the major hairy leaf sheath locus Hs (syn. Hsh) on chromosome 4H (111.3 cM) with high precision. The effects of the locus varied across the six different wild barley donors, with donor of HEB family 11 conferring the highest score of leaf sheath hairiness. Due to the high mapping resolution present in HEB-25, we were able to discuss physically linked pentatricopeptide repeat genes and subtilisin-like proteases as potential candidate genes underlying this locus. In this study, we proved that HEB-25 provides an appropriate tool to further understand the genetic control of leaf sheath hairiness in barley. Furthermore, our work represents a perfect starting position to clone the gene responsible for the 4H locus observed.
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Affiliation(s)
- Stephanie Saade
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
| | - Burcu Kutlu
- Ege University, Department of Biotechnology, Erzene, Bornova/İzmir, Turkey
| | - Vera Draba
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Karin Förster
- Institute of Agricultural and Nutritional Sciences, Department of Agronomy and Organic Farming, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Erika Schumann
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Department of Plant Breeding, Martin Luther University Halle-Wittenberg, Halle, Germany
- * E-mail:
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Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics 2017. [PMID: 29188438 DOI: 10.1007/s00438‐017‐1401‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.
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Affiliation(s)
- Youngjun Mo
- Department of Plant Sciences, University of California, Davis, CA, USA
- National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Luis Alejandro de Haro
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics 2017; 293:463-477. [PMID: 29188438 PMCID: PMC5854723 DOI: 10.1007/s00438-017-1401-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/23/2017] [Indexed: 11/23/2022]
Abstract
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.
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Affiliation(s)
- Youngjun Mo
- Department of Plant Sciences, University of California, Davis, CA, USA.,National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Luis Alejandro de Haro
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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Petit J, Bres C, Mauxion JP, Bakan B, Rothan C. Breeding for cuticle-associated traits in crop species: traits, targets, and strategies. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5369-5387. [PMID: 29036305 DOI: 10.1093/jxb/erx341] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/14/2017] [Indexed: 05/18/2023]
Abstract
Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement. To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits. Less information is available for staple crops such as rice, wheat or maize. Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species. Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties.
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Affiliation(s)
- Johann Petit
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| | - Cécile Bres
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| | | | | | - Christophe Rothan
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
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Wang Q, Pi J, Pan A, Shen J, Qu L. A novel sex-linked mutant affecting tail formation in Hongshan chicken. Sci Rep 2017; 7:10079. [PMID: 28855651 PMCID: PMC5577132 DOI: 10.1038/s41598-017-10943-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/16/2017] [Indexed: 01/11/2023] Open
Abstract
The Hongshan chicken is a Chinese indigenous breed that has two distinctly different tail types. Some chickens have stunted tails as compared to the normal phenotype, and they are termed rumpless. Rumplessness in other chicken breeds was caused by a reduction in the number of coccygeal vertebrae. However, X-ray examination showed that rumpless Hongshan chickens possess the normal number of coccygeal vertebrae. Our analyses of the main tail feathers and tissue sections led us to speculate that their stunted tail appearance may be the result of abnormal feather development. To investigate the genetic mechanism underlying rumplessness in Hongshan chickens, we analyzed the results of various crosses. The results indicated that rumplessness is a Z-linked dominant character. In addition, we chose some normal and rumpless individuals for pool-sequencing. Nucleotide diversity and Fst were calculated, and a selective sweep was detected on the Z chromosome. These analyses allowed us to reduce the search area to 71.8–72 Mb on the Z chromosome (galGal5.0). A pseudogene LOC431648 located in this region appeared a strong candidate involving in Wnt/β-catenin signaling pathway to regulate feather development in chickens.
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Affiliation(s)
- Qiong Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryonic Engineering and Molecular Breeding, Wuhan, Hubei Province, China
| | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryonic Engineering and Molecular Breeding, Wuhan, Hubei Province, China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryonic Engineering and Molecular Breeding, Wuhan, Hubei Province, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Besnard F, Koutsovoulos G, Dieudonné S, Blaxter M, Félix MA. Toward Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius tipulae To Identify Mutations Affecting Vulva Development. Genetics 2017; 206:1747-1761. [PMID: 28630114 PMCID: PMC5560785 DOI: 10.1534/genetics.117.203521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/15/2017] [Indexed: 12/30/2022] Open
Abstract
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in nonmodel species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development. The cov-3 locus encodes the O. tipulae ortholog of C. elegans mig-13, and we further show that Cel-mig-13 mutants also have an unsuspected vulval-development phenotype. In a virtuous circle, we were able to use the linkage information collected during mutant mapping to improve the genome assembly. These results showcase the promise of genome-enabled forward genetics in nonmodel species.
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Affiliation(s)
- Fabrice Besnard
- École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Paris Sciences et Lettres Research University, 75005, France
| | | | - Sana Dieudonné
- École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Paris Sciences et Lettres Research University, 75005, France
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, EH8 9YL, United Kingdom
| | - Marie-Anne Félix
- École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Paris Sciences et Lettres Research University, 75005, France
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57
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Barley Developmental Mutants: The High Road to Understand the Cereal Spike Morphology. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9020021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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58
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Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön CC, Scholz U. Towards a whole-genome sequence for rye (Secale cereale L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:853-869. [PMID: 27888547 DOI: 10.1111/tpj.13436] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Affiliation(s)
- Eva Bauer
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Ivan Barilar
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mihaela M Martis
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Bernd Hackauf
- Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Peer Wilde
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Karl Schmid
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
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Hisano H, Sakamoto K, Takagi H, Terauchi R, Sato K. Exome QTL-seq maps monogenic locus and QTLs in barley. BMC Genomics 2017; 18:125. [PMID: 28148242 PMCID: PMC5288901 DOI: 10.1186/s12864-017-3511-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/20/2017] [Indexed: 12/21/2022] Open
Abstract
Background QTL-seq, in combination with bulked segregant analysis and next-generation sequencing (NGS), is used to identify loci in small plant genomes, but is technically challenging to perform in species with large genomes, such as barley. A combination of exome sequencing and QTL-seq (exome QTL-seq) was used to map the mono-factorial Mendelian locus black lemma and pericarp (Blp) and QTLs for resistance to net blotch disease, a common disease of barley caused by the fungus Pyrenophora teres, which segregated in a population of 100 doubled haploid barley lines. Methods The provisional exome sequences were prepared by ordering the loci of expressed genes based on the genome information and concatenating genes with intervals of 200-bp spacer "N" for each chromosome. The QTL-seq pipeline was used to analyze short reads from the exome-captured library. Results In this study, short NGS reads of bulked total DNA samples from segregants with extreme trait values were subjected to exome capture, and the resulting exome sequences were aligned to the reference genome. SNP allele frequencies were compared to identify the locations of genes/QTLs responsible for the trait value differences between lines. For both objective traits examined, exome QTL-seq identified the monogenic Mendelian locus and associated QTLs. These findings were validated using conventional mapping approaches. Conclusions Exome QTL-seq broadens the utility of NGS-based gene/QTL mapping in organisms with large genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3511-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Kazuki Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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Kaur P, Gaikwad K. From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:2164. [PMID: 29312405 PMCID: PMC5742236 DOI: 10.3389/fpls.2017.02164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Exome sequencing represents targeted capture and sequencing of 1-2% of 'high-value genomic regions' (subset of the genome) which are enriched for functional variants and harbors low level of repetitive regions. We discuss here an overview of exome sequencing, ways to approach plant exomes, and advantages and applicability of this powerful approach in deciphering functional regions of genomes. Though initially this approach was developed as an alternative to whole genome sequencing (WGS), but the multitude of benefits conferred by sequence capture via hybridization approaches created a niche for itself to solve many of biological riddles, particularly for resolving phylogenetic distances. The technique has also proved to be successful in understanding the basis of natural and induced molecular variation, marker development and developing genomic resources for complex, wild and non-model species, which are still intractable for WGS efforts. Thus, with profound applications of this powerful sequencing strategy, near future is expected to witness a collective expansion of both techniques, i.e., sequence capture via hybridization for evolutionary and ecological research and WGS approaches for its universal accessibility.
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Li Z, Jiang L, Ma Y, Wei Z, Hong H, Liu Z, Lei J, Liu Y, Guan R, Guo Y, Jin L, Zhang L, Li Y, Ren Y, He W, Liu M, Htwe NMPS, Liu L, Guo B, Song J, Tan B, Liu G, Li M, Zhang X, Liu B, Shi X, Han S, Hua S, Zhou F, Yu L, Li Y, Wang S, Wang J, Chang R, Qiu L. Development and utilization of a new chemically-induced soybean library with a high mutation density . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:60-74. [PMID: 27774740 PMCID: PMC5248594 DOI: 10.1111/jipb.12505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/20/2016] [Indexed: 05/20/2023]
Abstract
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene (ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.
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Song J, Li Z, Liu Z, Guo Y, Qiu LJ. Next-Generation Sequencing from Bulked-Segregant Analysis Accelerates the Simultaneous Identification of Two Qualitative Genes in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:919. [PMID: 28620406 PMCID: PMC5449466 DOI: 10.3389/fpls.2017.00919] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/16/2017] [Indexed: 05/03/2023]
Abstract
Next-generation sequencing (NGS)-based bulked-segregant analysis (BSA) approaches have been proven successful for rapidly mapping genes in plant species. However, most such methods are based on mutants and usually only one gene controlling the mutant phenotype is identified. In this study, NGS-based BSA was employed to map simultaneously two qualitative genes controlling cotyledon color of seed in soybean. Yellow-cotyledon (YC) and green-cotyledon (GC) bulks from progenies of a biparental population (Zhonghuang 30 × Jiyu 102) were sequenced. The SNP-index of each SNP locus in YC and GC bulks was calculated and two genomic regions on chromosomes 1 and 11 harboring, respectively, loci qCC1 and qCC2 were identified by Δ(SNP-index) analysis. These two BSA-seq-derived loci were further validated with SSR markers and fine-mapped. qCC1 was mapped to a 30.7-kb region containing four annotated genes and qCC2 was mapped to a 67.7-kb region with nine genes. These two regions contained, respectively, genes D1 and D2, which had previously been identified by homology-based cloning as being associated with cotyledon color. Sequence analysis of the NGS data also identified a frameshift deletion in the coding region of D1. These results suggested that BSA-seq could accelerate the mapping of loci controlling qualitative traits, even if a trait is controlled by more than one locus.
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Affiliation(s)
| | | | | | - Yong Guo
- *Correspondence: Li-Juan Qiu, Yong Guo,
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Tränkner C, Lemnian IM, Emrani N, Pfeiffer N, Tiwari SP, Kopisch-Obuch FJ, Vogt SH, Müller AE, Schilhabel M, Jung C, Grosse I. A Detailed Analysis of the BR1 Locus Suggests a New Mechanism for Bolting after Winter in Sugar Beet ( Beta vulgaris L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1662. [PMID: 27895650 PMCID: PMC5107561 DOI: 10.3389/fpls.2016.01662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/21/2016] [Indexed: 05/29/2023]
Abstract
Sugar beet (Beta vulgaris ssp. vulgaris) is a biennial, sucrose-storing plant, which is mainly cultivated as a spring crop and harvested in the vegetative stage before winter. For increasing beet yield, over-winter cultivation would be advantageous. However, bolting is induced after winter and drastically reduces yield. Thus, post-winter bolting control is essential for winter beet cultivation. To identify genetic factors controlling bolting after winter, a F2 population was previously developed by crossing the sugar beet accessions BETA 1773 with reduced bolting tendency and 93161P with complete bolting after winter. For a mapping-by-sequencing analysis, pools of 26 bolting-resistant and 297 bolting F2 plants were used. Thereby, a single continuous homozygous region of 103 kb was co-localized to the previously published BR1 QTL for post-winter bolting resistance (Pfeiffer et al., 2014). The BR1 locus was narrowed down to 11 candidate genes from which a homolog of the Arabidopsis CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I (CPSF73-I) was identified as the most promising candidate. A 2 bp deletion within the BETA 1773 allele of BvCPSF73-Ia results in a truncated protein. However, the null allele of BvCPSF73-Ia might partially be compensated by a second BvCPSF73-Ib gene. This gene is located 954 bp upstream of BvCPSF73-Ia and could be responsible for the incomplete penetrance of the post-winter bolting resistance allele of BETA 1773. This result is an important milestone for breeding winter beets with complete bolting resistance after winter.
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Affiliation(s)
- Conny Tränkner
- Plant Breeding Institute, University of KielKiel, Germany
| | - Ioana M. Lemnian
- Institute of Computer Science, Martin Luther University Halle-WittenbergHalle, Germany
| | - Nazgol Emrani
- Plant Breeding Institute, University of KielKiel, Germany
| | - Nina Pfeiffer
- Plant Breeding Institute, University of KielKiel, Germany
| | | | | | | | | | - Markus Schilhabel
- Institute of Clinical Molecular Biology, University of KielKiel, Germany
| | - Christian Jung
- Plant Breeding Institute, University of KielKiel, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-WittenbergHalle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-JenaLeipzig, Germany
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Jia Q, Tan C, Wang J, Zhang XQ, Zhu J, Luo H, Yang J, Westcott S, Broughton S, Moody D, Li C. Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genomics 2016; 17:911. [PMID: 27835941 PMCID: PMC5106812 DOI: 10.1186/s12864-016-3247-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/02/2016] [Indexed: 12/04/2022] Open
Abstract
Background Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3247-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiaojun Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. .,Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou, 310018, China.
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hao Luo
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Sharon Westcott
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - Sue Broughton
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - David Moody
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
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Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH. Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 2016; 17:221. [PMID: 27795210 PMCID: PMC5087116 DOI: 10.1186/s13059-016-1082-1] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/10/2016] [Indexed: 11/18/2022] Open
Abstract
Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Simon G. Krattinger
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize. G3-GENES GENOMES GENETICS 2016; 6:2385-95. [PMID: 27261000 PMCID: PMC4978893 DOI: 10.1534/g3.116.030528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools.
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68
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Gardiner LJ, Bansept-Basler P, Olohan L, Joynson R, Brenchley R, Hall N, O'Sullivan DM, Hall A. Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:403-19. [PMID: 27144898 PMCID: PMC5026171 DOI: 10.1111/tpj.13204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 05/20/2023]
Abstract
Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | | | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Ryan Joynson
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Rachel Brenchley
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, PO Box 237, Whiteknights, Reading, RG6 6AR, UK
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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Jost M, Taketa S, Mascher M, Himmelbach A, Yuo T, Shahinnia F, Rutten T, Druka A, Schmutzer T, Steuernagel B, Beier S, Taudien S, Scholz U, Morgante M, Waugh R, Stein N. A Homolog of Blade-On-Petiole 1 and 2 (BOP1/2) Controls Internode Length and Homeotic Changes of the Barley Inflorescence. PLANT PHYSIOLOGY 2016; 171:1113-27. [PMID: 27208226 PMCID: PMC4902598 DOI: 10.1104/pp.16.00124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/08/2016] [Indexed: 05/17/2023]
Abstract
Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected.
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Affiliation(s)
- Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Shin Taketa
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Takahisa Yuo
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Fahimeh Shahinnia
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Arnis Druka
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Stefan Taudien
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Michele Morgante
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Robbie Waugh
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Stadt Seeland, Germany (M.J., Ma.M., A.H., F.S., T.R., T.S., B.S., S.B., U.S., N.S.);Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan (Sh.T., T.Y.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.);Leibniz Institute on Aging and Fritz-Lipmann Institute, 07745 Jena, Germany (St.T.);Applied Genomics Institute, University of Udine, 33100 Udine, Italy (Mi.M.); andDivision of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom (R.W.)
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Jöst M, Hensel G, Kappel C, Druka A, Sicard A, Hohmann U, Beier S, Himmelbach A, Waugh R, Kumlehn J, Stein N, Lenhard M. The INDETERMINATE DOMAIN Protein BROAD LEAF1 Limits Barley Leaf Width by Restricting Lateral Proliferation. Curr Biol 2016; 26:903-9. [PMID: 26996502 DOI: 10.1016/j.cub.2016.01.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/15/2015] [Accepted: 01/20/2016] [Indexed: 12/21/2022]
Abstract
Variation in the size, shape, and positioning of leaves as the major photosynthetic organs strongly impacts crop yield, and optimizing these aspects is a central aim of cereal breeding [1, 2]. Leaf growth in grasses is driven by cell proliferation and cell expansion in a basal growth zone [3]. Although several factors influencing final leaf size and shape have been identified from rice and maize [4-14], what limits grass leaf growth in the longitudinal or transverse directions during leaf development remains poorly understood. To identify factors involved in this process, we characterized the barley mutant broad leaf1 (blf1). Mutants form wider but slightly shorter leaves due to changes in the numbers of longitudinal cell files and of cells along the leaf length. These differences arise during primordia outgrowth because of more cell divisions in the width direction increasing the number of cell files. Positional cloning, analysis of independent alleles, and transgenic complementation confirm that BLF1 encodes a presumed transcriptional regulator of the INDETERMINATE DOMAIN family. In contrast to loss-of-function mutants, moderate overexpression of BLF1 decreases leaf width below wild-type levels. A functional BLF1-vYFP fusion protein expressed from the endogenous promoter shows a dynamic expression pattern in the shoot apical meristem and young leaf primordia. Thus, we propose that the BLF1 gene regulates barley leaf size by restricting cell proliferation in the leaf-width direction. Given the agronomic importance of canopy traits in cereals, identifying functionally different BLF1 alleles promises to allow for the generation of optimized cereal ideotypes.
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Affiliation(s)
- Moritz Jöst
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Götz Hensel
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Arnis Druka
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Uwe Hohmann
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Sebastian Beier
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Jochen Kumlehn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Nils Stein
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Michael Lenhard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany.
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72
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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73
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Borrill P, Adamski N, Uauy C. Genomics as the key to unlocking the polyploid potential of wheat. THE NEW PHYTOLOGIST 2015; 208:1008-22. [PMID: 26108556 DOI: 10.1111/nph.13533] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
Polyploidy has played a central role in plant genome evolution and in the formation of new species such as tetraploid pasta wheat and hexaploid bread wheat. Until recently, the high sequence conservation between homoeologous genes, together with the large genome size of polyploid wheat, had hindered genomic analyses in this important crop species. In the past 5 yr, however, the advent of next-generation sequencing has radically changed the wheat genomics landscape. Here, we review a series of advances in genomic resources and tools for functional genomics that are shifting the paradigm of what is possible in wheat molecular genetics and breeding. We discuss how understanding the relationship between homoeologues can inform approaches to modulate the response of quantitative traits in polyploid wheat; we also argue that functional redundancy has 'locked up' a wide range of phenotypic variation in wheat. We explore how genomics provides key tools to inform targeted manipulation of multiple homoeologues, thereby allowing researchers and plant breeders to unlock the full polyploid potential of wheat.
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Affiliation(s)
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS. Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:587-96. [PMID: 26386250 DOI: 10.1111/tpj.13029] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/17/2015] [Accepted: 09/08/2015] [Indexed: 05/03/2023]
Abstract
Although approaches for performing genome-wide association studies (GWAS) are well developed, conventional GWAS requires high-density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP-GWAS (extreme-phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well-characterized kernel row number trait, which was selected to enable comparisons between the results of XP-GWAS and conventional GWAS. An exome-sequencing strategy was used to focus sequencing resources on genes and their flanking regions. A total of 0.94 million variants were identified and served as evaluation markers; comparisons among pools showed that 145 of these variants were statistically associated with the kernel row number phenotype. These trait-associated variants were significantly enriched in regions identified by conventional GWAS. XP-GWAS was able to resolve several linked QTL and detect trait-associated variants within a single gene under a QTL peak. XP-GWAS is expected to be particularly valuable for detecting genes or alleles responsible for quantitative variation in species for which extensive genotyping resources are not available, such as wild progenitors of crops, orphan crops, and other poorly characterized species such as those of ecological interest.
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Affiliation(s)
- Jinliang Yang
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Haiying Jiang
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Center for Plant Genomics, Iowa State University, Ames, IA, 50011, USA
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Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. BMC Genomics 2015; 16:838. [PMID: 26494145 PMCID: PMC4619012 DOI: 10.1186/s12864-015-2015-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/06/2015] [Indexed: 11/28/2022] Open
Abstract
Background Leaf color variations are common in plants. Herein we describe a natural mutant of barley cultivar Edamai No.6, whs18, whose leaf color showed stable and inheritable stage-green-revertible-albino under field condition. Methods Bulked Segregant Analysis (BSA) based on SSR assay and Specific Length Amplified Fragment Sequencing (SLAF-seq) was used to map the candidate gene for this trait. Results We found that leaf color of whs18 was green at seedling stage, while the seventh or eighth leaf began to show etiolation, and albino leaves emerged after a short period. The newly emerged leaves began to show stripe white before jointing stage, and normal green leaves emerged gradually. The duration of whs18 with abnormal leaf color lasted for about 3 months, which had some negative impacts on yield-related-traits. Further investigations showed that the variation was associated with changes in chlorophyII content and chloroplast development. Genetic analysis revealed that the trait was controlled by a single recessive nuclear gene, and was designed as HvSGRA in this study. Based on the F2 population derived from Edamai No.9706 and whs18, we initially mapped the HvSGRA gene on the short arm of chromosome 2H using SSR and BSA. GBMS247 on 2HS showed co-segregation with HvSGRA. The genetic distance between the other marker GBM1187 and HvSGRA was 1.2 cM. Further analysis using BSA with SLAF-seq also identified this region as candidate region. Finally, HvSGRA interval was narrowed to 0.4 cM between morex_contig_160447 and morex_contig_92239, which were anchored to two adjacent FP contigs, contig_34437 and contig_46434, respectively. Furthermore, six putative genes with high-confidence in this interval were identified by POPSEQ. Further analysis showed that the substitution from C to A in the third exon of fructokinase-1-like gene generated a premature stop codon in whs18, which may lead to loss function of this gene. Conclusions Using SSR and SLAF-seq in conjunction with BSA, we mapped HvSGRA within two adjacent FP contigs of barley. The mutation of fructokinase-1-like gene in whs18 may cause the stage green-revertible albino of barley. The current study lays foundation for hierarchical map-based cloning of HvSGRA and utilizing the gene/trait as a visualized maker in molecular breeding in future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2015-1) contains supplementary material, which is available to authorized users.
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76
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Suzuki M, Sato Y, Wu S, Kang BH, McCarty DR. Conserved Functions of the MATE Transporter BIG EMBRYO1 in Regulation of Lateral Organ Size and Initiation Rate. THE PLANT CELL 2015; 27:2288-300. [PMID: 26276834 PMCID: PMC4568504 DOI: 10.1105/tpc.15.00290] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/06/2015] [Accepted: 07/23/2015] [Indexed: 05/18/2023]
Abstract
Genetic networks that determine rates of organ initiation and organ size are key regulators of plant architecture. Whereas several genes that influence the timing of lateral organ initiation have been identified, the regulatory pathways in which these genes operate are poorly understood. Here, we identify a class of genes implicated in regulation of the lateral organ initiation rate. Loss-of-function mutations in the MATE transporter encoded by maize (Zea mays) Big embryo 1 (Bige1) cause accelerated leaf and root initiation as well as enlargement of the embryo scutellum. BIGE1 is localized to trans-Golgi, indicating a possible role in secretion of a signaling molecule. Interestingly, phenotypes of bige1 bear striking similarity to cyp78a mutants identified in diverse plant species. We show that a CYP78A gene is upregulated in bige1 mutant embryos, suggesting a role for BIGE1 in feedback regulation of a CYP78A pathway. We demonstrate that accelerated leaf formation and early flowering phenotypes conditioned by mutants of Arabidopsis thaliana BIGE1 orthologs are complemented by maize Bige1, showing that the BIGE1 transporter has a conserved function in regulation of lateral organ initiation in plants. We propose that BIGE1 is required for transport of an intermediate or product associated with the CYP78A pathway.
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Affiliation(s)
- Masaharu Suzuki
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Yutaka Sato
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shan Wu
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Byung-Ho Kang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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78
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Ramirez-Gonzalez RH, Segovia V, Bird N, Fenwick P, Holdgate S, Berry S, Jack P, Caccamo M, Uauy C. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:613-24. [PMID: 25382230 DOI: 10.1111/pbi.12281] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 05/19/2023]
Abstract
The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq) of bulked pools to identify single-nucleotide polymorphisms (SNP) associated with Yr15. Over 27 000 genes with SNPs were identified between the parents, and then classified based on the results from the sequenced bulks. We calculated the bulk frequency ratio (BFR) of SNPs between resistant and susceptible bulks, selecting those showing sixfold enrichment/depletion in the corresponding bulks (BFR > 6). Using additional filtering criteria, we reduced the number of genes with a putative SNP to 175. The 35 SNPs with the highest BFR values were converted into genome-specific KASP assays using an automated bioinformatics pipeline (PolyMarker) which circumvents the limitations associated with the polyploid wheat genome. Twenty-eight assays were polymorphic of which 22 (63%) mapped in the same linkage group as Yr15. Using these markers, we mapped Yr15 to a 0.77-cM interval. The three most closely linked SNPs were tested across varieties and breeding lines representing UK elite germplasm. Two flanking markers were diagnostic in over 99% of lines tested, thus providing a reliable haplotype for marker-assisted selection in these breeding programmes. Our results demonstrate that the proposed methodology can be applied in polyploid F2 populations to generate high-resolution genetic maps across target intervals.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Cristobal Uauy
- John Innes Centre, Norwich, UK
- National Institute of Agricultural Botany, Cambridge, UK
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Tavakol E, Okagaki R, Verderio G, Shariati J V, Hussien A, Bilgic H, Scanlon MJ, Todt NR, Close TJ, Druka A, Waugh R, Steuernagel B, Ariyadasa R, Himmelbach A, Stein N, Muehlbauer GJ, Rossini L. The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. PLANT PHYSIOLOGY 2015; 168:164-74. [PMID: 25818702 PMCID: PMC4424007 DOI: 10.1104/pp.114.252882] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Tillers are vegetative branches that develop from axillary buds located in the leaf axils at the base of many grasses. Genetic manipulation of tillering is a major objective in breeding for improved cereal yields and competition with weeds. Despite this, very little is known about the molecular genetic bases of tiller development in important Triticeae crops such as barley (Hordeum vulgare) and wheat (Triticum aestivum). Recessive mutations at the barley Uniculme4 (Cul4) locus cause reduced tillering, deregulation of the number of axillary buds in an axil, and alterations in leaf proximal-distal patterning. We isolated the Cul4 gene by positional cloning and showed that it encodes a BROAD-COMPLEX, TRAMTRACK, BRIC-À-BRAC-ankyrin protein closely related to Arabidopsis (Arabidopsis thaliana) BLADE-ON-PETIOLE1 (BOP1) and BOP2. Morphological, histological, and in situ RNA expression analyses indicate that Cul4 acts at axil and leaf boundary regions to control axillary bud differentiation as well as the development of the ligule, which separates the distal blade and proximal sheath of the leaf. As, to our knowledge, the first functionally characterized BOP gene in monocots, Cul4 suggests the partial conservation of BOP gene function between dicots and monocots, while phylogenetic analyses highlight distinct evolutionary patterns in the two lineages.
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Affiliation(s)
- Elahe Tavakol
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ron Okagaki
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Gabriele Verderio
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Vahid Shariati J
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ahmed Hussien
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Hatice Bilgic
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Mike J Scanlon
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Natalie R Todt
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Timothy J Close
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Arnis Druka
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Robbie Waugh
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Burkhard Steuernagel
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Ruvini Ariyadasa
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Axel Himmelbach
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Nils Stein
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Gary J Muehlbauer
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
| | - Laura Rossini
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, 20133 Milan, Italy (E.T., G.V., A.Hu., L.R.);Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran (E.T.);Department of Agronomy and Plant Genetics (R.O., H.B., G.J.M.) and Department of Plant Biology (G.J.M.), University of Minnesota, St. Paul, Minnesota 55108;Parco Tecnologico Padano, 26900 Lodi, Italy (V.S.J., L.R.);Department of Plant Biology, Cornell University, Ithaca, New York 14853 (M.J.S., N.R.T.);Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 (T.J.C.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., R.W.); andLeibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany (B.S., R.A., A.Hi., N.S.)
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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.
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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
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81
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Bohra A, Singh NP. Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement. Biotechnol Lett 2015; 37:1529-39. [PMID: 25851953 DOI: 10.1007/s10529-015-1836-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/02/2015] [Indexed: 01/28/2023]
Abstract
Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India,
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82
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Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 2015. [PMID: 25637298 DOI: 10.1186/s13059‐015‐0582‐8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
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Affiliation(s)
- Jarrod A Chapman
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Aydın Buluç
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Evangelos Georganas
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Adam Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
| | - Veronika Strnadova
- Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Sunish Sehgal
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. .,Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Leonid Oliker
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Katherine A Yelick
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Jesse A Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA.
| | - Gary J Muehlbauer
- Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
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83
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Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 2015; 16:26. [PMID: 25637298 PMCID: PMC4373400 DOI: 10.1186/s13059-015-0582-8] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/06/2015] [Indexed: 11/10/2022] Open
Abstract
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
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Affiliation(s)
- Jarrod A Chapman
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Aydın Buluç
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Evangelos Georganas
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Adam Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
| | - Veronika Strnadova
- Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Sunish Sehgal
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. .,Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Leonid Oliker
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Katherine A Yelick
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Jesse A Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA.
| | - Gary J Muehlbauer
- Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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85
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Induced Genetic Variation, TILLING and NGS-Based Cloning. BIOTECHNOLOGICAL APPROACHES TO BARLEY IMPROVEMENT 2014. [DOI: 10.1007/978-3-662-44406-1_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wulff BBH, Moscou MJ. Strategies for transferring resistance into wheat: from wide crosses to GM cassettes. FRONTIERS IN PLANT SCIENCE 2014; 5:692. [PMID: 25538723 PMCID: PMC4255625 DOI: 10.3389/fpls.2014.00692] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/20/2014] [Indexed: 05/19/2023]
Abstract
The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed the genetic base by introducing extreme levels of uniformity on a vast spatial and temporal scale. This reduction in genetic complexity renders the crop vulnerable to new and emerging pests and pathogens. The wild relatives of wheat represent an important source of genetic variation for disease resistance. For nearly a century farmers, breeders, and cytogeneticists have sought to access this variation for crop improvement. Several barriers restricting interspecies hybridization and introgression have been overcome, providing the opportunity to tap an extensive reservoir of genetic diversity. Resistance has been introgressed into wheat from at least 52 species from 13 genera, demonstrating the remarkable plasticity of the wheat genome and the importance of such natural variation in wheat breeding. Two main problems hinder the effective deployment of introgressed resistance genes for crop improvement: (1) the simultaneous introduction of genetically linked deleterious traits and (2) the rapid breakdown of resistance when deployed individually. In this review, we discuss how recent advances in molecular genomics are providing new opportunities to overcome these problems.
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Affiliation(s)
- Brande B. H. Wulff
- Department of Crop Genetics, John Innes Centre, Norwich, Norfolk, UK
- *Correspondence: Brande B. H. Wulff, Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK e-mail: ; Matthew J. Moscou, The Sainsbury Laboratory, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK e-mail:
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich, Norfolk, UK
- *Correspondence: Brande B. H. Wulff, Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK e-mail: ; Matthew J. Moscou, The Sainsbury Laboratory, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK e-mail:
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