1
|
Sato K, Nakamura S, Fujita M. Regulation of Seed Dormancy Genes in Triticeae Species. Methods Mol Biol 2024; 2830:13-23. [PMID: 38977564 DOI: 10.1007/978-1-0716-3965-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Wild progenitors of Triticeae crops generally have long dormancy periods. Domesticated crops inherited these longer dormancy alleles from their wild progenitors, which have since been modified and selected during cultivation and utilization by humans. Thus, allelic combinations at different seed dormancy loci are currently represented in Triticeae germplasm preserved in seed repositories and gene banks as accessions and materials of breeding programs. Methods to evaluate seed dormancy are key to explore, analyze, and exploit optimal alleles in dormancy genes. Recent developments in genomics have accelerated the identification and analysis of seed dormancy loci in Triticeae species. Transgenic experiments have been conducted to validate if candidate genes affect seed dormancy and more recently have yielded an array of mutations derived from genome editing for practical applications. The information gathered on these seed dormancy loci provides a deeper knowledge of germplasm diversity and offers strategies to control seed dormancy in breeding programs in Triticeae crops.
Collapse
Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science & Resources, Okayama University, Kurashiki, Japan.
- Faculty of Agriculture, Setsunan University, Hirakata, Japan.
- Kazusa DNA Research Institute, Kisarazu, Japan.
| | | | | |
Collapse
|
2
|
Taketa S, Kim JS, Takahashi H, Yajima S, Koshiishi Y, Sotome T, Kato T, Mochida K. Genomic traces of Japanese malting barley breeding in two modern high-quality cultivars, 'Sukai Golden' and 'Sachiho Golden'. BREEDING SCIENCE 2023; 73:435-444. [PMID: 38737917 PMCID: PMC11082453 DOI: 10.1270/jsbbs.23031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/08/2023] [Indexed: 05/14/2024]
Abstract
Two modern high-quality Japanese malting barley cultivars, 'Sukai Golden' and 'Sachiho Golden', were subjected to RNA-sequencing of transcripts extracted from 20-day-old immature seeds. Despite their close relation, 2,419 Sukai Golden-specific and 3,058 Sachiho Golden-specific SNPs were detected in comparison to the genome sequences of two reference cultivars: 'Morex' and 'Haruna Nijo'. Two single nucleotide polymorphism (SNP) clusters respectively showing the incorporation of (1) the barley yellow mosaic virus (BaYMV) resistance gene rym5 from six-row non-malting Chinese landrace Mokusekko 3 on the long arm of 3H, and (2) the anthocyanin-less ant2 gene from a two-row Dutch cultivar on the long arm of 2H were detected specifically in 'Sukai Golden'. Using 221 recombinant inbred lines of a cross between 'Ishukushirazu' and 'Nishinochikara', another BaYMV resistance rym3 gene derived from six-row non-malting Japanese cultivar 'Haganemugi' was mapped to a 0.4-cM interval on the proximal region of 5H. Haplotype analysis of progenitor accessions of the two modern malting cultivars revealed that rym3 of 'Haganemugi' was independently introduced into 'Sukai Golden' and 'Sachiho Golden'. Residual chromosome 5H segments of 'Haganemugi' surrounding rym3 were larger in 'Sukai Golden'. Available results suggest possibilities for malting quality improvement by minimizing residual segments surrounding rym3.
Collapse
Affiliation(s)
- Shin Taketa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - June-Sik Kim
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hidekazu Takahashi
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima 960-1296, Japan
| | - Shunsuke Yajima
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yuichi Koshiishi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Toshinori Sotome
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
3
|
Akbari M, Sabouri H, Sajadi SJ, Yarahmadi S, Ahangar L, Abedi A, Katouzi M. Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses. Genes (Basel) 2022; 13:genes13112087. [PMID: 36360327 PMCID: PMC9690463 DOI: 10.3390/genes13112087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Abiotic stresses cause a significant decrease in productivity and growth in agricultural products, especially barley. Breeding has been considered to create resistance against abiotic stresses. Pyramiding genes for tolerance to abiotic stresses through selection based on molecular markers connected to Mega MQTLs of abiotic tolerance can be one of the ways to reach Golden Barley. In this study, 1162 original QTLs controlling 116 traits tolerant to abiotic stresses were gathered from previous research and mapped from various populations. A consensus genetic map was made, including AFLP, SSR, RFLP, RAPD, SAP, DArT, EST, CAPS, STS, RGA, IFLP, and SNP markers based on two genetic linkage maps and 26 individual linkage maps. Individual genetic maps were created by integrating individual QTL studies into the pre-consensus map. The consensus map covered a total length of 2124.43 cM with an average distance of 0.25 cM between markers. In this study, 585 QTLs and 191 effective genes related to tolerance to abiotic stresses were identified in MQTLs. The most overlapping QTLs related to tolerance to abiotic stresses were observed in MQTL6.3. Furthermore, three MegaMQTL were identified, which explained more than 30% of the phenotypic variation. MQTLs, candidate genes, and linked molecular markers identified are essential in barley breeding and breeding programs to develop produce cultivars resistant to abiotic stresses.
Collapse
Affiliation(s)
- Mahjoubeh Akbari
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
| | - Hossein Sabouri
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
- Correspondence: (H.S.); (M.K.); Tel.: +98-9111438917 (H.S.); +41-779660486 (M.K.)
| | - Sayed Javad Sajadi
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
| | - Saeed Yarahmadi
- Horticulture-Crops Reseaech Department, Golestan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Gorgan 4969186951, Iran
| | - Leila Ahangar
- Department of Plant Production, Collage of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad-e Kavus 4971799151, Iran
| | - Amin Abedi
- Department of Plant Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran
| | - Mahnaz Katouzi
- Crop Génome Dynamics Group, Agroscope Changins, 1260 Nyon, Switzerland
- Correspondence: (H.S.); (M.K.); Tel.: +98-9111438917 (H.S.); +41-779660486 (M.K.)
| |
Collapse
|
4
|
Rakkammal K, Priya A, Pandian S, Maharajan T, Rathinapriya P, Satish L, Ceasar SA, Sohn SI, Ramesh M. Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview. PLANTS (BASEL, SWITZERLAND) 2022; 11:2852. [PMID: 36365305 PMCID: PMC9655223 DOI: 10.3390/plants11212852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 05/22/2023]
Abstract
Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.
Collapse
Affiliation(s)
- Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Arumugam Priya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
| | - Theivanayagam Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin 683104, Kerala, India
| | - Periyasamy Rathinapriya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Lakkakula Satish
- Applied Phycology and Biotechnology Division, Marine Algal Research Station, Mandapam Camp, CSIR—Central Salt and Marine Chemicals Research Institute, Bhavnagar 623519, Tamil Nadu, India
| | | | - Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| |
Collapse
|
5
|
Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
Collapse
Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
6
|
Yoshikawa T, Hisano H, Hibara KI, Nie J, Tanaka Y, Itoh JI, Taketa S. A bifurcated palea mutant infers functional differentiation of WOX3 genes in flower and leaf morphogenesis of barley. AOB PLANTS 2022; 14:plac019. [PMID: 35669443 PMCID: PMC9162124 DOI: 10.1093/aobpla/plac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Barley (Hordeum vulgare) is the fourth most highly produced cereal in the world after wheat, rice and maize and is mainly utilized as malts and for animal feed. Barley, a model crop of the tribe Triticeae, is important in comparative analyses of Poaceae. However, molecular understanding about the developmental processes is limited in barley. Our previous work characterized one of two WUSCHEL-RELATED HOMEOBOX 3 (WOX3) genes present in the barley genome: NARROW LEAFED DWARF1 (NLD1). We demonstrated that NLD1 plays a pivotal role in the development of lateral organs. In the present study, we describe a bifurcated palea (bip) mutant of barley focusing on flower and leaf phenotypes. The palea in the bip mutant was split into two and develop towards inside the lemma surrounding the carpels and anthers. The bip mutant is devoid of lodicules, which develop in a pair at the base of the stamen within the lemma in normal barley. bip also exhibited malformations in leaves, such as narrow leaf due to underdeveloped leaf-blade width, and reduced trichome density. Map-based cloning and expression analysis indicated that BIP is identical to another barley WOX3 gene, named HvWOX3. The bip nld1 double mutant presented a more severe reduction in leaf-blade width and number of trichomes. By comparing the phenotypes and gene expression patterns of various WOX3 mutants, we concluded that leaf bilateral outgrowth and trichome development are promoted by both NLD1 and HvWOX3, but that HvWOX3 serves unique and pivotal functions in barley development that differ from those of NLD1.
Collapse
Affiliation(s)
- Takanori Yoshikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo 656-0484, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Ken-Ichiro Hibara
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo 656-0484, Japan
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Jilu Nie
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yuki Tanaka
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo 656-0484, Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Shin Taketa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| |
Collapse
|
7
|
Sakkour A, Mascher M, Himmelbach A, Haberer G, Lux T, Spannagl M, Stein N, Kawamoto S, Sato K. Chromosome-scale assembly of barley cv. 'Haruna Nijo' as a resource for barley genetics. DNA Res 2022; 29:dsac001. [PMID: 35022669 PMCID: PMC8798153 DOI: 10.1093/dnares/dsac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Cultivated barley (Hordeum vulgare ssp. vulgare) is used for food, animal feed, and alcoholic beverages and is widely grown in temperate regions. Both barley and its wild progenitor (H. vulgare ssp. spontaneum) have large 5.1-Gb genomes. High-quality chromosome-scale assemblies for several representative barley genotypes, both wild and domesticated, have been constructed recently to populate the nascent barley pan-genome infrastructure. Here, we release a chromosome-scale assembly of the Japanese elite malting barley cultivar 'Haruna Nijo' using a similar methodology as in the barley pan-genome project. The 4.28-Gb assembly had a scaffold N50 size of 18.9 Mb. The assembly showed high collinearity with the barley reference genome 'Morex' cultivar, with some inversions. The pseudomolecule assembly was characterized using transcript evidence of gene projection derived from the reference genome and de novo gene annotation achieved using published full-length cDNA sequences and RNA-Seq data for 'Haruna Nijo'. We found good concordance between our whole-genome assembly and the publicly available BAC clone sequence of 'Haruna Nijo'. Interesting phenotypes have since been identified in Haruna Nijo; its genome sequence assembly will facilitate the identification of the underlying genes.
Collapse
Affiliation(s)
- Areej Sakkour
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Martin Mascher
- Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Axel Himmelbach
- Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466 Seeland, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nils Stein
- Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466 Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075 Göttingen, Germany
| | - Shoko Kawamoto
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| |
Collapse
|
8
|
Bettgenhaeuser J, Hernández-Pinzón I, Dawson AM, Gardiner M, Green P, Taylor J, Smoker M, Ferguson JN, Emmrich P, Hubbard A, Bayles R, Waugh R, Steffenson BJ, Wulff BBH, Dreiseitl A, Ward ER, Moscou MJ. The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics. Nat Commun 2021; 12:6915. [PMID: 34824299 PMCID: PMC8617247 DOI: 10.1038/s41467-021-27288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Crop losses caused by plant pathogens are a primary threat to stable food production. Stripe rust (Puccinia striiformis) is a fungal pathogen of cereal crops that causes significant, persistent yield loss. Stripe rust exhibits host species specificity, with lineages that have adapted to infect wheat and barley. While wheat stripe rust and barley stripe rust are commonly restricted to their corresponding hosts, the genes underlying this host specificity remain unknown. Here, we show that three resistance genes, Rps6, Rps7, and Rps8, contribute to immunity in barley to wheat stripe rust. Rps7 cosegregates with barley powdery mildew resistance at the Mla locus. Using transgenic complementation of different Mla alleles, we confirm allele-specific recognition of wheat stripe rust by Mla. Our results show that major resistance genes contribute to the host species specificity of wheat stripe rust on barley and that a shared genetic architecture underlies resistance to the adapted pathogen barley powdery mildew and non-adapted pathogen wheat stripe rust.
Collapse
Affiliation(s)
- Jan Bettgenhaeuser
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | | | - Andrew M Dawson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Matthew Gardiner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
| | - John N Ferguson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Peter Emmrich
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amelia Hubbard
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, England, UK
| | - Rosemary Bayles
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, England, UK
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brande B H Wulff
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Antonín Dreiseitl
- Department of Integrated Plant Protection, Agrotest Fyto Ltd, Havlíčkova 2787, CZ-767 01, Kroměříž, Czech Republic
| | - Eric R Ward
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK
- AgBiome, Research Triangle Park, NC, 27709, USA
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, England, UK.
| |
Collapse
|
9
|
Sato K, Mascher M, Himmelbach A, Haberer G, Spannagl M, Stein N. Chromosome-scale assembly of wild barley accession "OUH602". G3 (BETHESDA, MD.) 2021; 11:jkab244. [PMID: 34568912 PMCID: PMC8473966 DOI: 10.1093/g3journal/jkab244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022]
Abstract
Barley (Hordeum vulgare) was domesticated from its wild ancestral form ca. 10,000 years ago in the Fertile Crescent and is widely cultivated throughout the world, except for in tropical areas. The genome size of both cultivated barley and its conspecific wild ancestor is approximately 5 Gb. High-quality chromosome-level assemblies of 19 cultivated and one wild barley genotype were recently established by pan-genome analysis. Here, we release another equivalent short-read assembly of the wild barley accession "OUH602." A series of genetic and genomic resources were developed for this genotype in prior studies. Our assembly contains more than 4.4 Gb of sequence, with a scaffold N50 value of over 10 Mb. The haplotype shows high collinearity with the most recently updated barley reference genome, "Morex" V3, with some inversions. Gene projections based on "Morex" gene models revealed 46,807 protein-coding sequences and 43,375 protein-coding genes. Alignments to publicly available sequences of bacterial artificial chromosome (BAC) clones of "OUH602" confirm the high accuracy of the assembly. Since more loci of interest have been identified in "OUH602," the release of this assembly, with detailed genomic information, should accelerate gene identification and the utilization of this key wild barley accession.
Collapse
Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland 06466, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland 06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen 37075, Germany
| |
Collapse
|
10
|
Taketa S, Hattori M, Takami T, Himi E, Sakamoto W. Mutations in a�Golden2-Like�Gene Cause Reduced Seed Weight in�Barley�albino lemma 1�Mutants. PLANT & CELL PHYSIOLOGY 2021; 62:447-457. [PMID: 33439257 DOI: 10.1093/pcp/pcab001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
The albino lemma 1 (alm1) mutants of barley (Hordeum vulgare L.) exhibit obvious chlorophyll-deficient hulls. Hulls are seed-enclosing tissues on the spike, consisting of the lemma and palea. The alm1 phenotype is also expressed in the pericarp, culm nodes and basal leaf sheaths, but leaf blades and awns are normal green. A single recessive nuclear gene controls tissue-specific alm1 phenotypic expression. Positional cloning revealed that the ALM1 gene encodes a Golden 2-like (GLK) transcription factor, HvGLK2, belonging to the GARP subfamily of Myb transcription factors. This finding was validated by genetic evidence indicating that all 10 alm1 mutants studied had a lesion in functionally important regions of HvGLK2, including the three alpha-helix domains, an AREAEAA motif and the GCT box. Transmission electron microscopy revealed that, in lemmas of the alm1.g mutant, the chloroplasts lacked thylakoid membranes, instead of stacked thylakoid grana in wild-type chloroplasts. Compared with wild type, alm1.g plants showed similar levels of leaf photosynthesis but reduced spike photosynthesis by 34%. The alm1.g mutant and the alm1.a mutant showed a reduction in 100-grain weight by 15.8% and 23.1%, respectively. As in other plants, barley has HvGLK2 and a paralog, HvGLK1. In flag leaves and awns, HvGLK2 and HvGLK1 are expressed at moderate levels, but in hulls, HvGLK1 expression was barely detectable compared with HvGLK2. Barley alm1/Hvglk2 mutants exhibit more severe phenotypes than glk2 mutants of other plant species reported to date. The severe alm1 phenotypic expression in multiple tissues indicates that HvGLK2 plays some roles that are nonredundant with HvGLK1.
Collapse
Affiliation(s)
- Shin Taketa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Momoko Hattori
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Eiko Himi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| |
Collapse
|
11
|
Hibara KI, Miya M, Benvenuto SA, Hibara-Matsuo N, Mimura M, Yoshikawa T, Suzuki M, Kusaba M, Taketa S, Itoh JI. Regulation of the plastochron by three many-noded dwarf genes in barley. PLoS Genet 2021; 17:e1009292. [PMID: 33970916 PMCID: PMC8136844 DOI: 10.1371/journal.pgen.1009292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/20/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022] Open
Abstract
The plastochron, the time interval between the formation of two successive leaves, is an important determinant of plant architecture. We genetically and phenotypically investigated many-noded dwarf (mnd) mutants in barley. The mnd mutants exhibited a shortened plastochron and a decreased leaf blade length, and resembled previously reported plastochron1 (pla1), pla2, and pla3 mutants in rice. In addition, the maturation of mnd leaves was accelerated, similar to pla mutants in rice. Several barley mnd alleles were derived from three genes-MND1, MND4, and MND8. Although MND4 coincided with a cytochrome P450 family gene that is a homolog of rice PLA1, we clarified that MND1 and MND8 encode an N-acetyltransferase-like protein and a MATE transporter-family protein, which are respectively orthologs of rice GW6a and maize BIGE1 and unrelated to PLA2 or PLA3. Expression analyses of the three MND genes revealed that MND1 and MND4 were expressed in limited regions of the shoot apical meristem and leaf primordia, but MND8 did not exhibit a specific expression pattern around the shoot apex. In addition, the expression levels of the three genes were interdependent among the various mutant backgrounds. Genetic analyses using the double mutants mnd4mnd8 and mnd1mnd8 indicated that MND1 and MND4 regulate the plastochron independently of MND8, suggesting that the plastochron in barley is controlled by multiple genetic pathways involving MND1, MND4, and MND8. Correlation analysis between leaf number and leaf blade length indicated that both traits exhibited a strong negative association among different genetic backgrounds but not in the same genetic background. We propose that MND genes function in the regulation of the plastochron and leaf growth and revealed conserved and diverse aspects of plastochron regulation via comparative analysis of barley and rice.
Collapse
Affiliation(s)
- Ken-Ichiro Hibara
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Japan
| | - Masayuki Miya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Sean Akira Benvenuto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoko Hibara-Matsuo
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Japan
| | | | | | - Masaharu Suzuki
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
| | - Makoto Kusaba
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shin Taketa
- Group of Genetic Resources and Functions, Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
12
|
Abstract
Barley (Hordeum vulgare), one of the most widely cultivated cereal crops, possesses a large genome of 5.1 Gbp. Through various international collaborations, the genome has recently been sequenced and assembled at the chromosome-scale by exploiting available genetic and genomic resources. Many wild and cultivated barley accessions have been collected and preserved around the world. These accessions are crucial to obtain diverse natural and induced barley variants. The barley bioresource project aims to investigate the diversity of this crop based on purified seed and DNA samples of a large number of collected accessions. The long-term goal of this project is to analyse the genome sequences of major barley accessions worldwide. In view of technical limitations, a strategy has been employed to establish the exome structure of a selected number of accessions and to perform high-quality chromosome-scale assembly of the genomes of several major representative accessions. For the future project, an efficient annotation pipeline is essential for establishing the function of genomes and genes as well as for using this information for sequence-based digital barley breeding. In this article, the author reviews the existing barley resources along with their applications and discuss possible future directions of research in barley genomics.
Collapse
Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| |
Collapse
|
13
|
Alipour H, Bai G, Zhang G, Bihamta MR, Mohammadi V, Peyghambari SA. Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references. PLoS One 2019; 14:e0208614. [PMID: 30615624 PMCID: PMC6322752 DOI: 10.1371/journal.pone.0208614] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 11/20/2018] [Indexed: 02/04/2023] Open
Abstract
Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular technology for genetic and breeding applications in bread wheat (Triticum aestivum L.) and many other plant species. Although GBS can discover millions of SNPs, a high rate of missing data is a major concern for many applications. Accurate imputation of those missing data can significantly improve the utility of GBS data. This study compared imputation accuracies among four genome references including three wheat references (Chinese Spring survey sequence, W7984, and IWGSC RefSeq v1.0) and one barley reference genome by comparing imputed data derived from low-depth sequencing to actual data from high-depth sequencing. After imputation, the average number of imputed data points was the highest in the B genome (~48.99%). The D genome had the lowest imputed data points (~15.02%) but the highest imputation accuracy. Among the four reference genomes, IWGSC RefSeq v1.0 reference provided the most imputed data points, but the lowest imputation accuracy for the SNPs with < 10% minor allele frequency (MAF). The W7984 reference, however, provided the highest imputation accuracy for the SNPs with < 10% MAF.
Collapse
Affiliation(s)
- Hadi Alipour
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
| | - Guorong Zhang
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Valiollah Mohammadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Seyed Ali Peyghambari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| |
Collapse
|
14
|
Mohanta TK, Bashir T, Hashem A, Abd Allah EF. Systems biology approach in plant abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 121:58-73. [PMID: 29096174 DOI: 10.1016/j.plaphy.2017.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/28/2017] [Accepted: 10/20/2017] [Indexed: 05/05/2023]
Abstract
Plant abiotic stresses are the major constraint on plant growth and development, causing enormous crop losses across the world. Plants have unique features to defend themselves against these challenging adverse stress conditions. They modulate their phenotypes upon changes in physiological, biochemical, molecular and genetic information, thus making them tolerant against abiotic stresses. It is of paramount importance to determine the stress-tolerant traits of a diverse range of genotypes of plant species and integrate those traits for crop improvement. Stress-tolerant traits can be identified by conducting genome-wide analysis of stress-tolerant genotypes through the highly advanced structural and functional genomics approach. Specifically, whole-genome sequencing, development of molecular markers, genome-wide association studies and comparative analysis of interaction networks between tolerant and susceptible crop varieties grown under stress conditions can greatly facilitate discovery of novel agronomic traits that protect plants against abiotic stresses.
Collapse
Affiliation(s)
- Tapan Kumar Mohanta
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Tufail Bashir
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Science, King Saud University, P.O. Box 24160, Riyadh, 11451, Saudi Arabia
| |
Collapse
|
15
|
Talukder SK, Saha MC. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses. FRONTIERS IN PLANT SCIENCE 2017; 8:1317. [PMID: 28798766 PMCID: PMC5526908 DOI: 10.3389/fpls.2017.01317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.
Collapse
|
16
|
Oozeki M, Sotome T, Haruyama N, Yamaguchi M, Watanabe H, Okiyama T, Kato T, Takayama T, Oyama M, Nagamine T, Suzuki Y, Toyoshima T, Sekiwa T, Oono K, Saito T, Usui M, Arai S, Kumekawa T, Suzuki E, Shirama K, Kihara M, Hoki T, Matsubara H, Ohsawa R. The two-row malting barley cultivar 'New Sachiho Golden' with null lipoxygenase-1 improves flavor stability in beer and was developed by marker-assisted selection. BREEDING SCIENCE 2017; 67:165-171. [PMID: 28588394 PMCID: PMC5445967 DOI: 10.1270/jsbbs.16104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/30/2016] [Indexed: 06/07/2023]
Abstract
Lipoxygenase-1 (LOX-1) null 'New Sachiho Golden' is a two-row malting barley (Hordeum vulgare L.) cultivar released in 2015 that was developed at the Tochigi Prefectural Agricultural Experimental Station by backcross breeding using the high-yield leading cultivar 'Sachiho Golden' as a recurrent parent and the LOX-1 null mutant 'Daikei LM1' as a non-recurrent parent. To develop 'New Sachiho Golden' we used a simple LOX activity assay and marker-assisted selection. This is the first LOX-1 null malting barley cultivar in Japan that is resistant to barley yellow mosaic virus (types I-III). Agronomic characteristics and malting qualities of 'New Sachiho Golden' were similar to those of 'Sachiho Golden', except that 'New Sachiho Golden' had no LOX activity in ungerminated grains and had clearly lower LOX activity during malting than 'Sachiho Golden'. The concentrations of a trans-2-nonenal (T2N) precursor in wort and beer made from 'New Sachiho Golden' were significantly lower than in those made from 'Sachiho Golden', both before and after storage.
Collapse
Affiliation(s)
- Mika Oozeki
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
- Faculty of Life and Environmental Science, University of Tsukuba,
1-1-1 Tennohdai, Tsukuba, Ibaraki 305-8572,
Japan
| | - Toshinori Sotome
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Naoto Haruyama
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Masahiro Yamaguchi
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Hirohisa Watanabe
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Takeshi Okiyama
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Tsuneo Kato
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Toshiyuki Takayama
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Makoto Oyama
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Takashi Nagamine
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
- Asahi Breweries, Ltd.,
1-23-1 Azumabashi, Sumida, Tokyo 130-8602,
Japan
| | - Yasuo Suzuki
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Takako Toyoshima
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Takahiro Sekiwa
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Kaori Oono
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Tetsuya Saito
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Masao Usui
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Shin Arai
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Terunobu Kumekawa
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Emiko Suzuki
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Kaori Shirama
- Tochigi Prefectural Agricultural Experiment Station,
1080 Kawaraya, Utsunomiya, Tochigi 320-0002,
Japan
| | - Makoto Kihara
- Sapporo Breweries Ltd.,
37-1 Kizaki, Oota, Gunma 370-0393,
Japan
| | - Takehiro Hoki
- Sapporo Breweries Ltd.,
37-1 Kizaki, Oota, Gunma 370-0393,
Japan
| | - Hideki Matsubara
- Asahi Breweries, Ltd.,
1-23-1 Azumabashi, Sumida, Tokyo 130-8602,
Japan
| | - Ryo Ohsawa
- Faculty of Life and Environmental Science, University of Tsukuba,
1-1-1 Tennohdai, Tsukuba, Ibaraki 305-8572,
Japan
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Hisano H, Tsujimura M, Yoshida H, Terachi T, Sato K. Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare). BMC Genomics 2016; 17:824. [PMID: 27776481 PMCID: PMC5078923 DOI: 10.1186/s12864-016-3159-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Background Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. vulgare ssp. vulgare) have cross compatibility and closely related genomes, although a significant number of nucleotide polymorphisms have been reported between their genomes. Results We determined the complete nucleotide sequences of the mitochondrial genomes of wild and cultivated barley. Two independent circular maps of the 525,599 bp barley mitochondrial genome were constructed by de novo assembly of high-throughput sequencing reads of barley lines H602 and Haruna Nijo, with only three SNPs detected between haplotypes. These mitochondrial genomes contained 33 protein-coding genes, three ribosomal RNAs, 16 transfer RNAs, 188 new ORFs, six major repeat sequences and several types of transposable elements. Of the barley mitochondrial genome-encoded proteins, NAD6, NAD9 and RPS4 had unique structures among grass species. Conclusions The mitochondrial genome of barley was similar to those of other grass species in terms of gene content, but the configuration of the genes was highly differentiated from that of other grass species. Mitochondrial genome sequencing is essential for annotating the barley nuclear genome; our mitochondrial sequencing identified a significant number of fragmented mitochondrial sequences in the reported nuclear genome sequences. Little polymorphism was detected in the barley mitochondrial genome sequences, which should be explored further to elucidate the evolution of barley. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3159-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Mai Tsujimura
- Plant Organelle Genomics Research Center and Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan
| | - Hideya Yoshida
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Toru Terachi
- Plant Organelle Genomics Research Center and Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
| |
Collapse
|
19
|
Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. Sci Rep 2016; 6:33199. [PMID: 27616653 PMCID: PMC5018957 DOI: 10.1038/srep33199] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 08/19/2016] [Indexed: 11/14/2022] Open
Abstract
Barley is one of the founder crops of Old world agriculture and has become the fourth most important cereal worldwide. Information on genome-scale DNA polymorphisms allows elucidating the evolutionary history behind domestication, as well as discovering and isolating useful genes for molecular breeding. Deep transcriptome sequencing enables the exploration of sequence variations in transcribed sequences; such analysis is particularly useful for species with large and complex genomes, such as barley. In this study, we performed RNA sequencing of 20 barley accessions, comprising representatives of several biogeographic regions and a wild ancestor. We identified 38,729 to 79,949 SNPs in the 19 domesticated accessions and 55,403 SNPs in the wild barley and revealed their genome-wide distribution using a reference genome. Genome-scale comparisons among accessions showed a clear differentiation between oriental and occidental barley populations. The results based on population structure analyses provide genome-scale properties of sub-populations grouped to oriental, occidental and marginal groups in barley. Our findings suggest that the oriental population of domesticated barley has genomic variations distinct from those in occidental groups, which might have contributed to barley’s domestication.
Collapse
|
20
|
SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley. Sci Rep 2016; 6:31741. [PMID: 27530597 PMCID: PMC4987670 DOI: 10.1038/srep31741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/26/2016] [Indexed: 11/08/2022] Open
Abstract
A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.
Collapse
|
21
|
Yoshikawa T, Tanaka SY, Masumoto Y, Nobori N, Ishii H, Hibara KI, Itoh JI, Tanisaka T, Taketa S. Barley NARROW LEAFED DWARF1 encoding a WUSCHEL-RELATED HOMEOBOX 3 (WOX3) regulates the marginal development of lateral organs. BREEDING SCIENCE 2016; 66:416-24. [PMID: 27436952 PMCID: PMC4902465 DOI: 10.1270/jsbbs.16019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) is the fourth most-produced cereal in the world and is mainly utilized as animal feed and malts. Recently barley attracts considerable attentions as healthy food rich in dietary fiber. However, limited knowledge is available about developmental aspects of barley leaves. In the present study, we investigated barley narrow leafed dwarf1 (nld1) mutants, which exhibit thin leaves accompanied by short stature. Detailed histological analysis revealed that leaf marginal tissues, such as sawtooth hairs and sclerenchymatous cells, were lacked in nld1, suggesting that narrowed leaf of nld1 was attributable to the defective development of the marginal regions in the leaves. The defective marginal developments were also appeared in internodes and glumes in spikelets. Map-based cloning revealed that NLD1 encodes a WUSCHEL-RELATED HOMEOBOX 3 (WOX3), an ortholog of the maize NARROW SHEATH genes. In situ hybridization showed that NLD1 transcripts were localized in the marginal edges of leaf primordia from the initiating stage. From these results, we concluded that NLD1 plays pivotal role in the increase of organ width and in the development of marginal tissues in lateral organs in barley.
Collapse
Affiliation(s)
- Takanori Yoshikawa
- School of Agricultural Regional Vitalization, Kibi International University,
Minamiawaji, Hyogo 656-0484,
Japan
- Corresponding author (e-mail: )
| | - Shin-Ya Tanaka
- School of Agricultural Regional Vitalization, Kibi International University,
Minamiawaji, Hyogo 656-0484,
Japan
| | - Yuuki Masumoto
- School of Agricultural Regional Vitalization, Kibi International University,
Minamiawaji, Hyogo 656-0484,
Japan
| | - Naoya Nobori
- School of Agricultural Regional Vitalization, Kibi International University,
Minamiawaji, Hyogo 656-0484,
Japan
| | - Hiroto Ishii
- School of Agricultural Regional Vitalization, Kibi International University,
Minamiawaji, Hyogo 656-0484,
Japan
| | - Ken-Ichiro Hibara
- Graduate School of Agricultural and Life Sciences, University of Tokyo,
Tokyo 113-8657,
Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, University of Tokyo,
Tokyo 113-8657,
Japan
| | - Takatoshi Tanisaka
- School of Agricultural Regional Vitalization, Kibi International University,
Minamiawaji, Hyogo 656-0484,
Japan
| | - Shin Taketa
- Group of Genetic Resources and Functions, Institute of Plant Science and Resources, Okayama University,
Kurashiki, Okayama 710-0046,
Japan
| |
Collapse
|
22
|
Sato K, Yamane M, Yamaji N, Kanamori H, Tagiri A, Schwerdt JG, Fincher GB, Matsumoto T, Takeda K, Komatsuda T. Alanine aminotransferase controls seed dormancy in barley. Nat Commun 2016; 7:11625. [PMID: 27188711 PMCID: PMC4873977 DOI: 10.1038/ncomms11625] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/13/2016] [Indexed: 01/08/2023] Open
Abstract
Dormancy allows wild barley grains to survive dry summers in the Near East. After domestication, barley was selected for shorter dormancy periods. Here we isolate the major seed dormancy gene qsd1 from wild barley, which encodes an alanine aminotransferase (AlaAT). The seed dormancy gene is expressed specifically in the embryo. The AlaAT isoenzymes encoded by the long and short dormancy alleles differ in a single amino acid residue. The reduced dormancy allele Qsd1 evolved from barleys that were first domesticated in the southern Levant and had the long dormancy qsd1 allele that can be traced back to wild barleys. The reduced dormancy mutation likely contributed to the enhanced performance of barley in industrial applications such as beer and whisky production, which involve controlled germination. In contrast, the long dormancy allele might be used to control pre-harvest sprouting in higher rainfall areas to enhance global adaptation of barley. Seed dormancy allows wild barley grains to survive dry summers in the Near East but has been selected against for industrial applications such as beer and whisky production that require quicker germination. Here Sato et al. show that Qsd1 is a major seed dormancy gene in barley and encodes an alanine aminotransferase.
Collapse
Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Miki Yamane
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Nami Yamaji
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Julian G Schwerdt
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Kazuyoshi Takeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| |
Collapse
|
23
|
Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Res 2016; 24:231-42. [DOI: 10.1007/s10577-016-9518-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/31/2016] [Accepted: 02/01/2016] [Indexed: 01/05/2023]
|
24
|
Sato K, Tanaka T, Shigenobu S, Motoi Y, Wu J, Itoh T. Improvement of barley genome annotations by deciphering the Haruna Nijo genome. DNA Res 2015; 23:21-8. [PMID: 26622062 PMCID: PMC4755524 DOI: 10.1093/dnares/dsv033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
Full-length (FL) cDNA sequences provide the most reliable evidence for the presence of genes in genomes. In this report, detailed gene structures of barley, whole genome shotgun (WGS) and additional transcript data of the cultivar Haruna Nijo were quality controlled and compared with the published Morex genome information. Haruna Nijo scaffolds have longer total sequence length with much higher N50 and fewer sequences than those in Morex WGS contigs. The longer Haruna Nijo scaffolds provided efficient FLcDNA mapping, resulting in high coverage and detection of the transcription start sites. In combination with FLcDNAs and RNA-Seq data from four different tissue samples of Haruna Nijo, we identified 51,249 gene models on 30,606 loci. Overall sequence similarity between Haruna Nijo and Morex genome was 95.99%, while that of exon regions was higher (99.71%). These sequence and annotation data of Haruna Nijo are combined with Morex genome data and released from a genome browser. The genome sequence of Haruna Nijo may provide detailed gene structures in addition to the current Morex barley genome information.
Collapse
Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Tsuyoshi Tanaka
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Yuka Motoi
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| |
Collapse
|
25
|
Ishihara A, Mizuno N, Islam RAKM, Doležel J, Endo TR, Nasuda S. Dissection of barley chromosomes 1H and 6H by the gametocidal system. Genes Genet Syst 2015; 89:203-14. [PMID: 25832747 DOI: 10.1266/ggs.89.203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We dissected barley chromosomes 1H and 6H added to common wheat by the gametocidal system and identified structural changes of the chromosomes by fluorescence in situ hybridization and genomic in situ hybridization. We found five aberrations of chromosome 1H, all of which lacked the long arm: one small fragment with the subtelomeric HvT01 sequence, one terminal deletion, and three telocentric chromosomes of the short arm. We established 33 dissection lines carrying single aberrant 6H chromosomes, of which 15 were deletions, 16 were translocations and two were isochromosomes. We conducted PCR analysis of the aberrant barley chromosomes using 75 and 81 EST markers specific to chromosomes 1H and 6H, respectively. This enabled us to construct a cytological map of chromosome 6H and to compare it to the previously reported genetic map and also to the physical map, which were released by the International Barley Genome Sequencing Consortium. The marker orders on the three maps were largely in agreement. The cytological map had better resolution in the proximal region of chromosome 6H than the corresponding genetic map. We discuss some of the discrepancies in marker order between the three maps that might be due to intraspecific polymorphism and gene duplication, as well as to technical problems inherent in the physical mapping process.
Collapse
Affiliation(s)
- Ayaka Ishihara
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
| | | | | | | | | | | |
Collapse
|
26
|
Mazaheri M, Kianian P, Kumar A, Mergoum M, Seetan R, Soltani A, Lund LI, Pirseyedi SM, Denton AM, Kianian SF. Radiation Hybrid Map of Barley Chromosome 3H. THE PLANT GENOME 2015; 8:eplantgenome2015.02.0005. [PMID: 33228309 DOI: 10.3835/plantgenome2015.02.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/14/2015] [Indexed: 06/11/2023]
Abstract
Assembly of the barley (Hordeum vulgare L.) genome is complicated by its large size (5.1 Gb) and proportion of repetitive elements (84%). This process is facilitated by high resolution maps for aligning bacterial artificial chromosome (BAC) contigs along chromosomes. Available genetic maps, however, do not provide accurate information on the physical position of a large portion of the genome located in recombination-poor regions. Radiation hybrid (RH) mapping is an alternative approach, which is based on radiation-induced deletions along the length of chromosomes. In this study, the first RH map for barley chromosome 3H was developed. In total, 373 in vivo RH lines were generated by irradiating wheat (Triticum aestivum L.)-barley chromosome 3H addition lines and crossing them to a normal wheat cultivar. Each RH informative line (containing deletions) had, on average, three deletions. The induced deletion size varied from 36.58 Kb to 576.00 Mb, with an average length of 52.42 Mb. This initial chromosome 3H radiation hybrid (3H-RH) map had a 9.53× higher resolution than an analogous genetic map, reaching a maximum of >262.40× resolution in regions around the centromere. The final RH map was 3066.1 cR in length, with a 0.76 Mb resolution. It was estimated that the map resolution can be improved to an average of 30.34 Kb by saturating the 3H-RH map with molecular markers. The generated RH panel enabled alignment of BAC and sequenced contigs as small as 1.50 Kb in size. The high resolution and the coverage of poor-recombination regions make RH maps an ideal resource for barley genome assembly, as well as other genetic studies.
Collapse
Affiliation(s)
- Mona Mazaheri
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Penny Kianian
- Dep. of Horticultural Science, Univ. of Minnesota, St. Paul, MN, 55108
| | - Ajay Kumar
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Mohamed Mergoum
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Raed Seetan
- Dep. of Math, Science, and Technology, Univ. of Minnesota, Crookston, MN
| | - Ali Soltani
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Lucy I Lund
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | | | - Anne M Denton
- Dep. of Computer Sciences, North Dakota State Univ., Fargo, ND, 58108
| | | |
Collapse
|
27
|
Himi E, Taketa S. Barley Ant17, encoding flavanone 3-hydroxylase (F3H), is a promising target locus for attaining anthocyanin/proanthocyanidin-free plants without pleiotropic reduction of grain dormancy. Genome 2015; 58:43-53. [PMID: 25932661 DOI: 10.1139/gen-2014-0189] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Preharvest sprouting is a serious problem in grain crop production because it causes quality deterioration and economic losses. It is well known that grain colour is closely associated with grain dormancy in wheat; white-grained lines without accumulating proanthocyanidins in testa tend to be more susceptible to preharvest sprouting than red ones. All available white-grained wheat lines are restricted to triple recessive mutations at the R loci (R-A1, R-B1, and R-D1), but barley is known to have 11 independent loci conferring the proanthocyanidin-free grain phenotype. In this study, we evaluated the dormancy levels of anthocyanin/proanthocyanidin-free ant17 mutants. Three ant17 mutants showed the same levels of dormancy as their respective wild types. Sequencing of three independent ant17 alleles detected a point mutation within the coding regions of flavanone-3-hydroxylase (F3H), which are predicted to cause a premature stop codon at different sites. The F3H locus completely cosegregated with the Ant17 position on the chromosome arm 2HL. Expression of the barley F3H gene was observed in pigmented tissues, but not in nonpigmented roots and stems. This result indicates that wheat F3H may be a promising new target locus for breeding white-grained lines with a practical level of preharvest sprouting resistance.
Collapse
Affiliation(s)
- Eiko Himi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | | |
Collapse
|
28
|
Wendler N, Mascher M, Nöh C, Himmelbach A, Scholz U, Ruge-Wehling B, Stein N. Unlocking the secondary gene-pool of barley with next-generation sequencing. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1122-31. [PMID: 25040223 DOI: 10.1111/pbi.12219] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 05/18/2023]
Abstract
Crop wild relatives (CWR) provide an important source of allelic diversity for any given crop plant species for counteracting the erosion of genetic diversity caused by domestication and elite breeding bottlenecks. Hordeum bulbosum L. is representing the secondary gene pool of the genus Hordeum. It has been used as a source of genetic introgressions for improving elite barley germplasm (Hordeum vulgare L.). However, genetic introgressions from H. bulbosum have yet not been broadly applied, due to a lack of suitable molecular tools for locating, characterizing, and decreasing by recombination and marker-assisted backcrossing the size of introgressed segments. We applied next-generation sequencing (NGS) based strategies for unlocking genetic diversity of three diploid introgression lines of cultivated barley containing chromosomal segments of its close relative H. bulbosum. Firstly, exome capture-based (re)-sequencing revealed large numbers of single nucleotide polymorphisms (SNPs) enabling the precise allocation of H. bulbosum introgressions. This SNP resource was further exploited by designing a custom multiplex SNP genotyping assay. Secondly, two-enzyme-based genotyping-by-sequencing (GBS) was employed to allocate the introgressed H. bulbosum segments and to genotype a mapping population. Both methods provided fast and reliable detection and mapping of the introgressed segments and enabled the identification of recombinant plants. Thus, the utilization of H. bulbosum as a resource of natural genetic diversity in barley crop improvement will be greatly facilitated by these tools in the future.
Collapse
Affiliation(s)
- Neele Wendler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | | | | | | | | |
Collapse
|
29
|
Fang Z, Gonzales AM, Clegg MT, Smith KP, Muehlbauer GJ, Steffenson BJ, Morrell PL. Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3 (BETHESDA, MD.) 2014; 4:1193-203. [PMID: 24760390 PMCID: PMC4455769 DOI: 10.1534/g3.114.010561] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/22/2014] [Indexed: 12/30/2022]
Abstract
Genetic differentiation in natural populations is driven by geographic distance and by ecological or physical features within and between natural habitats that reduce migration. The primary population structure in wild barley differentiates populations east and west of the Zagros Mountains. Genetic differentiation between eastern and western populations is uneven across the genome and is greatest on linkage groups 2H and 5H. Genetic markers in these two regions demonstrate the largest difference in frequency between the primary populations and have the highest informativeness for assignment to each population. Previous cytological and genetic studies suggest there are chromosomal structural rearrangements (inversions or translocations) in these genomic regions. Environmental association analyses identified an association with both temperature and precipitation variables on 2H and with precipitation variables on 5H.
Collapse
Affiliation(s)
- Zhou Fang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Ana M Gonzales
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| |
Collapse
|
30
|
Characterization and mapping of a Prbs gene controlling spike development in Hordeum vulgare L. Genes Genomics 2014. [DOI: 10.1007/s13258-013-0165-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
31
|
Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
Collapse
Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
| |
Collapse
|
32
|
Chen GD, Liu YX, Wei YM, McIntyre CL, Zhou MX, Zheng YL, Liu CJ. Major QTL for Fusarium crown rot resistance in a barley landrace. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2511-20. [PMID: 23824201 DOI: 10.1007/s00122-013-2151-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/20/2013] [Indexed: 05/09/2023]
Abstract
Fusarium crown rot (FCR) is a serious cereal disease in semi-arid regions worldwide. In assisting the effort of breeding cultivars with enhanced resistance, we identified several barley genotypes with high levels of FCR resistance. One of these genotypes, AWCS079 which is a barley landrace originating from Japan, was investigated by developing and assessing three populations of recombinant inbred lines. Two QTL, one located on the long arm of chromosome 1H (designated as Qcrs.cpi-1H) and the other on 3HL (designated as Qcrs.cpi-3H), were found to be responsible for the FCR resistance of this genotype. Qcrs.cpi-1H is novel as no other FCR loci have been reported on this chromosome arm. Qcrs.cpi-3H co-located with a reduced height (Rht) locus and the effectiveness of the former was significantly affected by the latter. The total phenotypic variance explained by these two QTL was over 60 %. Significant effects were detected for each of the QTL in each of the three populations assessed. The existence of these loci with major effects should not only facilitate breeding and exploitation of FCR-resistant barley cultivars but also their further characterization based on fine mapping and map-based gene cloning.
Collapse
Affiliation(s)
- G D Chen
- CSIRO Plant Industry, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | | | | | | | | | | | | |
Collapse
|
33
|
Joshi GP, Endo TR, Nasuda S. PCR and sequence analysis of barley chromosome 2H subjected to the gametocidal action of chromosome 2C. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2381-2390. [PMID: 23765160 DOI: 10.1007/s00122-013-2142-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/03/2013] [Indexed: 05/28/2023]
Abstract
Gametocidal (Gc) chromosomes induce various types of chromosomal mutations during gametogenesis in the chromosomes of common wheat and alien chromosomes added to common wheat. However, it is not yet known whether the Gc chromosome causes aberrations at the nucleotide level because mutations caused by Gc chromosomes have been studied only by cytological screening. In order to know whether the Gc chromosome induces point mutations, we conducted PCR analysis and sequencing with the progeny of a common wheat line that is disomic for barley chromosome 2H and monosomic for Gc chromosome 2C. We analyzed 18 2H-specific EST sequences using 81 progeny plants carrying a cytologically normal-appearing 2H chromosome and found no nucleotide changes in the analyzed 1,419 sequences (in total 647,075 bp). During this analysis, we found six plants for which some ESTs could not be PCR amplified, suggesting the presence of chromosomal mutations in these plants. The cytological and PCR analyses of the progeny of the six plants confirmed the occurrence of chromosomal mutations in the parental plants. These results suggested that the Gc chromosome mostly induced chromosomal aberrations, not nucleotide changes, and that the Gc-induced chromosomal mutations in the six plants occurred after fertilization.
Collapse
Affiliation(s)
- Giri Prasad Joshi
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto, Japan
| | | | | |
Collapse
|
34
|
Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc Natl Acad Sci U S A 2013; 110:13198-203. [PMID: 23878219 DOI: 10.1073/pnas.1221950110] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inflorescence architecture of barley (Hordeum vulgare L.) is common among the Triticeae species, which bear one to three single-flowered spikelets at each rachis internode. Triple spikelet meristem is one of the unique features of barley spikes, in which three spikelets (one central and two lateral spikelets) are produced at each rachis internode. Fertility of the lateral spikelets at triple spikelet meristem gives row-type identity to barley spikes. Six-rowed spikes show fertile lateral spikelets and produce increased grain yield per spike, compared with two-rowed spikes with sterile lateral spikelets. Thus, far, two loci governing the row-type phenotype were isolated in barley that include Six-rowed spike1 (Vrs1) and Intermedium-C. In the present study, we isolated Six-rowed spike4 (Vrs4), a barley ortholog of the maize (Zea mays L.) inflorescence architecture gene RAMOSA2 (RA2). Eighteen coding mutations in barley RA2 (HvRA2) were specifically associated with lateral spikelet fertility and loss of spikelet determinacy. Expression analyses through mRNA in situ hybridization and microarray showed that Vrs4 (HvRA2) controls the row-type pathway through Vrs1 (HvHox1), a negative regulator of lateral spikelet fertility in barley. Moreover, Vrs4 may also regulate transcripts of barley SISTER OF RAMOSA3 (HvSRA), a putative trehalose-6-phosphate phosphatase involved in trehalose-6-phosphate homeostasis implicated to control spikelet determinacy. Our expression data illustrated that, although RA2 is conserved among different grass species, its down-stream target genes appear to be modified in barley and possibly other species of tribe Triticeae.
Collapse
|
35
|
Silvar C, Perovic D, Nussbaumer T, Spannagl M, Usadel B, Casas A, Igartua E, Ordon F. Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces. PLoS One 2013; 8:e67336. [PMID: 23826271 PMCID: PMC3691219 DOI: 10.1371/journal.pone.0067336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/17/2013] [Indexed: 01/09/2023] Open
Abstract
Three quantitative trait loci (QTL) conferring broad spectrum resistance to powdery mildew, caused by the fungus Blumeria graminis f. sp. hordei, were previously identified on chromosomes 7HS, 7HL and 6HL in the Spanish barley landrace-derived lines SBCC097 and SBCC145. In the present work, a genome-wide putative linear gene index of barley (Genome Zipper) and the first draft of the physical, genetic and functional sequence of the barley genome were used to go one step further in the shortening and explicit demarcation on the barley genome of these regions conferring resistance to powdery mildew as well as in the identification of candidate genes. First, a comparative analysis of the target regions to the barley Genome Zippers of chromosomes 7H and 6H allowed the development of 25 new gene-based molecular markers, which slightly better delimit the QTL intervals. These new markers provided the framework for anchoring of genetic and physical maps, figuring out the outline of the barley genome at the target regions in SBCC097 and SBCC145. The outermost flanking markers of QTLs on 7HS, 7HL and 6HL defined a physical area of 4 Mb, 3.7 Mb and 3.2 Mb, respectively. In total, 21, 10 and 16 genes on 7HS, 7HL and 6HL, respectively, could be interpreted as potential candidates to explain the resistance to powdery mildew, as they encode proteins of related functions with respect to the known pathogen defense-related processes. The majority of these were annotated as belonging to the NBS-LRR class or protein kinase family.
Collapse
Affiliation(s)
- Cristina Silvar
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Johnston PA, Niks RE, Meiyalaghan V, Blanchet E, Pickering R. Rph22: mapping of a novel leaf rust resistance gene introgressed from the non-host Hordeum bulbosum L. into cultivated barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1613-25. [PMID: 23467993 DOI: 10.1007/s00122-013-2078-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 02/23/2013] [Indexed: 05/18/2023]
Abstract
A resistance gene (Rph22) to barley leaf rust caused by Puccinia hordei was introgressed from the non-host species Hordeum bulbosum into cultivated barley. The H. bulbosum introgression in line '182Q20' was located to chromosome 2HL using genomic in situ hybridisation (GISH). Using molecular markers it was shown to cover approximately 20 % of the genetic length of the chromosome. The introgression confers a very high level of resistance to P. hordei at the seedling stage that is not based on a hypersensitive reaction. The presence of the resistance gene increased the latency period of the leaf rust fungus and strongly reduced the infection frequency relative to the genetic background cultivar 'Golden Promise'. An F2 population of 550 individuals was developed and used to create a genetic map of the introgressed region and to determine the map position of the underlying resistance gene(s). The resistance locus, designated Rph22, was located to the distal portion of the introgression, co-segregating with markers H35_26334 and H35_45139. Flanking markers will be used to reduce the linkage drag, including gene(s) responsible for a yield penalty, around the resistance locus and to transfer the gene into elite barley germplasm. This genetic location is also known to harbour a QTL (Rphq2) for non-hypersensitive leaf rust resistance in the barley cultivar 'Vada'. Comparison of the 'Vada' and H. bulbosum resistances at this locus may lead to a better understanding of the possible association between host and non-host resistance mechanisms.
Collapse
Affiliation(s)
- Paul A Johnston
- The New Zealand Institute for Plant and Food Research Limited, 7608 Lincoln, New Zealand.
| | | | | | | | | |
Collapse
|
37
|
Lüpken T, Stein N, Perovic D, Habekuss A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Zhou R, Ariyadasa R, Taudien S, Platzer M, Martis M, Mayer K, Friedt W, Ordon F. Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1201-12. [PMID: 23456135 DOI: 10.1007/s00122-013-2047-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/13/2013] [Indexed: 05/20/2023]
Abstract
Soil-borne barley yellow mosaic virus disease, caused by different strains of Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), is one of the most important diseases of winter barley (Hordeum vulgare L.) in Europe and East Asia. The recessive resistance gene rym11 located in the centromeric region of chromosome 4HL is effective against all so far known strains of BaMMV and BaYMV in Germany. In order to isolate this gene, a high-resolution mapping population (10,204 meiotic events) has been constructed. F2 plants were screened with co-dominant flanking markers and segmental recombinant inbred lines (RILs) were tested for resistance to BaMMV under growth chamber and field conditions. Tightly linked markers were developed by exploiting (1) publicly available barley EST sequences, (2) employing barley synteny to rice, Brachypodium distachyon and sorghum and (3) using next-generation sequencing data of barley. Using this approach, the genetic interval was efficiently narrowed down from the initial 10.72 % recombination to 0.074 % recombination. A marker co-segregating with rym11 was developed providing the basis for gene isolation and efficient marker-assisted selection.
Collapse
Affiliation(s)
- Thomas Lüpken
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Chen G, Liu Y, Ma J, Zheng Z, Wei Y, McIntyre CL, Zheng YL, Liu C. A novel and major quantitative trait locus for fusarium crown rot resistance in a genotype of Wild Barley (Hordeum spontaneum L.). PLoS One 2013; 8:e58040. [PMID: 23536780 PMCID: PMC3594225 DOI: 10.1371/journal.pone.0058040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
Fusarium crown rot (FCR), caused by various Fusarium species, is a destructive disease of cereal crops in semiarid regions worldwide. As part of our contribution to the development of Fusarium resistant cultivars, we identified several novel sources of resistance by systematically assessing barley genotypes representing different geographical origins and plant types. One of these sources of resistance was investigated in this study by generating and analysing two populations of recombinant inbred lines. A major locus conferring FCR resistance, designated as Qcrs.cpi-4H, was detected in one of the populations (mapping population) and the effects of the QTL was confirmed in the other population. The QTL was mapped to the distal end of chromosome arm 4HL and it is effective against both of the Fusarium isolates tested, one F. pseudograminearum and the other F. graminearum. The QTL explains up to 45.3% of the phenotypic variance. As distinct from an earlier report which demonstrated co-locations of loci conferring FCR resistance and plant height in barley, a correlation between these two traits was not detected in the mapping population. However, as observed in a screen of random genotypes, an association between FCR resistance and plant growth rate was detected and a QTL controlling the latter was detected near the Qcrs.cpi-4H locus in the mapping population. Existing data indicate that, although growth rate may affect FCR resistance, different genes at this locus are likely involved in controlling these two traits.
Collapse
Affiliation(s)
- Guangdeng Chen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yaxi Liu
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Jun Ma
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhi Zheng
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - C. Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Chunji Liu
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
| |
Collapse
|
39
|
Li C, Wang A, Ma X, Pourkheirandish M, Sakuma S, Wang N, Ning S, Nevo E, Nawrath C, Komatsuda T, Chen G. An eceriferum locus, cer-zv, is associated with a defect in cutin responsible for water retention in barley (Hordeum vulgare) leaves. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:637-46. [PMID: 23124432 DOI: 10.1007/s00122-012-2007-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/13/2012] [Indexed: 05/08/2023]
Abstract
Drought limits plant growth and threatens crop productivity. A barley (Hordeum vulgare) ethylene imine-induced monogenic recessive mutant cer-zv, which is sensitive to drought, was characterized and genetically mapped in the present study. Detached leaves of cer-zv lost 34.2 % of their initial weight after 1 h of dehydration. The transpiration was much higher in cer-zv leaves than in wild-type leaves under both light and dark conditions. The stomata of cer-zv leaves functioned normally, but the cuticle of cer-zv leaves showed increased permeability to ethanol and toluidine blue dye. There was a 50-90 % reduction in four major cutin monomers, but no reduction in wax loads was found in the cer-zv mutant as compared with the wild type. Two F(2) mapping populations were established by the crosses of 23-19 × cer-zv and cer-zv × OUH602. More polymorphisms were found in EST sequences between cer-zv and OUH602 than between cer-zv and 23-19. cer-zv was located in a pericentromeric region on chromosome 4H in a 10.8 cM interval in the 23-19 × cer-zv map based on 186 gametes tested and a 1.7 cM interval in the cer-zv × OUH602 map based on 176 gametes tested. It co-segregated with EST marker AK251484 in both maps. The results indicated that the cer-zv mutant is defective in cutin, which might be responsible for the increased transpiration rate and drought sensitivity, and that the F(2) of cer-zv × OUH602 might better facilitate high resolution mapping of cer-zv.
Collapse
Affiliation(s)
- Chao Li
- Laboratory of Plant Stress Ecophysiology and Biotechnology, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Donggang West Road 320, Lanzhou, 730000, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Pérez-de-Castro AM, Vilanova S, Cañizares J, Pascual L, Blanca JM, Díez MJ, Prohens J, Picó B. Application of genomic tools in plant breeding. Curr Genomics 2012; 13:179-95. [PMID: 23115520 PMCID: PMC3382273 DOI: 10.2174/138920212800543084] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/16/2011] [Accepted: 10/11/2011] [Indexed: 02/08/2023] Open
Abstract
Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits.
Collapse
Affiliation(s)
- A M Pérez-de-Castro
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Okagaki RJ, Cho S, Kruger WM, Xu WW, Heinen S, Muehlbauer GJ. The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Funct Integr Genomics 2012; 13:33-41. [PMID: 23086595 DOI: 10.1007/s10142-012-0299-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 09/09/2012] [Accepted: 09/24/2012] [Indexed: 12/23/2022]
Abstract
Vegetative axillary meristem (AXM) activity results in the production of branches. In barley (Hordeum vulgare L.), vegetative AXM develop in the crown and give rise to modified branches, referred to as tillers. Mutations in the barley low-tillering mutant uniculm2 block vegetative AXM development and prevent tiller development. The objectives of this work were to examine gene expression in wild-type and cul2 mutant plants, fine map the CUL2 gene, and to examine synteny in the CUL2 region in barley with rice. RNA profiling experiments using two near-isogenic line pairs carrying either the cul2 mutant allele or wild-type CUL2 allele in different genetic backgrounds detected 28 unique gene transcripts exhibiting similar patterns of differential accumulation in both genetic backgrounds, indicating that we have identified key genes impacted by the CUL2 gene. Twenty-four genes had higher abundance in uniculm2 mutant tissues, and nearly half of the annotated genes likely function in stress-response or signal transduction pathways. Genetic mapping identified five co-segregating markers in 1,088 F2 individuals. These markers spanned the centromere region on chromosome 6H, and coincided with a 50-cM region on rice chromosome 2, indicating that it may be difficult to positionally clone CUL2. Taken together, the results revealed stress response and signal transduction pathways that are associated with the CUL2 gene, isolating CUL2 via positional cloning approaches that may be difficult, and the remnants of barley-rice synteny in the CUL2 region.
Collapse
Affiliation(s)
- Ron J Okagaki
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | | | | |
Collapse
|
42
|
A physical, genetic and functional sequence assembly of the barley genome. Nature 2012; 491:711-6. [PMID: 23075845 DOI: 10.1038/nature11543] [Citation(s) in RCA: 934] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/30/2012] [Indexed: 12/13/2022]
Abstract
Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
Collapse
|
43
|
Wang MJ, Zou HD, Lin ZS, Wu Y, Chen X, Yuan YP. Expressed sequence tag-PCR markers for identification of alien barley chromosome 2H in wheat. GENETICS AND MOLECULAR RESEARCH 2012; 11:3452-63. [PMID: 23079838 DOI: 10.4238/2012.september.25.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We developed EST-PCR markers specific to barley chromosome 2H, for the purpose of effectively tracing alien chromosomes or chromosome parts in the wheat genetic background. The target alien chromosome 2H confers high resistance to pre-harvest sprouting, which is a worldwide natural disaster in wheat. A total of 120 primer pairs were selected by combining the wheat group 2 chromosomes of the EST database and the genome sequences of the new model plant Brachypodium distachyon. Seventy-seven of 120 primer pairs were polymorphic and 31 of 120 primer pairs were monomorphic between a set of wheat-barley chromosome 2H disomic addition/substitution lines and their parents by agarose gel electrophoresis and polyacrylamide gel electrophoresis. Thirty of 77 polymorphic primer pairs including primer pair P120 derived from the basi gene were chromosome 2H-specific. These markers are expected to be valuable in screening of wheat-barley chromosome 2H recombination lines and pre-harvest sprouting resistant varieties.
Collapse
Affiliation(s)
- M J Wang
- College of Plant Science, Jilin University, Changchun, China
| | | | | | | | | | | |
Collapse
|
44
|
Taniguchi F, Fukuoka H, Tanaka J. Expressed sequence tags from organ-specific cDNA libraries of tea (Camellia sinensis) and polymorphisms and transferability of EST-SSRs across Camellia species. BREEDING SCIENCE 2012; 62:186-95. [PMID: 23136530 PMCID: PMC3405963 DOI: 10.1270/jsbbs.62.186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 04/06/2012] [Indexed: 05/19/2023]
Abstract
Tea is one of the most popular beverages in the world and the tea plant, Camellia sinensis (L.) O. Kuntze, is an important crop in many countries. To increase the amount of genomic information available for C. sinensis, we constructed seven cDNA libraries from various organs and used these to generate expressed sequence tags (ESTs). A total of 17,458 ESTs were generated and assembled into 5,262 unigenes. About 50% of the unigenes were assigned annotations by Gene Ontology. Some were homologous to genes involved in important biological processes, such as nitrogen assimilation, aluminum response, and biosynthesis of caffeine and catechins. Digital northern analysis showed that 67 unigenes were expressed differentially among the seven organs. Simple sequence repeat (SSR) motif searches among the unigenes identified 1,835 unigenes (34.9%) harboring SSR motifs of more than six repeat units. A subset of 100 EST-SSR primer sets was tested for amplification and polymorphism in 16 tea accessions. Seventy-one primer sets successfully amplified EST-SSRs and 70 EST-SSR loci were polymorphic. Furthermore, these 70 EST-SSR markers were transferable to 14 other Camellia species. The ESTs and EST-SSR markers will enhance the study of important traits and the molecular genetics of tea plants and other Camellia species.
Collapse
Affiliation(s)
- Fumiya Taniguchi
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87, Seto, Makurazaki, Kagoshima 898-0087, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba, Ibaraki 305-0001, Japan
- Corresponding author (e-mail: )
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Junichi Tanaka
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87, Seto, Makurazaki, Kagoshima 898-0087, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennohdai, Tsukuba, Ibaraki 305-0001, Japan
| |
Collapse
|
45
|
Rodríguez-Suárez C, Giménez MJ, Gutiérrez N, Avila CM, Machado A, Huttner E, Ramírez MC, Martín AC, Castillo A, Kilian A, Martín A, Atienza SG. Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:713-22. [PMID: 22048641 DOI: 10.1007/s00122-011-1741-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 10/18/2011] [Indexed: 05/24/2023]
Abstract
Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat-H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2H(ch), 3H(ch) and 5H(ch) in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.
Collapse
Affiliation(s)
- C Rodríguez-Suárez
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, 14080, Córdoba, Spain
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N. High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:373-84. [PMID: 21959909 DOI: 10.1007/s00122-011-1712-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 09/13/2011] [Indexed: 05/22/2023]
Abstract
Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC(7)F(3) nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.
Collapse
Affiliation(s)
- Fahimeh Shahinnia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany
| | | | | | | | | | | |
Collapse
|
47
|
Matsuda R, Iehisa JCM, Takumi S. Application of real-time PCR-based SNP detection for mapping of Net2, a causal D-genome gene for hybrid necrosis in interspecific crosses between tetraploid wheat and Aegilops tauschii. Genes Genet Syst 2012; 87:137-43. [DOI: 10.1266/ggs.87.137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
| | | | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University
| |
Collapse
|
48
|
Silvar C, Perovic D, Scholz U, Casas AM, Igartua E, Ordon F. Fine mapping and comparative genomics integration of two quantitative trait loci controlling resistance to powdery mildew in a Spanish barley landrace. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:49-62. [PMID: 21901548 DOI: 10.1007/s00122-011-1686-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 08/17/2011] [Indexed: 05/31/2023]
Abstract
The intervals containing two major quantitative trait loci (QTL) from a Spanish barley landrace conferring broad spectrum resistance to Blumeria graminis were subjected to marker saturation. First, all the available information on recently developed marker resources for barley was exploited. Then, a comparative genomic analysis of the QTL regions with other sequenced grass model species was performed. As a result of the first step, 32 new markers were added to the previous map and new flanking markers closer to both QTL were identified. Next, syntenic integration revealed that the barley target regions showed homology with regions on chromosome 6 of rice (Oryza sativa), chromosome 10 of Sorghum bicolor and chromosome 1 of Brachypodium distachyon. A nested insertion of ancestral syntenic blocks on Brachypodium chromosome 1 was confirmed. Based on sequence information of the most likely candidate orthologous genes, 23 new barley unigene-derived markers were developed and mapped within the barley target regions. The assessment of colinearity revealed an inversion on chromosome 7HL of barley compared to the other three grass species, and nearly perfect colinearity on chromosome 7HS. This two-step marker enrichment allowed for the refinement of the two QTL into much smaller intervals. Inspection of all predicted proteins for the barley unigenes identified within the QTL intervals did not reveal the presence of resistance gene candidates. This study demonstrates the usefulness of sequenced genomes for fine mapping and paves the way for the use of these two loci in barley breeding programs.
Collapse
Affiliation(s)
- Cristina Silvar
- Department of Genetics and Plant Production, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
| | | | | | | | | | | |
Collapse
|
49
|
Larson SR, Kishii M, Tsujimoto H, Qi L, Chen P, Lazo GR, Jensen KB, Wang RRC. Leymus EST linkage maps identify 4NsL-5NsL reciprocal translocation, wheat-Leymus chromosome introgressions, and functionally important gene loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:189-206. [PMID: 21915709 DOI: 10.1007/s00122-011-1698-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/29/2011] [Indexed: 05/31/2023]
Abstract
Allotetraploid (2n = 4x = 28) Leymus triticoides and Leymus cinereus are divergent perennial grasses, which form fertile hybrids. Genetic maps with n = 14 linkage groups (LG) comprised with 1,583 AFLP and 67 heterologous anchor markers were previously used for mapping quantitative trait loci (QTLs) in these hybrids, and chromosomes of other Leymus wildryes have been transferred to wheat. However, identifications of the x = 7 homoeologous groups were tenuous and genetic research has been encumbered by a lack of functional, conserved gene marker sequences. Herein, we mapped 350 simple sequence repeats and 26 putative lignin biosynthesis genes from a new Leymus EST library and constructed one integrated consensus map with 799 markers, including 375 AFLPs and 48 heterologous markers, spanning 2,381 centiMorgans. LG1b and LG6b were reassigned as LG6b* and LG1b*, respectively, and LG4Ns and LG4Xm were inverted so that all 14 linkage groups are aligned to the x = 7 Triticeae chromosomes based on EST alignments to barley and other reference genomes. Amplification of 146 mapped Leymus ESTs representing six of the seven homoeologous groups was shown for 17 wheat-Leymus chromosome introgression lines. Reciprocal translocations between 4L and 5L in both Leymus and Triticum monococcum were aligned to the same regions of Brachypodium chromosome 1. A caffeic acid O-methyltransferase locus aligned to fiber QTL peaks on Leymus LG7a and brown midrib mutations of maize and sorghum. Glaucousness genes on Leymus and wheat chromosome 2 were aligned to the same region of Brachypodium chromosome 5. Markers linked to the S self-incompatibility gene on Leymus LG1a cosegregated with markers on LG2b, possibly cross-linked by gametophytic selection. Homoeologous chromosomes 1 and 2 harbor the S and Z gametophytic self-incompatibility genes of Phalaris, Secale, and Lolium, but the Leymus chromosome-2 self-incompatibility gene aligns to a different region on Brachypodium chromosome 5. Nevertheless, cosegregation of self-incompatibility genes on Leymus presents a powerful system for mapping these loci.
Collapse
Affiliation(s)
- Steven R Larson
- US Department of Agriculture, Agriculture Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT, 84322-6300, USA.
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. PLANT & CELL PHYSIOLOGY 2011; 52:2017-38. [PMID: 22156726 PMCID: PMC3233218 DOI: 10.1093/pcp/pcr153] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions. Recent game-changing sequencing technologies have revitalized sequencing approaches in genomics and have produced opportunities for various emerging analytical applications. Driven by technological advances, several new omics layers such as the interactome, epigenome and hormonome have emerged. Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances.
Collapse
Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.
| | | |
Collapse
|