1
|
Tomaszewska P, Vorontsova MS, Renvoize SA, Ficinski SZ, Tohme J, Schwarzacher T, Castiblanco V, de Vega JJ, Mitchell RAC, Heslop-Harrison JS(P. Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species. ANNALS OF BOTANY 2023; 131:87-108. [PMID: 34874999 PMCID: PMC9904353 DOI: 10.1093/aob/mcab147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/06/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. METHODS Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. KEY RESULTS Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. CONCLUSIONS We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.
Collapse
Affiliation(s)
| | | | | | | | - Joseph Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | - J S (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
2
|
Frittelli A, Botticella E, Palombieri S, Masci S, Celletti S, Fontanella MC, Astolfi S, De Vita P, Volpato M, Sestili F. The suppression of TdMRP3 genes reduces the phytic acid and increases the nutrient accumulation in durum wheat grain. FRONTIERS IN PLANT SCIENCE 2023; 14:1079559. [PMID: 36743506 PMCID: PMC9890658 DOI: 10.3389/fpls.2023.1079559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Micronutrient malnutrition affects more than half of the world population. Reduced bioavailability of microelements in the raw materials is considered one of the main causes of mineral deficiency in populations whose diet is largely based on the consumption of staple crops. In this context, the production of low phytic acid (lpa) cereals is a main goal of the breeding programs, as phytic acid (PA) binds essential mineral cations such as iron (Fe), zinc (Zn), manganese (Mn), potassium (K), calcium (Ca) and magnesium (Mg) precipitating in the form of phytate salts poorly digested by monogastric animals, including humans, due to the lack of phytases in the digestive tract. Since PA limits the bioavailability of microelements, it is widely recognized as an anti-nutritional compound. A Targeting Induced Local Lesions IN Genomes (TILLING) approach has been undertaken to silence the genes encoding the TdABCC13 proteins, known as Multidrug-Resistance associated Proteins 3 (TdMRP3), transporters involved in the accumulation of PA inside the vacuole in durum wheat. The TdMRP3 complete null genotypes showed a significant reduction in the content of PA and were able to accumulate a higher amount of essential micronutrients (Fe, Zn, Mn) compared to the control. The number of spikelets and seeds per spike, traits associated with the agronomic performances, were reduced compared to the control, but the negative effect was in part balanced by the increased grain weight. The TdMRP3 mutant lines showed morphological differences in the root apparatus such as a significant decrease in the number of root tips, root length, volume and surface area and an increase in root average diameter compared to the control plants. These materials represent a promising basis for obtaining new commercial durum wheats with higher nutritional value.
Collapse
Affiliation(s)
- Arianna Frittelli
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| | - Ermelinda Botticella
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| | - Samuela Palombieri
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| | - Stefania Masci
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| | - Silvia Celletti
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| | - Maria Chiara Fontanella
- Department for Sustainable Process, Faculty of Agriculture, Food and Environmental Science (DiSTAS), Università Cattolica, Piacenza, Italy
| | - Stefania Astolfi
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | | | - Francesco Sestili
- Department of Agriculture and Forest Science (DAFNE), University of Tuscia, Viterbo, Italy
| |
Collapse
|
3
|
Stockinger EJ. The Breeding of Winter-Hardy Malting Barley. PLANTS 2021; 10:plants10071415. [PMID: 34371618 PMCID: PMC8309344 DOI: 10.3390/plants10071415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/20/2022]
Abstract
In breeding winter malting barley, one recurring strategy is to cross a current preferred spring malting barley to a winter barley. This is because spring malting barleys have the greatest amalgamation of trait qualities desirable for malting and brewing. Spring barley breeding programs can also cycle their material through numerous generations each year-some managing even six-which greatly accelerates combining desirable alleles to generate new lines. In a winter barley breeding program, a single generation per year is the limit when the field environment is used and about two generations per year if vernalization and greenhouse facilities are used. However, crossing the current favored spring malting barley to a winter barley may have its downsides, as winter-hardiness too may be an amalgamation of desirable alleles assembled together that confers the capacity for prolonged cold temperature conditions. In this review I touch on some general criteria that give a variety the distinction of being a malting barley and some of the general trends made in the breeding of spring malting barleys. But the main objective of this review is to pull together different aspects of what we know about winter-hardiness from the seemingly most essential aspect, which is survival in the field, to molecular genetics and gene regulation, and then finish with ideas that might help further our insight for predictability purposes.
Collapse
Affiliation(s)
- Eric J Stockinger
- Ohio Agricultural Research and Development Center (OARDC), Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691, USA
| |
Collapse
|
4
|
Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
| |
Collapse
|
5
|
Wang RRC, Li X, Robbins MD, Larson SR, Bushman SB, Jones TA, Thomas A. DNA sequence-based mapping and comparative genomics of the St genome of Pseudoroegneria spicata (Pursh) Á. Löve versus wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.). Genome 2020; 63:445-457. [PMID: 32384249 DOI: 10.1139/gen-2019-0152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bluebunch wheatgrass (referred to as BBWG) [Pseudoroegneria spicata (Pursh) Á. Löve] is an important rangeland Triticeae grass used for forage, conservation, and restoration. This diploid has the basic St genome that occurs also in many polyploid Triticeae species, which serve as a gene reservoir for wheat improvement. Until now, the St genome in diploid species of Pseudoroegneria has not been mapped. Using a double-cross mapping populations, we mapped 230 expressed sequence tag derived simple sequence repeat (EST-SSR) and 3468 genotyping-by-sequencing (GBS) markers to 14 linkage groups (LGs), two each for the seven homologous groups of the St genome. The 227 GBS markers of BBWG that matched those in a previous study helped identify the unclassified seven LGs of the St sub-genome among 21 LGs of Thinopyrum intermedium (Host) Barkworth & D.R. Dewey. Comparisons of GBS sequences in BBWG to whole-genome sequences in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) revealed that the St genome shared a homology of 35% and 24%, a synteny of 86% and 84%, and a collinearity of 0.85 and 0.86, with ABD and H, respectively. This first-draft molecular map of the St genome will be useful in breeding cereal and forage crops.
Collapse
Affiliation(s)
- Richard R-C Wang
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Matthew D Robbins
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Steve R Larson
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Shaun B Bushman
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Thomas A Jones
- U.S. Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT 84322-6300, USA
| | - Aaron Thomas
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815, USA
| |
Collapse
|
6
|
Qi J, Ni F, Wang X, Sun M, Cui Y, Wu J, Caplan A, Fu D. The anther-specific CYP704B is potentially responsible for MSG26 male sterility in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2413-2423. [PMID: 31209536 DOI: 10.1007/s00122-019-03363-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Plant male sterility is a valuable trait in breeding and hybrid seed production. The barley male-sterility gene msg26 was mapped to a 0.02-cM region that anchors to a 506-kb low-quality assembly between two cleaved amplified polymorphic sequence (CAPS) markers, SP1M14 and SP1M49. The barley gene HORVU4Hr1G074840, which encodes a putative cytochrome P450 CYP704B protein, appears to be a strong candidate for the MSG26 trait. Barley (Hordeum vulgare L.) is an important cereal crop worldwide. Traditional breeding in barley is time-consuming and labor-intensive. The use of male-sterile genotypes may significantly improve the efficacy of hybrid breeding and seed production. The barley accession 'GSHO745' is a spontaneous male-sterile mutant from the barley variety, 'Unitan'. The male sterility in 'GSHO745' is controlled by the recessive gene, msg26 (originally named as ms-u). We revealed that the barley plants homozygous for msg26 proceeded normally through Meiosis II until the tetrad stage, but became fully defective in the late uninucleate microspores and developed pollen-less anthers. Using seven barley F2 populations, we mapped MSG26 to a 0.02-cM region that anchored to a 506-kb low-quality assembly between two cleaved amplified polymorphic sequence markers, SP1M14 and SP1M49. The HORVU4Hr1G074840 gene that encodes a putative cytochrome P450 protein (CYP704B) was identified as the most plausible candidate for MSG26. First, HORVU4Hr1G074840 is located in a collinear region of the rice CYP704B2 and the maize CYP704B1. Both of these genes are essential for male gamete production. Second, the male-sterile allele of HORVU4Hr1G074840 in GSHO745 contained a 4-bp deletion in the last exon. The resulting frame shift causes a Gly436Gln substitution, scrambles the sequence of the remainder of the protein, and forms a new termination site at the 70th triplet of the shifted reading frame. We thus called the variant protein CYP704B:p.G436Qfs*70. Third, the barley HORVU4Hr1G074840 gene was specifically expressed in anthers. Altogether, HORVU4Hr1G074840 represents a strong candidate for MSG26 in barley.
Collapse
Affiliation(s)
- Juan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Fei Ni
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Xiao Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Meng Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yu Cui
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Allan Caplan
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Daolin Fu
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA.
- Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
| |
Collapse
|
7
|
Efremova TT, Chumanova EV, Trubacheeva NV, Pershina LA. Compensation Ability between the Chromosomes of Homoeologous Group 7 of Triticum aestivum L. and Hordeum marinum ssp. gussoneanum Hudson (2n = 28) and Analysis of the Transmission Frequency of Alien 7H1Lmar Chromosome through Gametes in the Progeny of Wheat–Barley Substitution Lines. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
8
|
Montiel EE, Badenhorst D, Lee LS, Literman R, Trifonov V, Valenzuela N. Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes. Cytogenet Genome Res 2016; 148:292-304. [DOI: 10.1159/000447478] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 11/19/2022] Open
Abstract
Turtle karyotypes are highly conserved compared to other vertebrates; yet, variation in diploid number (2n = 26-68) reflects profound genomic reorganization, which correlates with evolutionary turnovers in sex determination. We evaluate the published literature and newly collected comparative cytogenetic data (G- and C-banding, 18S-NOR, and telomere-FISH mapping) from 13 species spanning 2n = 28-68 to revisit turtle genome evolution and sex determination. Interstitial telomeric sites were detected in multiple lineages that underwent diploid number and sex determination turnovers, suggesting chromosomal rearrangements. C-banding revealed potential interspecific variation in centromere composition and interstitial heterochromatin at secondary constrictions. 18S-NORs were detected in secondary constrictions in a single chromosomal pair per species, refuting previous reports of multiple NORs in turtles. 18S-NORs are linked to ZW chromosomes in Apalone and Pelodiscus and to X (not Y) in Staurotypus. Notably, comparative genomics across amniotes revealed that the sex chromosomes of several turtles, as well as mammals and some lizards, are homologous to components of Xenopus tropicalis XTR1 (carrying Dmrt1). Other turtle sex chromosomes are homologous to XTR4 (carrying Wt1). Interestingly, all known turtle sex chromosomes, except in Trionychidae, evolved via inversions around Dmrt1 or Wt1. Thus, XTR1 appears to represent an amniote proto-sex chromosome (perhaps linked ancestrally to XTR4) that gave rise to turtle and other amniote sex chromosomes.
Collapse
|
9
|
Carmona A, de Bustos A, Jouve N, Cuadrado Á. Allopolyploidy and the complex phylogenetic relationships within the Hordeum brachyantherum taxon. Mol Phylogenet Evol 2016; 97:107-119. [PMID: 26790585 DOI: 10.1016/j.ympev.2016.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022]
Abstract
Hordeum brachyantherum Nevski includes two subspecies: the diploid (2×) subsp. californicum, and subsp. brachyantherum, which itself includes a tetraploid (4×) and a hexaploid (6×) cytotype. The phylogenetic relationships between these taxa and the origin of the polyploids remain controversial. To provide additional information to the many molecular phylogenetic analyses conducted within Hordeum, FISH-based karyotypes were produced for all subspecies/cytotypes within H. brachyantherum. Chromosomes of H. roshevitzii and H. marinum subsp. gussoneanum were also analysed since these species are potentially involved in the origin of the polyploids. For karyotyping, ten repetitive DNA sequences were screened to indentify repeats showing sufficient diversity in terms of copy number and localisation that they might serve as physical markers for distinguishing between each mitotic chromosome pair in all accessions. Genomic in situ hybridisation (GISH) was used to distinguish between subgenomes in polyploids. The karyotype maps allowed the assessment of the chromosomal diversity within species/cytotypes and the identification of possibly homoeologous chromosomes. The results show a wide divergence between the chromosomes of subsp. californicum and H. roshevitzii, and with their supposed derivatives in subsp. brachyantherum 4×. One of the three subgenomes of subsp. brachyantherum 6× is derived from subsp. gussoneanum with no genomic reorganisation (i.e., neither amplification nor loss of the repetitive DNA sequences analysed). It is generally accepted that subsp. brachyantherum 4× is the other progenitor of subsp. brachyantherum 6×, but the present results suggest this to be unlikely. The present findings thus show the cytogenetic diversity and genomic structure of H. brachyantherum, and reveal its complex evolutionary history, in which chromosomal diversification and allopolyploidy have played important roles.
Collapse
Affiliation(s)
- Alejandro Carmona
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Alfredo de Bustos
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Nicolás Jouve
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Ángeles Cuadrado
- Department of Biomedicine and Biotechnologies, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain.
| |
Collapse
|
10
|
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
|
11
|
Georgieva M, Gecheff K. Molecular Cytogenetic Characterization of a New Reconstructed Barley Karyotype. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
12
|
Kitanova M, Georgiev S. Transcriptional Activity of Translocated NORs in Barley (Hordeum Vulgare L.). BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Meglena Kitanova
- Sofia University “St. Kliment Ohridski”, Faculty of Biology, Sofia, Bulgaria
| | - Sevdalin Georgiev
- Sofia University “St. Kliment Ohridski”, Faculty of Biology, Sofia, Bulgaria
| |
Collapse
|
13
|
Papazova N, Hvarleva T, Atanassov A, Gecheff K. The Role of Cytosine Methylation for rRNA Gene Expression in Reconstructed Karyotypes of Barley. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2001.10819102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
14
|
Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U. Kmasker--a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet Genome Res 2013; 142:66-78. [PMID: 24335088 DOI: 10.1159/000356460] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
Specific localization of large genomic fragments by fluorescence in situ hybridization (FISH) is challenging in large- genome plant species due to the high content of repetitive sequences. We report the automated work flow (Kmasker) for in silico extraction of unique genomic sequences of large genomic fragments suitable for FISH in barley. This method can be widely used for the integration of genetic and cytogenetic maps in plants and other species with large and complex genomes if the probe sequence (e.g. BACs, sequence contigs) and a low coverage (8-fold) of unassembled sequences of the species of interest are available. Kmasker has been made publicly available as a web tool at http://webblast.ipk-gatersleben.de/kmasker.
Collapse
Affiliation(s)
- T Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | | | | | | | | |
Collapse
|
15
|
Stoilov L, Georgieva M, Manova V, Liu L, Gecheff K. Karyotype reconstruction modulates the sensitivity of barley genome to radiation-induced DNA and chromosomal damage. Mutagenesis 2012; 28:153-60. [DOI: 10.1093/mutage/ges065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
16
|
Huynh BL, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis JCR, Edwards J, Shirley N, Langridge P, Fleury D. Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. PLANT MOLECULAR BIOLOGY 2012; 80:299-314. [PMID: 22864927 DOI: 10.1007/s11103-012-9949-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/23/2012] [Indexed: 05/21/2023]
Abstract
Fructans are soluble carbohydrates with health benefits and possible roles in plant adaptation. Fructan biosynthetic genes were isolated using comparative genomics and physical mapping followed by BAC sequencing in barley. Genes encoding sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT) and sucrose:fructan 6-fructosyltransferase (6-SFT) were clustered together with multiple copies of vacuolar invertase genes and a transposable element on two barley BAC. Intron-exon structures of the genes were similar. Phylogenetic analysis of the fructosyltransferases and invertases in the Poaceae showed that the fructan biosynthetic genes may have evolved from vacuolar invertases. Quantitative real-time PCR was performed using leaf RNA extracted from three wheat cultivars grown under different conditions. The 1-SST, 1-FFT and 6-SFT genes had correlated expression patterns in our wheat experiment and in existing barley transcriptome database. Single nucleotide polymorphism (SNP) markers were developed and successfully mapped to a major QTL region affecting wheat grain fructan accumulation in two independent wheat populations. The alleles controlling high- and low- fructan in parental lines were also found to be associated in fructan production in a diverse set of 128 wheat lines. To the authors' knowledge, this is the first report on the mapping and sequencing of a fructan biosynthetic gene cluster and in particular, the isolation of a novel 1-FFT gene from barley.
Collapse
Affiliation(s)
- Bao-Lam Huynh
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond 5064, South Australia,
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Isidro J, Knox R, Singh A, Clarke F, Krishna P, DePauw R, Clarke J, Somers D. Brassinosteroid leaf unrolling QTL mapping in durum wheat. PLANTA 2012; 236:273-281. [PMID: 22350765 DOI: 10.1007/s00425-012-1603-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 01/28/2012] [Indexed: 05/31/2023]
Abstract
Brassinosteroids are a newly reported class of plant growth phytohormones found in plants throughout the plant kingdom. Functioning at very low concentrations, they play an essential role in improving biomass yield and stress tolerance. There are no reports in the literature of the genetic variability of responsiveness of brassinosteroids in wheat; most studies on brassinosteroids have focused on the physiological effects of exogenous addition of brassinosteroids. Our aim was to study the genetic variation in the responsiveness of a doubled haploid durum wheat population to three brassinosteroid concentrations using the leaf unrolling test, which is a simple bioassay to test brassinosteroid activity. An F(1)-derived doubled haploid population of 77 individuals from the cross Strongfield/Blackbird was used to construct a genetic map of 427 molecular marker loci. The leaf unrolling test was performed on the parents and doubled haploid genotypes of the population using 0.2, 2 and 20 nM brassinosteroid concentrations. The results indicated significant differences in leaf unrolling between the two parents, doubled haploid genotypes, treatments and genotype-by-treatment combinations. Transgressive segregation beyond Strongfield of leaf unrolling was observed for all concentrations, with the strongest response at 20 nM. Putative quantitative trait loci were revealed in the intervals Xgwm2-Xbarc45 on chromosome 3A and Xwmc643a-Xwmc625a on chromosome 3B. Additional quantitative trait loci were associated with markers Xwmc48a, Xwmc511, Xwmc89a and Xgwmc692 on chromosome 4B, and Xwmc17 on chromosome 7A. This work should enhance the understanding of the relationship between stress tolerance and productivity, and responsiveness to brassinosteroids.
Collapse
Affiliation(s)
- Julio Isidro
- Semiarid Prairie Agriculture Research Centre, Agriculture and Agri-Food Canada (AAFC), Swift Current, SK, S9H 3X2, Canada
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc Natl Acad Sci U S A 2012; 109:1176-81. [PMID: 22228301 DOI: 10.1073/pnas.1112041109] [Citation(s) in RCA: 235] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid, Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes. Importantly, 85% of plants exhibiting aneuploidy still had the expected chromosome number, mostly through reciprocal monosomy-trisomy of homeologous chromosomes (1:3 copies) or nullisomy-tetrasomy (0:4 copies). The extensive chromosomal variation still present after ca. 40 generations in this biennial species suggests that substantial and prolonged chromosomal instability might be common in natural populations after whole genome duplication. A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression.
Collapse
|
19
|
Kato A. High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures. Genome 2011; 54:151-9. [DOI: 10.1139/g10-098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The barley ( Hordeum vulgare L.) genome was screened to identify sequences that could be used for fluorescence in situ hybridization (FISH). From 2000 transformed bacterium colonies carrying barley clones, 56 colonies were selected on the basis of the patterns that their PCR products produced when subjected to agarose gel electrophoresis. Among them, 42 (75%) exhibited fluorescent signals on barley chromosomes after in situ hybridization using the directly labeled PCR products. Sequencing revealed seven clones, pHv-365, pHv-177, pHv-1112, pHv-689, pHv-1476, pHv-1889, and pHv-1972, to be newly identified FISH-positive sequences. The remainder possess previously described sequences such as 5S, GAA microsatellite, centromere repeats, HVT01, and pHvMWG2315 (324 bp repeat). It is shown here that a combination of five probes, which produce strong signals on barley chromosomes, pHv-38 (5S), pHv-365, pHv-961 (HVT01), GAA, and TAG microsatellites, offer unequivocal recognition of each chromosome. The combination of three probes, i.e., pHv-1123 (barley 324 bp repeat), GAA, and TAG, decorated entire chromosomes with fine dotted signals and was useful for detecting the break points of aberrant chromosomes. The signals’ distributions of pHv-177, pHv-1112, and TAG were highly polymorphic. An improved reprobing procedure and its usefulness are also discussed.
Collapse
Affiliation(s)
- Akio Kato
- Laboratory of Plant Breeding, Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-0823, Japan. (e-mail: )
| |
Collapse
|
20
|
Joshi GP, Nasuda S, Endo TR. Dissection and cytological mapping of barley chromosome 2H in the genetic background of common wheat. Genes Genet Syst 2011; 86:231-48. [DOI: 10.1266/ggs.86.231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Giri Prasad Joshi
- Laboratory of plant genetics, Graduate School of Agriculture, Kyoto University
| | - Shuhei Nasuda
- Laboratory of plant genetics, Graduate School of Agriculture, Kyoto University
| | - Takashi R. Endo
- Laboratory of plant genetics, Graduate School of Agriculture, Kyoto University
| |
Collapse
|
21
|
Pershina LA, Devyatkina EP, Belova LI, Trubacheeva NV, Arbuzova VS, Kravtsova LA. Features of alloplasmic wheat-barley substitution and addition lines (Hordeum marinum subsp. gussoneanum)-Triticum aestivum. RUSS J GENET+ 2009. [DOI: 10.1134/s102279540910010x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
22
|
Genomic diversity of germinating scutellum specific gene P23k in barley and wheat. Genetica 2009; 137:233-42. [PMID: 19641998 DOI: 10.1007/s10709-009-9394-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
Abstract
P23k is a 23 kDa protein involved in sugar translocation in the scutellum of germinating barley seeds. The present study was carried out to provide the genomic characterization for P23k gene in terms of copy number, chromosome mapping, genetic mapping and expression analysis in germinating sculletum in two major Triticeae crops, barley and wheat, and their relatives. Southern blotting showed that a variable copy number with different restriction fragment sizes was found among 15 Hordeum accessions, while low copy number were found to be conserved in 23 Triticum and 3 Aegilops accessions. Genetic and physical mapping study identified that the P23k gene is duplicated in wild and cultivated barley on chromosomes 1H, 2H, and 3H, and further tandem duplication on chromosomes 1H and 3H. In contrast, the wheat P23k is located on chromosome 3A of durum wheat and at the distal portion of the long arms of 3A and 3D chromosomes of bread wheat. Northern blotting showed remarkably high accumulation of P23k transcript in the germinating scutellum in cultivated and wild barley, whereas very few or no accumulation was detected in diploid, tetraploid, and hexaploid wheat accessions. The present study suggests a simple scenario where the ancestral P23k is encoded on the distal portion of an ancestral chromosome of homoeologous chromosome 3. Beside of polyploidy, dispersed and tandem duplications could trigger generation of the P23k family in the Hordeum lineage, while an ancestral P23k has been conserved in homoeologous 3A and 3D chromosomes in the wheat lineage.
Collapse
|
23
|
Kim NS, Fedak G, Han F, Cao W. Cytogenetic analyses of intergeneric hybrids between barley and nine species of Elymus. Genome 2008; 51:897-904. [PMID: 18956022 DOI: 10.1139/g08-074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wild species in the Triticeae tribe are very valuable resources for agronomic improvement in cereal crop species. Intergeneric hybrids were produced between several barley cultivars and perennial species in the genera Elymus, Thinopyrum, and Pseudoroegneria. Caryopsis formation and subsequent plantlet regeneration from embryo culture were variable depending on the hybrid combinations. Chromosome numbers and hybrid identity were confirmed by GISH analysis on the somatic cells of the hybrids. While the hybrids showed very robust vegetative growth and exceeded the parental spikes in size, their floral morphologies resembled that of the wild species. Meiotic chromosome analysis revealed that the bivalent formation frequency per cell ranged from 0.06 in Hordeum vulgare 'Betzes' x Elymus curvatus to 3.0 in Elymus humidus x H. vulgare 'Manley'. By GISH analysis on the meiocytes of the hybrid E. humidus x 'Manley', the frequency of autosyndetic bivalents exceeded the allosyndetic bivalent formation, which gave an insight into the genome constitution of E. humidus as an autoallohexploid species. Regardless of the low allosyndetic chromosome pairing between barley and E. humidus, this combination may be useful for further input, since E. humidus is known to carry many valuable genes for biotic and abiotic stress tolerance.
Collapse
Affiliation(s)
- N-S Kim
- Department of Molecular Biosciences, Kangwon National University, Chunchon, Korea
| | | | | | | |
Collapse
|
24
|
Bovill WD, Deveshwar P, Kapoor S, Able JA. Whole genome approaches to identify early meiotic gene candidates in cereals. Funct Integr Genomics 2008; 9:219-29. [PMID: 18836753 DOI: 10.1007/s10142-008-0097-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/16/2008] [Accepted: 09/16/2008] [Indexed: 11/25/2022]
Abstract
Early events during meiotic prophase I underpin not only viability but the variation of a species from generation to generation. Understanding and manipulating processes such as chromosome pairing and recombination are integral for improving plant breeding. This study uses comparative genetics, quantitative trait locus (QTL) analysis and a transcriptomics-based approach to identify genes that might have a role in genome-wide recombination control. Comparative genetics and the analysis of the yeast and Arabidopsis sequenced genomes has allowed the identification of early meiotic candidates that are conserved in wheat, rice and barley. Secondly, scoring recombination frequency as a phenotype for QTL analysis across wheat, rice and barley mapping populations has enabled us to identify genomic regions and candidate genes that could be involved in genome-wide recombination. Transcriptome data for candidate genes indicate that they are expressed in meiotic tissues. Candidates identified included a non-annotated expressed protein, a DNA topoisomerase 2-like candidate, RecG, RuvB and RAD54 homologues.
Collapse
Affiliation(s)
- William D Bovill
- School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
| | | | | | | |
Collapse
|
25
|
Li H, Vaillancourt R, Mendham N, Zhou M. Comparative mapping of quantitative trait loci associated with waterlogging tolerance in barley (Hordeum vulgare L.). BMC Genomics 2008; 9:401. [PMID: 18752688 PMCID: PMC2533678 DOI: 10.1186/1471-2164-9-401] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 08/27/2008] [Indexed: 11/10/2022] Open
Abstract
Background Resistance to soil waterlogging stress is an important plant breeding objective in high rainfall or poorly drained areas across many countries in the world. The present study was conducted to identify quantitative trait loci (QTLs) associated with waterlogging tolerance (e.g. leaf chlorosis, plant survival and biomass reduction) in barley and compare the QTLs identified across two seasons and in two different populations using a composite map constructed with SSRs, RFLP and Diversity Array Technology (DArT) markers. Results Twenty QTLs for waterlogging tolerance related traits were found in the two barley double haploid (DH) populations. Several of these QTLs were validated through replication of experiments across seasons or by co-location across populations. Some of these QTLs affected multiple waterlogging tolerance related traits, for example, QTL Qwt4-1 contributed not only to reducing barley leaf chlorosis, but also increasing plant biomass under waterlogging stress, whereas other QTLs controlled both leaf chlorosis and plant survival. Conclusion Improving waterlogging tolerance in barley is still at an early stage compared with other traits. QTLs identified in this study have made it possible to use marker assisted selection (MAS) in combination with traditional field selection to significantly enhance barley breeding for waterlogging tolerance. There may be some degree of homoeologous relationship between QTLs controlling barley waterlogging tolerance and that in other crops as discussed in this study.
Collapse
Affiliation(s)
- Haobing Li
- Tasmanian Institute of Agricultural Research and School of Agricultural Science, University of Tasmania, P,O, Box 46, Kings Meadows, TAS 7249, Australia.
| | | | | | | |
Collapse
|
26
|
Castiglione MR, Venora G, Ravalli C, Stoilov L, Gecheff K, Cremonini R. DNA methylation and chromosomal rearrangements in reconstructed karyotypes of Hordeum vulgare L. PROTOPLASMA 2008; 232:215-222. [PMID: 18274698 DOI: 10.1007/s00709-007-0275-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 05/23/2007] [Indexed: 05/25/2023]
Abstract
One standard and two reconstructed barley karyotypes were used to study the influence of chromosomal rearrangements on the distribution pattern of DNA methylation detectable at the chromosome level. Data obtained were also compared with Giemsa N-bands and high gene density regions that had been previously described. The effect of chromosomal reconstruction in barley seems to be decidedly prominent in the repositioning of genomic DNA methylation along metaphase chromosomes. In comparison to the standard karyotype, the DNA methylation pattern was found to vary not only in the reconstructed chromosomes but also in the other chromosomes of the complements not subjected to structural alterations. Moreover, differences may occur between corresponding regions of homologues. Some specific chromosomal bands, including the nucleolus-organizing regions, showed a relative constancy in the methylation pattern, but this was not the case when the two satellites were combined by translocation in chromosome 6H(5H) of line T-30. Our results suggest that epigenetic changes like DNA methylation may play an important role in the overall genome reorganization following chromosome reconstruction.
Collapse
|
27
|
Cuadrado A, Jouve N. Similarities in the chromosomal distribution of AG and AC repeats within and between Drosophila, human and barley chromosomes. Cytogenet Genome Res 2007; 119:91-9. [PMID: 18160787 DOI: 10.1159/000109624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 06/20/2007] [Indexed: 11/19/2022] Open
Abstract
Two simple sequence repeats (SSRs), AG and AC, were mapped directly in the metaphase chromosomes of man and barley (Hordeum vulgare L.), and in the metaphase and polytene chromosomes of Drosophila melanogaster. To this end, synthetic oligonucleotides corresponding to (AG)(12) and (AC)(8) were labelled by the random primer technique and used as probes in fluorescent in situ hybridisation (FISH) under high stringency and strict washing conditions. The distribution and intensity of the signals for the repeat sequences were found to be characteristic of the chromosomes and genomes of the three species analysed. The AC repeat sites were uniformly dispersed along the euchromatic segments of all three genomes; in fact, they were largely excluded from the heterochromatin. The Drosophila genome showed a high density of AC sequences on the X chromosome in both mitotic and polytene nuclei. In contrast, the AG repeats were associated with the euchromatic regions of the polytene chromosomes (and in high density on the X chromosome), but were only seen in specific heterochromatic regions in the mitotic chromosomes of all three species. In Drosophila, the AG repeats were exclusively distributed on the tips of the Y chromosome and near the centromere on both arms of chromosome 2. In barley and man, AG repeats were associated with the centromeres (of all chromosomes) and nucleolar organizer regions, respectively. The conserved chromosome distribution of AC within and between these three phylogenetically distant species, and the association of AG in specific chromosome regions with structural or functional properties, suggests that long clusters of these repeats may have some, as yet unknown, role.
Collapse
Affiliation(s)
- A Cuadrado
- Department of Cell Biology and Genetics, University of Alcalá, Madrid, Spain.
| | | |
Collapse
|
28
|
Cuadrado A, Jouve N. The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes. Chromosome Res 2007; 15:711-20. [PMID: 17874212 DOI: 10.1007/s10577-007-1156-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 04/26/2007] [Accepted: 04/26/2007] [Indexed: 10/22/2022]
Abstract
This paper is the first to report the long-range organization of all possible classes of trinucleotide motifs in a higher plant genome. Fluorescent in situ hybridization (FISH), employing the synthetic oligonucleotides (AAC)5, (AAG)5, (AAT)5, (AGG)5, (CAC)5, (CAT)5, (CAG)5, (ACT)5, (ACG)5 and (GCC)5, was used to characterize the nonrandom and motif-dependent distribution of tandem arrays of trinucleotide repeats in the metaphase chromosomes and interphase nuclei of barley (Hordeum vulgare L.). This provided detailed information on the sequence content of barley chromatin and allowed the saturation of the physical map of all barley chromosomes. The following conclusions were also drawn: (1) Except for (AAT)5 and (GCC)5, the studied repetitive motifs have a characteristic pattern of distribution in terms of their in situ FISH signals. Some permit the accurate identification of individual chromosomes. (2) (CAG)5, (CAT)5 and (ACT)5 are not found in all barley chromosomes. (3) With the exception of (ACT)5, the remaining trinucleotide repeats occur predominantly in the heterochromatin and are largely absent from the euchromatic regions. Moreover, (CAC)5, (ACG)5 and (CAG)5 are exclusively concentrated in the centromeres. The employment of simple synthetic probes for the identification of chromosomes and genomic characterization, and their importance in studies on genome organization, function and evolution, are discussed.
Collapse
Affiliation(s)
- Angeles Cuadrado
- Department of Cell Biology and Genetics, University of Alcalá, 28871 Alcalá de Henares, Madrid, Spain.
| | | |
Collapse
|
29
|
Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, Lundqvist U, Fujimura T, Matsuoka M, Matsumoto T, Yano M. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci U S A 2007; 104:1424-9. [PMID: 17220272 PMCID: PMC1783110 DOI: 10.1073/pnas.0608580104] [Citation(s) in RCA: 352] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Indexed: 11/18/2022] Open
Abstract
Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1.
Collapse
Affiliation(s)
- Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Ashida T, Nasuda S, Sato K, Endo TR. Dissection of barley chromosome 5H in common wheat. Genes Genet Syst 2007; 82:123-33. [PMID: 17507778 DOI: 10.1266/ggs.82.123] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We dissected barley chromosome 5H added to common wheat by a genetic method or the gametocidal system. Firstly, we induced chromosomal breaks in the offspring of a 5H addition line of common wheat carrying a gametocidal chromosome and cytologically screened for plants with structural chromosomal changes involving 5H, such as deletions and translocations. Secondly, we screened the progeny of such plants to establish common wheat lines carrying structurally changed chromosomes containing single segments of the dissected 5H. Using 23 representative 5H dissection lines, we physically mapped 97 barley EST markers assigned to 5H. The ESTs fell into 20 regions of 5H between the breakpoints of the 23 dissected segments, distributing rather evenly along the chromosome, with significantly higher frequency in the distal region of the long arm. The ESTs, in turn, allowed us to distinguish the breakpoints of dissected 5H segments. We demonstrated by PCR (polymerase chain reaction), as well as by in situ hybridization, that these dissected 5H segments were stably transmitted in the dissection lines. We discuss the usefulness of the 5H dissection lines for physical mapping of DNA markers. These 5H dissection lines are available from National BioResource Projects-Wheat, Japan.
Collapse
Affiliation(s)
- Taizo Ashida
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Japan
| | | | | | | |
Collapse
|
31
|
Liu S, Zhang X, Pumphrey MO, Stack RW, Gill BS, Anderson JA. Complex microcolinearity among wheat, rice, and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat. Funct Integr Genomics 2005; 6:83-9. [PMID: 16270217 DOI: 10.1007/s10142-005-0007-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 09/04/2005] [Accepted: 09/04/2005] [Indexed: 10/25/2022]
Abstract
A major quantitative trait locus (QTL), Qfhs.ndsu-3BS, for resistance to Fusarium head blight (FHB) in wheat has been identified and verified by several research groups. The objectives of this study were to construct a fine genetic map of this QTL region and to examine microcolinearity in the QTL region among wheat, rice, and barley. Two simple sequence repeat (SSR) markers (Xgwm533 and Xgwm493) flanking this QTL were used to screen for recombinants in a population of 3,156 plants derived from a single F(7) plant heterozygous for the Qfhs.ndsu-3BS region. A total of 382 recombinants were identified, and they were genotyped with two more SSR markers and eight sequence-tagged site (STS) markers. A fine genetic map of the Qfhs.ndsu-3BS region was constructed and spanned 6.3 cM. Based on replicated evaluations of homozygous recombinant lines for Type II FHB resistance, Qfhs.ndsu-3BS, redesignated as Fhb1, was placed into a 1.2-cM marker interval flanked by STS3B-189 and STS3B-206. Primers of STS markers were designed from wheat expressed sequence tags homologous to each of six barley genes expected to be located near this QTL region. A comparison of the wheat fine genetic map and physical maps of rice and barley revealed inversions and insertions/deletions. This suggests a complex microcolinearity among wheat, rice, and barley in this QTL region.
Collapse
Affiliation(s)
- Sixin Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | | | | | | | | | | |
Collapse
|
32
|
Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R. Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 2005; 274:515-27. [PMID: 16244872 DOI: 10.1007/s00438-005-0046-z] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Accepted: 08/20/2005] [Indexed: 10/25/2022]
Abstract
More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity. More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP, AFLP and SSR markers (1,237 loci in total). The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses. A set of known barley abiotic stress QTL was positioned on the linkage map, while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits. Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest. The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms.
Collapse
Affiliation(s)
- Nils Rostoks
- Genome Dynamics, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Taketa S, Ando H, Takeda K, Ichii M, von Bothmer R. Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA. ANNALS OF BOTANY 2005; 96:23-33. [PMID: 15829509 PMCID: PMC4246806 DOI: 10.1093/aob/mci147] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS The genus Hordeum exists at three ploidy levels (2x, 4x and 6x) and presents excellent material for investigating the patterns of polyploid evolution in plants. Here the aim was to clarify the ancestry of American polyploid species with the I genome. * METHODS Chromosomal locations of 5S and 18S-25S ribosomal RNA genes were determined by fluorescence in situ hybridization (FISH). In both polyploid and diploid species, variation in 18S-25S rDNA repeated sequences was analysed by the RFLP technique. * KEY RESULTS Six American tetraploid species were divided into two types that differed in the number of rDNA sites and RFLP profiles. Four hexaploid species were similar in number and location of both types of rDNA sites, but the RFLP profiles of 18S-25S rDNA revealed one species, H. arizonicum, with a different ancestry. * CONCLUSIONS Five American perennial tetraploid species appear to be alloploids having the genomes of an Asian diploid H. roshevitzii and an American diploid species. The North American annual tetraploid H. depressum is probably a segmental alloploid combining the two closely related genomes of American diploid species. A hexaploid species, H. arizonicum, involves a diploid species, H. pusillum, in its ancestry; both species share the annual growth habit and are distributed in North America. Polymorphisms of rDNA sites detected by FISH and RFLP analyses provide useful information to infer the phylogenetic relationships of I-genome Hordeum species because of their highly conserved nature during polyploid evolution.
Collapse
Affiliation(s)
- Shin Taketa
- Faculty of Agriculture, Kagawa University, Ikenobe, Miki, Kagawa 761-0795, Japan.
| | | | | | | | | |
Collapse
|
34
|
Morimoto R, Kosugi T, Nakamura C, Takumi S. Intragenic diversity and functional conservation of the three homoeologous loci of the KN1-type homeobox gene Wknox1 in common wheat. PLANT MOLECULAR BIOLOGY 2005; 57:907-24. [PMID: 15952073 DOI: 10.1007/s11103-005-3247-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 03/07/2005] [Indexed: 05/02/2023]
Abstract
Common wheat represents a typical allohexaploid species and provides a good experimental system for studying genomic alterations associated with allopolyploidization. We studied three homoeologous loci of wheat Wknox1 gene, which is highly homologous to the knotted1 (kn1)-like homeobox (KNOX) genes functioning at shoot apical meristems (SAM). Wknox1 transcripts were detected in SAM, and its overexpression caused abnormal leaf morphology with occasional ectopic leaves in transgenic tobacco plants. A comparative study of the three Wknox1 genomic sequences revealed accumulation of a large number of mutations including insertions and deletions, particularly in the fourth intron and the 5'-upstream region. Some structural mutations including MITE-insertions were allocated in the evolutionary lineage of the wheat genome, suggesting that they occurred at all stages of wheat evolution. A mutation rate was the highest in the Wknox1b locus, which is consistent with the known highest degree of differentiation in the B genome. Despite the structural differentiation, all three Wknox1 homoeologs showed an identical expression pattern in wheat and their promoter regions induced the conserved expression pattern in transgenic tobacco plants. A potential of the intragenic diversity in homoeologs of essential genes as a tool for studying the genome evolution associated with allopolyploidization was discussed.
Collapse
MESH Headings
- 5' Flanking Region/genetics
- Base Sequence
- Cloning, Molecular
- DNA Transposable Elements/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Evolution, Molecular
- Exons/genetics
- Gene Expression Profiling
- Genes, Plant/genetics
- Genetic Variation
- Genome, Plant
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/physiology
- Introns/genetics
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutation
- Plant Proteins/genetics
- Plant Proteins/physiology
- Plants, Genetically Modified
- Polymorphism, Single Nucleotide
- Polyploidy
- Protein Isoforms/genetics
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Analysis, DNA
- Sequence Deletion
- Sequence Homology, Nucleic Acid
- Triticum/genetics
- Triticum/physiology
Collapse
Affiliation(s)
- Ryoko Morimoto
- Laboratory of Plant Genetics, Department of Biological and Environmental Science, Faculty of Agriculture, and Graduate School of Science and Technology, Kobe University, 657-8501, Rokkodai-cho, Nada-ku, Kobe, Japan
| | | | | | | |
Collapse
|
35
|
Komatsuda T, Maxim P, Senthil N, Mano Y. High-density AFLP map of nonbrittle rachis 1 (btr1) and 2 (btr2) genes in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:986-95. [PMID: 15490100 DOI: 10.1007/s00122-004-1710-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2004] [Accepted: 04/15/2004] [Indexed: 05/18/2023]
Abstract
Wild relatives of barley disperse their seeds at maturity by means of their brittle rachis. In cultivated barley, brittleness of the rachis was lost during domestication. Nonbrittle rachis of occidental barley lines is controlled by a single gene (btr1) on chromosome 3H. However, nonbrittle rachis of oriental barley lines is controlled by a major gene (btr2) on chromosome 3H and two quantitative trait loci on chromosomes 5HL and 7H. This result suggests multiple mutations of the genes involved in the formation of brittle rachis in oriental lines. The btr1 and btr2 loci did not recombine in the mapping population analyzed. This result agrees with the theory of tight linkage between the two loci. A high-density amplified fragment-length polymorphism (AFLP) map of the btr1/btr2 region was constructed, providing an average density of 0.08 cM/locus. A phylogenetic tree based on the AFLPs showed clear separation of occidental and oriental barley lines. Thus, barley consists of at least two lineages as far as revealed by molecular markers linked to nonbrittle rachis genes.
Collapse
Affiliation(s)
- T Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | | | | | | |
Collapse
|
36
|
Stephens JL, Brown SE, Lapitan NLV, Knudson DL. Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 2004; 47:179-89. [PMID: 15060614 DOI: 10.1139/g03-084] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The primary objective of this study was to elucidate gene organization and to integrate the genetic linkage map for barley (Hordeum vulgare L.) with a physical map using ultrasensitive fluorescence in situ hybridization (FISH) techniques for detecting signals from restriction fragment length polymorphism (RFLP) clones. In the process, a single landmark plasmid, p18S5Shor, was constructed that identified and oriented all seven of the chromosome pairs. Plasmid p18S5Shor was used in all hybridizations. Fourteen cDNA probes selected from the linkage map for barley H. vulgare 'Steptoe' x H. vulgare 'Morex' (Kleinhofs et al. 1993) were mapped using an indirect tyramide signal amplification technique and assigned to a physical location on one or more chromosomes. The haploid barley genome is large and a complete physical map of the genome is not yet available; however, it was possible to integrate the linkage map and the physical locations of these cDNAs. An estimate of the ratio of base pairs to centimorgans was an average of 1.5 Mb/cM in the distal portions of the chromosome arms and 89 Mb/cM near the centromere. Furthermore, while it appears that the current linkage maps are well covered with markers along the length of each arm, the physical map showed that there are large areas of the genome that have yet to be mapped.
Collapse
Affiliation(s)
- J L Stephens
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
| | | | | | | |
Collapse
|
37
|
Kikuchi S, Taketa S, Ichii M, Kawasaki S. Efficient fine mapping of the naked caryopsis gene ( nud) by HEGS (High Efficiency Genome Scanning)/AFLP in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 108:73-78. [PMID: 12942174 DOI: 10.1007/s00122-003-1413-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2003] [Accepted: 05/12/2003] [Indexed: 05/24/2023]
Abstract
The hulled or naked caryopsis character of barley ( Hordeum vulgare L.) is an important trait for edibility and to follow its domestication process. A single recessive gene, nud, controls the naked caryopsis character, and is located on the long arm of chromosome 7H. To develop a fine map around the nud locus efficiently, the HEGS (High Efficiency Genome Scanning) electrophoresis system was combined with amplified fragment length polymorphism (AFLP). From bulked segregant analysis of 1,894 primer combinations, 12 AFLP fragments were selected as linked markers. For mapping, an F(2 )population of 151 individuals derived from a cross between Kobinkatagi (naked type) and Triumph (hulled type) was used. Seven AFLP markers were localized near the nud region. A fine map was developed with one-order higher resolution than before, along with the seven anchor markers. Among the seven linked AFLP markers (KT1-7), KT1, KT2 and KT6 were co-dominant, and the former two were detected for their single-nucleotide polymorphisms (SNPs) in the same length of fragments after electrophoresis with the non-denaturing gels of HEGS. The nud locus has co-segregated with KT3 and KT7, and was flanked by KT2 and KT4, at the 0.3-cM proximal and the 1.2-cM distal side, respectively. Four of these AFLP markers were converted into sequence-characterized amplified region (SCAR) markers, one of which was a dominant marker co-segregating with the nud gene.
Collapse
Affiliation(s)
- S Kikuchi
- Faculty of Agriculture, Kagawa University, Ikenobe, Miki-cho, Kita-gun, 761-0795, Kagawa, Japan
| | | | | | | |
Collapse
|
38
|
Kawahara T, Taketa S, Murai K. Differential effects of cultivated and wild barley 5H chromosomes on heading characters in wheat-barley chromosome addition lines. Hereditas 2003; 136:195-200. [PMID: 12471665 DOI: 10.1034/j.1601-5223.2002.1360303.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Wheat (Triticum aestivum L.)-barley (Hordeum vulgare L.) chromosome addition lines are possible vehicles for transferring barley genes into wheat. The barley 5H chromosome has genetic effects on the heading characters in wheat-barley addition lines: accelerating narrow-sense earliness, decreasing vernalization requirement and/or increasing photoperiodic sensitivity. To elucidate the effects of different 5H chromosomes under an identical wheat genetic background, two wheat-barley addition lines, i.e. cultivated barley 'New Golden' 5H chromosome added to 'Shinchunaga' wheat (Shi-NG5H) and wild barley H. vulgare ssp. spontaneum 5H chromosome added to 'Shinchunaga' wheat (Shi-Spn5H), were examined for their heading characters. The addition line Shi-NG5H showed a significantly lower vernalization requirement in comparison with 'Shinchunaga' wheat, whereas Shi-Spn5H did not. Furthermore, both NG5H and Spn5H chromosomes shortened narrow-sense earliness and increased photoperiodic sensitivity in wheat, but the effects of Spn5H were weaker than those of NG5H. The fact that NG5H and Spn5H showed differential effects on heading characters in wheat demonstrated that the heading characters were altered by the function of the barley genes located on 5H chromosomes, not merely by the aneuploid effect alone.
Collapse
Affiliation(s)
- Tomoko Kawahara
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka-cho, Yoshida-gun, Fukui 910-1195, Japan
| | | | | |
Collapse
|
39
|
Taketa S, Linde-Laursen I, Künzel G. Cytogenetic diversity. DEVELOPMENTS IN PLANT GENETICS AND BREEDING 2003. [DOI: 10.1016/s0168-7972(03)80008-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
40
|
Nagy ED, Molnár-Láng M, Linc G, Láng L. Identification of wheat-barley translocations by sequential GISH and two-colour FISH in combination with the use of genetically mapped barley SSR markers. Genome 2002; 45:1238-47. [PMID: 12502270 DOI: 10.1139/g02-068] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Five wheat-barley translocations in a wheat background were characterized through the combination of cytogenetic and molecular genetic approaches. The wheat chromosome segments involved in the translocations were identified using sequential GISH and two-colour FISH with the probes pSc119.2 and pAs1. The barley chromatin in these lines was identified using SSR markers. A total of 45 markers distributed over the total barley genome were selected from a recently published linkage map of barley and tested on the translocation lines. The following translocations were identified: 2DS.2DL-1HS, 3HS.3BL, 6BS.6BL-4HL, 4D-5HS, and 7DL.7DS-5HS. Wheat-barley disomic and ditelosomic addition lines for the chromosomes 3HS, 4H, 4HL, 5H, 5HL, and 6HS were used to determine the correct location of 21 markers and the position of the centromere. An intragenomic translocation breakpoint was detected on the short arm of the barley chromosome 5H with the help of SSR marker analysis. Physical mapping of the SSR markers on chromosomes 1H and 5H was carried out using the intragenomic and the interspecific translocation breakpoints, as well as the centromere, as physical landmarks.
Collapse
Affiliation(s)
- E D Nagy
- Agricultural Research Institute of the Hungarian Academy of Sciences, H-2462, Martonvasar, P.O. Box 19, Hungary
| | | | | | | |
Collapse
|
41
|
Hernández P, Dorado G, Martín A. Cross-species amplification of the Hordeum chilense genome using barley sequence-tagged-sites (STSs). Hereditas 2002; 135:243-6. [PMID: 12152342 DOI: 10.1111/j.1601-5223.2001.00243.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A selection of 51 barley Sequence-Tagged Sites (STSs) were studied for their utility in Hordeum chilense. They included four primer sets from wheat origin and six primer sets from oat origin. Forty-four primer pairs amplified H. chilense products consistently. Five primer pairs were suitable for studying the introgression of H. chilense in wheat because they amplified H. chilense products of distinct size. Six of the STSs showed polymorphism between different H. chilense accessions. The results showed that barley STSs could be useful for the genetic characterization of H. chilense, tritordeums and derived introgression lines.
Collapse
Affiliation(s)
- P Hernández
- Instituto de Agricultura Sostenible (CSIC), Apdo. 4084, 14080 Córdoba, Spain.
| | | | | |
Collapse
|
42
|
Taketa S, Choda M, Ohashi R, Ichii M, Takeda K. Molecular and physical mapping of a barley gene on chromosome arm 1 HL that causes sterility in hybrids with wheat. Genome 2002; 45:617-25. [PMID: 12175064 DOI: 10.1139/g02-024] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Addition of the long arm of barley chromosome 1H (1HL) to wheat causes severe meiotic abnormalities and complete sterility of the plants. To map the barley gene responsible for the 1H-induced sterility of wheat, a series of addition lines of translocated 1H chromosomes were developed from the crosses between the wheat 'Shinchunaga' and five reciprocal translocation lines derived from the barley line St.13559. Examination of the seed fertility of the addition lines revealed that the sterility gene is located in the interstitial 25% region of the 1HL arm. The genetic location of the sterility gene was also estimated by physically mapping sequence-tagged site (STS) markers and simple-sequence repeat (SSR) markers with known map locations. The sterility gene is designated Shw (sterility in hybrids with wheat). Comparison of the present physical map of 1HL with two previously published genetic maps revealed a paucity of markers in the proximal 30% region and non-random distribution of SSR markers. Two inconsistencies in marker order were found between the present physical map and the consensus genetic map of group 1 chromosomes of Triticeae. On the basis of the effects on meiosis and chromosomal location, the relationship of the present sterility gene with other fertility-related genes of Triticeae is discussed.
Collapse
Affiliation(s)
- Shin Taketa
- Faculty of Agriculture, Kagawa University, Ikenobe, Kita-gun, Japan.
| | | | | | | | | |
Collapse
|
43
|
Ohno R, Takumi S, Nakamura C. Expression of a cold-responsive Lt-Cor gene and development of freezing tolerance during cold acclimation in wheat (Triticum aestivum L.). JOURNAL OF EXPERIMENTAL BOTANY 2001; 52:2367-2374. [PMID: 11709586 DOI: 10.1093/jexbot/52.365.2367] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Time-courses of the development of freezing tolerance and the expression of a cold-responsive gene wlt10 were monitored during cold acclimation in wheat (Triticum aestivum L.). Bioassay showed that cold acclimation conferred much higher freezing tolerance on a winter cultivar than a spring cultivar. Northern blot analysis showed that the expression of wlt10 encoding a novel wheat member of a cereal-specific LT-COR protein family was specifically induced by low temperature. A freezing-tolerant winter cultivar accumulated the mRNA more rapidly and for a longer period than a susceptible spring cultivar. The increase in the amount of mRNA was temporary but the peak occurred at the time when the maximum level of freezing tolerance was attained. The mRNA accumulated more in the leaves than in the roots, and different light/dark regimes modulated the level of mRNA accumulation. Genomic Southern blot analyses using the nulli-tetrasomic series showed that the wlt10 homologues were located on the homologous group 2 chromosomes.
Collapse
Affiliation(s)
- R Ohno
- Laboratory of Plant Genetics, Department of Biological and Environmental Science, Faculty of Agriculture, Kobe University, 1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | | | | |
Collapse
|
44
|
Taketa S, Ando H, Takeda K, von Bothmer R. Physical locations of 5S and 18S-25S rDNA in Asian and American diploid Hordeum species with the I genome. Heredity (Edinb) 2001; 86:522-30. [PMID: 11554968 DOI: 10.1046/j.1365-2540.2001.00768.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The physical locations of 5S and 18S-25S rDNA sequences in 15 diploid Hordeum species with the I genome were examined by double-target in situ hybridization with pTa71 (18S-25S rDNA) and pTa794 (5S rDNA) clones as probes. All the three Asian species had a species-specific rDNA pattern. In 12 American species studied, eight different rDNA types were found. The type reported previously in H. chilense (the 'chilense' type) was observed in eight American species. The chilense type had double 5S rDNA sites - two sites on one chromosome arm separated by a short distance - and two pairs of major 18S-25S rDNA sites on two pairs of satellite chromosomes. The other seven types found in American species were similar to the chilense type and could be derived from the chilense type through deletion, reduction or addition of a rDNA site. Intraspecific polymorphisms were observed in three American species. The overall similarity in rDNA patterns among American species indicates the close relationships between North and South American species and their derivation from a single ancestral source. The differences in the distribution patterns of 5S and 18S-25S rDNA between Asian and American species suggest differentiation between the I genomes of Asian and American species. The 5S and 18S-25S rDNA sites are useful chromosome markers for delimiting Asian species, but have limited value as a taxonomic character in American species. On the basis of rDNA patterns, karyotype evolution and phylogeny of the I-genome diploid species are discussed.
Collapse
Affiliation(s)
- S Taketa
- Faculty of Agriculture, Kagawa University, Ikenobe, Miki, Kagawa 761-0795, Japan.
| | | | | | | |
Collapse
|
45
|
Künzel G, Gecheff KI, Schubert I. Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: First post-treatment mitosis versus viable offspring. Genome 2001. [DOI: 10.1139/g00-104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translocation breakpoints (TBs) induced by ionizing radiation are nonrandomly distributed along barley chromosomes. When first post-treatment mitoses were evaluated, centromeres and the heterochromatin-containing proximal segments tended to be more than randomly involved, and terminal segments to be less than randomly involved in translocations. Contrary to this, small chromosomal regions in median and distal arm positions, characterized by high recombination rates and high gene density, were identified as preferred sites for the origination of viable translocations, probably due to deviations in chromatin organization. Apparently, the position of a TB has an influence on the rate of viability versus elimination of the carrier cells. Surprisingly, TBs within centromeres and heterochromatin-containing segments seem to be more harmful for survival than those induced in gene-rich regions.Key words: Hordeum vulgare, radiation-induced chromosome breaks, translocation lines, breakpoint distribution.
Collapse
|
46
|
Baum BR, Johnson DA. The 5S rRNA gene units in the native New World annual Hordeum species (Triticeae: Poaceae). ACTA ACUST UNITED AC 2000. [DOI: 10.1139/b00-131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have employed a polymerase chain reaction (PCR) based approach to amplify 5S rDNA sequences from 20 accessions representing five Hordeum species native to the Americas. Sequence analysis of 88 clones revealed three sets of orthologous sequences in Hordeum pusillum Nutt. and two sets in the other four species. The long H1 unit class, previously known in Hordeum bulbosum L., Hordeum marinum L. s.l., Hordeum murinum L. s.l., Hordeum spontaneum Boiss., and Hordeum vulgare L., was found also in Hordeum depressum (Scribner & Smith) Rydberg and in H. pusillum; however, the majority of the sequences fell within two new classes of orthologous sequences. Sequences of the long H2 unit class were found in four species but not in H. depressum. Sequences of the long Y2 unit class were found in all five species. The long H2 and long Y2 unit classes appear to be unique to this group of five, mostly annual, North and South American species. Cladistic analysis of the orthologous sequences from the species with the long H1 unit class places the long H1 sequence of Hordeum flexuosum Steudel in the same clade with H. murinum, whereas H. depressum is more closely related to the perennial species, Hordeum bogdanii Wilenski and H. bulbosum. This association differs from previously described species relationships and it may be that the gene tree differs from the species tree. A cladistic analysis of paralogous sequences of the two new unit classes defined in this study together with the long H1, the long Y1 and the long X2 unit classes uncovered in previous work in Hordeum, was performed. Based upon these analyses, we hypothesize that the possible order of divergence was first the division into two branches leading to the long H1 unit class and the long H2 unit class; the lineage leading to the long H2 class was further divided to give rise to branches leading to the long Y1, the long Y2 and the long X2 classes.Key words: 5S rDNA, genomes, haplomes, unit classes, Hordeum, Triticeae.
Collapse
|
47
|
Ramsay L, Macaulay M, degli Ivanissevich S, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R. A simple sequence repeat-based linkage map of barley. Genetics 2000; 156:1997-2005. [PMID: 11102390 PMCID: PMC1461369 DOI: 10.1093/genetics/156.4.1997] [Citation(s) in RCA: 292] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F(1) of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.
Collapse
Affiliation(s)
- L Ramsay
- Unit of Genomics, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Ma Z, Steffenson BJ, Prom LK, Lapitan NL. Mapping of quantitative trait Loci for fusarium head blight resistance in barley. PHYTOPATHOLOGY 2000; 90:1079-88. [PMID: 18944470 DOI: 10.1094/phyto.2000.90.10.1079] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
ABSTRACT Fusarium head blight (FHB) is a devastating disease that causes significant reductions in yield and quality in wheat and barley. Barley grains infected with deoxynivalenol (DON), a vomitoxin produced by Fusarium graminearum, are rejected for malting and brewing. Among six-rowed barley cultivars tested thus far, only cv. Chevron exhibited resistance. This study was conducted to map genes and to identify DNA markers for marker-assisted breeding for FHB resistance in cv. Chevron with restriction fragment length polymorphism (RFLP) markers. A doubled haploid (DH) population was created from a cross between cv. Chevron and susceptible cv. Stander. Seven field experiments were conducted in four different locations in 2 years. A RFLP map containing 211 loci and covering over 1,000 centimorgans (cM) of the genome was used to map quantitative trait loci (QTL) associated with relatively low FHB severity and DON concentration. Morphological traits differing between the parents were also measured: heading date, plant height, spike angle, number of nodes per cm of rachis in the spike, and kernel plumpness. Many of the QTL for FHB and DON coincided with QTLs for these morphological traits. The "fix-QTL" algorithm in Mapmaker QTL was used to remove the part of the variance for FHB resistance that may be explained by heading date or plant height. Results from this study suggest that QTLs with major effects for FHB resistance probably do not exist in cv. Chevron. Three QTL intervals, Xcmwg706-Xbcd441 on chromosome 1H, Xbcd307b-Xcdo684b on chromosome 2H, and Xcdo959b-Xabg472 on chromosome 4H, that are not associated with late heading or height may be useful for marker-assisted selection.
Collapse
|
49
|
Yang YF, Furuta Y, Fukatani Y, Islam AK. Compensating ability in pollen fertilization between group-6 and -7 homoeologous chromosomes of barley and wheat. Genes Genet Syst 2000; 75:251-8. [PMID: 11245218 DOI: 10.1266/ggs.75.251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
By using alpha-amylase isozymes as markers for chromosomes of homoeologous groups 6 and 7, we analyzed the segregation of chromosome constitution in the progenies from crosses between double-ditelosomic or ditelosomic lines of hexaploid wheat cultivar 'Chinese Spring' (CS) as the female parent and double-monosomic F1 hybrids of CS x wheat-barley substitution lines for barley chromosomes 6H or 7H. From this analysis we estimated the transmission rate via pollen of barley chromosomes 6H and 7H in the double-monosomics and evaluated the compensating ability between barley and wheat chromosomes in homoeologous groups 6 and 7. The results indicated that both 6H and 7H showed their highest compensating ability for their respective homoeologous wheat chromosomes 6A (37.5% transmission rate) and 7A (39.4%), intermediate for 6D (34.1%) and 7D (29.6%), and lowest for 6B (26.6%) and 7B (22.6%) chromosomes.
Collapse
Affiliation(s)
- Y F Yang
- Faculty of Agriculture, Gifu University, Japan
| | | | | | | |
Collapse
|
50
|
Murai K, Taketa S, Islam AK, Shepherd KW. Barley allele-specific amplicons useful for identifying wheat-barley recombinant chromosomes. Genes Genet Syst 2000; 75:131-9. [PMID: 10984837 DOI: 10.1266/ggs.75.131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Barley (Hordeum vulgare L.) is potentially a new source of genes for wheat (Triticum aestivum L.) improvement. Wheat-barley chromosome recombinant lines provide a means for introgressing barley genes to wheat genome by chromosome engineering, and since these are expected to occur only rarely in special cytogenetic stocks, an efficient selection skill is necessary to identify them. To convert RFLP markers to barley allele-specific PCR markers useful for effective production of wheat-barley recombinant lines, 91 primer sets derived from RFLP clones which were previously mapped to the barley chromosomes were examined for PCR amplification using 'Chinese Spring' wheat, 'Betzes' barley and the wheat-barley chromosome addition lines. The polymorphisms were detected by an agarose gel electrophoresis of the PCR products without digestion with restriction enzymes. Out of 81 primer sets producing polymorphisms between the wheat and barley genomes, 26 amplified barley chromosome-specific DNAs which were confirmed to be located on the same chromosome as the RFLP markers by using the wheat-barley chromosome addition lines. These amplified DNAs represent barley allele-specific amplicons, which distinguish barley alleles from their wheat homoeologous counterparts. The present investigation revealed a higher probability for obtaining allele-specific amplicons from genomic DNA-derived RFLP markers than from cDNA-derived ones. The barley allele-specific amplicons developed in this study, namely, four for chromosome 2H, two for 3H, seven for 4H, eight for 5H, one for 6H and four for 7H, are suitable for identifying 'Chinese Spring' wheat- 'Betzes' barley recombinant chromosomes. However, one out of eight barley allele-specific amplicons on chromosome 5H did not detect a unique barley band in a 'New Golden' barley chromosome 5H addition line of 'Shinchunaga' wheat, indicating there may be a need to reconstruct allele-specific amplicons with different barley cultivars.
Collapse
Affiliation(s)
- K Murai
- Department of Bioscience, Fukui Prefectural University, Japan.
| | | | | | | |
Collapse
|