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Türkösi E, Szakács É, Ivanizs L, Farkas A, Gaál E, Said M, Darkó É, Cséplő M, Mikó P, Doležel J, Molnár-Láng M, Molnár I, Kruppa K. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:7. [PMID: 38263978 PMCID: PMC10803699 DOI: 10.1007/s11032-024-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01439-y.
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Affiliation(s)
- Edina Türkösi
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Éva Szakács
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - László Ivanizs
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - András Farkas
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Eszter Gaál
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Éva Darkó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mónika Cséplő
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Péter Mikó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
| | - Márta Molnár-Láng
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - István Molnár
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Klaudia Kruppa
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
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Deng P, Du X, Wang Y, Yang X, Cheng X, Huang C, Li T, Li T, Chen C, Zhao J, Wang C, Liu X, Tian Z, Ji W. GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:36. [PMID: 38291310 DOI: 10.1007/s00122-023-04538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE A total of 90,000 capture probes derived from wheat and Thinopyrum elongatum were integrated into one chip, which served as an economical genotype for explorating Thinopyrumspecies and their derivatives. Thinopyrum species play a crucial role as a source of new genetic variations for enhancing wheat traits, including resistance to both abiotic and biotic factors. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is essential following the introduction of alien genetic material into wheat, but this task remains challenging. This study aimed to develop a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information by genotyping using a target sequencing system. This GenoBaits®WheatplusEE array included 90,000 capture probes derived from two species and integrated into one chip, with 10,000 and 80,000 originating from wheat and Th. elongatum, respectively. The capture probes were strategically positioned in genes and evenly distributed across the genome, facilitating the development of a roadmap for identifying each alien gene. The array was applied to the high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species and their derivatives. Our results demonstrated that the GenoBaits®WheatplusEE array could be used for direct identification of the breakpoint of alien segments, determine copy number of alien chromosomes, and reveal variations in wheat chromosomes by a single round of target sequencing of the sample. Additionally, we could efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and polymorphisms in essential genes (e.g., Fhb7 gene) among Thinopyrum species and their derivatives. We hope that GenoBaits®WheatplusEE will become a widely adopted tool for exporting wild germplasm for wheat improvement in the future.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Xiaoying Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofang Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenxi Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingting Li
- College of Bioengineering, Yangling Vocational Technical College, Yangling, 712100, Shaanxi, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zengrong Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Kroupin PY, Yurkina AI, Ulyanov DS, Karlov GI, Divashuk MG. Comparative Characterization of Pseudoroegneria libanotica and Pseudoroegneria tauri Based on Their Repeatome Peculiarities. PLANTS (BASEL, SWITZERLAND) 2023; 12:4169. [PMID: 38140496 PMCID: PMC10747672 DOI: 10.3390/plants12244169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St., 42, 127550 Moscow, Russia (D.S.U.)
- Federal Research Center “Nemchinovka”, Bolshoi Blvd., 30 Bld. 1, Skolkovo Innovation Center, 121205 Moscow, Russia
- National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123182 Moscow, Russia
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Kroupin PY, Ulyanov DS, Karlov GI, Divashuk MG. The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae. Chromosoma 2023:10.1007/s00412-023-00789-4. [PMID: 36905415 DOI: 10.1007/s00412-023-00789-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/16/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023]
Abstract
Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for "classical" wheat probes (pSc119.2 and Afa family) and "universal" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.
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Affiliation(s)
- Pavel Yu Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia.
| | - Daniil S Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
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Kroupin PY, Badaeva ED, Sokolova VM, Chikida NN, Belousova MK, Surzhikov SA, Nikitina EA, Kocheshkova AA, Ulyanov DS, Ermolaev AS, Khuat TML, Razumova OV, Yurkina AI, Karlov GI, Divashuk MG. Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae. FRONTIERS IN PLANT SCIENCE 2022; 13:980764. [PMID: 36325551 PMCID: PMC9621091 DOI: 10.3389/fpls.2022.980764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D (Abdolmalaki et al., 2019) XcrXcr and 2n = 6x = 42, D1D (Abdolmalaki et al., 2019) XcrXcrD2D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Ekaterina D. Badaeva
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Victoria M. Sokolova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Nadezhda N. Chikida
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Maria Kh. Belousova
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Nikitina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Alina A. Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Aleksey S. Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Thi Mai Luong Khuat
- Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam
| | - Olga V. Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
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Türkösi E, Ivanizs L, Farkas A, Gaál E, Kruppa K, Kovács P, Szakács É, Szőke-Pázsi K, Said M, Cápal P, Griffiths S, Doležel J, Molnár I. Transfer of the ph1b Deletion Chromosome 5B From Chinese Spring Wheat Into a Winter Wheat Line and Induction of Chromosome Rearrangements in Wheat- Aegilops biuncialis Hybrids. FRONTIERS IN PLANT SCIENCE 2022; 13:875676. [PMID: 35769292 PMCID: PMC9234525 DOI: 10.3389/fpls.2022.875676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/09/2022] [Indexed: 06/10/2023]
Abstract
Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the Pairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of the Ph1 locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the original ph1b mutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, the ph1b mutation was transferred from two CSph1b mutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1 ph1b/ph1b exhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. The ph1b mutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialis F1 hybrids, predominantly with the Mb-genome chromosomes of Aegilops relative to those of the Ub genome. High frequency of wheat-Aegilops chromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialis amphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1b mutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.
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Affiliation(s)
- Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
- Institute of Genetics and Biotechnology, Szent István Campus, MATE, Gödöllő, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Mahmoud Said
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Giza, Egypt
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | | | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
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Grewal S, Coombes B, Joynson R, Hall A, Fellers J, Yang CY, Scholefield D, Ashling S, Isaac P, King IP, King J. Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines. THE PLANT GENOME 2022; 15:e20193. [PMID: 35102721 DOI: 10.1002/tpg2.20193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 05/23/2023]
Abstract
Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
- Current address: Limagrain Europe, Clermont-Ferrand, France
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - John Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Cai-Yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Peter Isaac
- iDna Genetics Ltd., Norwich Research Park, Norwich, UK
| | - Ian P King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
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King J, Grewal S, Othmeni M, Coombes B, Yang CY, Walter N, Ashling S, Scholefield D, Walker J, Hubbart-Edwards S, Hall A, King IP. Introgression of the Triticum timopheevii Genome Into Wheat Detected by Chromosome-Specific Kompetitive Allele Specific PCR Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:919519. [PMID: 35720607 PMCID: PMC9198554 DOI: 10.3389/fpls.2022.919519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/12/2022] [Indexed: 05/08/2023]
Abstract
Triticum timopheevii (2n = 28, A t A t GG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat Triticum aestivum (2n = 42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-T. timopheevii introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the A t and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the A t and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3A t , 4G, and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of T. timopheevii. A majority of these KASP markers were also found to be T. timopheevii subgenome specific with 182 detecting A t subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the A t segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour in situ hybridisation analysis. Together these homozygous wheat-T. timopheevii ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.
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Affiliation(s)
- Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- Surbhi Grewal,
| | - Manel Othmeni
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nicola Walter
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jack Walker
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Ian Phillip King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
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9
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Yang G, Zheng Q, Hu P, Li H, Luo Q, Li B, Li Z. Cytogenetic identification and molecular marker development for the novel stripe rust-resistant wheat- Thinopyrum intermedium translocation line WTT11. ABIOTECH 2021; 2:343-356. [PMID: 36304423 PMCID: PMC9590478 DOI: 10.1007/s42994-021-00060-3] [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: 02/03/2021] [Accepted: 08/23/2021] [Indexed: 02/02/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. Xiaoyan 78829, a partial amphidiploid developed by crossing common wheat with Thinopyrum intermedium, is immune to wheat stripe rust. To transfer the resistance gene of this excellent germplasm resource to wheat, the translocation line WTT11 was produced by pollen irradiation and assessed for immunity to stripe rust races CYR32, CYR33 and CYR34. A novel stripe rust-resistance locus derived from Th. intermedium was confirmed by linkage and diagnostic marker analyses. Molecular cytogenetic analyses revealed that WTT11 carries a TTh·2DL translocation. The breakpoint of 1B was located at 95.5 MB, and the alien segments were found to be homoeologous to wheat-group chromosomes 6 and 7 according to a wheat660K single-nucleotide polymorphism (SNP) array analysis. Ten previously developed PCR-based markers were confirmed to rapidly trace the alien segments of WTT11, and 20 kompetitive allele-specific PCR (KASP) markers were developed to enable genotyping of Th. intermedium and common wheat. Evaluation of agronomic traits in two consecutive crop seasons uncovered some favorable agronomic traits in WTT11, such as lower plant height and longer main panicles, that may be applicable to wheat improvement. As a novel genetic resource, the new resistance locus may be useful for wheat disease-resistance breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00060-3.
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Affiliation(s)
- Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
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10
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Adonina IG, Timonova EM, Salina EA. Introgressive Hybridization of Common Wheat: Results and Prospects. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421030029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Yang G, Boshoff WHP, Li H, Pretorius ZA, Luo Q, Li B, Li Z, Zheng Q. Chromosomal composition analysis and molecular marker development for the novel Ug99-resistant wheat-Thinopyrum ponticum translocation line WTT34. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1587-1599. [PMID: 33677639 DOI: 10.1007/s00122-021-03796-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/16/2021] [Indexed: 05/12/2023]
Abstract
A novel Ug99-resistant wheat-Thinopyrum ponticum translocation line was produced, its chromosomal composition was analyzed and specific markers were developed. Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn (Pgt) has seriously threatened global wheat production since Ug99 race TTKSK was first detected in Uganda in 1998. Thinopyrum ponticum is near immune to Ug99 races and may be useful for enhancing wheat disease resistance. Therefore, developing new wheat-Th. ponticum translocation lines that are resistant to Ug99 is crucial. In this study, a novel wheat-Th. ponticum translocation line, WTT34, was produced. Seedling and field evaluation revealed that WTT34 is resistant to Ug99 race PTKST. The resistance was derived from the alien parent Th. ponticum. Screening WTT34 with markers linked to Sr24, Sr25, Sr26, Sr43, and SrB resulted in the amplification of different DNA fragments from Th. ponticum, implying WTT34 carries at least one novel stem rust resistance gene. Genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and multi-color GISH (mc-GISH) analyses indicated that WTT34 carries a T5DS·5DL-Th translocation, which was consistent with wheat660K single-nucleotide polymorphism (SNP) array results. The SNP array also uncovered a deletion event in the terminal region of chromosome 1D. Additionally, the homeology between alien segments and the wheat chromosomes 2A and 5D was confirmed. Furthermore, 51 PCR-based markers derived from the alien segments of WTT34 were developed based on specific-locus amplified fragment sequencing (SLAF-seq). These markers may enable wheat breeders to rapidly trace Th. ponticum chromosomal segments carrying Ug99 resistance gene(s).
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Affiliation(s)
- Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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12
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Grewal S, Guwela V, Newell C, Yang CY, Ashling S, Scholefield D, Hubbart-Edwards S, Burridge A, Stride A, King IP, King J. Generation of Doubled Haploid Wheat- Triticum urartu Introgression Lines and Their Characterisation Using Chromosome-Specific KASP Markers. FRONTIERS IN PLANT SCIENCE 2021; 12:643636. [PMID: 34054892 PMCID: PMC8155260 DOI: 10.3389/fpls.2021.643636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/19/2021] [Indexed: 05/07/2023]
Abstract
Wheat is one of the most important food and protein sources in the world and although, in recent years wheat breeders have achieved yield gains, they are not sufficient to meet the demands of an ever-growing population. Development of high yielding wheat varieties, resilient to abiotic and biotic stress resulting from climate change, has been limited by wheat's narrow genetic base. In contrast to wheat, the wild relatives of wheat provide a vast reservoir of genetic variation for most, if not all, agronomic traits. Previous studies by the authors have shown the transfer of genetic variation from T. urartu into bread wheat. However, before the introgression lines can be exploited for trait analysis, they are required to have stable transmission of the introgressions to the next generation. In this work, we describe the generation of 86 doubled haploid (DH) wheat-T. urartu introgression lines that carry homozygous introgressions which are stably inherited. The DH lines were characterised using the Axiom® Wheat Relative Genotyping Array and 151 KASP markers to identify 65 unique T. urartu introgressions in a bread wheat background. DH production has helped accelerate the breeding process and facilitated the early release of homozygous wheat-T. urartu introgression lines. Together with the KASP markers, this valuable resource could greatly advance identification of beneficial alleles that can be used in wheat improvement.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Veronica Guwela
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Claire Newell
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Alex Stride
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
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13
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McAusland L, Vialet-Chabrand S, Jauregui I, Burridge A, Hubbart-Edwards S, Fryer MJ, King IP, King J, Pyke K, Edwards KJ, Carmo-Silva E, Lawson T, Murchie EH. Variation in key leaf photosynthetic traits across wheat wild relatives is accession dependent not species dependent. THE NEW PHYTOLOGIST 2020; 228:1767-1780. [PMID: 32910841 DOI: 10.1111/nph.16832] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/03/2020] [Indexed: 05/26/2023]
Abstract
The wild relatives of modern wheat represent an underutilized source of genetic and phenotypic diversity and are of interest in breeding owing to their wide adaptation to diverse environments. Leaf photosynthetic traits underpin the rate of production of biomass and yield and have not been systematically explored in the wheat relatives. This paper identifies and quantifies the phenotypic variation in photosynthetic, stomatal, and morphological traits in up to 88 wheat wild relative accessions across five genera. Both steady-state measurements and dynamic responses to step changes in light intensity are assessed. A 2.3-fold variation for flag leaf light and CO2 -saturated rates of photosynthesis Amax was observed. Many accessions showing higher and more variable Amax , maximum rates of carboxylation, electron transport, and Rubisco activity when compared with modern genotypes. Variation in dynamic traits was also significant; with distinct genus-specific trends in rates of induction of nonphotochemical quenching and rate of stomatal opening. We conclude that utilization of wild relatives for improvement of photosynthesis is supported by the existence of a high degree of natural variation in key traits and should consider not only genus-level properties but variation between individual accessions.
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Affiliation(s)
- Lorna McAusland
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | | | - Iván Jauregui
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | | | - Stella Hubbart-Edwards
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Michael J Fryer
- School of Life Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Ian P King
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Julie King
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Kevin Pyke
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
| | | | | | - Tracy Lawson
- School of Life Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Erik H Murchie
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, LE12 5RD, UK
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14
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Singh AK, Lo K, Dong C, Zhang P, Trethowan RM, Sharp PJ. Development of RNA-seq-based molecular markers for characterizing Thinopyrum bessarabicum and Secale introgressions in wheat. Genome 2020; 63:525-534. [PMID: 32762630 DOI: 10.1139/gen-2020-0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequence-based markers have added a new dimension in the efficiency of identifying alien introgressions in wheat. Expressed sequence tag-sequence tagged sites (EST-STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum- and Secale anatolicum-specific EST-STS markers and their application in tracing respective alien chromatin introgressions in wheat. The parental lines, Chinese Spring (CS), ISR991.1 (CS/Th. bessarabicum amphidiploid), and ISR1049.2 (CS/Secale anatolicum amphidiploid), were used as core experimental materials. Using comparative analysis of RNA-Seq data, 10 903 and 10 660 candidate sequences specific to Th. bessarabicum and S. anatolicum, respectively, were assembled and identified. To validate the genome specificity of these candidate sequences, 68 and 64 EST-STS markers were developed from randomly selected candidate sequences of Th. bessarabicum and S. anatolicum, respectively, and tested on sets of alien addition lines. Fifty-five and 53 markers for Th. bessarabicum and S. anatolicum chromatin, respectively, were assigned to chromosomal location(s), covering all seven chromosomes. Approximately 83% of S. anatolicum-specific markers were transferable to S. cereale. The genome-specific candidate sequences identified and the EST-STS markers developed will be valuable resources for exploitation of Th. bessarabicum and Secale species diversity in wheat and triticale breeding.
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Affiliation(s)
- Amit K Singh
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Richard M Trethowan
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Peter J Sharp
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW 2570, Australia
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15
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Singh AK, Zhang P, Dong C, Li J, Singh S, Trethowan RM, Sharp PJ. Development and molecular cytogenetic characterization of Thinopyrum bessarabicum introgression lines in hexaploid and tetraploid wheats. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2117-2130. [PMID: 32198597 DOI: 10.1007/s00122-020-03581-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
A variety of Thinopyrum bessarabicum introgressions in both hexaploid and tetraploid wheats were generated and characterized by molecular cytogenetic analysis. Six wheat-J genome recombinants were identified with ND-FISH and GISH. Diploid wheatgrass, Thinopyrum bessarabicum (2n = 2x = 14, EbEb or JbJb or JJ), is a well-known alien source of salinity tolerance and disease resistance for wheat improvement. The true genetic potential and effect of such introgressions into wheat can be best studied in chromosomal addition or substitution lines. Here, we report the generation and characterization of various categories of Th. bessarabicum derivatives in both hexaploid and tetraploid cultivated wheats. Sequential non-denaturing fluorescence in situ hybridization (ND-FISH) and genomic in situ hybridization (GISH) are robust techniques to visualize the size of alien introgressions and breakpoints. We identified a complete set of monosomic addition lines into both bread wheat and durum wheat, except for 7J in durum wheat, by sequential ND-FISH and GISH. We also characterized alien derivatives belonging to various classes including mono-telosomic additions, disomic additions, monosomic substitutions, double monosomic substitutions, monosomic substitution-monosomic additions, double monosomic additions, and multiple monosomic additions into both bread and durum wheats. In addition, various wheat-Th. bessarabicum recombinant chromosomes were also detected in six alien derivatives. These wheat-Th. bessarabicum derivatives will provide useful cytogenetic resources for improvement of both hexaploid and tetraploid wheats.
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Affiliation(s)
- Amit K Singh
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia.
| | - Chongmei Dong
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Jianbo Li
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Smriti Singh
- Bihar Agricultural University, Sabour, Bihar, 813210, India
| | - Richard M Trethowan
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Peter J Sharp
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia.
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16
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Baker L, Grewal S, Yang CY, Hubbart-Edwards S, Scholefield D, Ashling S, Burridge AJ, Przewieslik-Allen AM, Wilkinson PA, King IP, King J. Exploiting the genome of Thinopyrum elongatum to expand the gene pool of hexaploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2213-2226. [PMID: 32313991 PMCID: PMC7311493 DOI: 10.1007/s00122-020-03591-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/31/2020] [Indexed: 05/23/2023]
Abstract
One hundred and thirty four introgressions from Thinopyrum elongatum have been transferred into a wheat background and were characterised using 263 SNP markers. Species within the genus Thinopyrum have been shown to carry genetic variation for a very wide range of traits including biotic and abiotic stresses and quality. Research has shown that one of the species within this genus, Th. elongatum, has a close relationship with the genomes of wheat making it a highly suitable candidate to expand the gene pool of wheat. Homoeologous recombination, in the absence of the Ph1 gene, has been exploited to transfer an estimated 134 introgressions from Th. elongatum into a hexaploid wheat background. The introgressions were detected and characterised using 263 single nucleotide polymorphism markers from a 35 K Axiom® Wheat-Relative Genotyping Array, spread across seven linkage groups and validated using genomic in situ hybridisation. The genetic map had a total length of 187.8 cM and the average chromosome length was 26.8 cM. Comparative analyses of the genetic map of Th. elongatum and the physical map of hexaploid wheat confirmed previous work that indicated good synteny at the macro-level, although Th. elongatum does not contain the 4A/5A/7B translocation found in wheat.
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Affiliation(s)
- Lauren Baker
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Surbhi Grewal
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Cai-Yun Yang
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stella Hubbart-Edwards
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Duncan Scholefield
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephen Ashling
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Amanda J Burridge
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | | | - Paul A Wilkinson
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Ian P King
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Julie King
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
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17
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Fernández-Gómez J, Talle B, Tidy AC, Wilson ZA. Accurate staging of reproduction development in Cadenza wheat by non-destructive spike analysis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3475-3484. [PMID: 32255487 PMCID: PMC7307855 DOI: 10.1093/jxb/eraa156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 04/06/2020] [Indexed: 05/22/2023]
Abstract
Wheat is one of the most important crops in the world; however, loss of genetic variability and abiotic stress caused by variable climatic conditions threaten future productivity. Reproduction is critical for wheat yield; however, pollen development is amongst the developmental stages most sensitive to stresses such as heat, cold, or drought. A better understanding of how anther and pollen development is regulated is needed to help produce more resilient crops and ensure future yield increases. However, in cereals such as wheat, barley, and rice, flowers form within the developing pseudostem and therefore accurate staging of floral materials is extremely challenging. This makes detailed phenotypic and molecular analysis of floral development very difficult, particularly when limited plant material is available, for example with mutant or transgenic lines. Here we present an accurate approach to overcome this problem, by non-destructive staging of reproduction development in Cadenza, the widely used spring wheat research variety. This uses a double-scale system whereby anther and pollen development can be predicted in relation to spike size and spike position within the pseudostem. This system provides an easy, reproducible method that facilitates accurate sampling and analysis of floral materials, to enable anther and pollen developmental research.
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Affiliation(s)
- José Fernández-Gómez
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Correspondence: or
| | - Behzad Talle
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Alison C Tidy
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Correspondence: or
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18
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Zhou C, Dong Z, Zhang T, Wu J, Yu S, Zeng Q, Han D, Tong W. Genome-Scale Analysis of Homologous Genes among Subgenomes of Bread Wheat ( Triticum aestivum L.). Int J Mol Sci 2020; 21:ijms21083015. [PMID: 32344734 PMCID: PMC7215433 DOI: 10.3390/ijms21083015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) revealed a total of 88,733 high-confidence homologous genes of four major types (1:1:1, 1:1:0, 0:1:1 and 1:0:1) among the A, B and D subgenomes of wheat. This data was used to compare homologous gene densities among chromosomes, clarify their distribution and correspondence relationship, and compare their functional enrichment. The average density of 1:1:1 homologous genes was about 10 times more than the density of the other three types of homologous genes, although the homologous gene densities of the various chromosomes were similar within each homologous type. Three regions of exceptional density were detected in 1:1:1 homologous genes, the isolate peak on the tail of chromosome 4A, and the desert regions at the start of chromosome 7A and 7D. The correspondence between homologous genes of the wheat subgenomes demonstrated translocation between the tail segments of chromosome 4A and 5A, and the inversion of the segment of original 5A and 7B into the tail of 4A. The homologous genes on the inserting segments of 5A and 7B to 4A were highly enriched in nitrogen, primary metabolite and small molecular metabolism processes, compared with genes on other regions of the original 4A chromosome. This study provides a refined genome-scale reference of homologous genes for wheat molecular research and breeding, which will help to broaden the application of the wheat genome and can be used as a template for research on other polyploid plants.
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Affiliation(s)
- Caie Zhou
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhaonian Dong
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Ting Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Jianhui Wu
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shizhou Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling 712100, China
- Correspondence: (D.H.); (W.T.); Tel.: +86-29-87081317 (D.H.); Fax: +86-29-87081317 (D.H.)
| | - Wei Tong
- College of Agronomy, Northwest A&F University, Yangling 712100, China
- Correspondence: (D.H.); (W.T.); Tel.: +86-29-87081317 (D.H.); Fax: +86-29-87081317 (D.H.)
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19
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Xu J, Wang L, Deal KR, Zhu T, Ramasamy RK, Luo MC, Malvick J, You FM, McGuire PE, Dvorak J. Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1227-1241. [PMID: 31980837 DOI: 10.1007/s00122-020-03544-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
We introgressed wheatgrass germplasm from the octoploid amphiploid Triticum aestivum× Lophopyrum elongatum into wheat by manipulating the wheat Ph1 gene and discovered and characterized 130 introgression lines harboring single or, in various combinations, complete and recombined L. elongatum chromosomes. Diploid wheatgrass Lophopyrum elongatum (genomes EE) possesses valuable traits for wheat genetics and breeding. We evaluated several strategies for introgression of this germplasm into wheat. To detect it, we developed and validated multiplexed sets of Sequenom MassARRAY single nucleotide polymorphism (SNP) markers, which differentiated disomic and monosomic L. elongatum chromosomes from wheat chromosomes. We identified 130 introgression lines (ILs), which harbored 108 complete and 89 recombined L. elongatum chromosomes. Of the latter, 59 chromosomes were recombined by one or more crossovers and 30 were involved in centromeric (Robertsonian) translocations or were telocentric. To identify wheat chromosomes substituted for or recombined with L. elongatum chromosomes, we genotyped the ILs with the wheat 90-K Infinium SNP array. We found that most of the wheat 90-K probes correctly detected their targets in the L. elongatum genome and showed that some wheat SNPs are ancient and had originated prior to the divergence of the wheat and L. elongatum lineages. Of the 130 ILs, 52% were homozygous for Ph1 deletion and thus are staged to be recombined further. We failed to detect in the L. elongatum genome the 4/5 reciprocal translocation that has been reported in Thinopyrum bessarabicum and several other Triticeae genomes.
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Affiliation(s)
- Jiale Xu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ramesh K Ramasamy
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Julia Malvick
- Veterinary Genetics Laboratory, University of California, Davis, CA, 95616, USA
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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20
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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21
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Han G, Liu S, Jin Y, Jia M, Ma P, Liu H, Wang J, An D. Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.). BMC Genomics 2020; 21:206. [PMID: 32131733 PMCID: PMC7057559 DOI: 10.1186/s12864-020-6624-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/25/2020] [Indexed: 02/01/2023] Open
Abstract
Background Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will facilitate the transfer and utilization of elite genes derived from rye in wheat breeding. Results In the present study, five rye cultivars including Imperial, German White, Jingzhouheimai, Baili and Guyuan were sequenced by specific-locus amplified fragment sequencing (SLAF-seq) to develop large-scale rye-specific markers. Based on SLAF-seq and bioinformatics analyses, a total of 404 universal PCR-based and a whole set of Kompetitive allele-specific PCR (KASP) markers specific for the 14 individual rye chromosome arms were developed and validated. Additionally, two KASP markers specific for 1RS and 2RL were successfully applied in the detection of 1RS translocations in a natural population and 2RL chromosome arms in wheat-rye derived progenies that conferred adult resistance to powdery mildew. Conclusion The 404 PCR-based markers and 14 KASP markers specific for the 14 individual rye chromosome arms developed in this study can enrich the marker densities for gene mapping and accelerate the utilization of rye-derived genes in wheat improvement. Especially, the KASP markers achieved high-throughput and accurate detection of rye chromatin in wheat background, thus can be efficiently used in marker-assisted selection (MAS). Besides, the strategy of rye-specific PCR-based markers converting into KASP markers was high-efficient and low-cost, which will facilitate the tracing of alien genes, and can also be referred for other wheat relatives.
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Affiliation(s)
- Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiyu Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuli Jin
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Mengshu Jia
- School of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Pengtao Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China.,School of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Jing Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, Hebei, China. .,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
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22
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Grewal S, Hubbart‐Edwards S, Yang C, Devi U, Baker L, Heath J, Ashling S, Scholefield D, Howells C, Yarde J, Isaac P, King IP, King J. Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:743-755. [PMID: 31465620 PMCID: PMC7004896 DOI: 10.1111/pbi.13241] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/17/2019] [Indexed: 05/23/2023]
Abstract
For future food security, it is important that wheat, one of the most widely consumed crops in the world, can survive the threat of abiotic and biotic stresses. New genetic variation is currently being introduced into wheat through introgressions from its wild relatives. For trait discovery, it is necessary that each introgression is homozygous and hence stable. Breeding programmes rely on efficient genotyping platforms for marker-assisted selection (MAS). Recently, single nucleotide polymorphism (SNP)-based markers have been made available on high-throughput Axiom® SNP genotyping arrays. However, these arrays are inflexible in their design and sample numbers, making their use unsuitable for long-term MAS. SNPs can potentially be converted into Kompetitive allele-specific PCR (KASP™) assays that are comparatively cost-effective and efficient for low-density genotyping of introgression lines. However, due to the polyploid nature of wheat, KASP assays for homoeologous SNPs can have difficulty in distinguishing between heterozygous and homozygous hybrid lines in a backcross population. To identify co-dominant SNPs, that can differentiate between heterozygotes and homozygotes, we PCR-amplified and sequenced genomic DNA from potential single-copy regions of the wheat genome and compared them to orthologous copies from different wild relatives. A panel of 620 chromosome-specific KASP assays have been developed that allow rapid detection of wild relative segments and provide information on their homozygosity and site of introgression in the wheat genome. A set of 90 chromosome-nonspecific assays was also produced that can be used for genotyping introgression lines. These multipurpose KASP assays represent a powerful tool for wheat breeders worldwide.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Stella Hubbart‐Edwards
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Urmila Devi
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Lauren Baker
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Jack Heath
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Caroline Howells
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | | | - Peter Isaac
- IDna Genetics Ltd.Norwich Research ParkNorwichUK
| | - Ian P. King
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
| | - Julie King
- Nottingham BBSRC Wheat Research CentreSchool of BiosciencesUniversity of NottinghamLoughboroughLeicestershireUK
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23
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Souza RCD, Marques DDA, de Carvalho Filho MM, Oliveira ARDS, Siqueira WJ, Benko-Iseppon AM, Brasileiro-Vidal AC. Genome composition and pollen viability of Jatropha (Euphorbiaceae) interspecific hybrids by Genomic In Situ Hybridization (GISH). Genet Mol Biol 2020; 42:e20190112. [PMID: 32059051 PMCID: PMC7198012 DOI: 10.1590/1678-4685-gmb-2019-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/10/2019] [Indexed: 11/24/2022] Open
Abstract
Interspecific hybridization is required for the development of Jatropha
curcas L. improved cultivars, due to its narrow genetic basis. The
present study aimed to analyze the parental genomic composition of F1
and BC1F1 generations derived from interspecific crosses
(J. curcas/J. integerrima and J. curcas/J.
multifida) by GISH (Genomic In Situ
Hybridization), and the meiotic index and pollen viability of F1
hybrids. In F1 cells from both hybrids, 11 chromosomes of each
parental was observed, as expected, but chromosome rearrangement events could be
detected using rDNA chromosome markers, suggesting unbalanced cells. In the
BC1F1, both hybrids had 22 chromosomes, suggesting
that only n = 11 gametes were viable in the next generation.
However, GISH allowed the identification of three and two alien chromosomes in
J. curcas//J. integerrima and J. curcas//J.
multifida BC1F1 hybrids, respectively,
suggesting a preferential transmission of J. curcas chromosomes
for both hybrids. Pollen viability in F1 hybrids derived from
J. curcas/J. integerrima crosses were higher (82-83%) than
those found for J. curcas/J. multifida (68%), showing
post-meiotic problems in these last hybrids, with dyads, triads, polyads, and
micronuclei as post-meiosis results. The here presented cytogenetic
characterization of interspecific hybrids and their backcross progenies can
contribute to the selection of the best genotypes for future assisted breeding
of J. curcas.
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Affiliation(s)
- Rosilda Cintra de Souza
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
| | | | | | | | | | | | - Ana Christina Brasileiro-Vidal
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
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24
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Wang Y, Cao Q, Zhang J, Wang S, Chen C, Wang C, Zhang H, Wang Y, Ji W. Cytogenetic Analysis and Molecular Marker Development for a New Wheat- Thinopyrum ponticum 1J s (1D) Disomic Substitution Line With Resistance to Stripe Rust and Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2020; 11:1282. [PMID: 32973841 PMCID: PMC7472378 DOI: 10.3389/fpls.2020.01282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/06/2020] [Indexed: 05/03/2023]
Abstract
Thinopyrum ponticum (2n = 10x = 70), a member of the tertiary gene pool of wheat (Triticum aestivum L.), harbors many biotic and abiotic stress resistance genes. CH10A5, a novel disomic substitution line from a cross of T. aestivum cv. 7182 and Th. ponticum, was characterized by cytogenetic identification, in situ hybridization, molecular marker analysis, and morphological investigation of agronomic traits and disease resistance. Cytological observations showed that CH10A5 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genome in situ hybridization (GISH) analysis indicated that two of its chromosomes came from the Js genome of Th. ponticum, and wheat 15K array mapping and fluorescence in situ hybridization (FISH) revealed that chromosome 1D was absent from CH10A5. Polymorphic analysis of molecular markers indicated that the pair of alien chromosomes belonged to homoeologous group one, designated as 1Js. Thus, CH10A5 was a wheat-Th. ponticum 1Js (1D) disomic substitution line. Field disease resistance trials demonstrated that the introduced Th. ponticum chromosome 1Js was probably responsible for resistance to both stripe rust and powdery mildew at the adult stage. Based on specific-locus amplified fragment sequencing (SLAF-seq), 507 STS molecular markers were developed to distinguish chromosome 1Js genetic material from that of wheat. Of these, 49 STS markers could be used to specifically identify the genetic material of Th. ponticum. CH10A5 will increase the resistance gene diversity of wheat breeding materials, and the markers developed here will permit further tracing of heterosomal chromosome fragments in the future.
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Affiliation(s)
- Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Qiang Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Siwen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
- *Correspondence: Wanquan Ji,
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25
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Divashuk MG, Karlov GI, Kroupin PY. Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species. PLANTS 2019; 9:plants9010015. [PMID: 31877707 PMCID: PMC7020174 DOI: 10.3390/plants9010015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Diploid and polyploid wild species of Triticeae have complex relationships, and the understanding of their evolution and speciation could help to increase the usability of them in wheat breeding as a source of genetic diversity. The diploid species Pseudoroegneria spicata (St), Thinopyrum bessarabicum (Jb), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (JrJvsSt, where indices r, v, and s stand for the partial relation to the genomes of Secale, Dasypyrum, and Pseudoroegneria, respectively). We quantified 10 families of transposable elements (TEs) in P. spicata, Th. bessarabicum, D. villosum (per one genome), and Th. intermedium (per one average subgenome) using the quantitative real time PCR assay and compared their abundance within the studied genomes as well as between them. Sabrina was the most abundant among all studied elements in P. spicata, D. villosum, and Th. intermedium, and among Ty3/Gypsy elements in all studied species. Among Ty1/Copia elements, Angela-A and WIS-A showed the highest and close abundance with the exception of D. villosum, and comprised the majority of all studied elements in Th. bessarabicum. Sabrina, BAGY2, and Angela-A showed similar abundance among diploids and in Th. intermedium hexaploid; Latidu and Barbara demonstrated sharp differences between diploid genomes. The relationships between genomes of Triticeae species based on the studied TE abundance and the role of TEs in speciation and polyploidization in the light of the current phylogenetic models is discussed.
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Affiliation(s)
- Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
| | - Pavel Yu. Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia; (M.G.D.)
- Centre for Molecular Biotechnology, Russian State Agrarian University-Timiryazev Agricultural Academy, Moscow 127550, Russia
- Correspondence:
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26
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Badaeva ED, Surzhikov SA, Agafonov AV. Molecular-cytogenetic analysis of diploid wheatgrass Thinopyrum bessarabicum (Savul. and Rayss) A. Löve. COMPARATIVE CYTOGENETICS 2019; 13:389-402. [PMID: 31844506 PMCID: PMC6904353 DOI: 10.3897/compcytogen.v13i4.36879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Thinopyrum bessarabicum (T. Săvulescu & T. Rayss, 1923) A. Löve, 1980 is diploid (2n=2x=14, JJ or EbEb), perennial self-fertilizing rhizomatous maritime beach grass, which is phylogenetically close to another diploid wheatgrass species, Agropyron elongatum (N. Host, 1797) P. de Beauvois, 1812. The detailed karyotype of Th. bessarabicum was constructed based on FISH with six DNA probes representing 5S and 45S rRNA gene families and four tandem repeats. We found that the combination of pAesp_SAT86 (= pTa-713) probe with pSc119.2 or pAs1/ pTa-535 allows the precise identification of all J-genome chromosomes. Comparison of our data with the results of other authors showed that karyotypically Th. bessarabicum is distinct from A. elongatum. On the other hand, differences between the J-genome chromosomes of Th. bessarabicum and the chromosomes of hexaploid Th. intermedium (N. Host, 1797) M. Barkworth & D.R. Dewey, 1985 and decaploid Th. ponticum (J. Podpěra, 1902) Z.-W. Liu & R.-C. Wang, 1993 in the distribution of rDNA loci and hybridization patterns of pSc119.2 and pAs1 probes could be an indicative of (1) this diploid species was probably not involved in the origin of these polyploids or (2) it could has contributed the J-genome to Th. intermedium and Th. ponticum, but it was substantially modified over the course of speciation.
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Affiliation(s)
- Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences. Gubkina str. 3, Moscow 117333, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscowRussia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences. Vavilova str. 34, Moscow 117334, RussiaN.I. Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences. Vavilova str. 34, Moscow 117334, RussiaN.I. Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Alexander V. Agafonov
- Central Siberian Botanical Garden, Russian Academy of Sciences, Siberian Branch, Zolotodolinskaya st., 101, Novosibirsk 630090, RussiaCentral Siberian Botanical Garden, Russian Academy of SciencesNovosibirskRussia
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Li H, Wang L, Luo MC, Nie F, Zhou Y, McGuire PE, Distelfeld A, Dai X, Song CP, Dvorak J. Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3265-3276. [PMID: 31529271 DOI: 10.1007/s00122-019-03423-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/06/2019] [Indexed: 05/21/2023]
Abstract
Su1-Ph1, which we previously introgressed into wheat from Aegilops speltoides, is a potent suppressor of Ph1 and a valuable tool for gene introgression in tetraploid wheat. We previously introgressed Su1-Ph1, a suppressor of the wheat Ph1 gene, from Aegilops speltoides into durum wheat cv Langdon (LDN). Here, we evaluated the utility of the introgressed suppressor for inducing introgression of alien germplasm into durum wheat. We built LDN plants heterozygous for Su1-Ph1 that simultaneously contained a single LDN chromosome 5B and a single Ae. searsii chromosome 5Sse, which targeted them for recombination. We genotyped 28 BC1F1 and 84 F2 progeny with the wheat 90-K Illumina single-nucleotide polymorphism assay and detected extensive recombination between the two chromosomes, which we confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH). We constructed BC1F1 and F2 genetic maps that were 65.31 and 63.71 cM long, respectively. Recombination rates between the 5B and 5Sse chromosomes were double the expected rate computed from their meiotic pairing, which we attributed to selection against aneuploid gametes. Recombination rate between 5B and 5Sse was depressed compared to that between 5B chromosomes in the proximal region of the long arm. We integrated ND-FISH signals into the genetic map and constructed a physical map, which we used to map a 172,188,453-bp Ph1 region. Despite the location of the region in a low-recombination region of the 5B chromosome, we detected three crossovers in it. Our data show that Su1-Ph1 is a valuable tool for gene introgression and gene mapping based on recombination between homoeologous chromosomes in wheat.
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Affiliation(s)
- Hao Li
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Fang Nie
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yun Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Xiongtao Dai
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Devi U, Grewal S, Yang CY, Hubbart-Edwards S, Scholefield D, Ashling S, Burridge A, King IP, King J. Development and characterisation of interspecific hybrid lines with genome-wide introgressions from Triticum timopheevii in a hexaploid wheat background. BMC PLANT BIOLOGY 2019; 19:183. [PMID: 31060503 PMCID: PMC6501383 DOI: 10.1186/s12870-019-1785-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/17/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Triticum timopheevii (2n = 4x = 28; AtAtGG), is an important source for new genetic variation for wheat improvement with genes for potential disease resistance and salt tolerance. By generating a range of interspecific hybrid lines, T. timopheevii can contribute to wheat's narrow gene-pool and be practically utilised in wheat breeding programmes. Previous studies that have generated such introgression lines between wheat and its wild relatives have been unable to use high-throughput methods to detect the presence of wild relative segments in such lines. RESULTS A whole genome introgression approach, exploiting homoeologous recombination in the absence of the Ph1 locus, has resulted in the transfer of different chromosome segments from both the At and G genomes of T. timopheevii into wheat. These introgressions have been detected and characterised using single nucleotide polymorphism (SNP) markers present on a high-throughput Axiom® Genotyping Array. The analysis of these interspecific hybrid lines has resulted in the detection of 276 putative unique introgressions from T. timopheevii, thereby allowing the generation of a genetic map of T. timopheevii containing 1582 SNP markers, spread across 14 linkage groups representing each of the seven chromosomes of the At and G genomes of T. timopheevii. The genotyping of the hybrid lines was validated through fluorescence in situ hybridisation (FISH). Comparative analysis of the genetic map of T. timopheevii and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of inter- and intra-genomic translocations within the At and G genomes of T. timopheevii that have been previously only detected through cytological techniques. CONCLUSIONS In this work, we report a set of SNP markers present on a high-throughput genotyping array, able to detect the presence of T. timopheevii in a hexaploid wheat background making it a potentially valuable tool for marker assisted selection (MAS) in wheat pre-breeding programs. These valuable resources of high-density molecular markers and wheat-T. timopheevii hybrid lines will greatly enhance the work being undertaken for wheat improvement through wild relative introgressions.
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Affiliation(s)
- Urmila Devi
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Surbhi Grewal
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Cai-Yun Yang
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stella Hubbart-Edwards
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Duncan Scholefield
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Stephen Ashling
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Amanda Burridge
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, UK
| | - Ian P King
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
| | - Julie King
- Division of Plant and Cop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK.
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Cseh A, Yang C, Hubbart-Edwards S, Scholefield D, Ashling SS, Burridge AJ, Wilkinson PA, King IP, King J, Grewal S. Development and validation of an exome-based SNP marker set for identification of the St, J r and J vs genomes of Thinopyrym intermedium in a wheat background. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1555-1570. [PMID: 30767030 PMCID: PMC6476854 DOI: 10.1007/s00122-019-03300-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/02/2019] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Cytogenetic analysis and array-based SNP genotyping of wheat- Th. intermedium introgression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes of Th. intermedium (StJ r J vs , 2 n = 6 x = 42). Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat-Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.
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Affiliation(s)
- Andras Cseh
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Molecular Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Stephen S Ashling
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | | | - Ian P King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Division of Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, UK.
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Türkösi E, Darko E, Rakszegi M, Molnár I, Molnár-Láng M, Cseh A. Development of a new 7BS.7HL winter wheat-winter barley Robertsonian translocation line conferring increased salt tolerance and (1,3;1,4)-β-D-glucan content. PLoS One 2018; 13:e0206248. [PMID: 30395616 PMCID: PMC6218033 DOI: 10.1371/journal.pone.0206248] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023] Open
Abstract
Interspecific hybridization between bread wheat (Triticum aestivum, 2n = 42) and related species allows the transfer of agronomic and quality traits, whereby subsequent generations comprise an improved genetic background and can be directly applied in wheat breeding programmes. While wild relatives are frequently used as sources of agronomically favourable traits, cultivated species can also improve wheat quality and stress resistance. A salt-tolerant 'Asakaze'/'Manas' 7H disomic addition line (2n = 44) with elevated β-glucan content, but with low fertility and an unstable genetic background was developed in an earlier wheat-barley prebreeding programme. The aim of the present study was to take this hybridization programme further and transfer the favourable barley traits into a more stable genetic background. Taking advantage of the breakage-fusion mechanism of univalent chromosomes, the 'Rannaya' winter wheat 7B monosomic line was used as female partner to the 7H addition line male, leading to the development of a compensating wheat/barley Robertsonian translocation line (7BS.7HL centric fusion, 2n = 42) exhibiting higher salt tolerance and elevated grain β-glucan content. Throughout the crossing programme, comprising the F1-F4 generations, genomic in situ hybridization, fluorescence in situ hybridization and chromosome-specific molecular markers were used to trace and identify the wheat and barley chromatin. Investigations on salt tolerance during germination and on the (1,3;1,4)-β-D-glucan (mixed-linkage glucan [MLG]) content of the seeds confirmed the salt tolerance and elevated grain MLG content of the translocation line, which can be directly applied in current wheat breeding programmes.
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Affiliation(s)
- Edina Türkösi
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Eva Darko
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Marianna Rakszegi
- Cereal Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - István Molnár
- Maize Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Márta Molnár-Láng
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - András Cseh
- Molecular Breeding Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
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Zhang W, Zhu X, Zhang M, Chao S, Xu S, Cai X. Meiotic homoeologous recombination-based mapping of wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2381-2395. [PMID: 30109393 DOI: 10.1007/s00122-018-3160-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/03/2018] [Indexed: 05/09/2023]
Abstract
We physically dissected and mapped wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum based on meiotic homoeologous recombination, providing a unique physical framework for genome studies. Common wheat has a large and complex genome with narrow genetic diversity and various degrees of recombination between the A, B, and D subgenomes. This has limited the homologous recombination-based genome studies in wheat. Here, we exploited meiotic homoeologous recombination for molecular mapping of wheat chromosome 2B and its homoeologue 2S from Aegilops speltoides and 2E from Thinopyrum elongatum. The 2B-2S and 2B-2E recombination was induced by the ph1b mutant, and recovered using molecular markers and fluorescent genomic in situ hybridization (FGISH). A total of 112 2B-2S and 87 2B-2E recombinants involving different chromosome regions were developed and physically delineated by FGISH. The 2B-2S and 2B-2E recombination hotspots mapped to the subterminal regions on both arms. Recombination hotspots with the highest recombination rates mapped to the short arms. Eighty-three 2B-2S and 67 2B-2E recombinants were genotyped using the wheat 90 K SNP arrays. Based on the genotyping results and FGISH patterns of the recombinants, chromosomes 2B, 2S, and 2E were partitioned into 93, 66, and 46 bins, respectively. In total, 1037 SNPs physically mapped onto distinct bins of these three homoeologous chromosomes. A homoeologous recombination-based bin map was constructed for chromosome 2B, providing a unique physical framework for genome studies in wheat and its relatives. Meiotic homoeologous recombination also facilitates gene introgression to diversify the wheat genome for germplasm development. Therefore, homoeologous recombination-based studies enhance understanding of the wheat genome and its homoeologous counterparts from wild grasses, and expand the genetic variability of the wheat genome.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Mingyi Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Shiaoman Chao
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND, 58102, USA
| | - Steven Xu
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
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Grewal S, Hubbart-Edwards S, Yang C, Scholefield D, Ashling S, Burridge A, Wilkinson PA, King IP, King J. Detection of T. urartu Introgressions in Wheat and Development of a Panel of Interspecific Introgression Lines. FRONTIERS IN PLANT SCIENCE 2018; 9:1565. [PMID: 30420865 PMCID: PMC6216105 DOI: 10.3389/fpls.2018.01565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
Tritcum urartu (2n = 2x = 14, AuAu), the A genome donor of wheat, is an important source for new genetic variation for wheat improvement due to its high photosynthetic rate and disease resistance. By facilitating the generation of genome-wide introgressions leading to a variety of different wheat-T. urartu translocation lines, T. urartu can be practically utilized in wheat improvement. Previous studies that have generated such introgression lines have been unable to successfully use cytological methods to detect the presence of T. urartu in these lines. Many have, thus, used a variety of molecular markers with limited success due to the low-density coverage of these markers and time-consuming nature of the techniques rendering them unsuitable for large-scale breeding programs. In this study, we report the generation of a resource of single nucleotide polymorphic (SNP) markers, present on a high-throughput SNP genotyping array, that can detect the presence of T. urartu in a hexaploid wheat background making it a potentially valuable tool in wheat pre-breeding programs. A whole genome introgression approach has resulted in the transfer of different chromosome segments from T. urartu into wheat which have then been detected and characterized using these SNP markers. The molecular analysis of these wheat-T. urartu recombinant lines has resulted in the generation of a genetic map of T. urartu containing 368 SNP markers, spread across all seven chromosomes of T. urartu. Comparative analysis of the genetic map of T. urartu and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of the 4/5 translocation in T. urartu also present in the A genome of wheat. A panel of 17 wheat-T. urartu recombinant lines, which consisted of introgressed segments that covered the whole genome of T. urartu, were also selected for self-fertilization to provide a germplasm resource for future trait analysis. This valuable resource of high-density molecular markers specifically designed for detecting wild relative chromosomes and a panel of stable interspecific introgression lines will greatly enhance the efficiency of wheat improvement through wild relative introgressions.
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Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Caiyun Yang
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Paul Anthony Wilkinson
- Cereal Genomics Lab, Life Sciences Building, School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, Plant and Crop Sciences, School of Biosciences, The University of Nottingham, Loughborough, United Kingdom
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Tang S, Tang Z, Qiu L, Yang Z, Li G, Lang T, Zhu W, Zhang J, Fu S. Developing New Oligo Probes to Distinguish Specific Chromosomal Segments and the A, B, D Genomes of Wheat ( Triticum aestivum L.) Using ND-FISH. FRONTIERS IN PLANT SCIENCE 2018; 9:1104. [PMID: 30093909 PMCID: PMC6070686 DOI: 10.3389/fpls.2018.01104] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/09/2018] [Indexed: 05/03/2023]
Abstract
Non-denaturing FISH (ND-FISH) technology has been widely used to study the chromosomes of Triticeae species because of its convenience. The oligo probes for ND-FISH analysis of wheat (Triticum aestivum L.) chromosomes are still limited. In this study, the whole genome shotgun assembly sequences (IWGSC WGA v0.4) and the first version of the reference sequences (IWGSC RefSeq v1.0) of Chinese Spring (T. aestivum L.) were used to find new tandem repeats. One hundred and twenty oligo probes were designed according to the new tandem repeats and used for ND-FISH analysis of chromosomes of wheat Chinese Spring. Twenty nine of the 120 oligo probes produce clear or strong signals on wheat chromosomes. Two of the 29 oligo probes can be used to conveniently distinguish wheat A-, B-, and D-genome chromosomes. Sixteen of the 29 oligo probes only produce clear or strong signals on the subtelomeric regions of 1AS, 5AS, 7AL, 4BS, 5BS, and 3DS arms, on the telomeric regions of 1AL, 5AL, 2BS, 3BL, 6DS, and 7DL arms, on the intercalary regions of 4AL and 2DL arms, and on the pericentromeric regions of 3DL and 6DS arms. Eleven of the 29 oligo probes generate distinct signal bands on several chromosomes and they are different from those previously reported. In addition, the short and long arms of 6D chromosome have been confirmed. The new oligo probes developed in this study are useful and convenient for distinguishing wheat chromosomes or specific segments of wheat chromosomes.
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Affiliation(s)
- Shuyao Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Zongxiang Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Ling Qiu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
| | - Zujun Yang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Guangrong Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Tao Lang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenqian Zhu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Jiehong Zhang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
| | - Shulan Fu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Shulan Fu,
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