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Chepurnov GY, Ovchinnikova ES, Blinov AG, Chikida NN, Belousova MK, Goncharov NP. Analysis of the Structural Organization and Expression of the Vrn-D1 Gene Controlling Growth Habit (Spring vs. Winter) in Aegilops tauschii Coss. PLANTS (BASEL, SWITZERLAND) 2023; 12:3596. [PMID: 37896059 PMCID: PMC10610194 DOI: 10.3390/plants12203596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]
Abstract
The duration of the vegetative period is an important agronomic characteristic of cereal crops. It is mainly influenced by the Vrn (response to vernalization) and Ppd (response to photoperiod) genes. In this work, we searched for alleles of several known genes of these two systems of response to external conditions in 15 accessions of Aegilops tauschii Coss. (syn. Ae. squarrosa L.), with the aim of studying the impact these alleles have on the vegetative period duration and growth habit. As a result, three allelic variants have been found for the Vrn-D1 gene: (i) one intact (winter type), (ii) one with a 5437 bp deletion in the first intron and (iii) one previously undescribed allele with a 3273 bp deletion in the first intron. It has been shown that the spring growth habit of Ae. tauschii can be developed due to the presence of a new allele of the Vrn-D1 gene. Significant differences in expression levels between the new allelic variant of the Vrn-D1 gene and the intact allele vrn-D1 were confirmed by qPCR. The new allele can be introgressed into common wheat to enhance the biodiversity of the spring growth habit and vegetative period duration of plants.
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Affiliation(s)
- Grigory Yurievich Chepurnov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
| | - Ekaterina Sergeevna Ovchinnikova
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
| | - Alexander Genadevich Blinov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
| | - Nadezhda Nikolaevna Chikida
- Division of Wheat Genetic Resources, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia;
| | - Mariya Khasbulatovna Belousova
- Wheat Laboratory, Dagestan Experimental Station—The Branch of the Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Vavilovo Village, Derbent District, 368600 Saint Petersburg, Russia;
| | - Nikolay Petrovich Goncharov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
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Multiomics Based Association Mapping in Wheat Reveals Genetic Architecture of Quality and Allergenic Related Proteins. Int J Mol Sci 2023; 24:ijms24021485. [PMID: 36674997 PMCID: PMC9866442 DOI: 10.3390/ijms24021485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Wheat is an important staple crop since its proteins contribute to human and animal nutrition and are important for its end-use quality. However, wheat proteins can also cause adverse human reactions for a large number of people. We performed a genome wide association study (GWAS) on 114 proteins quantified by LC-MS-based proteomics and expressed in an environmentally stable manner in 148 wheat cultivars with a heritability > 0.6. For 54 proteins, we detected quantitative trait loci (QTL) that exceeded the Bonferroni-corrected significance threshold and explained 17.3−84.5% of the genotypic variance. Proteins in the same family often clustered at a very close chromosomal position or the potential homeolog. Major QTLs were found for four well-known glutenin and gliadin subunits, and the QTL segregation pattern in the protein encoding the high molecular weight glutenin subunit Dx5 could be confirmed by SDS gel-electrophoresis. For nine potential allergenic proteins, large QTLs could be identified, and their measured allele frequencies open the possibility to select for low protein abundance by markers as long as their relevance for human health has been conclusively demonstrated. A potential allergen was introduced in the beginning of 1980s that may be linked to the cluster of resistance genes introgressed on chromosome 2AS from Triticum ventricosum. The reported sequence information for the 54 major QTLs can be used to design efficient markers for future wheat breeding.
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Varotto S, Krugman T, Aiese Cigliano R, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3987-4003. [PMID: 35678824 PMCID: PMC9729329 DOI: 10.1007/s00122-022-04122-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padova, Viale dell'Università, 16 35020, Legnaro, Italy.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beersheba, 84105, Israel
| | - Ankica Kondić-Špika
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Fillipos A Aravanopoulos
- Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, GR54006, Greece
| | - Monica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Federica Consiglio
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Università 133, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Acad Sci, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
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4
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Hanif U, Alipour H, Gul A, Jing L, Darvishzadeh R, Amir R, Munir F, Ilyas MK, Ghafoor A, Siddiqui SU, St Amand P, Bernado A, Bai G, Sonder K, Rasheed A, He Z, Li H. Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study. THE PLANT GENOME 2021; 14:e20096. [PMID: 34275212 DOI: 10.1002/tpg2.20096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/31/2021] [Indexed: 05/21/2023]
Abstract
Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.
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Affiliation(s)
- Uzma Hanif
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Hadi Alipour
- Dep. of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia Univ., Urmia, Iran
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Li Jing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
| | - Reza Darvishzadeh
- Dep. of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia Univ., Urmia, Iran
| | - Rabia Amir
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Abdul Ghafoor
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Sadar Uddin Siddiqui
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Paul St Amand
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernado
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Kai Sonder
- International Wheat and Maize Improvement Center (CIMMYT), Texcoco, Mexico
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
- Dep. of Plant Sciences, Quaid-i-Azam Univ., Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
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5
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Zhou Y, Bai S, Li H, Sun G, Zhang D, Ma F, Zhao X, Nie F, Li J, Chen L, Lv L, Zhu L, Fan R, Ge Y, Shaheen A, Guo G, Zhang Z, Ma J, Liang H, Qiu X, Hu J, Sun T, Hou J, Xu H, Xue S, Jiang W, Huang J, Li S, Zou C, Song CP. Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. NATURE PLANTS 2021; 7:774-786. [PMID: 34045708 DOI: 10.1038/s41477-021-00934-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/30/2021] [Indexed: 05/04/2023]
Abstract
Increasing crop production is necessary to feed the world's expanding population, and crop breeders often utilize genetic variations to improve crop yield and quality. However, the narrow diversity of the wheat D genome seriously restricts its selective breeding. A practical solution is to exploit the genomic variations of Aegilops tauschii via introgression. Here, we established a rapid introgression platform for transferring the overall genetic variations of A. tauschii to elite wheats, thereby enriching the wheat germplasm pool. To accelerate the process, we assembled four new reference genomes, resequenced 278 accessions of A. tauschii and constructed the variation landscape of this wheat progenitor species. Genome comparisons highlighted diverse functional genes or novel haplotypes with potential applications in wheat improvement. We constructed the core germplasm of A. tauschii, including 85 accessions covering more than 99% of the species' overall genetic variations. This was crossed with elite wheat cultivars to generate an A. tauschii-wheat synthetic octoploid wheat (A-WSOW) pool. Laboratory and field analysis with two examples of the introgression lines confirmed its great potential for wheat breeding. Our high-quality reference genomes, genomic variation landscape of A. tauschii and the A-WSOW pool provide valuable resources to facilitate gene discovery and breeding in wheat.
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Affiliation(s)
- Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Guiling Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Dale Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Feifei Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Xinpeng Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Fang Nie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jingyao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing, China
| | - Linlin Lv
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lele Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ruixiao Fan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yifan Ge
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Aaqib Shaheen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Guanghui Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Zhen Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jianchao Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Huihui Liang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaolong Qiu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiamin Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ting Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jingyi Hou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hongxing Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Changsong Zou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
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Schaart JG, Salentijn EMJ, Goryunova SV, Chidzanga C, Esselink DG, Gosman N, Bentley AR, Gilissen LJWJ, Smulders MJM. Exploring the alpha-gliadin locus: the 33-mer peptide with six overlapping coeliac disease epitopes in Triticum aestivum is derived from a subgroup of Aegilops tauschii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:86-94. [PMID: 33369792 PMCID: PMC8248119 DOI: 10.1111/tpj.15147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 05/28/2023]
Abstract
Most alpha-gliadin genes of the Gli-D2 locus on the D genome of hexaploid bread wheat (Triticum aestivum) encode for proteins with epitopes that can trigger coeliac disease (CD), and several contain a 33-mer peptide with six partly overlapping copies of three epitopes, which is regarded as a remarkably potent T-cell stimulator. To increase genetic diversity in the D genome, synthetic hexaploid wheat lines are being made by hybridising accessions of Triticum turgidum (AB genome) and Aegilops tauschii (the progenitor of the D genome). The diversity of alpha-gliadins in A. tauschii has not been studied extensively. We analysed the alpha-gliadin transcriptome of 51 A. tauschii accessions representative of the diversity in A. tauschii. We extracted RNA from developing seeds and performed 454 amplicon sequencing of the first part of the alpha-gliadin genes. The expression profile of allelic variants of the alpha-gliadins was different between accessions, and also between accessions of the Western and Eastern clades of A. tauschii. Generally, both clades expressed many allelic variants not found in bread wheat. In contrast to earlier studies, we detected the 33-mer peptide in some A. tauschii accessions, indicating that it was introduced along with the D genome into bread wheat. In these accessions, transcripts with the 33-mer peptide were present at lower frequencies than in bread wheat varieties. In most A. tauschii accessions, however, the alpha-gliadins do not contain the epitope, and this may be exploited, through synthetic hexaploid wheats, to breed bread wheat varieties with fewer or no coeliac disease epitopes.
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Affiliation(s)
- Jan G. Schaart
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Elma M. J. Salentijn
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Svetlana V. Goryunova
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Present address:
FSBSI Lorch Potato Research InstituteKraskovo140051Russia
- Present address:
Institute of General GeneticsRussian Academy of ScienceMoscow119333Russia
| | - Charity Chidzanga
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Present address:
University of AdelaideSchool of Agriculture, Food and WineWaite CampusUrrbraeSouth Australia5064Australia
| | - Danny G. Esselink
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Nick Gosman
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
- Present address:
Gosman AssociatesAg‐Biotech Consultingthe StreetBressingham, DissIP22 2BLUK
| | - Alison R. Bentley
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
- Present address:
International Maize and Wheat Improvement Center (CIMMYT)TexcocoMexico
| | - Luud J. W. J. Gilissen
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Allergy Consortium WageningenDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Marinus J. M. Smulders
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Allergy Consortium WageningenDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
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7
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Przewieslik-Allen AM, Wilkinson PA, Burridge AJ, Winfield MO, Dai X, Beaumont M, King J, Yang CY, Griffiths S, Wingen LU, Horsnell R, Bentley AR, Shewry P, Barker GLA, Edwards KJ. The role of gene flow and chromosomal instability in shaping the bread wheat genome. NATURE PLANTS 2021; 7:172-183. [PMID: 33526912 DOI: 10.1038/s41477-020-00845-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/18/2020] [Indexed: 05/02/2023]
Abstract
Bread wheat (Triticum aestivum) is one of the world's most important crops; however, a low level of genetic diversity within commercial breeding accessions can significantly limit breeding potential. In contrast, wheat relatives exhibit considerable genetic variation and so potentially provide a valuable source of novel alleles for use in breeding new cultivars. Historically, gene flow between wheat and its relatives may have contributed novel alleles to the bread wheat pangenome. To assess the contribution made by wheat relatives to genetic diversity in bread wheat, we used markers based on single nucleotide polymorphisms to compare bread wheat accessions, created in the past 150 years, with 45 related species. We show that many bread wheat accessions share near-identical haplotype blocks with close relatives of wheat's diploid and tetraploid progenitors, while some show evidence of introgressions from more distant species and structural variation between accessions. Hence, introgressions and chromosomal rearrangements appear to have made a major contribution to genetic diversity in cultivar collections. As gene flow from relatives to bread wheat is an ongoing process, we assess the impact that introgressions might have on future breeding strategies.
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Affiliation(s)
| | - Paul A Wilkinson
- Life Sciences, University of Bristol, Bristol, UK
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | - Xiaoyang Dai
- Life Sciences, University of Bristol, Bristol, UK
| | | | - Julie King
- Plant Sciences Building, School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - Cai-Yun Yang
- Plant Sciences Building, School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | | | | | | | - Alison R Bentley
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Mexico
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8
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Identification of a hard kernel texture line of synthetic allohexaploid wheat reducing the puroindoline accumulation on the D genome from Aegilops tauschii. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.102964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Takumi S, Mitta S, Komura S, Ikeda TM, Matsunaka H, Sato K, Yoshida K, Murai K. Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars. PLoS One 2020; 15:e0228397. [PMID: 31986184 PMCID: PMC6984701 DOI: 10.1371/journal.pone.0228397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/14/2020] [Indexed: 12/03/2022] Open
Abstract
The breeding of agriculturally useful genes from wild crop relatives must take into account recent and future climate change. In Japan, the development of early heading wheat cultivars without the use of any major gene controlling the heading date is desired to avoid overlap of the harvesting time before the rainy season. Here, we backcrossed two early heading lines of a synthetic hexaploid wheat, derived from a crossing between durum wheat and the wild wheat progenitor Aegilops tauschii, with four Japanese elite cultivars to develop early heading lines of bread wheat. In total, nine early heading lines that showed a heading date two to eight days earlier than their parental cultivars in field conditions were selected and established from the selfed progenies of the two- or three-times backcrossed populations. The whole appearance and spike shape of the selected early heading lines looked like their parental wheat cultivars. The mature grains of the selected lines had the parental cultivars’ characteristics, although the grains exhibited longer and narrower shapes. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines. The introgression regions could shorten wheat heading date, and their chromosomal positions were dependent on the backcrossed wheat cultivars. Therefore, early heading synthetic hexaploid wheat is useful for fine-tuning of the heading date through introgression of Ae. tauschii chromosomal regions.
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Affiliation(s)
- Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
- * E-mail: (ST); (KM)
| | - Seito Mitta
- Fukui Prefectural University, Eiheiji, Yoshida, Fukui, Japan
| | - Shoya Komura
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Tatsuya M. Ikeda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Hiroshima, Japan
| | - Hitoshi Matsunaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Koji Murai
- Fukui Prefectural University, Eiheiji, Yoshida, Fukui, Japan
- * E-mail: (ST); (KM)
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10
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Ivanizs L, Monostori I, Farkas A, Megyeri M, Mikó P, Türkösi E, Gaál E, Lenykó-Thegze A, Szőke-Pázsi K, Szakács É, Darkó É, Kiss T, Kilian A, Molnár I. Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time. FRONTIERS IN PLANT SCIENCE 2019; 10:1531. [PMID: 31824545 PMCID: PMC6882925 DOI: 10.3389/fpls.2019.01531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/01/2019] [Indexed: 06/02/2023]
Abstract
Understanding the genetic diversity of Aegilops biuncialis, a valuable source of agronomical useful genes, may significantly facilitate the introgression breeding of wheat. The genetic diversity and population structure of 86 Ae. biuncialis genotypes were investigated by 32700 DArT markers with the simultaneous application of three statistical methods- neighbor-joining clustering, Principal Coordinate Analysis, and the Bayesian approach to classification. The collection of Ae. biuncialis accessions was divided into five groups that correlated well with their eco-geographic habitat: A (North Africa), B (mainly from Balkans), C (Kosovo and Near East), D (Turkey, Crimea, and Peloponnese), and E (Azerbaijan and the Levant region). The diversity between the Ae. biuncialis accessions for a phenological trait (heading time), which is of decisive importance in the adaptation of plants to different eco-geographical environments, was studied over 3 years. A comparison of the intraspecific variation in the heading time trait by means of analysis of variance and principal component analysis revealed four phenotypic categories showing association with the genetic structure and geographic distribution, except for minor differences. The detailed exploration of genetic and phenologic divergence provides an insight into the adaptation capacity of Ae. biuncialis, identifying promising genotypes that could be utilized for wheat improvement.
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Affiliation(s)
- László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - István Monostori
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Mária Megyeri
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Péter Mikó
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Edina Türkösi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Eszter Gaál
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | | | - Kitti Szőke-Pázsi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Éva Szakács
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Tibor Kiss
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Andrzej Kilian
- University of Canberra, Diversity Array Technologies, Canberra, ACT, Australia
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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11
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Brewster C, Hayes F, Fenner N. Ozone Tolerance Found in Aegilops tauschii and Primary Synthetic Hexaploid Wheat. PLANTS (BASEL, SWITZERLAND) 2019; 8:E195. [PMID: 31261799 PMCID: PMC6681361 DOI: 10.3390/plants8070195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022]
Abstract
Modern wheat cultivars are increasingly sensitive to ground level ozone, with 7-10% mean yield reductions in the northern hemisphere. In this study, three of the genome donors of bread wheat, Triticum urartu (AA), T. dicoccoides (AABB), and Aegilops tauschii (DD) along with a modern wheat cultivar (T. aestivum 'Skyfall'), a 1970s cultivar (T. aestivum 'Maris Dove'), and a line of primary Synthetic Hexaploid Wheat were grown in 6 L pots of sandy loam soil in solardomes (Bangor, North Wales) and exposed to low (30 ppb), medium (55 ppb), and high (110 ppb) levels of ozone over 3 months. Measurements were made at harvest of shoot biomass and grain yield. Ae. tauschii appeared ozone tolerant with no significant effects of ozone on shoot biomass, seed head biomass, or 1000 grain + husk weight even under high ozone levels. In comparison, T. urartu had a significant reduction in 1000 grain + husk weight, especially under high ozone (-26%). The older cultivar, 'Maris Dove', had a significant reduction in seed head biomass (-9%) and 1000 grain weight (-11%) but was less sensitive than the more recent cultivar 'Skyfall', which had a highly significant reduction in its seed head biomass (-21%) and 1000 grain weight (-27%) under high ozone. Notably, the line of primary Synthetic Hexaploid Wheat was ozone tolerant, with no effect on total seed head biomass (-1%) and only a 5% reduction in 1000 grain weight under high ozone levels. The potential use of synthetic wheat in breeding ozone tolerant wheat is discussed.
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Affiliation(s)
- Clare Brewster
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor LL57 2UW, UK.
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK.
| | - Felicity Hayes
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor LL57 2UW, UK
| | - Nathalie Fenner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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12
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Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Johnson R, Enk J, Periyannan S, Singh N, Asyraf Md Hatta M, Athiyannan N, Cheema J, Yu G, Kangara N, Ghosh S, Szabo LJ, Poland J, Bariana H, Jones JDG, Bentley AR, Ayliffe M, Olson E, Xu SS, Steffenson BJ, Lagudah E, Wulff BBH. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat Biotechnol 2019; 37:139-143. [PMID: 30718880 DOI: 10.1038/s41587-018-0007-9] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 12/12/2018] [Indexed: 01/17/2023]
Abstract
Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum resistance in domesticated crops. We combined association genetics with R gene enrichment sequencing (AgRenSeq) to exploit pan-genome variation in wild diploid wheat and rapidly clone four stem rust resistance genes. AgRenSeq enables R gene cloning in any crop that has a diverse germplasm panel.
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Affiliation(s)
- Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Kumar Gaurav
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sutha Chandramohan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Yunming Long
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Ryan Johnson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Jacob Enk
- Arbor Biosciences, Ann Arbor, MI, USA
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Narinder Singh
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, UK.,Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Naveenkumar Athiyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia.,Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Les J Szabo
- US Department of Agriculture, Agriculture Research Service, Cereal Disease Laboratory, St. Paul, MN, USA
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Harbans Bariana
- The University of Sydney Plant Breeding Institute, Cobbitty, New South Wales, Australia
| | | | | | - Mick Ayliffe
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Eric Olson
- Michigan State University, East Lansing, MI, USA
| | - Steven S Xu
- US Department of Agriculture, Agriculture Research Service, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, Fargo, ND, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, Australia
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13
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Przewieslik-Allen AM, Burridge AJ, Wilkinson PA, Winfield MO, Shaw DS, McAusland L, King J, King IP, Edwards KJ, Barker GLA. Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2019; 9:1993. [PMID: 30733728 PMCID: PMC6354564 DOI: 10.3389/fpls.2018.01993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.
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Affiliation(s)
| | | | | | | | - Daniel S. Shaw
- Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Lorna McAusland
- Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Julie King
- Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Ian P. King
- Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom
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14
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Nishijima R, Yoshida K, Sakaguchi K, Yoshimura SI, Sato K, Takumi S. RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat. Int J Mol Sci 2018; 19:E3749. [PMID: 30486239 PMCID: PMC6321645 DOI: 10.3390/ijms19123749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 11/16/2022] Open
Abstract
Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.
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Affiliation(s)
- Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kohei Sakaguchi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Shin-Ichi Yoshimura
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan.
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15
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Okada M, Ikeda TM, Yoshida K, Takumi S. Effect of the U genome on grain hardness in nascent synthetic hexaploids derived from interspecific hybrids between durum wheat and Aegilops umbellulata. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Brunazzi A, Scaglione D, Talini RF, Miculan M, Magni F, Poland J, Enrico Pè M, Brandolini A, Dell'Acqua M. Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:670-684. [PMID: 29573496 DOI: 10.1111/tpj.13888] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 01/06/2018] [Accepted: 02/19/2018] [Indexed: 05/22/2023]
Abstract
Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next-generation sequencing was used to generate 1.3 million genome-wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the Au subgenome of modern wheat. A set of 75 511 high-quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R2 = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the Au subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome-wide association approach, identifying several marker-environment associations (MEAs). Fifty-seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding.
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Affiliation(s)
- Alice Brunazzi
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.zza Martiri della Libertà 33, Pisa, 56127, Italy
| | - Davide Scaglione
- Institute of Applied Genomics, Via J. Linussio, 51 ZIU, Udine, 33100, Italy
| | - Rebecca Fiorella Talini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.zza Martiri della Libertà 33, Pisa, 56127, Italy
| | - Mara Miculan
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.zza Martiri della Libertà 33, Pisa, 56127, Italy
| | - Federica Magni
- Institute of Applied Genomics, Via J. Linussio, 51 ZIU, Udine, 33100, Italy
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton PSC, Manhattan, KS, 66506, USA
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.zza Martiri della Libertà 33, Pisa, 56127, Italy
| | - Andrea Brandolini
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Via Po 14, Roma, 00198, Italy
| | - Matteo Dell'Acqua
- Institute of Life Sciences, Scuola Superiore Sant'Anna, P.zza Martiri della Libertà 33, Pisa, 56127, Italy
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17
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Yan L, Liu Z, Xu H, Zhang X, Zhao A, Liang F, Xin M, Peng H, Yao Y, Sun Q, Ni Z. Transcriptome analysis reveals potential mechanisms for different grain size between natural and resynthesized allohexaploid wheats with near-identical AABB genomes. BMC PLANT BIOLOGY 2018; 18:28. [PMID: 29402221 PMCID: PMC5799976 DOI: 10.1186/s12870-018-1248-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/24/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Common wheat is a typical allohexaploid species (AABBDD) derived from the interspecific crossing between allotetraploid wheat (AABB) and Aegilops tauschii (DD). Wide variation in grain size and shape observed among Aegilops tauschii can be retained in synthetic allohexaploid wheats, but the underlying mechanism remains enigmatic. Here, the natural and resynthesized allohexaploid wheats with near-identical AB genomes and different D genomes (TAA10 and XX329) were employed for analysis. RESULTS Significant differences in grain size and weight between TAA10 and XX329 were observed at the early stages of development, which could be mainly attributed to the higher growth rates of the pericarp and endosperm cells in XX329 compared to TAA10. Furthermore, comparative transcriptome analysis identified that 8891 of 69,711 unigenes (12.75%) were differentially expressed between grains at 6 days after pollination (DAP) of TAA10 and XX329, including 5314 up-regulated and 3577 down-regulated genes in XX329 compared to TAA10. The MapMan functional annotation and enrichment analysis revealed that the differentially expressed genes were significantly enriched in categories of cell wall, carbohydrate and hormone metabolism. Notably, consistent with the up-regulation of sucrose synthase genes in resynthesized relative to natural allohexaploid wheat, the resynthesized allohexaploid wheat accumulated much higher contents of glucose and fructose in 6-DAP grains than those of the natural allohexaploid wheat. CONCLUSIONS These data indicated that the genetic variation of the D genome induced drastic alterations of gene expression in grains of the natural and resynthesized allohexaploid wheats, which may contribute to the observed differences in grain size and weight.
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Affiliation(s)
- Lei Yan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhenshan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Huanwen Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoping Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035 China
| | - Fei Liang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
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18
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Okada M, Yoshida K, Takumi S. Hybrid incompatibilities in interspecific crosses between tetraploid wheat and its wild diploid relative Aegilops umbellulata. PLANT MOLECULAR BIOLOGY 2017; 95:625-645. [PMID: 29090430 DOI: 10.1007/s11103-017-0677-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 10/22/2017] [Indexed: 05/10/2023]
Abstract
Hybrid abnormalities, severe growth abortion and grass-clump dwarfism, were found in the tetraploid wheat/Aegilops umbellulata hybrids, and the gene expression changes were conserved in the hybrids with those in other wheat synthetic hexaploids. Aegilops umbellulata Zhuk., a diploid goatgrass species with a UU genome, has been utilized as a genetic resource for wheat breeding. Here, we examine the reproductive barriers between tetraploid wheat cultivar Langdon (Ldn) and various Ae. umbellulata accessions by conducting interspecific crossings. Through systematic cross experiments, three types of hybrid incompatibilities were found: seed production failure in crosses, hybrid growth abnormalities and sterility in the ABU hybrids. Hybrid incompatibilities were widely distributed over the entire range of the natural species, and in about 50% of the cross combinations between tetraploid Ldn and Ae. umbellulata accessions, ABU F1 hybrids showed one of two abnormal growth phenotypes: severe growth abortion (SGA) or grass-clump dwarfism. Expression of the shoot meristem maintenance-related and cell cycle-related genes was markedly repressed in crown tissues of hybrids showing SGA, suggesting dysfunction of mitotic cell division in the shoot apices. The grass-clump dwarf phenotype may be explained by down-regulation of wheat APETALA1-like MADS box genes, which act as flowering promoters, and altered expression in crown tissues of the miR156/SPLs module, which controls tiller number and branching. These gene expression changes in growth abnormalities were well conserved between the Ldn/Ae. umbellulata plants and interspecific hybrids from crosses of Ldn and wheat D-genome progenitor Ae. tauschii.
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Affiliation(s)
- Moeko Okada
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, 332-0012, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan.
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19
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Nishijima R, Ikeda TM, Takumi S. Genetic mapping reveals a dominant awn-inhibiting gene related to differentiation of the variety anathera in the wild diploid wheat Aegilops tauschii. Genetica 2017; 146:75-84. [PMID: 29101627 DOI: 10.1007/s10709-017-9998-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
Aegilops tauschii, a wild wheat relative, is the D-genome donor of common wheat. Subspecies and varieties of Ae. tauschii are traditionally classified based on differences in their inflorescence architecture. However, the genetic information for their diversification has been quite limited in the wild wheat relatives. The variety anathera has no awn on the lemma, but the genetic basis for this diagnostic character is unknown. Wide variations in awn length traits at the top and middle spikes were found in the Ae. tauschii core collection, and the awn length at the middle spike was significantly smaller in the eastward-dispersed sublineage than in those in other sublineages. To clarify loci controlling the awnless phenotype of var. anathera, we measured awn length of an intervariety F2 mapping population, and found that the F2 individuals could be divided into two groups mainly based on the awn length at the middle of spike, namely short and long awn groups, significantly fitting a 3:1 segregation ratio, which indicated that a single locus controls the awnless phenotype. The awnless locus, Anathera (Antr), was assigned to the distal region of the short arm of chromosome 5D. Quantitative trait locus analysis using the awn length data of each F2 individual showed that only one major locus was at the same chromosomal position as Antr. These results suggest that a single dominant allele determines the awnless diagnostic character in the variety anathera. The Antr dominant allele is a novel gene inhibiting awn elongation in wheat and its relatives.
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Affiliation(s)
- Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Tatsuya M Ikeda
- Western Region Agricultural Research Center of the National Agriculture and Food Research Organization, 6-12-1 Nishi-fukatsucho, Fukuyama, Hiroshima, 721-8514, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan.
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20
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Matsuda R, Iehisa JCM, Sakaguchi K, Ohno R, Yoshida K, Takumi S. Global gene expression profiling related to temperature-sensitive growth abnormalities in interspecific crosses between tetraploid wheat and Aegilops tauschii. PLoS One 2017; 12:e0176497. [PMID: 28463975 PMCID: PMC5413045 DOI: 10.1371/journal.pone.0176497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/10/2017] [Indexed: 12/17/2022] Open
Abstract
Triploid wheat hybrids between tetraploid wheat and Aegilops tauschii sometimes show abnormal growth phenotypes, and the growth abnormalities inhibit generation of wheat synthetic hexaploids. In type II necrosis, one of the growth abnormalities, necrotic cell death accompanied by marked growth repression occurs only under low temperature conditions. At normal temperature, the type II necrosis lines show grass-clump dwarfism with no necrotic symptoms, excess tillers, severe dwarfism and delayed flowering. Here, we report comparative expression analyses to elucidate the molecular mechanisms of the temperature-dependent phenotypic plasticity in the triploid wheat hybrids. We compared gene and small RNA expression profiles in crown tissues to characterize the temperature-dependent phenotypic plasticity. No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Some microRNAs, including miR156, were up-regulated, whereas the levels of transcripts of the miR156 target genes SPLs, known to inhibit tiller and branch number, were reduced in crown tissues of the grass-clump dwarf lines at the normal temperature. Unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype. Dramatic alteration of gene expression profiles, including miRNA levels, in crown tissues is associated with the temperature-dependent phenotypic plasticity in type II necrosis/grass-clump dwarf wheat hybrids.
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Affiliation(s)
- Ryusuke Matsuda
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Julio Cesar Masaru Iehisa
- Departmento de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Kouhei Sakaguchi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Ryoko Ohno
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kentaro Yoshida
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shigeo Takumi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- * E-mail:
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Jouanin A, Gilissen LJWJ, Boyd LA, Cockram J, Leigh FJ, Wallington EJ, van den Broeck HC, van der Meer IM, Schaart JG, Visser RGF, Smulders MJM. Food processing and breeding strategies for coeliac-safe and healthy wheat products. Food Res Int 2017; 110:11-21. [PMID: 30029701 DOI: 10.1016/j.foodres.2017.04.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 01/01/2023]
Abstract
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients. The first approach is based on food processing strategies, which aim to remove gliadins or all gluten from edible products. We find that several of the candidate food processing techniques to produce low gluten-immunogenic products from wheat already exist. The second approach focuses on wheat breeding strategies to remove immunogenic epitopes from the gluten proteins, while maintaining their food-processing properties. A combination of breeding strategies, including mutation breeding and possibly genome editing, will be necessary to produce coeliac-safe wheat. Individuals suffering from CD and people genetically susceptible who may develop CD after prolonged gluten consumption would benefit from reduced CD-immunogenic wheat. Although the production of healthy and less CD-toxic wheat varieties and food products will be challenging, increasing global demand may require these issues to be addressed in the near future by food processing and cereal breeding companies.
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Affiliation(s)
- Aurélie Jouanin
- Wageningen University & Research, Wageningen, The Netherlands; NIAB, Cambridge CB3 0LE, UK
| | | | | | | | | | | | | | | | - Jan G Schaart
- Wageningen University & Research, Wageningen, The Netherlands
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Nishijima R, Okamoto Y, Hatano H, Takumi S. Quantitative trait locus analysis for spikelet shape-related traits in wild wheat progenitor Aegilops tauschii: Implications for intraspecific diversification and subspecies differentiation. PLoS One 2017; 12:e0173210. [PMID: 28264068 PMCID: PMC5338802 DOI: 10.1371/journal.pone.0173210] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/16/2017] [Indexed: 11/19/2022] Open
Abstract
Wild diploid wheat Aegilops tauschii, the D-genome progenitor of common wheat, carries large genetic variation in spikelet and grain morphology. Two differentiated subspecies of Ae. tauschii, subspecies tauschii and strangulata, have been traditionally defined based on differences in spikelet morphology. Here, we first assessed six spikelet shape-related traits among 199 Ae. tauschii accessions, and found that the accessions belonging to TauL1major lineage produced significantly longer spikes, higher spikelet density, and shorter, narrower spikelets than another major lineage, TauL2, in which the strangulata accessions are included. Next, we performed quantitative trait locus (QTL) analysis of the spikelet and grain shape using three mapping populations derived from interlineage crosses between TauL1 and TauL2 to identify the genetic loci for the morphological variations of the spikelet and grain shape in Ae. tauschii. Three major QTL regions for the examined traits were detected on chromosomes 3D, 4D and 7D. The 3D and 4D QTL regions for several spikelet shape-related traits were conserved in the three mapping populations, which indicated that the 3D and 4D QTLs contribute to divergence of the two major lineages. The 7D QTLs were found only in a mapping population from a cross of the two subspecies, suggesting that these 7D QTLs may be closely related to subspecies differentiation in Ae. tauschii. Thus, QTL analysis for spikelet and grain morphology may provide useful information to elucidate the evolutionary processes of intraspecific differentiation.
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Affiliation(s)
- Ryo Nishijima
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Yuki Okamoto
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Hitoshi Hatano
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Shigeo Takumi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
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23
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Sakaguchi K, Nishijima R, Iehisa JCM, Takumi S. Fine mapping and genetic association analysis of Net2, the causative D-genome locus of low temperature-induced hybrid necrosis in interspecific crosses between tetraploid wheat and Aegilops tauschii. Genetica 2016; 144:523-533. [PMID: 27502693 DOI: 10.1007/s10709-016-9920-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/02/2016] [Indexed: 12/20/2022]
Abstract
Hybrid necrosis has been observed in many interspecific hybrids from crosses between tetraploid wheat and the wheat D-genome donor Aegilops tauschii. Type II necrosis is a kind of hybrid incompatibility that is specifically characterized by low-temperature induction and growth suppression. Two complementary genes, Net1 on the AB genome and Net2 on the D genome, putatively control type II necrosis in ABD triploids and synthetic hexaploid wheat. Toward map-based cloning of Net2, a fine map around the Net2 region on 2DS was constructed in this study. Using the draft genome sequence of Ae. tauschii and the physical map of the barley genome, the Net2 locus was mapped within a 0.6 cM interval between two closely linked markers. Although local chromosomal rearrangements were observed in the Net2-corresponding region between the barley/Brachypodium and Ae. tauschii genomes, the two closely linked markers were significantly associated with type II necrosis in Ae. tauschii. These results suggest that these markers will aid efficient selection of Net2 non-carrier individuals from the Ae. tauschii population and intraspecific progeny, and could help with introgression of agriculturally important genes from Ae. tauschii to common wheat.
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Affiliation(s)
- Kouhei Sakaguchi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Julio Cesar Masaru Iehisa
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.
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Nguyen AT, Nishijima R, Kajimura T, Murai K, Takumi S. Quantitative trait locus analysis for flowering-related traits using two F2 populations derived from crosses between Japanese common wheat cultivars and synthetic hexaploids. Genes Genet Syst 2016; 90:89-98. [PMID: 26399768 DOI: 10.1266/ggs.90.89] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Flowering time is an important trait for Japanese wheat breeding. Aegilops tauschii, the D-genome donor of hexaploid wheat, is a useful resource to enlarge the D-genome diversity of common wheat. Previously, we identified flowering-related QTLs in F2 populations of synthetic hexaploid wheat lines between the tetraploid wheat cultivar Langdon and Ae. tauschii accessions. Here, to evaluate the usefulness of the early-flowering alleles from Ae. tauschii for Japanese wheat breeding, QTL analyses were conducted in two F2 populations derived from crosses between Japanese wheat cultivars and early-flowering lines of synthetic hexaploid wheat. Only two chromosomal regions controlling flowering-related traits were identified, on chromosomes 2DS and 5AL in the mapping populations, and no previously identified QTLs were found in the synthetic hexaploid lines. The strong effect of the 2DS QTL, putatively corresponding to Ppd-D1, was considered to hide any significant expression of other QTLs with small effects on flowering-related traits. When F2 individuals carrying Ae. tauschii-homozygous alleles around the 2DS QTL region were selected, the Ae. tauschii-derived alleles of the previously identified flowering QTLs partly showed an early-flowering phenotype compared with the Japanese wheat-derived alleles. Thus, some early-flowering alleles from Ae. tauschii may be useful for production of early-flowering Japanese wheat cultivars.
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Affiliation(s)
- Anh T Nguyen
- Graduate School of Agricultural Science, Kobe University
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25
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Welling MT, Shapter T, Rose TJ, Liu L, Stanger R, King GJ. A Belated Green Revolution for Cannabis: Virtual Genetic Resources to Fast-Track Cultivar Development. FRONTIERS IN PLANT SCIENCE 2016; 7:1113. [PMID: 27524992 PMCID: PMC4965456 DOI: 10.3389/fpls.2016.01113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/13/2016] [Indexed: 05/18/2023]
Abstract
Cannabis is a predominantly diecious phenotypically diverse domesticated genus with few if any extant natural populations. International narcotics conventions and associated legislation have constrained the establishment, characterization, and use of Cannabis genetic resource collections. This has resulted in the underutilization of genepool variability in cultivar development and has limited the inclusion of secondary genepools associated with genetic improvement strategies of the Green Revolution. The structured screening of ex situ germplasm and the exploitation of locally-adapted intraspecific traits is expected to facilitate the genetic improvement of Cannabis. However, limited attempts have been made to establish the full extent of genetic resources available for pre-breeding. We present a thorough critical review of Cannabis ex situ genetic resources, and discuss recommendations for conservation, pre-breeding characterization, and genetic analysis that will underpin future cultivar development. We consider East Asian germplasm to be a priority for conservation based on the prolonged historical cultivation of Cannabis in this region over a range of latitudes, along with the apparent high levels of genetic diversity and relatively low representation in published genetic resource collections. Seed cryopreservation could improve conservation by reducing hybridization and genetic drift that may occur during Cannabis germplasm regeneration. Given the unique legal status of Cannabis, we propose the establishment of a global virtual core collection based on the collation of consistent and comprehensive provenance meta-data and the adoption of high-throughput DNA sequencing technologies. This would enable representative core collections to be used for systematic phenotyping, and so underpin breeding strategies for the genetic improvement of Cannabis.
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Affiliation(s)
- Matthew T. Welling
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Tim Shapter
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
- Ecofibre Industries Operations Pty LtdMaleny, QLD, Australia
| | - Terry J. Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Rhia Stanger
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
- *Correspondence: Graham J. King
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26
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Yokota H, Iehisa JCM, Shimosaka E, Takumi S. Line differences in Cor/Lea and fructan biosynthesis-related gene transcript accumulation are related to distinct freezing tolerance levels in synthetic wheat hexaploids. JOURNAL OF PLANT PHYSIOLOGY 2015; 176:78-88. [PMID: 25577733 DOI: 10.1016/j.jplph.2014.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/11/2014] [Accepted: 12/11/2014] [Indexed: 05/18/2023]
Abstract
In common wheat, cultivar differences in freezing tolerance are considered to be mainly due to allelic differences at two major loci controlling freezing tolerance. One of the two loci, Fr-2, is coincident with a cluster of genes encoding C-repeat binding factors (CBFs), which induce downstream Cor/Lea genes during cold acclimation. Here, we conducted microarray analysis to study comprehensive changes in gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related to cold acclimation in leaves of seedlings and crown tissues of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines that contain the A and B genomes from the tetraploid wheat cultivar Langdon and the diverse D genomes originating from different Aegilops tauschii accessions with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR showed increased transcript levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes in more freezing-tolerant lines than in sensitive lines. After a 14-day LT treatment, a significant difference in fructan accumulation was observed among the four lines. Therefore, the fructan biosynthetic pathway is associated with cold acclimation in development of wheat freezing tolerance and is another pathway related to diversity in freezing tolerance, in addition to the CBF-mediated Cor/Lea expression pathway.
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Affiliation(s)
- Hirokazu Yokota
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Julio C M Iehisa
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Etsuo Shimosaka
- Hokkaido Agricultural Research Center of the National Agriculture and Food Research Organization, Hitsujigaoka 1, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan.
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27
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28
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Hirao K, Nishijima R, Sakaguchi K, Takumi S. Fine mapping of Hch1, the causal D-genome gene for hybrid chlorosis in interspecific crosses between tetraploid wheat and Aegilops tauschii. Genes Genet Syst 2015; 90:283-91. [DOI: 10.1266/ggs.15-00035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Kana Hirao
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University
| | - Ryo Nishijima
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University
| | - Kohei Sakaguchi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University
| | - Shigeo Takumi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University
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Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown‐Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:787-96. [PMID: 24646323 PMCID: PMC4265271 DOI: 10.1111/pbi.12183] [Citation(s) in RCA: 1067] [Impact Index Per Article: 106.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/18/2023]
Affiliation(s)
- Shichen Wang
- Department of Plant Pathology Kansas State University Manhattan KS USA
| | - Debbie Wong
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Kerrie Forrest
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Alexandra Allen
- School of Biological Sciences University of Bristol Bristol UK
| | - Shiaoman Chao
- US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory Fargo ND USA
| | - Bevan E. Huang
- Commonwealth Scientific and Industrial Research Organization Computational Informatics and Food Futures National Research Flagship Dutton Park Qld Australia
| | - Marco Maccaferri
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Silvio Salvi
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Sara G. Milner
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Genomics Research Centre Fiorenzuola d'arda Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Cereal Research Centre Foggia Italy
| | - Alex Whan
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gary Barker
- School of Biological Sciences University of Bristol Bristol UK
| | | | | | - Morten Lillemo
- Department of Plant Sciences Norwegian University of Life Sciences Ås Norway
| | - Diane Mather
- Waite Research Institute School of Agriculture, Food and Wine University of Adelaide Urrbrae SA Australia
| | | | - Rudy Dolferus
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gina Brown‐Guedira
- US Department of Agriculture–Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory Raleigh NC USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution University of Haifa Mount Carmel Haifa Israel
| | - Alina R. Akhunova
- K‐State Integrated Genomics Facility Kansas State University Manhattan KS USA
| | - Catherine Feuillet
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Jerome Salse
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Michele Morgante
- Department of Crop and Environmental Sciences University of Udine Via delle Scienze Udine Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ming‐Cheng Luo
- Department of Plant Sciences University of California Davis CA USA
| | - Jan Dvorak
- Department of Plant Sciences University of California Davis CA USA
| | - Matthew Morell
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences University of California Davis CA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | | | | | - Colin Cavanagh
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | | | - Matthew Hayden
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Eduard Akhunov
- Department of Plant Pathology Kansas State University Manhattan KS USA
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Mikó P, Megyeri M, Farkas A, Molnár I, Molnár-Láng M. Molecular cytogenetic identification and phenotypic description of a new synthetic amphiploid, Triticum timococcum (A tA tGGA mA m). GENETIC RESOURCES AND CROP EVOLUTION 2014; 62:55-66. [PMID: 26412939 PMCID: PMC4579857 DOI: 10.1007/s10722-014-0135-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 05/26/2014] [Indexed: 05/24/2023]
Abstract
A recently developed synthetic amphiploid, Triticum timococcum Kost., nom. nud. (2n = 6x = 42, AtAtGGAmAm) is described in the present study. This hexaploid taxon was developed by colchicine treatment in Martonvásár from the hybrid of a selected accession of Triticum timopheevii Zhuk. (2n = 4x = 28, AtAtGG) and a prebred semi-dwarf line of Triticum monococcum L. (2n = 2x = 14, AmAm). A detailed cytomolecular examination was carried out using the sequential multicolour fluorescence and genomic in situ hybridization techniques (FISH and mcGISH). It was proved that T. timococcum has 42 chromosomes originating from its parents. The chromosomes of the A genomes of T. monococcum and T. timopheevii could be distinguished in the amphiploid using FISH. The successful discrimination of the chromosomes was supported by the karyotypes of the three genomes and the successful optimization of the mcGISH technique for the A and G chromosomes achieved in the present study. A phenotypic evaluation was also carried out under natural and artificial growing conditions in 2012 and 2013. Based on the results, T. timococcum has intermediate characteristics in terms of spike (spikelet) shape and plant height, while it is similar to the female parent, T. timopheevii regarding pubescence. Like its parents, T. timococcum showed outstanding resistance to the main fungal diseases of wheat. T. timococcum headed later and developed longer and looser spikes, fewer tillers and only a third as many seeds than its parents. The third generation of T. timococcum was able to develop an acceptable number of seeds, even taking into account the reduced germination ability in the field.
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Affiliation(s)
- Péter Mikó
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462 Martonvásár, Hungary
| | - Mária Megyeri
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462 Martonvásár, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462 Martonvásár, Hungary
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462 Martonvásár, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, PO Box 19, 2462 Martonvásár, Hungary
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31
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Iehisa JCM, Matsuura T, Mori IC, Yokota H, Kobayashi F, Takumi S. Identification of quantitative trait loci for abscisic acid responsiveness in the D-genome of hexaploid wheat. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:830-841. [PMID: 24877675 DOI: 10.1016/j.jplph.2014.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 06/03/2023]
Abstract
In crop species such as wheat, abiotic stresses and preharvest sprouting reduce grain yield and quality. The plant hormone abscisic acid (ABA) plays important roles in abiotic stress tolerance and seed dormancy. In previous studies, we evaluated ABA responsiveness of 67 Aegilops tauschii accessions and their synthetic hexaploid wheat lines, finding wide variation that was due to the D-genome. In this study, quantitative trait locus (QTL) analysis was performed using an F2 population derived from crosses of highly ABA-responsive and less-responsive synthetic wheat lines. A significant QTL was detected on chromosome 6D, in a similar location to that reported for ABA responsiveness using recombinant inbred lines derived from common wheat cultivars Mironovskaya 808 and Chinese Spring. A comparative map and physiological and expression analyses of the 6D QTL suggested that this locus involved in line differences among wheat synthetics is different from that involved in cultivar differences in common wheat. The common wheat 6D QTL was found to affect seed dormancy and the regulation of cold-responsive/late embryogenesis abundant genes during dehydration. However, in synthetic wheat, we failed to detect any association of ABA responsiveness with abiotic stress tolerance or seed dormancy, at least under our experimental conditions. Development of near-isogenic lines will be important for functional analyses of the synthetic wheat 6D QTL.
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Affiliation(s)
- Julio C M Iehisa
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Izumi C Mori
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Hirokazu Yokota
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Fuminori Kobayashi
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan.
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32
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Rasheed A, Xia X, Ogbonnaya F, Mahmood T, Zhang Z, Mujeeb-Kazi A, He Z. Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis. BMC PLANT BIOLOGY 2014; 14:128. [PMID: 24884376 PMCID: PMC4057600 DOI: 10.1186/1471-2229-14-128] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/17/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Grain size and shape greatly influence grain weight which ultimately enhances grain yield in wheat. Digital imaging (DI) based phenomic characterization can capture the three dimensional variation in grain size and shape than has hitherto been possible. In this study, we report the results from using digital imaging of grain size and shape to understand the relationship among different components of this trait, their contribution to enhance grain weight, and to identify genomic regions (QTLs) controlling grain morphology using genome wide association mapping with high density diversity array technology (DArT) and allele-specific markers. RESULTS Significant positive correlations were observed between grain weight and grain size measurements such as grain length (r = 0.43), width, thickness (r = 0.64) and factor from density (FFD) (r = 0.69). A total of 231 synthetic hexaploid wheats (SHWs) were grouped into five different sub-clusters by Bayesian structure analysis using unlinked DArT markers. Linkage disequilibrium (LD) decay was observed among DArT loci > 10 cM distance and approximately 28% marker pairs were in significant LD. In total, 197 loci over 60 chromosomal regions and 79 loci over 31 chromosomal regions were associated with grain morphology by genome wide analysis using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. They were mainly distributed on homoeologous group 2, 3, 6 and 7 chromosomes. Twenty eight marker-trait associations (MTAs) on the D genome chromosomes 2D, 3D and 6D may carry novel alleles with potential to enhance grain weight due to the use of untapped wild accessions of Aegilops tauschii. Statistical simulations showed that favorable alleles for thousand kernel weight (TKW), grain length, width and thickness have additive genetic effects. Allelic variations for known genes controlling grain size and weight, viz. TaCwi-2A, TaSus-2B, TaCKX6-3D and TaGw2-6A, were also associated with TKW, grain width and thickness. In silico functional analysis predicted a range of biological functions for 32 DArT loci and receptor like kinase, known to affect plant development, appeared to be common protein family encoded by several loci responsible for grain size and shape. CONCLUSION Conclusively, we demonstrated the application and integration of multiple approaches including high throughput phenotyping using DI, genome wide association studies (GWAS) and in silico functional analysis of candidate loci to analyze target traits, and identify candidate genomic regions underlying these traits. These approaches provided great opportunity to understand the breeding value of SHWs for improving grain weight and enhanced our deep understanding on molecular genetics of grain weight in wheat.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
| | - Francis Ogbonnaya
- Grain Research and Development Corporation (GRDC), Barton, ACT 2600, Australia
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Zongwen Zhang
- Bioversity International c/o CAAS, 12 Zhongguancun South Street, Beijing 100081, China
| | - Abdul Mujeeb-Kazi
- National Institute of Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing 100081, China
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Iehisa JCM, Shimizu A, Sato K, Nishijima R, Sakaguchi K, Matsuda R, Nasuda S, Takumi S. Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:261-71. [PMID: 24158251 DOI: 10.1007/s00122-013-2215-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/14/2013] [Indexed: 05/19/2023]
Abstract
13,347 high-confidence SNPs were discovered through transcriptome sequencing of Aegilops tauschii, which are useful for genomic analysis and molecular breeding of hexaploid wheat. In organisms with large and complex genomes, such as wheat, RNA-seq analysis is cost-effective for discovery of genome-wide single nucleotide polymorphisms (SNPs). In this study, deep sequencing of the spike transcriptome from two Aegilops tauschii accessions representing two major lineages led to the discovery of 13,347 high-confidence (HC) SNPs in 4,872 contigs. After removing redundant SNPs detected in the leaf transcriptome from the same accessions in an earlier study, 10,589 new SNPs were discovered. In total, 5,642 out of 5,808 contigs with HC SNPs were assigned to the Ae. tauschii draft genome sequence. On average, 732 HC polymorphic contigs were mapped in silico to each Ae. tauschii chromosome. Based on the polymorphic data, we developed markers to target the short arm of chromosome 2D and validated the polymorphisms using 20 Ae. tauschii accessions. Of the 29 polymorphic markers, 28 were successfully mapped to 2DS in the diploid F2 population of Ae. tauschii. Among ten hexaploid wheat lines, which included wheat synthetics and common wheat cultivars, 25 of the 43 markers were polymorphic. In the hexaploid F2 population between a common wheat cultivar and a synthetic wheat line, 23 of the 25 polymorphic markers between the parents were available for genotyping of the F2 plants and 22 markers mapped to chromosome 2DS. These results indicate that molecular markers that developed from polymorphisms between two distinct lineages of Ae. tauschii might be useful for analysis not only of the diploid, but also of the hexaploid wheat genome.
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Okamoto Y, Nguyen AT, Yoshioka M, Iehisa JC, Takumi S. Identification of quantitative trait loci controlling grain size and shape in the D genome of synthetic hexaploid wheat lines. BREEDING SCIENCE 2013; 63:423-9. [PMID: 24399915 PMCID: PMC3859354 DOI: 10.1270/jsbbs.63.423] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/15/2013] [Indexed: 05/24/2023]
Abstract
Synthetic hexaploid wheat is an effective genetic resource for transferring agronomically important genes from Aegilops tauschii to common wheat. Wide variation in grain size and shape, one of the main targets for wheat breeding, has been observed among Ae. tauschii accessions. To identify the quantitative trait loci (QTLs) responsible for grain size and shape variation in the wheat D genome under a hexaploid genetic background, six parameters related to grain size and shape were measured using SmartGrain digital image software and QTL analysis was conducted using four F2 mapping populations of wheat synthetic hexaploids. In total, 18 QTLs for the six parameters were found on five of the seven D-genome chromosomes. The identified QTLs significantly contributed to the variation in grain size and shape among the synthetic wheat lines, implying that the D-genome QTLs might be at least partly functional in hexaploid wheat. Thus, synthetic wheat lines with diverse D genomes from Ae. tauschii are useful resources for the identification of agronomically important loci that function in hexaploid wheat.
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