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He G, Zhang Y, Liu P, Jing Y, Zhang L, Zhu Y, Kong X, Zhao H, Zhou Y, Sun J. The transcription factor TaLAX1 interacts with Q to antagonistically regulate grain threshability and spike morphogenesis in bread wheat. THE NEW PHYTOLOGIST 2021; 230:988-1002. [PMID: 33521967 DOI: 10.1111/nph.17235] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
The domestication gene Q is largely responsible for the widespread cultivation of wheat because it confers multiple domestication traits. However, the underlying molecular mechanisms of how Q regulates these domestication traits remain unclear. In this study, we identify a Q-interacting protein TaLAX1, a basic helix-loop-helix transcription factor, through yeast two-hybrid assays. Using biochemical and genetic approaches, we explore the roles of TaLAX1 in regulating wheat domestication traits. Overexpression of TaLAX1 produces phenotypes, reminiscent of the q allele; loss-of-function Talax1 mutations confer compact spikes, largely similar to the Q-overexpression wheat lines. The two transcription factors TaLAX1 and Q disturb each other's activity to antagonistically regulate the expression of the lignin biosynthesis-related gene TaKNAT7-4D. More interestingly, a natural variation (InDel, +/- TATA), which occurs in the promoter of TaLAX1, is associated with the promoter activity difference between the D subgenome of bread wheat and its ancestor Aegilops tauschii accession T093. This study reveals that the transcription factor TaLAX1 physically interacts with Q to antagonistically regulate wheat domestication traits and a natural variation (InDel, +/- TATA) is associated with the diversification of TaLAX1 promoter activity.
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Affiliation(s)
- Guanhua He
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yunwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yexing Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Identification of QTLs and a Candidate Gene for Reducing Pre-Harvest Sprouting in Aegilops tauschii- Triticum aestivum Chromosome Segment Substitution Lines. Int J Mol Sci 2021; 22:ijms22073729. [PMID: 33918469 PMCID: PMC8038248 DOI: 10.3390/ijms22073729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/03/2022] Open
Abstract
Wheat pre-harvest sprouting (PHS) causes serious losses in wheat yield. In this study, precise mapping was carried out in the chromosome segment substitution lines (CSSL) F2 population generated by a direct cross of Zhoumai 18 (PHS-sensitive) and Aegilops tauschii accession T093 (highly PHS-resistant). Three Ae. tauschii-derived quantitative trait loci (QTLs), QDor.3D.1, QDor.3D.2, and QDor.3D.3, were detected on chromosome 3DL using four simple sequence repeats (SSR) markers and 10 developed Kompetitive allele-specific PCR (KASP) markers. Alongside these QTL results, the RNA-Seq and qRT-PCR analysis revealed expression levels of TraesCS3D01G466100 in the QDor.3D.2 region that were significantly higher in CSSLs 495 than in Zhoumai 18 during the seed imbibition treatment. The cDNA sequencing results of TraesCS3D01G466100 showed two single nucleotide polymorphisms (SNPs), resulting in two changed amino acid substitutions between Zhoumai 18 and line 495, and the 148 nt amino acid substitution of TraesCS3D01G466100, derived from Ae. tauschii T093, which may play an important role in the functioning of ubiquitin ligase enzymes 3 (E3) according to the homology protein analysis, which could lead to differential PHS-resistance phenotypes. Taken together, our results may foster a better understanding of the mechanism of PHS resistance and are potentially valuable for marker-assisted selection in practical wheat breeding efforts.
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Mei F, Chen B, Li F, Zhang Y, Kang Z, Wang X, Mao H. Overexpression of the wheat NAC transcription factor TaSNAC4-3A gene confers drought tolerance in transgenic Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:37-50. [PMID: 33454635 DOI: 10.1016/j.plaphy.2021.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/04/2021] [Indexed: 05/07/2023]
Abstract
NAC transcription factors (TFs) play critical roles in plant abiotic stress responses. However, information on the roles of NAC TFs is limited in wheat (Triticum aestivum L.). In this study, we isolated three wheat TaSNAC4 homeologous genes, TaSNAC4-3A, TaSNAC4-3B, and TaSNAC4-3D, and characterized the function of TaSNAC4-3A in plant drought tolerance. TaSNAC4 is highly expressed in seedling leaves, and expression is induced by various abiotic stresses. Transient expression and transactivation assays showed that TaSNAC4-3A is localized to the nucleus, and the C-terminal region has transcriptional activation activity. Overexpression of TaSNAC4-3A in Arabidopsis led to stimulated germination and root growth when exposed to salt and osmotic stresses, and drought stress tolerance was significantly increased in the TaSNAC4-3A transgenic lines. When compared to the control plants, the transgenic lines overexpressing TaSNAC4-3A exhibited reduced stomatal aperture size under drought stress, and therefore had lower water loss rates. In addition, the overexpression of TaSNAC4-3A led to abscisic acid (ABA) hypersensitivity at the root elongation and seed germination stages. Further transcriptomic analysis demonstrated that there was a significant up-regulation of stress responsive genes in the TaSNAC4-3A transgenic lines. Our findings have revealed the important role of TaSNAC4-3A in plant drought tolerance.
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Affiliation(s)
- Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China; College of Plant Science, Tarim University, Alar, Xinjiang, 843300, China
| | - Xiaojing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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54
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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55
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Zhang W, Sun Y, Liu J, Xu C, Zou X, Chen X, Liu Y, Wu P, Yang X, Zhou S. DNA barcoding of Oryza: conventional, specific, and super barcodes. PLANT MOLECULAR BIOLOGY 2021; 105:215-228. [PMID: 32880855 PMCID: PMC7858216 DOI: 10.1007/s11103-020-01054-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.
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Affiliation(s)
- Wen Zhang
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuzhe Sun
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia Liu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China
| | - Chao Xu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xinhui Zou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xun Chen
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Landscape Architecture, Northeast Forestry University, Haerbin, 150040, China
| | - Yanlei Liu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Wu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueying Yang
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, China, Beijing, 100038, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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56
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Saintenac C, Cambon F, Aouini L, Verstappen E, Ghaffary SMT, Poucet T, Marande W, Berges H, Xu S, Jaouannet M, Favery B, Alassimone J, Sánchez-Vallet A, Faris J, Kema G, Robert O, Langin T. A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch. Nat Commun 2021; 12:433. [PMID: 33469010 PMCID: PMC7815785 DOI: 10.1038/s41467-020-20685-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
The poverty of disease resistance gene reservoirs limits the breeding of crops for durable resistance against evolutionary dynamic pathogens. Zymoseptoria tritici which causes Septoria tritici blotch (STB), represents one of the most genetically diverse and devastating wheat pathogens worldwide. No fully virulent Z. tritici isolates against synthetic wheats carrying the major resistant gene Stb16q have been identified. Here, we use comparative genomics, mutagenesis and complementation to identify Stb16q, which confers broad-spectrum resistance against Z. tritici. The Stb16q gene encodes a plasma membrane cysteine-rich receptor-like kinase that was recently introduced into cultivated wheat and which considerably slows penetration and intercellular growth of the pathogen.
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Affiliation(s)
- Cyrille Saintenac
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
| | - Florence Cambon
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
| | - Lamia Aouini
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands ,grid.169077.e0000 0004 1937 2197Present Address: Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA
| | - Els Verstappen
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands
| | - Seyed Mahmoud Tabib Ghaffary
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands ,Present Address: Seed and Plant Improvement Research Department, Safiabad Agricultural and Natural Resources Research and Education Center, AREEO, Dezful, Iran
| | - Théo Poucet
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France ,grid.11480.3c0000000121671098Present Address: Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain ,grid.412041.20000 0001 2106 639XPresent Address: Université de Bordeaux, 146 rue Leo-Saignat, Bordeaux, Cedex 33076 France
| | - William Marande
- grid.507621.7CNRGV (Centre National des Ressources Génomiques Végétales), INRAE, UPR 1258 Castanet-Tolosan, France
| | - Hélène Berges
- grid.507621.7CNRGV (Centre National des Ressources Génomiques Végétales), INRAE, UPR 1258 Castanet-Tolosan, France ,grid.508749.7Present Address: Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA 02139 USA
| | - Steven Xu
- grid.463419.d0000 0001 0946 3608United States Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Maëlle Jaouannet
- grid.4444.00000 0001 2112 9282INRAE, Université Côte d’Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Bruno Favery
- grid.4444.00000 0001 2112 9282INRAE, Université Côte d’Azur, CNRS, ISA, 06903 Sophia Antipolis, France
| | - Julien Alassimone
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Andrea Sánchez-Vallet
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland ,grid.5690.a0000 0001 2151 2978Present Address: Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA). Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón Madrid, Spain
| | - Justin Faris
- grid.463419.d0000 0001 0946 3608United States Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Gert Kema
- grid.4818.50000 0001 0791 5666Wageningen University and Research (Wageningen Plant Research, Biointeractions and Plant Health), PO Box 16, 6700AA Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University (Laboratory of Phytopathology), 6700AA Wageningen, The Netherlands
| | - Oliver Robert
- Florimond-Desprez, 3 rue Florimond-Desprez, BP 41, 59242 Cappelle-en-Pevele, France
| | - Thierry Langin
- grid.503180.f0000 0004 0613 5360Université Clermont Auvergne, INRAE, GDEC, 63000 Clermont-Ferrand, France
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In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions. Biosci Rep 2020; 40:226968. [PMID: 33275764 PMCID: PMC7724613 DOI: 10.1042/bsr20201188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
The importance of wheat yellow rust disease, caused by Puccinia striiformis f. sp. tritici (Pst), has increased substantially due to the emergence of aggressive new Pst races in the last couple of decades. In an era of escalating human populations and climate change, it is vital to understand the infection mechanism of Pst in order to develop better strategies to combat wheat yellow disease. The present study focuses on the identification of small secreted proteins (SSPs) and candidate-secreted effector proteins (CSEPs) that are used by the pathogen to support infection and control disease development. We generated de novo assembled transcriptomes of Pst collected from wheat fields in central Anatolia. We inoculated both susceptible and resistant seedlings with Pst and analyzed haustoria formation. At 10 days post-inoculation (dpi), we analyzed the transcriptomes and identified 10550 Differentially Expressed Unigenes (DEGs), of which 6072 were Pst-mapped. Among those Pst-related genes, 227 were predicted as PstSSPs. In silico characterization was performed using an approach combining the transcriptomic data and data mining results to provide a reliable list to narrow down the ever-expanding repertoire of predicted effectorome. The comprehensive analysis detected 14 Differentially Expressed Small-Secreted Proteins (DESSPs) that overlapped with the genes in available literature data to serve as the best CSEPs for experimental validation. One of the CSEPs was cloned and studied to test the reliability of the presented data. Biological assays show that the randomly selected CSEP, Unigene17495 (PSTG_10917), localizes in the chloroplast and is able to suppress cell death induced by INF1 in a Nicotiana benthamiana heterologous expression system.
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Zhao Y, Dong L, Jiang C, Wang X, Xie J, Rashid MAR, Liu Y, Li M, Bu Z, Wang H, Ma X, Sun S, Wang X, Bo C, Zhou T, Kong L. Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization. BMC Biol 2020; 18:188. [PMID: 33267868 PMCID: PMC7713161 DOI: 10.1186/s12915-020-00917-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/05/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. RESULTS Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. CONCLUSIONS The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Luhao Dong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Conghui Jiang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xueqiang Wang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jianyin Xie
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, People's Republic of China
| | | | - Yanhe Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Mengyao Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhimu Bu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xin Ma
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Silong Sun
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xiaoqian Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Cunyao Bo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Tingting Zhou
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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Liu Z, Zhu H, Zhou J, Jiang S, Wang Y, Kuang J, Ji Q, Peng J, Wang J, Gao L, Bai M, Jian J, Ke W. Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1673-1684. [PMID: 33073434 DOI: 10.1111/tpj.15029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7 191 010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.
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Affiliation(s)
- Zhengwei Liu
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Honglian Zhu
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Juhong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Sanjie Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Yun Wang
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jing Kuang
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Qun Ji
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jie Wang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China
- BGI-Agro Seed Service (Wuhan) Co Ltd, Wuhan, 430090, People's Republic of China
| | - Li Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Mingzhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Weidong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
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Chandra S, Satapathy L, Basu S, Jha SK, Kumar M, Mukhopadhyay K. Characterization of the leaf rust responsive ARF genes in wheat (Triticum aestivum L.). PLANT CELL REPORTS 2020; 39:1639-1654. [PMID: 32892289 DOI: 10.1007/s00299-020-02591-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/26/2020] [Indexed: 05/09/2023]
Abstract
Genome-wide identification, classification, functional characterization and expression analysis of Auxin Responsive Factor (ARF) gene family in wheat reveal their attributes and role during leaf rust infection. Auxins are important plant growth regulators that also impact plant-pathogen interaction. Auxin responsive factors (ARF) are plant specific transcription factors that control responses to auxins. Whole genome investigation of ARF gene family is limited in allohexaploid wheat (Triticum aestivum L.). Comprehensive study of this gene family was carried out by employing the currently available reference genome sequence of wheat. In total, 27 ARF genes were identified and located on the wheat genome as well as were positioned on wheat chromosome arms. Additionally, examination of the predicted genes unveiled a decent degree of relatedness within and among the phylogenetic clades. Leaf rust, caused by the obligate biotrophic fungal pathogen Puccinia triticina, is responsible for drastic loss of wheat crop worldwide reducing grain yield by 10-90%. Expression profiling of ARF genes in retort to leaf rust infection indicated their differential regulation during this plant-pathogen interaction. Highest expression of ARF genes were observed at 12 hpi that was maintained up to 72 hpi during incompatible interaction, whereas the high expression levels receded at 48 hpi during compatible interactions. Few of the identified ARF genes were likely to be post-transcriptionally regulated by microRNAs. Many light and stress responsive elements were detected in the promoter regions of ARF genes. Microsynteny analysis showed the conservation of ARF genes within the members of the Poaceae family. This study provides fundamental details for understanding the different types of ARF genes in wheat and there putative roles during leaf rust-wheat interaction.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lopamudra Satapathy
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Faculty of Agriculture, Usha Martin University, Angara, Ranchi, Jharkhand, 835103, India
| | - Srirupa Basu
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | | | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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Zeng X, Tagiri A, Kikuchi S, Sassa H, Komatsuda T. The Ectopic Expression of Btr2 in Aegilops tauschii Switches the Disarticulation Layer From Above to Below the Rachis Node. FRONTIERS IN PLANT SCIENCE 2020; 11:582622. [PMID: 33240300 PMCID: PMC7680762 DOI: 10.3389/fpls.2020.582622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/13/2020] [Indexed: 05/31/2023]
Abstract
Seed dispersal among wild species belonging to the tribe Triticeae is typically achieved by the formation of a brittle rachis. The trait relies on the development of a disarticulation layer, most frequently above the rachis node (resulting in wedge type dispersal units), but in some species below the rachis node (resulting in barrel type dispersal units). The genes responsible for the former type are the complementary pair Btr1 and Btr2, while the genetic basis of the latter type has yet to be determined. Aegilops tauschii forms barrel type dispersal units and previous study showed this species lacked an intact copy of Btr1. Here it has been demonstrated that Ae. tauschii carries two of Btr2; and that Btr2 transcript is present in a region below the rachis node where the abscission zone forms. The implication is that in this species, the Btr2 product is involved in the formation of barrel type dispersal units.
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Affiliation(s)
- Xiaoxue Zeng
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Akemi Tagiri
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
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62
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Li Q, Li B, Wang J, Chang X, Mao X, Jing R. TaPUB15
, a U‐Box E3 ubiquitin ligase gene from wheat, enhances salt tolerance in rice. Food Energy Secur 2020. [DOI: 10.1002/fes3.250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Qiaoru Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Bo Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China
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63
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Bakhshi B, Fard EM. Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191017151708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Aegilops tauschii is a wild relative of bread wheat. This species has been
reported as the donor of bread wheat D genome. There are also several reports that mentioned the
importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have
been reported as the essential regulatory elements in stress response.
Objective:
Therefore, it is important to discover novel miRNAs involved in stress tolerance in this
species. The aim of the current study was to predict novel miRNAs in Ae. tauschii and also
uncover their potential role in stress response.
Methods:
For this purpose, ESTs, TSAs, and miRBase databases were obtained and used to
predict new miRNAs.
Results:
Our results discovered nine novel stem-loop miRNAs. These predicted miRNAs could be
introduced as the new members of previously identified miRNA families in Ae. tauschii, including
miR156, miR168, miR169, and miR319. The result indicating that miR397 and miR530 are novel
families in this species. Furthermore, several novel stem-loop miRNAs predicted for T. aestivum
showed remarkable similarities to novel Ae. tauschii stem-loops.
Conclusion:
Our results demonstrated that predicted novel miRNAs could play a significant role
in stress response.
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Affiliation(s)
- Behnam Bakhshi
- Horticulture Crops Research Department, Sistan Agricultural and Natural Resources Research and Education Center, AREEO, Zabol, Iran
| | - Ehsan Mohseni Fard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
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Jacott CN, Boden SA. Feeling the heat: developmental and molecular responses of wheat and barley to high ambient temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5740-5751. [PMID: 32667992 PMCID: PMC7540836 DOI: 10.1093/jxb/eraa326] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
The increasing demand for global food security in the face of a warming climate is leading researchers to investigate the physiological and molecular responses of cereals to rising ambient temperatures. Wheat and barley are temperate cereals whose yields are adversely affected by high ambient temperatures, with each 1 °C increase above optimum temperatures reducing productivity by 5-6%. Reproductive development is vulnerable to high-temperature stress, which reduces yields by decreasing grain number and/or size and weight. In recent years, analysis of early inflorescence development and genetic pathways that control the vegetative to floral transition have elucidated molecular processes that respond to rising temperatures, including those involved in the vernalization- and photoperiod-dependent control of flowering. In comparison, our understanding of genes that underpin thermal responses during later developmental stages remains poor, thus highlighting a key area for future research. This review outlines the responses of developmental genes to warmer conditions and summarizes our knowledge of the reproductive traits of wheat and barley influenced by high temperatures. We explore ways in which recent advances in wheat and barley research capabilities could help identify genes that underpin responses to rising temperatures, and how improved knowledge of the genetic regulation of reproduction and plant architecture could be used to develop thermally resilient cultivars.
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Affiliation(s)
- Catherine N Jacott
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, UK
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
- Correspondence:
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Ye CY, Wu D, Mao L, Jia L, Qiu J, Lao S, Chen M, Jiang B, Tang W, Peng Q, Pan L, Wang L, Feng X, Guo L, Zhang C, Kellogg EA, Olsen KM, Bai L, Fan L. The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation. MOLECULAR PLANT 2020; 13:1298-1310. [PMID: 32622997 DOI: 10.1016/j.molp.2020.07.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 05/20/2023]
Abstract
The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. In this study, we generated and analyzed high-quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola), and hexaploid (E. crus-galli) Echinochloa species. Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization, contrary to their significant expansionduring wheat polyploidization, suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. In addition, distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E. crus-galli and bread wheat. Collectively, our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization. The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lingfeng Mao
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lei Jia
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Sangting Lao
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Meihong Chen
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Bowen Jiang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiong Peng
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Lang Pan
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Lifeng Wang
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China
| | - Xiaoxiao Feng
- Agricultural Experiment Station, Zhejiang University, Hangzhou 310058, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Chulong Zhang
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | | | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha 410125, China.
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
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66
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Li GZ, Li HX, Xu MJ, Wang PF, Xiao XH, Kang GZ. Functional characterization and regulatory mechanism of wheat CPK34 kinase in response to drought stress. BMC Genomics 2020; 21:577. [PMID: 32831009 PMCID: PMC7444251 DOI: 10.1186/s12864-020-06985-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Drought is one of the most adverse environmental factors limiting crop productions and it is important to identify key genetic determinants for food safety. Calcium-dependent protein kinases (CPKs) are known to be involved in plant growth, development, and environmental stresses. However, biological functions and regulatory mechanisms of many plant CPKs have not been explored. In our previous study, abundance of the wheat CPK34 (TaCPK34) protein was remarkably upregulated in wheat plants suffering from drought stress, inferring that it could be involved in this stress. Therefore, here we further detected its function and mechanism in response to drought stress. RESULTS Transcripts of the TaCPK34 gene were significantly induced after PEG-stimulated water deficiency (20% PEG6000) or 100 μM abscisic acid (ABA) treatments. The TaCPK34 gene was transiently silenced in wheat genome by using barley stripe mosaic virus-induced silencing (BSMV-VIGS) method. After 14 days of drought stress, the transiently TaCPK34-silenced wheat seedlings showed more sensitivity compared with control, and the plant biomasses and relative water contents significantly decreased, whereas soluble sugar and MDA contents increased. The iTRAQ-based quantitative proteomics was employed to measure the protein expression profiles in leaves of the transiently TaCPK34-silenced wheat plants after drought stress. There were 6103 proteins identified, of these, 51 proteins exhibited significantly altered abundance, they were involved in diverse function. And sequence analysis on the promoters of genes, which encoded the above identified proteins, indicated that some promoters harbored some ABA-responsive elements. We determined the interactions between TaCPK34 and three identified proteins by using bimolecular fluorescent complementation (BiFC) method and our data indicated that TaCPK34directly interacted with the glutathione S-transferase 1 and prx113, respectively. CONCLUSIONS Our study suggested that the TaCPK34 gene played positive roles in wheat response to drought stress through directly or indirectly regulating the expression of ABA-dependent manner genes, which were encoding identified proteins from iTRAQ-based quantitative proteomics. And it could be used as one potential gene to develop crop cultivars with improved drought tolerance.
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Affiliation(s)
- Ge-Zi Li
- National Engineering Research Centre for Wheat, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Han-Xiao Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Meng-Jun Xu
- National Engineering Research Centre for Wheat, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Peng-Fei Wang
- National Engineering Research Centre for Wheat, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Xiang-Hong Xiao
- National Engineering Research Centre for Wheat, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China
| | - Guo-Zhang Kang
- National Engineering Research Centre for Wheat, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China. .,National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, Henan Province, People's Republic of China.
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67
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Bilgrami SS, Ramandi HD, Shariati V, Razavi K, Tavakol E, Fakheri BA, Mahdi Nezhad N, Ghaderian M. Detection of genomic regions associated with tiller number in Iranian bread wheat under different water regimes using genome-wide association study. Sci Rep 2020; 10:14034. [PMID: 32820220 PMCID: PMC7441066 DOI: 10.1038/s41598-020-69442-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/09/2020] [Indexed: 11/09/2022] Open
Abstract
Two of the important traits for wheat yield are tiller and fertile tiller number, both of which have been thought to increase cereal yield in favorable and unfavorable environments. A total of 6,349 single nucleotide polymorphism (SNP) markers from the 15 K wheat Infinium array were employed for genome-wide association study (GWAS) of tillering number traits, generating a physical distance of 14,041.6 Mb based on the IWGSC wheat genome sequence. GWAS analysis using Fixed and random model Circulating Probability Unification (FarmCPU) identified a total of 47 significant marker-trait associations (MTAs) for total tiller number (TTN) and fertile tiller number (FTN) in Iranian bread wheat under different water regimes. After applying a 5% false discovery rate (FDR) threshold, a total of 13 and 11 MTAs distributed on 10 chromosomes were found to be significantly associated with TTN and FTN, respectively. Linked single nucleotide polymorphisms for IWB39005 (2A) and IWB44377 (7A) were highly significantly associated (FDR < 0.01) with TTN and FTN traits. Moreover, to validate GWAS results, meta-analysis was performed and 30 meta-QTL regions were identified on 11 chromosomes. The integration of GWAS and meta-QTLs revealed that tillering trait in wheat is a complex trait which is conditioned by the combined effects of minor changes in multiple genes. The information provided by this study can enrich the currently available candidate genes and genetic resources pools, offering evidence for subsequent analysis of genetic adaptation of wheat to different climatic conditions of Iran and other countries.
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Affiliation(s)
- Sayedeh Saba Bilgrami
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Vahid Shariati
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Khadijeh Razavi
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Elahe Tavakol
- Department of Plant Production and Genetics, Shiraz University, Shiraz, Iran
| | - Barat Ali Fakheri
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Nafiseh Mahdi Nezhad
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mostafa Ghaderian
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Zhou GC, Li W, Zhang YM, Liu Y, Zhang M, Meng GQ, Li M, Wang YL. Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species. Front Genet 2020; 11:737. [PMID: 32754204 PMCID: PMC7365912 DOI: 10.3389/fgene.2020.00737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022] Open
Abstract
Nucleotide-binding site (NBS)-type disease resistance genes (R genes) play key roles in plant immune responses and have co-evolved with pathogens over the course of plant lifecycles. Comparative genomic studies tracing the dynamic evolution of NBS-encoding genes have been conducted using many important plant lineages. However, studies on Sapindaceae species have not been performed. In this study, a discrepant number of NBS-encoding genes were identified in the genomes of Xanthoceras sorbifolium (180), Dinnocarpus longan (568), and Acer yangbiense (252). These genes were unevenly distributed and usually clustered as tandem arrays on chromosomes, with few existed as singletons. The phylogenetic analysis revealed that NBS-encoding genes formed three monophyletic clades, RPW8-NBS-LRR (RNL), TIR-NBS-LRR (TNL), and CC-NBS-LRR (CNL), which were distinguished by amino acid motifs. The NBS-encoding genes of the X. sorbifolium, D. longan, and A. yangbiense genomes were derived from 181 ancestral genes (three RNL, 23 TNL, and 155 CNL), which exhibited dynamic and distinct evolutionary patterns due to independent gene duplication/loss events. Specifically, X. sorbifolium exhibited a “first expansion and then contraction” evolutionary pattern, while A. yangbiense and D. longan exhibited a “first expansion followed by contraction and further expansion” evolutionary pattern. However, further expansion in D. longan was stronger than in A. yangbiense after divergence, suggesting that D. longan gained more genes in response to various pathogens. Additionally, the ancient and recent expansion of CNL genes generated the dominance of this subclass in terms of gene numbers, while the low copy number status of RNL genes was attributed to their conserved functions.
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Affiliation(s)
- Guang-Can Zhou
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Wen Li
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Guo-Qing Meng
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Min Li
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yi-Lei Wang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
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Andersen EJ, Nepal MP, Purintun JM, Nelson D, Mermigka G, Sarris PF. Wheat Disease Resistance Genes and Their Diversification Through Integrated Domain Fusions. Front Genet 2020; 11:898. [PMID: 32849852 PMCID: PMC7422411 DOI: 10.3389/fgene.2020.00898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
Plants are in a constant evolutionary arms race with their pathogens. At the molecular level, the plant nucleotide-binding leucine-rich repeat receptors (NLRs) family has coevolved with rapidly evolving pathogen effectors. While many NLRs utilize variable leucine-rich repeats (LRRs) to detect effectors, some have gained integrated domains (IDs) that may be involved in receptor activation or downstream signaling. The major objectives of this project were to identify NLR genes in wheat (Triticum aestivum L.) and assess IDs associated with immune signaling (e.g., kinase and transcription factor domains). We identified 2,151 NLR-like genes in wheat, of which 1,298 formed 547 gene clusters. Among the non-toll/interleukin-1 receptor NLR (non-TNL)-like genes, 1,552 encode LRRs, 802 are coiled-coil (CC) domain-encoding (CC-NBS-LRR or CNL) genes, and three encode resistance to powdery mildew 8 (RPW8) domains (RPW8-NBS-LRR or RNL). The expansion of the NLR gene family in wheat is attributable to its origin by recent polyploidy events. Gene clusters were likely formed by tandem duplications, and wheat NLR phylogenetic relationships were similar to those in barley and Aegilops. We also identified wheat NLR-ID fusion proteins as candidates for NLR functional diversification, often as kinase and transcription factor domains. Comparative analyses of the IDs revealed evolutionary conservation of more than 80% amino acid sequence similarity. Homology assessment indicates that these domains originated as functional non-NLR-encoding genes that were incorporated into NLR-encoding genes through duplication events. We also found that many of the NLR-ID genes encode alternative transcripts that include or exclude IDs, a phenomenon that seems to be conserved among species. To verify this, we have analyzed the alternative transcripts that include or exclude an ID of an NLR-ID from another monocotyledon species, rice (Oryza sativa). This indicates that plants employ alternative splicing to regulate IDs, possibly using them as baits, decoys, and functional signaling components. Genomic and expression data support the hypothesis that wheat uses alternative splicing to include and exclude IDs from NLR proteins.
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Affiliation(s)
- Ethan J Andersen
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Jordan M Purintun
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Dillon Nelson
- Department of Math, Science and Technology, Oglala Lakota College, Kyle, SD, United States
| | | | - Panagiotis F Sarris
- Department of Biology, University of Crete, Crete, Greece.,Institute of Molecular Biology and Biotechnology, FORTH, Crete, Greece.,School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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Zeng X, Mishina K, Jia J, Distelfeld A, Maughan PJ, Kikuchi S, Sassa H, Komatsuda T. The Brittle Rachis Trait in Species Belonging to the Triticeae and Its Controlling Genes Btr1 and Btr2. FRONTIERS IN PLANT SCIENCE 2020; 11:1000. [PMID: 32793251 PMCID: PMC7387508 DOI: 10.3389/fpls.2020.01000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/18/2020] [Indexed: 05/31/2023]
Abstract
In many non-cultivated angiosperm species, seed dispersal is facilitated by the shattering of the seed head at maturity; in the Triticeae tribe, to which several of the world's most important cereals belong, shattering takes the form of a disarticulation of the rachis. The products of the genes Btr1 and Btr2 are both required for disarticulation to occur above the rachis nodes within the genera Hordeum (barley) and Triticum/Aegilops (wheat). Here, it has been shown that both Btr1 and Btr2 are specific to the Triticeae tribe, although likely paralogs (Btr1-like and Btr2-like) are carried by the family Poaceae including Triticeae. Aegilops tauschii (the donor of the bread wheat D genome) lacks a copy of Btr1 and disarticulation in this species occurs below, rather than above the rachis node; thus, the product of Btr1 appears to be required for disarticulation to occur above the rachis node.
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Affiliation(s)
- Xiaoxue Zeng
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Juqing Jia
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Peter Jeff Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
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71
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Liu C, Wang J, Sun P, Yu J, Meng F, Zhang Z, Guo H, Wei C, Li X, Shen S, Wang X. Illegitimate Recombination Between Homeologous Genes in Wheat Genome. FRONTIERS IN PLANT SCIENCE 2020; 11:1076. [PMID: 32849677 PMCID: PMC7396543 DOI: 10.3389/fpls.2020.01076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/30/2020] [Indexed: 05/30/2023]
Abstract
Polyploidies produce a large number of duplicated regions and genes in genomes, which have a long-term impact and stimulate genetic innovation. The high similarity between homeologous chromosomes, forming different subgenomes, or homologous regions after genome repatterning, may permit illegitimate DNA recombination. Here, based on gene colinearity, we aligned the (sub)genomes of common wheat (Triticum aestivum, AABBDD genotype) and its relatives, including Triticum urartu (AA), Aegilops tauschii (DD), and T. turgidum ssp. dicoccoides (AABB) to detect the homeologous (paralogous or orthologous) colinear genes within and between (sub)genomes. Besides, we inferred more ancient paralogous regions produced by a much ancient grass-common tetraploidization. By comparing the sequence similarity between paralogous and orthologous genes, we assumed abnormality in the topology of constructed gene trees, which could be explained by gene conversion as a result of illegitimate recombination. We found large numbers of inferred converted genes (>2,000 gene pairs) suggested long-lasting genome instability of the hexaploid plant, and preferential donor roles by DD genes. Though illegitimate recombination was much restricted, duplicated genes produced by an ancient whole-genome duplication, which occurred millions of years ago, also showed evidence of likely gene conversion. As to biological function, we found that ~40% catalytic genes in colinearity, including those involved in starch biosynthesis, were likely affected by gene conversion. The present study will contribute to understanding the functional and structural innovation of the common wheat genome.
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Affiliation(s)
- Chao Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- National Key Laboratory for North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhikang Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- National Key Laboratory for North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding, China
- Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Navarro-Escalante L, Zhao C, Shukle R, Stuart J. BSA-Seq Discovery and Functional Analysis of Candidate Hessian Fly ( Mayetiola destructor) Avirulence Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:956. [PMID: 32670342 PMCID: PMC7330099 DOI: 10.3389/fpls.2020.00956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 06/10/2020] [Indexed: 05/17/2023]
Abstract
The Hessian fly (HF, Mayetiola destructor) is a plant-galling parasite of wheat (Triticum spp.). Seven percent of its genome is composed of highly diversified signal-peptide-encoding genes that are transcribed in HF larval salivary glands. These observations suggest that they encode effector proteins that are injected into wheat cells to suppress basal wheat immunity and redirect wheat development towards gall formation. Genetic mapping has determined that mutations in four of these genes are associated with HF larval survival (virulence) on plants carrying four different resistance (R) genes. Here, this line of investigation was pursued further using bulked-segregant analysis combined with whole genome resequencing (BSA-seq). Virulence to wheat R genes H6, Hdic, and H5 was examined. Mutations associated with H6 virulence had been mapped previously. Therefore, we used H6 to test the capacity of BSA-seq to map virulence using a field-derived HF population. This was the first time a non-structured HF population had been used to map HF virulence. Hdic virulence had not been mapped previously. Using a structured laboratory population, BSA-seq associated Hdic virulence with mutations in two candidate effector-encoding genes. Using a laboratory population, H5 virulence was previously positioned in a region spanning the centromere of HF autosome 2. BSA-seq resolved H5 virulence to a 1.3 Mb fragment on the same chromosome but failed to identify candidate mutations. Map-based candidate effectors were then delivered to Nicotiana plant cells via the type III secretion system of Burkholderia glumae bacteria. These experiments demonstrated that the genes associated with virulence to wheat R genes H6 and H13 are capable of suppressing plant immunity. Results are consistent with the hypothesis that effector proteins underlie the ability of HFs to survive on wheat.
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Affiliation(s)
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Richard Shukle
- USDA-ARS and Department of Entomology, Purdue University, West Lafayette, IN, United States
| | - Jeffrey Stuart
- Department of Entomology, Purdue University, West Lafayette, IN, United States
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Guan J, Garcia DF, Zhou Y, Appels R, Li A, Mao L. The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:221-229. [PMID: 32561470 PMCID: PMC7801200 DOI: 10.1016/j.gpb.2019.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 08/15/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023]
Abstract
In the year 2018, the world witnessed the finale of the race to sequence the genome of the world's most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced. At different stages, multiple versions of genome sequences of the same variety (e.g., Chinese Spring) were produced by several groups with their special strategies. Finally, 16 years after the rice genome was finished and 9 years after that of maize, the wheat research community now possesses its own reference genome. Armed with these genomics tools, wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution, domestication, genetic and epigenetic regulation of homoeolog expression, as well as defining its genetic diversity and breeding on the genome level. The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.
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Affiliation(s)
- Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Diego F Garcia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yun Zhou
- Collaborative Innovation Center of Crop Stress Biology & Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng 475004, China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, La Trobe University, Melbourne, VIC 3083, Australia
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles. G3-GENES GENOMES GENETICS 2020; 10:2021-2032. [PMID: 32295768 PMCID: PMC7263691 DOI: 10.1534/g3.120.401288] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world's most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.
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Xie DF, Tan JB, Yu Y, Gui LJ, Su DM, Zhou SD, He XJ. Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences. ANNALS OF BOTANY 2020; 125:1039-1055. [PMID: 32239179 PMCID: PMC7262478 DOI: 10.1093/aob/mcaa024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/01/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. METHODS In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. RESULTS Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. CONCLUSIONS Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Jin-Bo Tan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Lin-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
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Wang N, Xie Y, Li Y, Wu S, Li S, Guo Y, Wang C. High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat. PLANTS 2020; 9:plants9060698. [PMID: 32486195 PMCID: PMC7355531 DOI: 10.3390/plants9060698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
Early leaf senescence negatively impacts the grain yield in wheat (Triticum aestivum L.). Induced mutants provide an important resource for mapping and cloning of genes for early leaf senescence. In our previous study, Els2, a single incomplete dominance gene, that caused early leaf senescence phenotype in the wheat mutant LF2099, had been mapped on the long arm of chromosome 2B. The objective of this study was to develop molecular markers tightly linked to the Els2 gene and construct a high-resolution map surrounding the Els2 gene. Three tightly linked single-nucleotide polymorphism (SNP) markers were obtained from the Illumina Wheat 90K iSelect SNP genotyping array and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. To saturate the Els2 region, the Axiom® Wheat 660K SNP array was used to screen bulked extreme phenotype DNA pools, and 9 KASP markers were developed. For fine mapping of the Els2 gene, these KASP markers and previously identified polymorphic markers were analyzed in a large F2 population of the LF2099 × Chinese Spring cross. The Els2 gene was located in a 0.24-cM genetic region flanked by the KASP markers AX-111643885 and AX-111128667, which corresponded to a physical interval of 1.61 Mb in the Chinese Spring chromosome 2BL containing 27 predicted genes with high confidence. The study laid a foundation for a map-based clone of the Els2 gene controlling the mutation phenotype and revealing the molecular regulatory mechanism of wheat leaf senescence.
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Jiang C, Kan J, Ordon F, Perovic D, Yang P. Bymovirus-induced yellow mosaic diseases in barley and wheat: viruses, genetic resistances and functional aspects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1623-1640. [PMID: 32008056 DOI: 10.1007/s00122-020-03555-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/24/2020] [Indexed: 05/20/2023]
Abstract
Bymovirus-induced yellow mosaic diseases seriously threaten global production of autumn-sown barley and wheat, which are two of the presently most important crops around the world. Under natural field conditions, the diseases are caused by infection of soil-borne plasmodiophorid Polymyxa graminis-transmitted bymoviruses of the genus Bymovirus of the family Potyviridae. Focusing on barley and wheat, this article summarizes the achievements on taxonomy, geography and host specificity of these disease-conferring viruses, as well as the genetics of resistance in barley, wheat and wild relatives. Moreover, based on recent progress of barley and wheat genomics, germplasm resources and large-scale sequencing, the exploration and isolation of corresponding resistant genes from wheat and barley as well as relatives, no matter what a large and complicated genome is present, are becoming feasible and are discussed. Furthermore, the foreseen advances on cloning of the resistance or susceptibility-encoding genes, which will provide the possibility to explore the functional interaction between host plants and soil-borne viral pathogens, are discussed as well as the benefits for marker-assisted resistance breeding in barley and wheat.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute (JKI), 06484, Quedlinburg, Germany
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, People's Republic of China.
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Bernhardt N, Brassac J, Dong X, Willing EM, Poskar CH, Kilian B, Blattner FR. Genome-wide sequence information reveals recurrent hybridization among diploid wheat wild relatives. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:493-506. [PMID: 31821649 DOI: 10.1111/tpj.14641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/13/2019] [Accepted: 11/28/2019] [Indexed: 05/07/2023]
Abstract
Many conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome-wide sequence information, independent data were obtained from genotyping-by-sequencing and a target-enrichment experiment that returned 244 low-copy nuclear loci. The data were analyzed using Bayesian, likelihood and coalescent-based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat-group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species except Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa except Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat-group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case for tetraploid and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.
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Affiliation(s)
- Nadine Bernhardt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Xue Dong
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Plant Germplasm and Genomics Centre, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Eva-Maria Willing
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - C Hart Poskar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
- Global Crop Diversity Trust, 53113, Bonn, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
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Chen JD, Zheng C, Ma JQ, Jiang CK, Ercisli S, Yao MZ, Chen L. The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant. HORTICULTURE RESEARCH 2020; 7:63. [PMID: 32377354 PMCID: PMC7192901 DOI: 10.1038/s41438-020-0288-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/02/2020] [Accepted: 03/08/2020] [Indexed: 05/07/2023]
Abstract
Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. sinensis var. sinensis and successfully ordered 2984.7 Mb (94.7%) scaffolds into 15 chromosomes. The scaffold N50 of the improved genome was 218.1 Mb, ~157-fold higher than that of the draft genome. Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly. We clarified that only one Camellia recent tetraploidization event (CRT, 58.9-61.7 million years ago (Mya)) occurred after the core-eudicot common hexaploidization event (146.6-152.7 Mya). Meanwhile, 9243 genes (28.6%) occurred in tandem duplication, and most of these expanded after the CRT event. These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response. Sixty-four catechin- and caffeine-related quantitative trait loci (QTLs) were anchored to chromosome assembly. Of these, two catechin-related QTL hotspots were derived from the CRT event, which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms. The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs.
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Affiliation(s)
- Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Chao Zheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Ming-Zhe Yao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
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80
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Kroupin PY, Chernook AG, Bazhenov MS, Karlov GI, Goncharov NP, Chikida NN, Divashuk MG. Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes. PLoS One 2020; 15:e0231704. [PMID: 32298343 PMCID: PMC7162470 DOI: 10.1371/journal.pone.0231704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/30/2020] [Indexed: 11/18/2022] Open
Abstract
The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii.
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Affiliation(s)
- Pavel Yu. Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Anastasiya G. Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Mikhail S. Bazhenov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nadezhda N. Chikida
- Federal Research Center Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg, Russia
| | - Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University–Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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81
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Feng K, Cui L, Wang L, Shan D, Tong W, Deng P, Yan Z, Wang M, Zhan H, Wu X, He W, Zhou X, Ji J, Zhang G, Mao L, Karafiátová M, Šimková H, Doležel J, Du X, Zhao S, Luo M, Han D, Zhang C, Kang Z, Appels R, Edwards D, Nie X, Weining S. The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:732-742. [PMID: 31471988 PMCID: PMC7004910 DOI: 10.1111/pbi.13240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/27/2019] [Accepted: 08/15/2019] [Indexed: 05/03/2023]
Abstract
Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication-related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.
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Affiliation(s)
- Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
- College of Bioscience and EngineeringJiangxi Agricultural UniversityNanchangJiangxiChina
| | - Le Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Dai Shan
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry InformationHuazhong Agricultural UniversityWuhanChina
| | - Mengxing Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Haoshuang Zhan
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaotong Wu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | | | | | | | | | - Long Mao
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureThe National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Shancen Zhao
- BGI Institute of Applied AgricultureBGI‐ShenzhenShenzhenChina
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Chi Zhang
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Rudi Appels
- State Agriculture Biotechnology CentreSchool of Veterinary and Life SciencesAustralia Export Grains Innovation CentreMurdoch UniversityPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
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82
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Jain N, Rani S, Sharma C, Sinha N, Singh A, Sharma JB, Prasad P, Saripalli G, Sharma PK, Balyan HS, Gupta PK, Prabhu KV. Large-scale stage-specific regulation of gene expression during host-pathogen interactions in CSP44 bread wheat carrying APR gene Lr48. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:203-225. [PMID: 32007128 DOI: 10.1071/fp18336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Genome-wide transcriptome analysis was undertaken in a leaf-rust resistant bread wheat line CSP44 (selected from Australian cv. Condor) carrying the adult plant resistance (APR) gene Lr48. Two pre-adult plant (P-AP) susceptible stages (S48 and S96) and two adult plant (AP) resistant stages (R48 and R96) were used for RNA-seq. At the susceptible P-AP stage (during S48 to S96), expression increased in 2062 genes, and declined in 130 genes; 1775 of 2062 differentially expressed genes (DEGs) also exhibited high expression during early incompatible stage R48. Comparison of S96 with R96 showed that the expression of 80 genes was enhanced and that of 208 genes declined at the AP stage. At the resistant AP stage (during R48 to R96), expression of mere 25 genes increased and that of 126 genes declined. Apparently, the resistance during late adult stage (R96) is caused by regulation of the expression of relatively fewer genes, although at pre-adult stage (S48 to S96), expression of large number of genes increased; expression of majority of these genes kept on increasing during adult stage at R48 also. These and other results of the present study suggest that APR may mimic some kind of systemic acquired resistance (SAR). The host-specific DEGs belonged to 10 different classes including genes involved in defence, transport, epigenetics, photosynthesis, genes encoding some transcription factors etc. The pathogen (Puccinia triticina) specific DEGs (including three genes encoding known biotrophic effectors) seem to help the pathogen in infection/growth through large-scale stage-specific enhanced expression of host's genes. A putative candidate gene for Lr48 containing protein kinase domain (its ortholog in rice encoding OsWAK8) was also identified.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sushma Rani
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chanchal Sharma
- Chaudhary Charan Singh University, Meerut 250004, UP, India; and Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan City, Gyeongbook 38453, South Korea
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anupam Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jai Bhagwan Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla 171002, India
| | | | | | | | | | - Kumble Vinod Prabhu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; and Protection of Plant Varieties and Farmers' Rights Authority, Govt. of India, Ministry of Agriculture & Farmers Welfare, New Delhi 110012 (India)
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83
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Li S, Chen N, Li F, Mei F, Wang Z, Cheng X, Kang Z, Mao H. Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2020; 20:50. [PMID: 32005165 PMCID: PMC6993422 DOI: 10.1186/s12870-020-2252-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many studies in Arabidopsis and rice have demonstrated that HD-Zip transcription factors play important roles in plant development and responses to abiotic stresses. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, the function of the HD-Zip proteins in wheat is still largely unknown. RESULTS To explore the potential biological functions of HD-Zip genes in wheat, we performed a bioinformatics and gene expression analysis of the HD-Zip family. We identified 113 HD-Zip members from wheat and classified them into four subfamilies (I-IV) based on phylogenic analysis against proteins from Arabidopsis, rice, and maize. Most HD-Zip genes are represented by two to three homeoalleles in wheat, which are named as TaHDZX_ZA, TaHDZX_ZB, or TaHDZX_ZD, where X denotes the gene number and Z the wheat chromosome on which it is located. TaHDZs in the same subfamily have similar protein motifs and intron/exon structures. The expression profiles of TaHDZ genes were analysed in different tissues, at different stages of vegetative growth, during seed development, and under drought stress. We found that most TaHDZ genes, especially those in subfamilies I and II, were induced by drought stress, suggesting the potential importance of subfamily I and II TaHDZ members in the responses to abiotic stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaHDZ5-6A displayed enhanced drought tolerance, lower water loss rates, higher survival rates, and higher proline content under drought conditions. Additionally, the transcriptome analysis identified a number of differentially expressed genes between 35S::TaHDZ5-6A transgenic and wild-type plants, many of which are involved in stress response. CONCLUSIONS Our results will facilitate further functional analysis of wheat HD-Zip genes, and also indicate that TaHDZ5-6A may participate in regulating the plant response to drought stress. Our experiments show that TaHDZ5-6A holds great potential for genetic improvement of abiotic stress tolerance in crops.
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Affiliation(s)
- Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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84
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Singh AK, Singh N, Kumar S, Kumari J, Singh R, Gaba S, Yadav MC, Grover M, Chaurasia S, Kumar R. Identification and evolutionary analysis of polycistronic miRNA clusters in domesticated and wild wheat. Genomics 2020; 112:2334-2348. [PMID: 31926215 DOI: 10.1016/j.ygeno.2020.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/31/2022]
Abstract
MicroRNAs are ~22 nucleotide long non-coding RNAs that regulate gene expression at posttranscriptional level. Genome-wide analysis was performed to identify polycistronic miRNAs from wheat. Total 89 polycistronic miRNAs were identified in bread wheat which were distributed on three component sub-genomes (A = 26, B = 33 and D = 30). Except some, most of the identified polycistronic miRNAs were also present in other cultivated and wild wheat species. Expression of 11 identified polycistronic miRNAs could be validated using previously assembled transcriptomes, RNA-seq/s-RNA seq data of cultivated and wild wheats and RT-PCR. Polycistronic miRNAs orthologs were also localized on rice and Brachypodium genomes. As a case study, we also analyzed molecular evolution of miR395 family polycistrons in wheat. Both tandem and segmental duplications contributed to expansion of miR395 family polycistrons. Our findings provide a comprehensive view on wheat polycitronic miRNAs that will enable their in-depth functional analysis in the future.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.
| | - Nidhi Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Sundeep Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Sonam Gaba
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Mahesh C Yadav
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Monendra Grover
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
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85
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Dong Z, Tian X, Ma C, Xia Q, Wang B, Chen Q, Sehgal SK, Friebe B, Li H, Liu W. Physical Mapping of Pm57, a Powdery Mildew Resistance Gene Derived from Aegilops searsii. Int J Mol Sci 2020; 21:E322. [PMID: 31947730 PMCID: PMC6982159 DOI: 10.3390/ijms21010322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/01/2022] Open
Abstract
Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is one of many severe diseases that threaten bread wheat (Triticum aestivum L.) yield and quality worldwide. The discovery and deployment of powdery mildew resistance genes (Pm) can prevent this disease epidemic in wheat. In a previous study, we transferred the powdery mildew resistance gene Pm57 from Aegilops searsii into common wheat and cytogenetically mapped the gene in a chromosome region with the fraction length (FL) 0.75-0.87, which represents 12% segment of the long arm of chromosome 2Ss#1. In this study, we performed RNA-seq using RNA extracted from leaf samples of three infected and mock-infected wheat-Ae. searsii 2Ss#1 introgression lines at 0, 12, 24, and 48 h after inoculation with Bgt isolates. Then we designed 79 molecular markers based on transcriptome sequences and physically mapped them to Ae. searsii chromosome 2Ss#1- in seven intervals. We used these markers to identify 46 wheat-Ae. searsii 2Ss#1 recombinants induced by ph1b, a deletion mutant of pairing homologous (Ph) genes. After analyzing the 46 ph1b-induced 2Ss#1L recombinants in the region where Pm57 is located with different Bgt-responses, we physically mapped Pm57 gene on the long arm of 2Ss#1 in a 5.13 Mb genomic region, which was flanked by markers X67593 (773.72 Mb) and X62492 (778.85 Mb). By comparative synteny analysis of the corresponding region on chromosome 2B in Chinese Spring (T. aestivum L.) with other model species, we identified ten genes that are putative plant defense-related (R) genes which includes six coiled-coil nucleotide-binding site-leucine-rich repeat (CNL), three nucleotide-binding site-leucine-rich repeat (NL) and a leucine-rich receptor-like repeat (RLP) encoding proteins. This study will lay a foundation for cloning of Pm57, and benefit the understanding of interactions between resistance genes of wheat and powdery mildew pathogens.
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Affiliation(s)
- Zhenjie Dong
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Xiubin Tian
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Chao Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Qing Xia
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Beilin Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Qifan Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA;
| | - Bernd Friebe
- Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506-5502, USA;
| | - Huanhuan Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
| | - Wenxuan Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; (Z.D.); (X.T.); (C.M.); (Q.X.); (B.W.); (Q.C.)
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86
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Budak H, Kaya SB, Cagirici HB. Long Non-coding RNA in Plants in the Era of Reference Sequences. FRONTIERS IN PLANT SCIENCE 2020; 11:276. [PMID: 32226437 PMCID: PMC7080850 DOI: 10.3389/fpls.2020.00276] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/21/2020] [Indexed: 05/04/2023]
Abstract
The discovery of non-coding RNAs (ncRNAs), and the subsequent elucidation of their functional roles, was largely delayed due to the misidentification of non-protein-coding parts of DNA as "junk DNA," which forced ncRNAs into the shadows of their protein-coding counterparts. However, over the past decade, insight into the important regulatory roles of ncRNAs has led to rapid progress in their identification and characterization. Of the different types of ncRNAs, long non-coding RNAs (lncRNAs), has attracted considerable attention due to their mRNA-like structures and gene regulatory functions in plant stress responses. While RNA sequencing has been commonly used for mining lncRNAs, a lack of widespread conservation at the sequence level in addition to relatively low and highly tissue-specific expression patterns challenges high-throughput in silico identification approaches. The complex folding characteristics of lncRNA molecules also complicate target predictions, as the knowledge about the interaction interfaces between lncRNAs and potential targets is insufficient. Progress in characterizing lncRNAs and their targets from different species may hold the key to efficient identification of this class of ncRNAs from transcriptomic and potentially genomic resources. In wheat and barley, two of the most important crops, the knowledge about lncRNAs is very limited. However, recently published high-quality genomes of these crops are considered as promising resources for the identification of not only lncRNAs, but any class of molecules. Considering the increasing demand for food, these resources should be used efficiently to discover molecular mechanisms lying behind development and a/biotic stress responses. As our understanding of lncRNAs expands, interactions among ncRNA classes, as well as interactions with the coding sequences, will likely define novel functional networks that may be modulated for crop improvement.
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Affiliation(s)
- Hikmet Budak
- Montana BioAgriculture, Inc., Bozeman, MT, United States
- *Correspondence: Hikmet Budak,
| | - Sezgi Biyiklioglu Kaya
- Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabancı University, Istanbul, Turkey
| | - Halise Busra Cagirici
- Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabancı University, Istanbul, Turkey
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87
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Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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88
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Qian C, Yan X, Shi Y, Yin H, Chang Y, Chen J, Ingvarsson PK, Nevo E, Ma XF. Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations. Heredity (Edinb) 2020; 124:62-76. [PMID: 31527784 PMCID: PMC6906298 DOI: 10.1038/s41437-019-0264-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/06/2023] Open
Abstract
Flowering time is one of the most critical traits for plants' life cycles, which is influenced by various environment changes, such as global warming. Previous studies have suggested that to guarantee reproductive success, plants have shifted flowering times to adapt to global warming. Although many studies focused on the molecular mechanisms of early flowering, little was supported by the repeated sampling at different time points through the changing climate. To fully dissect the temporal and spatial evolutionary genetics of flowering time, we investigated nucleotide variation in ten flowering time candidate genes and nine reference genes for the same ten wild-barley populations sampled 28 years apart (1980-2008). The overall genetic differentiation was significantly greater in the descendant populations (2008) compared with the ancestral populations (1980); however, local adaptation tests failed to detect any single-nucleotide polymorphism (SNP)/indel under spatial-diversifying selection at either time point. By contrast, the WFABC (Wright-Fisher ABC-based approach) that detected 54 SNPs/indels was under strong selection during the past 28 generations. Moreover, all these 54 alleles were segregated in the ancestral populations, but fixed in the descendent populations. Among the top ten SNPs/indels, seven were located in genes of FT1 (FLOWERING TIME LOCUS T 1), CO1 (CONSTANS-LIKE PROTEIN 1), and VRN-H2 (VERNALIZATION-H2), which have been documented to be associated with flowering time regulation in barley cultivars. This study might suggest that all ten populations have undergone parallel evolution over the past few decades in response to global warming, and even an overwhelming local adaptation and ecological differentiation.
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Affiliation(s)
- Chaoju Qian
- Department of Ecology and Agriculture Research, Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Xia Yan
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Yong Shi
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 450002, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, SE-750 07, Uppsala, Sweden
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.
| | - Xiao-Fei Ma
- Department of Ecology and Agriculture Research, Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
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89
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90
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Yang Z, Li X, Liao H, Hu L, Peng C, Wang S, Huang X, Bao Z. A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:731-742. [PMID: 31473865 DOI: 10.1007/s10126-019-09918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Yantai Fisheries Research Institute, Yantai, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shenhai Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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91
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Molecular evolution and structural variations in nuclear encoded chloroplast localized heat shock protein 26 (sHSP26) from genetically diverse wheat species. Comput Biol Chem 2019; 83:107144. [PMID: 31751884 DOI: 10.1016/j.compbiolchem.2019.107144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 07/01/2019] [Accepted: 10/05/2019] [Indexed: 11/20/2022]
Abstract
Heat shock proteins are an important class of molecular chaperones known to impart tolerance under high temperature stress. sHSP26, a member of small heat shock protein subfamily is specifically involved in protecting plant's photosynthetic machinery. The present study aimed at identifying and characterizing sequence and structural variations in sHSP26 from genetically diverse progenitor and non-progenitor species of wheat. In silico analysis identified three paralogous copies of TaHSP26 to reside on short arm of chromosome 4A while one homeologue each was localized on long arm of chromosome 4B and 4D of cultivated bread wheat. Wild DD-genome donor Aegilops tauschii carried an additional sHSP26 gene (AET4Gv20569400) which was absent in the cultivated DD genome of bread wheat. In vitro amplification of this novel gene in wild accessions of Ae. tauschii and synthetic hexaploid wheat but not in cultivated bread wheat validated this finding. Further, significant length polymorphism could be identified in exon1 from diverse sHSP26 sequences. Multiple sequence alignment of procured sequences revealed numerous sSNPs and nsSNPs. D3A, P125 L, Q242 K were designated as homeolog specific- while A49 G as non-progenitor specific amino acid replacements. A 9-bp indel in TmHSP26-1(GA) translated into a deletion of SPM amino acid segment in chloroplast specific conserved consensus region III. High degree of divergence in nucleotide sequence between cultivated and wild species appeared in the form of higher ω values (Ka/Ks >1) indicating positive selection during the course of evolution. Phylogenetic analysis elucidated ancestral relationships between wheat sHSP26 proteins and orthologous proteins across plant kingdom. Overall, data mining approach may be employed as an effective pre-breeding strategy to identify and mobilize novel stress responsive genes and distinct allelic variants from wider germplasm collections of wheat to enhance climate resilience of present day elite wheat cultivars.
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92
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Badaeva ED, Fisenko AV, Surzhikov SA, Yankovskaya AA, Chikida NN, Zoshchuk SA, Belousova MK, Dragovich AY. Genetic Heterogeneity of a Diploid Grass Aegilops tauschii Revealed by Chromosome Banding Methods and Electrophoretic Analysis of the Seed Storage Proteins (Gliadins). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419110024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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93
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Bhattacharya S, Dhar S, Banerjee A, Ray S. Structural, functional, and evolutionary analysis of late embryogenesis abundant proteins (LEA) in Triticum aestivum: A detailed molecular level biochemistry using in silico approach. Comput Biol Chem 2019; 82:9-24. [DOI: 10.1016/j.compbiolchem.2019.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 10/26/2022]
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94
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Yu K, Liu D, Chen Y, Wang D, Yang W, Yang W, Yin L, Zhang C, Zhao S, Sun J, Liu C, Zhang A. Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4671-4688. [PMID: 31226200 PMCID: PMC6760303 DOI: 10.1093/jxb/erz247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/15/2019] [Indexed: 05/12/2023]
Abstract
Understanding the genetic architecture of grain size is a prerequisite to manipulating grain development and improving the potential crop yield. In this study, we conducted a whole genome-wide quantitative trait locus (QTL) mapping of grain-size-related traits by constructing a high-density genetic map using 109 recombinant inbred lines of einkorn wheat. We explored the candidate genes underlying QTLs through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 single nucleotide polymorphism markers assigned to 1551 bins on seven chromosomes. Strong collinearity and high genome coverage of this map were revealed by comparison with physical maps of wheat and barley. Six grain size-related traits were surveyed in five environments. In total, 42 QTLs were identified; these were assigned to 17 genomic regions on six chromosomes and accounted for 52.3-66.7% of the phenotypic variation. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing identified 4959 genes differentially expressed between the two parental lines. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTLs, indicating that the starch biosynthesis pathway plays a vital role in grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat; identification of the underlying genes enables understanding of grain development and wheat genetic improvement. Furthermore, the map facilitates quantitative trait mapping, map-based cloning, genome assembly, and comparative genomics in wheat taxa.
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Affiliation(s)
- Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- Science and Technology Department, State Tobacco Monopoly Administration, Beijing, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wei Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Lixin Yin
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Chi Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Correspondence: and
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Correspondence: and
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95
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Yu K, Liu D, Chen Y, Wang D, Yang W, Yang W, Yin L, Zhang C, Zhao S, Sun J, Liu C, Zhang A. Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping and transcriptomic profiling. JOURNAL OF EXPERIMENTAL BOTANY 2019. [PMID: 31226200 DOI: 10.1101/377820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding the genetic architecture of grain size is a prerequisite to manipulating grain development and improving the potential crop yield. In this study, we conducted a whole genome-wide quantitative trait locus (QTL) mapping of grain-size-related traits by constructing a high-density genetic map using 109 recombinant inbred lines of einkorn wheat. We explored the candidate genes underlying QTLs through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 single nucleotide polymorphism markers assigned to 1551 bins on seven chromosomes. Strong collinearity and high genome coverage of this map were revealed by comparison with physical maps of wheat and barley. Six grain size-related traits were surveyed in five environments. In total, 42 QTLs were identified; these were assigned to 17 genomic regions on six chromosomes and accounted for 52.3-66.7% of the phenotypic variation. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing identified 4959 genes differentially expressed between the two parental lines. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTLs, indicating that the starch biosynthesis pathway plays a vital role in grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat; identification of the underlying genes enables understanding of grain development and wheat genetic improvement. Furthermore, the map facilitates quantitative trait mapping, map-based cloning, genome assembly, and comparative genomics in wheat taxa.
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Affiliation(s)
- Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- Science and Technology Department, State Tobacco Monopoly Administration, Beijing, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wei Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Lixin Yin
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Chi Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shancen Zhao
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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97
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Wang B, Li X, Chen W, Kong L. Isobaric tags for relative and absolute quantification-based proteomic analysis of defense responses triggered by the fungal pathogen Fusarium graminearum in wheat. J Proteomics 2019; 207:103442. [PMID: 31326557 DOI: 10.1016/j.jprot.2019.103442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/22/2019] [Accepted: 07/07/2019] [Indexed: 01/07/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease worldwide that is predominantly caused by the fungal pathogen Fusarium graminearum. The aim of this work was to study differentially abundant protein species of near-isogenic lines A061-3 and A061-4 with the final goal of elucidating the molecular mechanisms of their differential resistance to F. graminearum. The objectives were accomplished using isobaric tags for relative and absolute quantification (iTRAQ) with mass spectrometry (MS). Lines A061-3 and A061-4 were resistant and susceptible to F. graminearum, respectively. At four post-inoculation points, 11,070 protein species were identified, of which 762 were differentially abundant. Gene Ontology enrichment analysis showed that most differentially abundant protein species participated in 18 biological processes after inoculation. Further analysis demonstrated that crucial metabolic pathways like plant-pathogen interaction had increased abundance. Real-time quantitative PCR (qRT-PCR) analysis revealed increased gene products of eight selected genes in plant-pathogen interaction. This investigation provides a basic bioinformatics-based characterization of differentially abundant protein species during early stages against F. graminearum. SIGNIFICANCE: FHB leads to severe yield loss and reduction in grain quality in wheat and other small grain cereals. Although extensive studies have focused on wheat resistance against F. graminearum, the molecular mechanism of FHB resistance in wheat remains to be further elucidated. In the present study, Kyoto Encyclopedia of Genes and Genomes analysis indicated that ten pathways were putatively associated with FHB resistance. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) showed that a valuable set of differentially abundant protein species including pathogenesis-related protein species were identified for further discovery of candidate genes for FHB resistance. This investigation provides new insights into the molecular mechanisms associated with FHB resistance and as well as a foundation for future studies.
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Affiliation(s)
- Biao Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Xuefeng Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Wuying Chen
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China.
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98
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Rufo R, Alvaro F, Royo C, Soriano JM. From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. PLoS One 2019; 14:e0219867. [PMID: 31306459 PMCID: PMC6629082 DOI: 10.1371/journal.pone.0219867] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/02/2019] [Indexed: 11/18/2022] Open
Abstract
Assessment of genetic diversity and population structure in crops is essential for breeding and germplasm conservation. A collection of 354 bread wheat genotypes, including Mediterranean landraces and modern cultivars representative of the ones most widely grown in the Mediterranean Basin, were characterized with 11196 single nucleotide polymorphism (SNP) markers. Total genetic diversity (HT) and polymorphic information content (PIC) were 0.36 and 0.30 respectively for both landraces and modern cultivars. Linkage disequilibrium for the modern cultivars was higher than for the landraces (0.18 and 0.12, respectively). Analysis of the genetic structure showed a clear geographical pattern for the landraces, which were clustered into three subpopulations (SPs) representing the western, northern and eastern Mediterranean, whereas the modern cultivars were structured according to the breeding programmes that developed them: CIMMYT/ICARDA, France/Italy, and Balkan/eastern European countries. The modern cultivars showed higher genetic differentiation (GST) and lower gene flow (0.1673 and 2.49, respectively) than the landraces (0.1198 and 3.67, respectively), indicating a better distinction between subpopulations. The maximum gene flow was observed between landraces from the northern Mediterranean SPs and the modern cultivars released mainly by French and Italian breeding programmes.
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Affiliation(s)
- Rubén Rufo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Fanny Alvaro
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
- * E-mail:
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99
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Cheng H, Liu J, Wen J, Nie X, Xu L, Chen N, Li Z, Wang Q, Zheng Z, Li M, Cui L, Liu Z, Bian J, Wang Z, Xu S, Yang Q, Appels R, Han D, Song W, Sun Q, Jiang Y. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biol 2019; 20:136. [PMID: 31300020 PMCID: PMC6624984 DOI: 10.1186/s13059-019-1744-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/22/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.
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Affiliation(s)
- Hong Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Jing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Ming Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zihua Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Jianxin Bian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Qixin Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
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Physical information of 2705 PCR-based molecular markers and the evaluation of their potential use in wheat. J Genet 2019. [DOI: 10.1007/s12041-019-1114-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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