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Abdelrahman M, Gorafi YSA, Sulieman S, Jogaiah S, Gupta A, Tsujimoto H, Nguyen HT, Herrera-Estrella L, Tran LSP. Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38935838 DOI: 10.1111/tpj.16887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.
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Affiliation(s)
- Mostafa Abdelrahman
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Yasir Serag Alnor Gorafi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kitashirakawa, 606-8502, Kyoto, Japan
| | - Saad Sulieman
- Department of Agronomy, Faculty of Agriculture, University of Khartoum, Khartoum North, 13314, Sudan
| | - Sudisha Jogaiah
- Department of Environmental Science, Central University of Kerala, Periye, Kasaragod, 671316, Kerala, India
| | - Aarti Gupta
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Henry T Nguyen
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, Missouri, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
- Unidad de Genomica Avanzada, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional, Irapuato, 36821, Mexico
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
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2
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Asuke S, Morita K, Shimizu M, Abe F, Terauchi R, Nago C, Takahashi Y, Shibata M, Yoshioka M, Iwakawa M, Kishi-Kaboshi M, Su Z, Nasuda S, Handa H, Fujita M, Tougou M, Hatta K, Mori N, Matsuoka Y, Kato K, Tosa Y. Evolution of wheat blast resistance gene Rmg8 accompanied by differentiation of variants recognizing the powdery mildew fungus. NATURE PLANTS 2024; 10:971-983. [PMID: 38898164 DOI: 10.1038/s41477-024-01711-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/25/2024] [Indexed: 06/21/2024]
Abstract
Wheat blast, a devastating disease having spread recently from South America to Asia and Africa, is caused by Pyricularia oryzae (synonym of Magnaporthe oryzae) pathotype Triticum, which first emerged in Brazil in 1985. Rmg8 and Rmg7, genes for resistance to wheat blast found in common wheat and tetraploid wheat, respectively, recognize the same avirulence gene, AVR-Rmg8. Here we show that an ancestral resistance gene, which had obtained an ability to recognize AVR-Rmg8 before the differentiation of Triticum and Aegilops, has expanded its target pathogens. Molecular cloning revealed that Rmg7 was an allele of Pm4, a gene for resistance to wheat powdery mildew on 2AL, whereas Rmg8 was its homoeologue on 2BL ineffective against wheat powdery mildew. Rmg8 variants with the ability to recognize AVR-Rmg8 were distributed not only in Triticum spp. but also in Aegilops speltoides, Aegilops umbellulata and Aegilops comosa. This result suggests that the origin of resistance gene(s) recognizing AVR-Rmg8 dates back to the time before differentiation of A, B, S, U and M genomes, that is, ~5 Myr before the emergence of its current target, the wheat blast fungus. Phylogenetic analyses suggested that, in the evolutionary process thereafter, some of their variants gained the ability to recognize the wheat powdery mildew fungus and evolved into genes controlling dual resistance to wheat powdery mildew and wheat blast.
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Affiliation(s)
- Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kohei Morita
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Fumitaka Abe
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Centre, Kitakami, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Chika Nago
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yoshino Takahashi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Mai Shibata
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Motohiro Yoshioka
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Mizuki Iwakawa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Mitsuko Kishi-Kaboshi
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Zhuo Su
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hirokazu Handa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Makoto Tougou
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Koichi Hatta
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Naoki Mori
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
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3
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Tan W, Zhou P, Huang X, Liao R, Wang X, Wu Y, Ni Z, Shi T, Yu X, Zhang H, Ma C, Gao F, Ma Y, Bai Y, Hayat F, Omondi OK, Coulibaly D, Gao Z. Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot. HORTICULTURE RESEARCH 2024; 11:uhae103. [PMID: 38689698 PMCID: PMC11059810 DOI: 10.1093/hr/uhae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.
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Affiliation(s)
- Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruyu Liao
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Xiaoan Wang
- Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yaoyao Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiqin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chengdong Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufan Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Faisal Hayat
- Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ouma Kenneth Omondi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Crops, Horticulture and Soils, Faculty of Agriculture, Egerton University, P.O. Box 536, Egerton 20115, Kenya
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Agricultural Sciences and Techniques-Horticulture, Rural Polytechnic Institute for Training and Applied Research (IPR/IFRA) of Katibougou, Koulikoro B.P.224, Mali
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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4
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Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nat Commun 2023; 14:6072. [PMID: 37770474 PMCID: PMC10539295 DOI: 10.1038/s41467-023-41833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuyong Pang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China.
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5
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Hasanpour K, Aalami A, Seraj RGM, Hosseini R, Naeimi S, Esmaeilzadeh-Salestani K. Identification of drought-tolerant hub genes in Iranian KC-2226 genotype of Aegilops tauschii using transcriptomic analysis. Sci Rep 2023; 13:9499. [PMID: 37308505 DOI: 10.1038/s41598-023-36133-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
Aegilops tauschii, as a donor of D genome to the bread wheat with a valuable source of resistance to different biotic and abiotic stresses, is used to improve the quality of wheat cultivars. Every genotype has a specific genetic content, the investigation of which can lead to the identification of useful genes such as stress tolerance genes, including drought. Therefore, 23 genotypes of Ae. tauschii were selected to evaluate their morphological and physiological traits under greenhouse conditions. Among them, a superior tolerant genotype (KC-2226) was chosen for transcriptomic analysis. Our result showed that 5007 and 3489 genes were deferentially up- and downregulated, respectively. Upregulated genes were involved in photosynthesis, glycolysis/gluconeogenesis, and amino acid biosynthesis whereas downregulated genes were often engaged in DNA synthesis, replication, repair and topological changes. The result of protein-protein interaction network analysis showed that AT1G76550 (1.46), AT1G20950 (1.42), IAR4 (1.19), and PYD2 (1.16) among upregulated genes and THY-1 (44), PCNA1 (41) and TOPII (22) among down-regulated genes had the highest interactions with other genes. In conclusion, Ae. tauschii employs elevated transcription of specific genes involved in photosynthesis, glycolysis and gluconeogenesis and amino acid biosynthesis pathways rather than genes active in DNA synthesis and repair to provide the energy needed for the plant to survive under stress conditions.
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Affiliation(s)
- Keyvan Hasanpour
- Department of Agricultural Biotechnology, University of Guilan, University Campus 2, Rasht, Iran
| | - Ali Aalami
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
| | - Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Ramin Hosseini
- Department of Biotechnology, Faculty of Agriculture and Natural Resource, Imam Khomeini International University, Qazvin, Iran
| | - Shahram Naeimi
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, 19858-13111, Iran
| | - Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
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6
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Yang Y, Cui L, Lu Z, Li G, Yang Z, Zhao G, Kong C, Li D, Chen Y, Xie Z, Chen Z, Zhang L, Xia C, Liu X, Jia J, Kong X. Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat. PLANT COMMUNICATIONS 2023:100567. [PMID: 36855304 PMCID: PMC10363506 DOI: 10.1016/j.xplc.2023.100567] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.
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Affiliation(s)
- Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Licao Cui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongxu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jizeng Jia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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7
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Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. Nat Commun 2022; 13:1607. [PMID: 35338132 PMCID: PMC8956640 DOI: 10.1038/s41467-022-29132-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance. Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
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8
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Li LF, Zhang ZB, Wang ZH, Li N, Sha Y, Wang XF, Ding N, Li Y, Zhao J, Wu Y, Gong L, Mafessoni F, Levy AA, Liu B. Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome. MOLECULAR PLANT 2022; 15:488-503. [PMID: 34979290 DOI: 10.1016/j.molp.2021.12.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/11/2021] [Accepted: 12/28/2021] [Indexed: 05/23/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Fabrizio Mafessoni
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.
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9
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Seni S, Kaur S, Malik P, Yadav IS, Sirohi P, Chauhan H, Kaur A, Chhuneja P. Transcriptome based identification and validation of heat stress transcription factors in wheat progenitor species Aegilops speltoides. Sci Rep 2021; 11:22049. [PMID: 34764387 PMCID: PMC8586331 DOI: 10.1038/s41598-021-01596-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/01/2021] [Indexed: 11/10/2022] Open
Abstract
Wheat, one of the major cereal crops worldwide, get adversely affected by rising global temperature. We have identified the diploid B genome progenitor of wheat, Aegilops speltoides (SS), as a potential donor for heat stress tolerance. Therefore, the present work was planned to study the total transcriptome profile of heat stress-tolerant Ae. speltoides accession pau3809 (AS3809) and compare with that of tetraploid and hexaploid wheat cultivars PDW274 and PBW725, respectively. The comparative transcriptome was utilized to identify and validate heat stress transcription factors (HSFs), the key genes involved in imparting heat stress tolerance. Transcriptome analysis led to the identification of a total of 74 K, 68 K, and 76 K genes in AS3809, PDW274, and PBW725, respectively. There was a high uniformity of GO profiles under the biological, molecular, and cellular functions across the three wheat transcriptomes, suggesting the conservation of gene function. Twelve HSFs having the highest FPKM value were identified in the AS3809 transcriptome data, while six of these HSFs namely HSFA3, HSFA5, HSFA9, HSFB2a, HSFB2b, and HSFC1b, were validated with qRT PCR. These six HSFs were identified as an important component of thermotolerance in AS3809 as evident from their comparative higher expression under heat stress.
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Affiliation(s)
- Sushmita Seni
- grid.412577.20000 0001 2176 2352School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Palvi Malik
- grid.412577.20000 0001 2176 2352School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Inderjit Singh Yadav
- grid.412577.20000 0001 2176 2352School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Parul Sirohi
- grid.19003.3b0000 0000 9429 752XDepartment of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 India
| | - Harsh Chauhan
- grid.19003.3b0000 0000 9429 752XDepartment of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667 India
| | - Amandeep Kaur
- grid.412577.20000 0001 2176 2352School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
| | - Parveen Chhuneja
- grid.412577.20000 0001 2176 2352School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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10
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Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses. Int J Mol Sci 2021; 22:ijms222011017. [PMID: 34681677 PMCID: PMC8541341 DOI: 10.3390/ijms222011017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/18/2021] [Accepted: 09/19/2021] [Indexed: 02/02/2023] Open
Abstract
Aegilops tauschii (Coss.) is an aggressive and serious annual grass weed in China. Its DD genome is a rich source of genetic material and performs better under different abiotic stress conditions (salinity, drought, temperature, etc.). Reverse-transcribed quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for reference gene selection and validation. This work aimed to evaluate the stability of reference gene expression in Ae. tauschii under different abiotic stresses (salinity, drought, hot, and cold) and developmental stages (seedling and development). The results show that the ubiquitin-conjugating enzyme E2 36-like (UBC36) and protein microrchidia 2-like (HSP) are the most stable genes under control and salinity conditions, respectively. Under drought stress conditions, UBC36 is more stable as compared with others. Glyceraldehyde-3-phosphate dehydrogenase (GADPH) is the most stable reference gene during heat stress conditions and thioredoxin-like protein (YLS) under cold stress condition. Phosphate2A serine/threonine-protein phosphatase 2A (PP2A) and eukaryotic translation initiation factor 3 (ETIF3) are the most stable genes at seedling and developmental stages. Intracellular transport protein (CAC) is recommended as the most stable gene under different abiotic stresses and at developmental stages. Furthermore, the relative expression levels of NHX1 and DREB under different levels of salinity and drought stress conditions varied with the most (HSP and UBC36) and least (YLS and ACT) stable genes. This study provides reliable reference genes for understanding the tolerance mechanisms in Ae. tauschii under different abiotic stress conditions.
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11
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RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species. Funct Integr Genomics 2021; 21:535-542. [PMID: 34405283 DOI: 10.1007/s10142-021-00799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/08/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
The release of high-quality chromosome-level genome sequences of members of the Triticeae tribe has greatly facilitated genetic and genomic analyses of important crops such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the large diploid genome size of Triticeae plants (ca. 5 Gbp), transcript analysis is an important method for identifying genetic and genomic differences among Triticeae species. In this review, we summarize our results of RNA-Seq analyses of diploid wheat accessions belonging to the genera Aegilops and Triticum. We also describe studies of the molecular relationships among these accessions and provide insight into the evolution of common hexaploid wheat. DNA markers based on polymorphisms within species can be used to map loci of interest. Even though the genome sequence of diploid Aegilops tauschii, the D-genome donor of common wheat, has been released, the diploid barley genome continues to provide key information about the physical structures of diploid wheat genomes. We describe how a series of RNA-Seq analyses of wheat relatives has helped uncover the structural and evolutionary features of genomic and genetic systems in wild and cultivated Triticeae species.
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12
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Mahlandt A, Rawat N, Leonard J, Venglat P, Datla R, Meier N, Gill BS, Riera-Lizarazu O, Coleman G, Murphy AS, Tiwari VK. High-resolution mapping of the Mov-1 locus in wheat by combining radiation hybrid (RH) and recombination-based mapping approaches. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2303-2314. [PMID: 33830295 DOI: 10.1007/s00122-021-03827-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
This work reports a quick method that integrates RH mapping and genetic mapping to map the dominant Mov-1 locus to a 1.1-Mb physical interval with a small number of candidate genes. Bread wheat is an important crop for global human population. Identification of genes and alleles controlling agronomic traits is essential toward sustainably increasing crop production. The unique multi-ovary (MOV) trait in wheat holds potential for improving yields and is characterized by the formation of 2-3 grains per spikelet. The genetic basis of the multi-ovary trait is known to be monogenic and dominant in nature. Its precise mapping and functional characterization is critical to utilizing this trait in a feasible manner. Previous mapping efforts of the locus controlling multiple ovary/pistil formation in the hexaploid wheat have failed to produce a consensus for a particular chromosome. We describe a mapping strategy integrating radiation hybrid mapping and high-resolution genetic mapping to locate the chromosomal position of the Mov-1 locus in hexaploid wheat. We used RH mapping approach using a panel of 188 lines to map the Mov-1 locus in the terminal part of long arm of wheat chromosome 2D with a map resolution of 1.67 Mb/cR1500. Then using a genetic population of MOV × Synthetic wheat of F2 lines, we delineated the Mov-1 locus to a 1.1-Mb physical region with a small number of candidate genes. This demonstrates the value of this integrated strategy to mapping dominant genes in wheat.
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Affiliation(s)
- Alexander Mahlandt
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Jeff Leonard
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, USA
| | - Prakash Venglat
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Nathan Meier
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Gary Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Angus S Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA.
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Alotaibi F, Alharbi S, Alotaibi M, Al Mosallam M, Motawei M, Alrajhi A. Wheat omics: Classical breeding to new breeding technologies. Saudi J Biol Sci 2021; 28:1433-1444. [PMID: 33613071 PMCID: PMC7878716 DOI: 10.1016/j.sjbs.2020.11.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 12/26/2022] Open
Abstract
Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.
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Affiliation(s)
- Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Saif Alharbi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Majed Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mobarak Al Mosallam
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | | | - Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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14
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Zeng X, Chen G, Wang L, Tagiri A, Kikuchi S, Sassa H, Komatsuda T. The unique disarticulation layer formed in the rachis of Aegilops longissima probably results from the spatial co-expression of Btr1 and Btr2. ANNALS OF BOTANY 2021; 127:297-304. [PMID: 32766735 PMCID: PMC7872126 DOI: 10.1093/aob/mcaa147] [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: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS The brittle rachis trait is a feature of many wild grasses, particularly within the tribe Triticeae. Wild Hordeum and Triticum species form a disarticulation layer above the rachis node, resulting in the production of wedge-type dispersal units. In Aegilops longissima, only one or two of the nodes in the central portion of its rachis are brittle. In Triticeae species, the formation of a disarticulation layer above the rachis node requires the co-transcription of the two dominant and complementary genes Btr1 and Btr2. This study aims to establish whether homologues of Btr1 and/or Btr2 underlie the unusual brittle rachis phenotype observed in Ae. longissima. METHODS Scanning electron microscopy was used to examine the disarticulation surfaces. Quantitative RT-PCR and RNA in situ hybridization experiments were used to identify gene expression in the immature inflorescence. KEY RESULTS Analysis based on scanning electron microscopy was able to demonstrate that the disarticulation surfaces formed in the Ae. longissima rachis are morphologically indistinguishable from those formed in the rachises of wild Hordeum and Triticum species. RNA in situ hybridization showed that in the immature Ae. longissima inflorescence, the intensity of Btr1 transcription varied from high at the rachis base to low at its apex, while that of Btr2 was limited to the nodes in the central to distal portion of the rachis. CONCLUSIONS The disarticulation pattern shown by Ae. longissima results from the limitation of Btr1 and Btr2 co-expression to nodes lying in the centre of the rachis.
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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
| | - Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Lei Wang
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 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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15
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Zhang Y, Fan C, Chen Y, Wang RRC, Zhang X, Han F, Hu Z. Genome evolution during bread wheat formation unveiled by the distribution dynamics of SSR sequences on chromosomes using FISH. BMC Genomics 2021; 22:55. [PMID: 33446108 PMCID: PMC7809806 DOI: 10.1186/s12864-020-07364-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic regions of chromosomes, are the effective marker for tracing the genomic DNA sequence variations. However, to date the distribution dynamics of SSRs on chromosomes of bread wheat and its donors, including diploid and tetraploid Triticum urartu, Aegilops speltoides, Aegilops tauschii, Triticum turgidum ssp. dicocoides, reflecting the genome evolution events during bread wheat formation had not been comprehensively investigated. RESULTS The genome evolution was studied by comprehensively comparing the distribution patterns of (AAC)n, (AAG)n, (AGC)n and (AG)n in bread wheat Triticum aestivum var. Chinese Spring and its progenitors T. urartu, A. speltoides, Ae. tauschii, wild tetroploid emmer wheat T. dicocoides, and cultivated emmer wheat T. dicoccum. Results indicated that there are specific distribution patterns in different chromosomes from different species for each SSRs. They provided efficient visible markers for identification of some individual chromosomes and SSR sequence evolution tracing from the diploid progenitors to hexaploid wheat. During wheat speciation, the SSR sequence expansion occurred predominately in the centromeric and pericentromeric regions of B genome chromosomes accompanied by little expansion and elimination on other chromosomes. This result indicated that the B genome might be more sensitive to the "genome shock" and more changeable during wheat polyplodization. CONCLUSIONS During the bread wheat evolution, SSRs including (AAC)n, (AAG)n, (AGC)n and (AG)n in B genome displayed the greatest changes (sequence expansion) especially in centromeric and pericentromeric regions during the polyploidization from Ae. speltoides S genome, the most likely donor of B genome. This work would enable a better understanding of the wheat genome formation and evolution and reinforce the viewpoint that B genome was originated from S genome.
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Affiliation(s)
- Yingxin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Richard R-C Wang
- United States Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Utah State University, Logan, UT, 84322-6300, USA
| | - Xiangqi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Agriculture, University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Production of synthetic wheat lines to exploit the genetic diversity of emmer wheat and D genome containing Aegilops species in wheat breeding. Sci Rep 2020; 10:19698. [PMID: 33184344 PMCID: PMC7661528 DOI: 10.1038/s41598-020-76475-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Due to the accumulation of various useful traits over evolutionary time, emmer wheat (Triticum turgidum subsp. dicoccum and dicoccoides, 2n = 4x = 28; AABB), durum wheat (T. turgidum subsp. durum, 2n = 4x = 28; AABB), T. timopheevii (2n = 4x = 28; AAGG) and D genome containing Aegilops species offer excellent sources of novel variation for the improvement of bread wheat (T. aestivum L., AABBDD). Here, we made 192 different cross combinations between diverse genotypes of wheat and Aegilops species including emmer wheat × Ae. tauschii (2n = DD or DDDD), durum wheat × Ae. tauschii, T. timopheevii × Ae. tauschii, Ae. crassa × durum wheat, Ae. cylindrica × durum wheat and Ae. ventricosa × durum wheat in the field over three successive years. We successfully recovered 56 different synthetic hexaploid and octaploid F2 lines with AABBDD, AABBDDDD, AAGGDD, D1D1XcrXcrAABB, DcDcCcCcAABB and DvDvNvNvAABB genomes via in vitro rescue of F1 embryos and spontaneous production of F2 seeds on the Fl plants. Cytogenetic analysis of F2 lines showed that the produced synthetic wheat lines were generally promising stable amphiploids. Contribution of D genome bearing Aegilops and the less-investigated emmer wheat genotypes as parents in the crosses resulted in synthetic amphiploids which are a valuable resource for bread wheat breeding.
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17
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Hall ND, Zhang H, Mower JP, McElroy JS, Goertzen LR. The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content within Poaceae. Genome Biol Evol 2020; 12:3684-3697. [PMID: 31665327 PMCID: PMC7145533 DOI: 10.1093/gbe/evz229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Plant mitochondrial (mt) genome assembly provides baseline data on size, structure, and gene content, but resolving the sequence of these large and complex organelle genomes remains challenging due to fragmentation, frequent recombination, and transfers of DNA from neighboring plastids. The mt genome for Eleusine indica (Poaceae: goosegrass) is comprehensibly analyzed here, providing key reference data for an economically significant invasive species that is also the maternal parent of the allotetraploid crop Finger millet (Eleusine coracana). The assembled E. indica genome contains 33 protein coding genes, 6 rRNA subunits, 24 tRNA, 8 large repetitive regions 15 kb of transposable elements across a total of 520,691 bp. Evidence of RNA editing and loss of rpl2, rpl5, rps14, rps11, sdh4, and sdh3 genes is evaluated in the context of an updated survey of mt genomic gene content across the grasses through an analysis of publicly available data. Hypothesized patterns of Poaceae mt gene loss are examined in a phylogenetic context to clarify timing, showing that rpl2 was transferred to the nucleus from the mitochondrion prior to the origin of the PACMAD clade.
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Affiliation(s)
- Nathan D Hall
- Department of Biological Sciences, Auburn University
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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18
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Kaushik M, Rai S, Venkadesan S, Sinha SK, Mohan S, Mandal PK. Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors. Genes (Basel) 2020; 11:E509. [PMID: 32380773 PMCID: PMC7290843 DOI: 10.3390/genes11050509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022] Open
Abstract
Wheat grain development after anthesis is an important biological process, in which major components of seeds are synthesised, and these components are further required for germination and seed vigour. We have made a comparative RNA-Seq analysis between hexaploid wheat and its individual diploid progenitors to know the major differentially expressed genes (DEGs) involved during grain development. Two libraries from each species were generated with an average of 55.63, 55.23, 68.13, and 103.81 million reads, resulting in 79.3K, 113.7K, 90.6K, and 121.3K numbers of transcripts in AA, BB, DD, and AABBDD genome species respectively. Number of expressed genes in hexaploid wheat was not proportional to its genome size, but marginally higher than that of its diploid progenitors. However, to capture all the transcripts in hexaploid wheat, sufficiently higher number of reads was required. Functional analysis of DEGs, in all the three comparisons, showed their predominance in three major classes of genes during grain development, i.e., nutrient reservoirs, carbohydrate metabolism, and defence proteins; some of them were subsequently validated through real time quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Further, developmental stage-specific gene expression showed most of the defence protein genes expressed during initial developmental stages in hexaploid contrary to the diploids at later stages. Genes related to carbohydrates anabolism expressed during early stages, whereas catabolism genes expressed at later stages in all the species. However, no trend was observed in case of different nutrient reservoirs gene expression. This data could be used to study the comparative gene expression among the three diploid species and homeologue-specific expression in hexaploid.
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Affiliation(s)
- Megha Kaushik
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
- Amity Institute of Biotechnology (AIB), Amity University, Sector 125, Noida, Uttar Pradesh 201313, India;
| | - Shubham Rai
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
| | - Sureshkumar Venkadesan
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
| | - Sumedha Mohan
- Amity Institute of Biotechnology (AIB), Amity University, Sector 125, Noida, Uttar Pradesh 201313, India;
| | - Pranab Kumar Mandal
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
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19
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Rasheed A, Takumi S, Hassan MA, Imtiaz M, Ali M, Morgunov AI, Mahmood T, He Z. Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1503-1520. [PMID: 31897516 DOI: 10.1007/s00122-019-03523-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Muhammad Adeel Hassan
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Mohsin Ali
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Alex I Morgunov
- International Maize and Wheat Improvement Center (CIMMYT), Yenimahalle, Ankara, 06170, Turkey
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
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20
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Bariah I, Keidar-Friedman D, Kashkush K. Identification and characterization of large-scale genomic rearrangements during wheat evolution. PLoS One 2020; 15:e0231323. [PMID: 32287287 PMCID: PMC7156093 DOI: 10.1371/journal.pone.0231323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/20/2020] [Indexed: 12/25/2022] Open
Abstract
Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they might have occurred via unequal intra-strand recombination or double-strand break (DSB) events. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.
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Affiliation(s)
- Inbar Bariah
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
- * E-mail:
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21
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Okada M, Michikawa A, Yoshida K, Nagaki K, Ikeda TM, Takumi S. Phenotypic effects of the U-genome variation in nascent synthetic hexaploids derived from interspecific crosses between durum wheat and its diploid relative Aegilops umbellulata. PLoS One 2020; 15:e0231129. [PMID: 32240263 PMCID: PMC7117738 DOI: 10.1371/journal.pone.0231129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022] Open
Abstract
Aegilops umbellulata is a wild diploid wheat species with the UU genome that is an important genetic resource for wheat breeding. To exploit new synthetic allohexaploid lines available as bridges for wheat breeding, a total of 26 synthetic hexaploid lines were generated through crossing between the durum wheat cultivar Langdon and 26 accessions of Ae. umbellulata. In nascent synthetic hexaploids with the AABBUU genome, the presence of the set of seven U-genome chromosomes was confirmed with U-genome chromosome-specific markers developed based on RNA-seq-derived data from Ae. umbellulata. The AABBUU synthetic hexaploids showed large variations in flowering- and morphology-related traits, and these large variations transmitted well from the parental Ae. umbellulata accessions. However, the variation ranges in most traits examined were reduced under the AABBUU hexaploid background compared with under the diploid parents. The AABBUU and AABBDD synthetic hexaploids were clearly discriminated by several morphological traits, and an increase of plant height and in the number of spikes and a decrease of spike length were commonly observed in the AABBUU synthetics. Thus, interspecific differences in several morphological traits between Ae. umbellulata and A. tauschii largely affected the basic plant architecture of the synthetic hexaploids. In conclusion, the AABBUU synthetic hexaploid lines produced in the present study are useful resources for the introgression of desirable genes from Ae. umbellulata to common wheat.
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Affiliation(s)
- Moeko Okada
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Asami Michikawa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Tatsuya M. Ikeda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Hiroshima, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- * E-mail:
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22
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Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BBH, Uauy C. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife 2020; 9:e55646. [PMID: 32208137 PMCID: PMC7093151 DOI: 10.7554/elife.55646] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of BirminghamBirminghamUnited Kingdom
| | - Jemima Brinton
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | | | | | - William D Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and BioinformaticsFiorenzuola d'ArdaItaly
| | | | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Brett Ford
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | | | - Sadiye Hayta
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt LuciaAustralia
| | | | - Julie King
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington CampusLoughboroughUnited Kingdom
| | - Marco Maccaferrri
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - Università di Bologna (University of Bologna)BolognaItaly
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Curtis J Pozniak
- Crop Development Centre, University of SaskatchewanSaskatoonCanada
| | | | | | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food (CSIRO)CanberraAustralia
| | - Luzie U Wingen
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Brande BH Wulff
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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23
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Tanaka S, Yoshida K, Sato K, Takumi S. Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops. BMC Genomics 2020; 21:246. [PMID: 32192452 PMCID: PMC7083043 DOI: 10.1186/s12864-020-6664-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
Background Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome nomenclatures have been defined. However, evaluations of genome differentiation based on genome-wide nucleotide variations are still limited, especially in the three genomes of the genus Aegilops: Ae. caudata L. (CC genome), Ae. comosa Sibth. et Sm. (MM genome), and Ae. uniaristata Vis. (NN genome). To reveal the genome differentiation of these diploid species, we first performed RNA-seq-based polymorphic analyses for C, M, and N genomes, and then expanded the analysis to include the 12 diploid species of Triticum and Aegilops. Results Genetic divergence of the exon regions throughout the entire chromosomes in the M and N genomes was larger than that between A- and Am-genomes. Ae. caudata had the second highest genetic diversity following Ae. speltoides, the putative B genome donor of common wheat. In the phylogenetic trees derived from the nuclear and chloroplast genome-wide polymorphism data, the C, D, M, N, U, and S genome species were connected with short internal branches, suggesting that these diploid species emerged during a relatively short period in the evolutionary process. The highly consistent nuclear and chloroplast phylogenetic topologies indicated that nuclear and chloroplast genomes of the diploid Triticum and Aegilops species coevolved after their diversification into each genome, accounting for most of the genome differentiation among the diploid species. Conclusions RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. speltoides. Phylogenomic and epigenetic analyses of intergenic and centromeric regions could be essential for clarifying the mechanisms behind this inconsistency.
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Affiliation(s)
- Sayaka Tanaka
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan
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24
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Takumi S, Mitta S, Komura S, Ikeda TM, Matsunaka H, Sato K, Yoshida K, Murai K. Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars. PLoS One 2020; 15:e0228397. [PMID: 31986184 PMCID: PMC6984701 DOI: 10.1371/journal.pone.0228397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/14/2020] [Indexed: 12/03/2022] Open
Abstract
The breeding of agriculturally useful genes from wild crop relatives must take into account recent and future climate change. In Japan, the development of early heading wheat cultivars without the use of any major gene controlling the heading date is desired to avoid overlap of the harvesting time before the rainy season. Here, we backcrossed two early heading lines of a synthetic hexaploid wheat, derived from a crossing between durum wheat and the wild wheat progenitor Aegilops tauschii, with four Japanese elite cultivars to develop early heading lines of bread wheat. In total, nine early heading lines that showed a heading date two to eight days earlier than their parental cultivars in field conditions were selected and established from the selfed progenies of the two- or three-times backcrossed populations. The whole appearance and spike shape of the selected early heading lines looked like their parental wheat cultivars. The mature grains of the selected lines had the parental cultivars’ characteristics, although the grains exhibited longer and narrower shapes. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines. The introgression regions could shorten wheat heading date, and their chromosomal positions were dependent on the backcrossed wheat cultivars. Therefore, early heading synthetic hexaploid wheat is useful for fine-tuning of the heading date through introgression of Ae. tauschii chromosomal regions.
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Affiliation(s)
- Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
- * E-mail: (ST); (KM)
| | - Seito Mitta
- Fukui Prefectural University, Eiheiji, Yoshida, Fukui, Japan
| | - Shoya Komura
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Tatsuya M. Ikeda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Hiroshima, Japan
| | - Hitoshi Matsunaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Koji Murai
- Fukui Prefectural University, Eiheiji, Yoshida, Fukui, Japan
- * E-mail: (ST); (KM)
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25
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Fatima F, McCallum BD, Pozniak CJ, Hiebert CW, McCartney CA, Fedak G, You FM, Cloutier S. Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics. FRONTIERS IN PLANT SCIENCE 2020; 11:583738. [PMID: 33304363 PMCID: PMC7701059 DOI: 10.3389/fpls.2020.583738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/15/2020] [Indexed: 05/22/2023]
Abstract
Leaf rust caused by Puccinia triticina is the most widespread rust disease of wheat. As pathogen populations are constantly evolving, identification of novel sources of resistance is necessary to maintain disease resistance and stay ahead of this plant-pathogen evolutionary arms race. The wild genepool of wheat is a rich source of genetic diversity, accounting for 44% of the Lr genes identified. Here we performed a genome-wide association study (GWAS) on a diverse germplasm of 385 accessions, including 27 different Triticum and Aegilops species. Genetic characterization using the wheat 90 K array and subsequent filtering identified a set of 20,501 single nucleotide polymorphic (SNP) markers. Of those, 9,570 were validated using exome capture and mapped onto the Chinese Spring reference sequence v1.0. Phylogenetic analyses illustrated four major clades, clearly separating the wild species from the T. aestivum and T. turgidum species. GWAS was conducted using eight statistical models for infection types against six leaf rust isolates and leaf rust severity rated in field trials for 3-4 years at 2-3 locations in Canada. Functional annotation of genes containing significant quantitative trait nucleotides (QTNs) identified 96 disease-related loci associated with leaf rust resistance. A total of 21 QTNs were in haplotype blocks or within flanking markers of at least 16 known Lr genes. The remaining significant QTNs were considered loci that putatively harbor new Lr resistance genes. Isolation of these candidate genes will contribute to the elucidation of their role in leaf rust resistance and promote their usefulness in marker-assisted selection and introgression.
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Affiliation(s)
- Fizza Fatima
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curtis J. Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curt A. McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Sylvie Cloutier,
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26
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Michikawa A, Yoshida K, Okada M, Sato K, Takumi S. Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat. Mol Genet Genomics 2019; 294:1327-1341. [PMID: 31187273 DOI: 10.1007/s00438-019-01581-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/24/2019] [Indexed: 12/20/2022]
Abstract
A survey of genome-wide polymorphisms between closely related species is required to understand the molecular basis of the evolutionary differentiation of their genomes. Two wild diploid wheat species, namely Triticum monococcum ssp. aegilopoides and T. urartu, are closely related and harbour the Am and A genomes, respectively. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat subspecies aegilopoides. Although subspecies aegilopoides has been a useful genetic resource in wheat breeding, genome-wide molecular markers for this subspecies have not been sufficiently developed. Here, we describe the detection of genome-wide polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The SNPs and indels, detected using the A genome of common wheat as the reference genome, covered the entire chromosomes of these species. The polymorphism information facilitated a comparison of the genetic diversity of einkorn wheat with that of two related diploid Aegilops species, namely, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the addition of aegilopoides subspecies chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genomes. In addition, the CAPS markers permitted linkage map construction in mapping populations of aegilopoides subspecies accessions. Therefore, these RNA-seq data provide information for further breeding of closely related species with no reference genome sequence data.
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Affiliation(s)
- Asami Michikawa
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501, Japan.
| | - Moeko Okada
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Hyogo, 657-8501, Japan.
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