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Zhang J, Jie Y, Yan L, Wang M, Dong Y, Pang Y, Ren C, Song J, Chen X, Li X, Zhang P, Yang D, Zhang Y, Qi Z, Ru Z. Development and identification of a novel wheat-Thinopyrum ponticum disomic substitution line DS5Ag(5D) with new genes conferring resistance to powdery mildew and leaf rust. BMC PLANT BIOLOGY 2024; 24:718. [PMID: 39069623 DOI: 10.1186/s12870-024-05433-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Powdery mildew (caused by Blumeria graminis f. sp. tritici (Bgt)) and leaf rust (caused by Puccinia triticina (Pt)) are prevalent diseases in wheat (Triticum aestivum L.) production. Thinopyrum ponticum (2n = 10x = 70, EeEeEbEbExExStStStSt) contains genes that confer high levels of resistance to these diseases. RESULTS An elite wheat-Th. ponticum disomic substitution line, DS5Ag(5D), was developed in the Bainong Aikang 58 (AK58) background. The line was assessed using genomic in situ hybridization (GISH), oligo-nucleotide probe multiplex (ONPM) fluorescence in situ hybridization (FISH), and molecular markers. Twenty eight chromosome-specific molecular markers were identified for the alien chromosome, and 22 of them were co-dominant. Additionally, SNP markers from the wheat 660 K SNP chip were utilized to confirm chromosome identification and they provide molecular tools for tagging the chromosome in concern. The substitution line demonstrated high levels of resistance to powdery mildew throughout its growth period and to leaf rust at the adult stage. Based on the resistance evaluation of five F5 populations between the substitution lines and wheat genotypes with different levels of sensitivity to the two diseases. Results showed that the resistance genes located on 5Ag confered stable resistance against both diseases across different backgrounds. Resistance spectrum analysis combined with diagnostic marker detection of known resistance genes of Th. ponticum revealed that 5Ag contained two novel genes, Pm5Ag and Lr5Ag, which conferred resistance to powdery mildew and leaf rust, respectively. CONCLUSIONS In this study, a novel wheat-Th. ponticum disomic substitution line DS5Ag(5D) was successfully developed. The Th. ponticum chromosome 5Ag contain new resistance genes for powdery mildew and leaf rust. Chromosomic-specific molecular markers were generated and they can be used to track the 5Ag chromosome fragments. Consequently, this study provides new elite germplasm resources and molecular markers to facilitate the breeding of wheat varieties that is resistant to powdery mildew and leaf rust.
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Affiliation(s)
- Jinlong Zhang
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yize Jie
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Linjie Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Mengmeng Wang
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Yilong Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yunfei Pang
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Cuicui Ren
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Jie Song
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Xiangdong Chen
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Xiaojun Li
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Peipei Zhang
- College of Plant Protection, State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Dongyan Yang
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Yang Zhang
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Zhengang Ru
- School of Agriculture, Center of Wheat Research, Henan Key Laboratory of Hybrid Wheat, Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China.
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Niu J, Wang W, Wang Z, Chen Z, Zhang X, Qin Z, Miao L, Yang Z, Xie C, Xin M, Peng H, Yao Y, Liu J, Ni Z, Sun Q, Guo W. Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing. Genome Biol 2024; 25:171. [PMID: 38951917 PMCID: PMC11218387 DOI: 10.1186/s13059-024-03315-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources. RESULTS We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions. Key CNVb markers are linked with trait-associated introgressions, such as the 1RS·1BL translocation and 2NvS translocation, and the beneficial alleles, such as the end-use quality allele Glu-D1d (Dx5 + Dy10) and the semi-dwarf r-e-z allele. Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. We also develop a user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), for exploring the CNVb profiles over ever-increasing wheat accessions, and also propose a QR-code-like representation of individual digital CNVb fingerprint. This platform also allows uploading new CNVb profiles for comparison with stored varieties. CONCLUSIONS The CNVb-based approach provides a low-cost and high-throughput genotyping strategy for enabling digitalized wheat germplasm management and modern breeding with precise and practical decision-making.
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Affiliation(s)
- Jianxia Niu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Zhe Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoyu Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Pei D, Yu X, Fu W, Ma X, Fang J. The evolution and formation of centromeric repeats analysis in Vitis vinifera. PLANTA 2024; 259:99. [PMID: 38522063 DOI: 10.1007/s00425-024-04374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
MAIN CONCLUSION Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed. Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.
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Affiliation(s)
- Dan Pei
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xue Yu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weihong Fu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Ma
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Jinggui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China.
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He Y, He J, Zhao Y, Zhang S, Rao X, Wang H, Wang Z, Song A, Jiang J, Chen S, Chen F. Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution. Chromosome Res 2024; 32:5. [PMID: 38502277 DOI: 10.1007/s10577-024-09749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.
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Affiliation(s)
- Yanze He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Zhao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuangshuang Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Rao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haibin Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Zhenxing Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Aiping Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Jiafu Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Sumei Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China.
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Li H, Men W, Ma C, Liu Q, Dong Z, Tian X, Wang C, Liu C, Gill HS, Ma P, Zhang Z, Liu B, Zhao Y, Sehgal SK, Liu W. Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein. Nat Commun 2024; 15:2449. [PMID: 38503771 PMCID: PMC10951266 DOI: 10.1038/s41467-024-46814-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.
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Affiliation(s)
- Huanhuan Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Wenqiang Men
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Chao Ma
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Qianwen Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Zhenjie Dong
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, PR China
| | - Xiubin Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Chaoli Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250000, PR China
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, 264005, PR China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Yue Zhao
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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Jiang C, Liu X, Yang Z, Li G. Chromosome Rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting. PLANTS (BASEL, SWITZERLAND) 2023; 12:3268. [PMID: 37765432 PMCID: PMC10535892 DOI: 10.3390/plants12183268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
As a perennial herb in Triticeae, Elymus dahuricus is widely distributed in Qinghai-Tibetan Plateau and Central Asia. It has been used as high-quality fodders for improving degraded grassland. The genomic constitution of E. dahuricus (2n = 6x = 42) has been revealed as StStHHYY by cytological approaches. However, the universal karyotyping nomenclature system of E. dahuricus is not fully established by traditional fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). In this study, the non-denaturing fluorescent in situ hybridization (ND-FISH) using 14 tandem-repeat oligos could effectively distinguish the entire E. dahuricus chromosomes pairs, while Oligo-FISH painting by bulked oligo pools based on wheat-barley collinear regions combined with GISH analysis, is able to precisely determine the linkage group and sub-genomes of the individual E. dahuricus chromosomes. We subsequently established the 42-chromosome karyotype of E. dahuricus with distinctive chromosomal FISH signals, and characterized a new type of intergenomic rearrangement between 2H and 5Y. Furthermore, the comparative chromosomal localization of the centromeric tandem repeats and immunostaining by anti-CENH3 between cultivated barley (Hordeum vulgare L.) and E. dahuricus suggests that centromere-associated sequences in H subgenomes were continuously changing during the process of polyploidization. The precise karyotyping system based on ND-FISH and Oligo-FISH painting methods will be efficient for describing chromosomal rearrangements and evolutionary networks for polyploid Elymus and their related species.
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Affiliation(s)
| | | | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; (C.J.); (X.L.)
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; (C.J.); (X.L.)
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Xu S, Lyu Z, Zhang N, Li M, Wei X, Gao Y, Cheng X, Ge W, Li X, Bao Y, Yang Z, Ma X, Wang H, Kong L. Genetic mapping of the wheat leaf rust resistance gene Lr19 and development of translocation lines to break its linkage with yellow pigment. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:200. [PMID: 37639002 DOI: 10.1007/s00122-023-04425-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
KEY MESSAGE The leaf rust resistance gene Lr19, which is present on the long arm of chromosome 7E1 in Thinopyrum ponticum, was mapped within a 0.3-cM genetic interval, and translocation lines were developed to break its linkage with yellow pigmentation The leaf rust resistance locus Lr19, which was transferred to wheat (Triticum aestivum) from its relative Thinopyrum ponticum in 1966, still confers broad resistance to most known races of the leaf rust pathogen Puccinia triticina (Pt) worldwide. However, this gene has not previously been fine-mapped, and its tight linkage with a gene causing yellow pigmentation has limited its application in bread wheat breeding. In this study, we genetically mapped Lr19 using a bi-parental population from a cross of two wheat-Th. ponticum substitution lines, the Lr19-carrying line 7E1(7D) and the leaf rust-susceptible line 7E2(7D). Genetic analysis of the F2 population and the F2:3 families showed that Lr19 was a single dominant gene. Genetic markers allowed the gene to be mapped within a 0.3-cM interval on the long arm of Th. ponticum chromosome 7E1, flanked by markers XsdauK3734 and XsdauK2839. To reduce the size of the Th. ponticum chromosome segment carrying Lr19, the Chinese Spring Ph1b mutant was employed to promote recombination between the homoeologous chromosomes of the wheat chromosome 7D and the Th. ponticum chromosome 7E1. Two translocation lines with short Th. ponticum chromosome fragments carrying Lr19 were identified using the genetic markers closely linked to Lr19. Both translocation lines were resistant to 16 Pt races collected throughout China. Importantly, the linkage between Lr19 and yellow pigment content was broken in one of the lines. Thus, the Lr19 linked markers and translocation lines developed in this study are valuable resources in marker-assisted selection as part of common wheat breeding programs.
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Affiliation(s)
- Shoushen Xu
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhongfan Lyu
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Na Zhang
- College of Plant Protection, Technological Innovation Center for Biological Control Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071001, Hebei, People's Republic of China
| | - Mingzhu Li
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xinyi Wei
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Yuhang Gao
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xinxin Cheng
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Wenyang Ge
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xuefeng Li
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Yinguang Bao
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichun, People's Republic of China
| | - Xin Ma
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Hongwei Wang
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Lingrang Kong
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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9
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Zhao J, Li X, Qiao L, Zheng X, Wu B, Guo M, Feng M, Qi Z, Yang W, Zheng J. Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:37. [PMID: 36897407 DOI: 10.1007/s00122-023-04283-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.
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Affiliation(s)
- Jiajia Zhao
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaohua Li
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Meijun Guo
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
- Jinzhong University, Jinzhong, China
| | - Meichen Feng
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wude Yang
- College of Agriculture, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taigu, China.
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China.
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10
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Wu N, He Z, Fang J, Liu X, Shen X, Zhang J, Lei Y, Xia Y, He H, Liu W, Chu C, Wang C, Qi Z. Chromosome diversity in Dasypyrum villosum, an important genetic and trait resource for hexaploid wheat engineering. ANNALS OF BOTANY 2023; 131:185-198. [PMID: 35451455 PMCID: PMC9904354 DOI: 10.1093/aob/mcac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/20/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Dasypyrum villosum (2n = 2x = 14) harbours potentially beneficial genes for hexaploid and tetraploid wheat improvement. Highly diversified chromosome variation exists among and within accessions due to its open-pollination nature. The wheat-D. villosum T6VS·6AL translocation was widely used in breeding mainly because gene Pm21 in the 6VS segment conferred high and lasting powdery mildew resistance. However, the widespread use of this translocation may narrow the genetic base of wheat. A better solution is to utilize diversified D. villosum accessions as the genetic source for wheat breeding. Analysis of cytological and genetic polymorphisms among D. villosum accessions also provides genetic evolution information on the species. Using cytogenetic and molecular tools we analysed genetic polymorphisms among D. villosum accessions and developed consensus karyotypes to assist the introgression of beneficial genes from D. villosum into wheat. METHODS A multiplex probe of repeats for FISH, GISH and molecular markers were used to detect chromosome polymorphisms among D. villosum accessions. Polymorphic signal block types, chromosome heterogeneity and heterozygosity, and chromosome polymorphic information content were used in genetic diversity analysis. KEY RESULTS Consensus karyotypes of D. villosum were developed, and the homoeologous statuses of individual D. villosum chromosomes relative to wheat were determined. Tandem repeat probes of pSc119.2, (GAA)10 and the AFA family produced high-resolution signals and not only showed different signal patterns in D. villosum chromosomes but also revealed the varied distribution of tandem repeats among chromosomes and accessions. A total of 106 polymorphic chromosomes were identified from 13 D. villosum accessions and high levels of chromosomal heterozygosity and heterogeneity were observed. A subset of 56 polymorphic chromosomes was transferred into durum wheat through wide crosses, and seven polymorphic chromosomes are described in two newly developed durum-D. villosum amphidiploids. CONCLUSIONS Consensus karyotypes of D. villosum and oligonucleotide FISH facilitated identification of polymorphic signal blocks and a high level of chromosomal heterozygosity and heterogeneity among D. villosum accessions, seen in newly developed amphiploids. The abundant genetic diversity of D. villosum and range of alleles, exploitable through interploid crosses, backcrosses and recombination (chromosome engineering), allow introduction of biotic and abiotic stress resistances into wheat, translating into increasing yield, end-use quality and crop sustainability.
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Affiliation(s)
- Nan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziming He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaxin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xia Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhong Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yating Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Huagang He
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Chenggen Chu
- USDA-ARS, Sugarbeet & Potato Research Unit, Fargo, ND 58102, USA
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11
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Cheng M, Li X, Cui H, Sun H, Deng T, Song X, Song R, Wang T, Wang Z, Wang H, Wang X. FISH-based "pan" and "core" karyotypes reveal genetic diversification of Roegneria ciliaris. J Genet Genomics 2023; 50:135-138. [PMID: 35753677 DOI: 10.1016/j.jgg.2022.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Affiliation(s)
- Menghao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xingyue Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huimin Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tianshuo Deng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rongrong Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Tong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute/Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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12
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Zhao J, Zheng X, Qiao L, Yang C, Wu B, He Z, Tang Y, Li G, Yang Z, Zheng J, Qi Z. Genome-wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1447-1461. [PMID: 36345647 DOI: 10.1111/tpj.16023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome-wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a doubled haploid population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.
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Affiliation(s)
- Jiajia Zhao
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingwei Zheng
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Ling Qiao
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Chenkang Yang
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Bangbang Wu
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Ziming He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqing Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Jun Zheng
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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13
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Tomaszewska P, Schwarzacher T, Heslop-Harrison JS(P. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. FRONTIERS IN PLANT SCIENCE 2022; 13:1026364. [PMID: 36483968 PMCID: PMC9725029 DOI: 10.3389/fpls.2022.1026364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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14
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Shi P, Sun H, Liu G, Zhang X, Zhou J, Song R, Xiao J, Yuan C, Sun L, Wang Z, Lou Q, Jiang J, Wang X, Wang H. Chromosome painting reveals inter-chromosomal rearrangements and evolution of subgenome D of wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:55-67. [PMID: 35998122 DOI: 10.1111/tpj.15926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/16/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aegilops species represent the most important gene pool for breeding bread wheat (Triticum aestivum). Thus, understanding the genome evolution, including chromosomal structural rearrangements and syntenic relationships among Aegilops species or between Aegilops and wheat, is important for both basic genome research and practical breeding applications. In the present study, we attempted to develop subgenome D-specific fluorescence in situ hybridization (FISH) probes by selecting D-specific oligonucleotides based on the reference genome of Chinese Spring. The oligo-based chromosome painting probes consisted of approximately 26 000 oligos per chromosome and their specificity was confirmed in both diploid and polyploid species containing the D subgenome. Two previously reported translocations involving two D chromosomes have been confirmed in wheat varieties and their derived lines. We demonstrate that the oligo painting probes can be used not only to identify the translocations involving D subgenome chromosomes, but also to determine the precise positions of chromosomal breakpoints. Chromosome painting of 56 accessions of Ae. tauschii from different origins led us to identify two novel translocations: a reciprocal 3D-7D translocation in two accessions and a complex 4D-5D-7D translocation in one accession. Painting probes were also used to analyze chromosomes from more diverse Aegilops species. These probes produced FISH signals in four different genomes. Chromosome rearrangements were identified in Aegilops umbellulata, Aegilops markgrafii, and Aegilops uniaristata, thus providing syntenic information that will be valuable for the application of these wild species in wheat breeding.
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Affiliation(s)
- Peiyao Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Xu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jiawen Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Rongrong Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Li Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, MSU AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
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15
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Zhang W, Tang Z, Luo J, Li G, Yang Z, Yang M, Yang E, Fu S. Location of Tandem Repeats on Wheat Chromosome 5B and the Breakpoint on the 5BS Arm in Wheat Translocation T7BS.7BL-5BS Using Single-Copy FISH Analysis. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11182394. [PMID: 36145797 PMCID: PMC9502598 DOI: 10.3390/plants11182394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/05/2022] [Accepted: 09/12/2022] [Indexed: 06/13/2023]
Abstract
Wheat (Triticum aestivum L.) is rich in tandem repeats, and this is helpful in studying its karyotypic evolution. Some tandem repeats have not been assembled into the wheat genome sequence. Alignment using the blastn tool in the B2DSC web server indicated that the genomic sequence of 5B chromosome (IWGSC RefSeq v2.1) does not contain the tandem repeat pTa-275, and the tandem repeat (GA)26 distributed throughout the whole 5B chromosome. The nondenaturing fluorescence in situ hybridization (ND-FISH) using the oligonucleotide (oligo) probes derived from pTa-275 and (GA)26 indicated that one signal band of pTa-275 and two signal bands of (GA)26 appeared on the 5B chromosome of Chinese Spring wheat, indicating the aggregative distribution patterns of the two kinds of tandem repeats. Single-copy FISH indicated that the clustering region of pTa-275 and the two clustering regions of (GA)26 were located in ~160-201 Mb, ~153-157 Mb, and ~201-234 Mb intervals, respectively. Using ND-FISH and single-copy FISH technologies, the translocation breakpoint on the 5BS portion of the translocation T7BS.7BL-5BS, which exists widely in north-western European wheat cultivars, was located in the region from 157,749,421 bp to 158,555,080 bp (~0.8 Mb), and this region mainly contains retrotransposons, and no gene was found. The clustering regions of two kinds of tandem repeats on wheat chromosome 5B were determined and this will be helpful to improve the future sequence assembly of this chromosome. The sequence characteristics of the translocation breakpoint on the translocation T7BS.7BL-5BS obtained in this study are helpful to understand the mechanism of wheat chromosome translocation.
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Affiliation(s)
- Wei Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Manyu Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
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Men W, Fan Z, Ma C, Zhao Y, Wang C, Tian X, Chen Q, Miao J, He J, Qian J, Sehgal SK, Li H, Liu W. Mapping of the novel powdery mildew resistance gene Pm2Mb from Aegilops biuncialis based on ph1b-induced homoeologous recombination. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2993-3003. [PMID: 35831461 DOI: 10.1007/s00122-022-04162-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
A novel powdery mildew resistance gene Pm2Mb from Aegilops biuncialis was transferred into common wheat and mapped to chromosome 2MbL bin FL 0.49-0.66 by molecular cytogenetic analysis of 2Mb recombinants. Aegilops biuncialis, a wild relative of common wheat, is highly resistant to powdery mildew. Previous studies identified that chromosome 2Mb in Chinese Spring (CS)-Ae. biuncialis 2Mb disomic addition line TA7733 conferred high resistance to powdery mildew, and the resistance gene was temporarily designated as Pm2Mb. In this study, a total of 65 CS-Ae. biuncialis 2Mb recombinants were developed by ph1b-induced homoeologous recombination and they were grouped into 12 different types based on the presence of different markers of 2Mb-specificity. Segment sizes and breakpoints of each 2Mb recombinant type were further characterized using in situ hybridization and molecular marker analyses. Powdery mildew responses of each type were assessed by inoculation of each 2Mb recombinant-derived F2 progenies using the isolate E05. Combined analyses of in situ hybridization, molecular markers and powdery mildew resistance data of the 2Mb recombinants, the gene Pm2Mb was cytologically located to an interval of FL 0.49-0.66 in the long arm of 2Mb, where 19 2Mb-specific markers were located. Among the 65 2Mb recombinants, T-11 (T2DS.2DL-2MbL) and T-12 (Ti2DS.2DL-2MbL-2DL) contained a small 2MbL segment harboring Pm2Mb. Besides, a physical map of chromosome 2Mb was constructed with 70 2Mb-specific markers in 10 chromosomal bins and the map showed that submetacentric chromosome 2Mb of Ae. biuncialis was rearranged by a terminal intrachromosomal translocation. The newly developed 2Mb recombinants with powdery mildew resistance, the 2Mb-specific molecular markers and the physical map of chromosome 2Mb will benefit wheat disease breeding as well as fine mapping and cloning of Pm2Mb.
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Affiliation(s)
- Wenqiang Men
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Ziwei Fan
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Chao Ma
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Yue Zhao
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Chaoli Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiubin Tian
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Qifan Chen
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jingnan Miao
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jinqiu He
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jiajun Qian
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Huanhuan Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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17
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Zou Y, Luo J, Tang Z, Fu S. Variations of wheat ( Triticum aestivum L.) chromosomes caused by the 5A chromosomes with complex cytological structure. FRONTIERS IN PLANT SCIENCE 2022; 13:992934. [PMID: 36105696 PMCID: PMC9465395 DOI: 10.3389/fpls.2022.992934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
To study the effects of structural alterations of chromosomes caused by tandem repeats on the meiotic recombination, the wheat (Triticum aestivum L.) 5A chromosomes with different structure from ten wheat cultivars were used to investigate their meiotic recombination using non-denaturing fluorescence in situ hybridization (ND-FISH) technology. Fifteen cross combinations were carried out and they were divided into seven F1 categories. The structural difference between the intercalary regions of the long arms of the two 5A chromosomes (5AL) in the F1 categories III, VI, and VII was greater than that in the categories I and II, subsequently, the recombination frequencies in the distal regions of the 5AL arm in the progenies from the three categories were significantly lower than that from the categories I and II. For the two 5A chromosomes in the F1 categories VI and VII, the structural differences in the distal regions of both of the two arms were greater than that in the categories IV and V. So, the recombination frequencies in the intercalary region of the 5AL arm in the progeny from the categories IV and V were higher than that in the progeny from the categories VI and VII. The breakage of 5A chromosome together with the 5A translocations and the breakage of some other chromosomes were observed in the progeny from the F1 categories V, VI, and VII. These chromosomal variations were not observed in the progenies from the other four F1 categories. In conclusion, the smaller structural difference between the 5A chromosomes in distal regions of the two arms resulted in a higher recombination frequency in interstitial region and vice versa. The 5A chromosome with complex cytological structure can be used to induce genetic variations of wheat genome.
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Affiliation(s)
- Yang Zou
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Jie Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
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18
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Li M, Yuan Y, Ni F, Li X, Wang H, Bao Y. Characterization of Two Wheat- Thinopyrum ponticum Introgression Lines With Pyramiding Resistance to Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2022; 13:943669. [PMID: 35909780 PMCID: PMC9335053 DOI: 10.3389/fpls.2022.943669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew is one of the most devastating foliar diseases in wheat production. The wild relative Thinopyrum ponticum (2n = 10x = 70) has been widely used in wheat genetic improvement due to its superior resistance to both biotic and abiotic stresses. In the present study, two wheat-Th. ponticum introgression lines named SN0293-2 and SN0293-7 were developed from the progenies of a cross between the octoploid Trititrigia SNTE20 and common wheat, including the elite cultivar Jimai 22. They had a novel powdery mildew resistance gene (temporarily named PmSN0293) putatively from Th. ponticum pyramided with Pm2 and Pm52, exhibiting excellent Pm resistance at both the seedling and adult stages. Sequential GISH-FISH detected no signal of Th. ponticum in these two lines but a pair of T1BL·1RS in SN0293-2. Chromosomal structural variations were also observed obviously in SN0293-2 and SN0293-7. Through the Wheat 660K SNP array, 157 SNPs, 134 of which were on 6A, were found to be specific to Th. ponticum. Based on the data combined with DNA re-sequencing, seven specific markers, including one CAPS marker on 2B and six CAPS and Indel markers on 6A, were developed, confirming their wheat-Th. ponticum introgression nature. Furthermore, the two lines displayed positive plant height and produced more kernels and higher 1,000-grain weight. Excellent resistance with desirable agronomic traits makes them valuable in wheat breeding programs.
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Affiliation(s)
- Mingzhu Li
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
- Bureau of Agriculture and Rural Affairs of Linqing, Liaocheng, China
| | - Yuanyuan Yuan
- Crop Research Institute, Jinan Academy of Agricultural Sciences, Jinan, China
| | - Fei Ni
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
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19
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Türkösi E, Ivanizs L, Farkas A, Gaál E, Kruppa K, Kovács P, Szakács É, Szőke-Pázsi K, Said M, Cápal P, Griffiths S, Doležel J, Molnár I. Transfer of the ph1b Deletion Chromosome 5B From Chinese Spring Wheat Into a Winter Wheat Line and Induction of Chromosome Rearrangements in Wheat- Aegilops biuncialis Hybrids. FRONTIERS IN PLANT SCIENCE 2022; 13:875676. [PMID: 35769292 PMCID: PMC9234525 DOI: 10.3389/fpls.2022.875676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/09/2022] [Indexed: 06/10/2023]
Abstract
Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the Pairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of the Ph1 locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the original ph1b mutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, the ph1b mutation was transferred from two CSph1b mutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1 ph1b/ph1b exhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. The ph1b mutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialis F1 hybrids, predominantly with the Mb-genome chromosomes of Aegilops relative to those of the Ub genome. High frequency of wheat-Aegilops chromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialis amphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1b mutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.
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Affiliation(s)
- Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
- Institute of Genetics and Biotechnology, Szent István Campus, MATE, Gödöllő, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Mahmoud Said
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Giza, Egypt
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | | | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
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20
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Tian X, Chen Q, Ma C, Men W, Liu Q, Zhao Y, Qian J, Fan Z, Miao J, He J, Sehgal SK, Li H, Liu W. Development and Characterization of Triticum aestivum- Aegilops longissima 6S l Recombinants Harboring a Novel Powdery Mildew Resistance Gene Pm6Sl. FRONTIERS IN PLANT SCIENCE 2022; 13:918508. [PMID: 35720614 PMCID: PMC9201914 DOI: 10.3389/fpls.2022.918508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew of wheat is a foliar disease that is spread worldwide. Cultivation of resistant varieties is the most effective, economical, and environmentally friendly strategy to curb this disease. Powdery mildew resistance genes (Pm) are the primary resources for resistance breeding, and new Pm genes are in constant demand. Previously, we identified Aegilops longissima chromosome 6Sl#3 as a carrier of powdery mildew resistance and designated the resistance gene as Pm6Sl. Here, we reported the design of 24 markers specific to 6Sl#3 on the basis of the full-length cDNA sequences of 6Sl#3 donor Ae. longissma accession TA1910, and the development of wheat-Ae. longissima 6Sl#3 introgression stocks by ph1b-induced homoeologous recombination. Further, 6Sl#3 introgression lines were identified and characterized by integration analysis of powdery mildew responses, in situ hybridization, and molecular markers and Pm6Sl was mapped to a distal interval of 42.80 Mb between markers Ael58410 and Ael57699 in the long arm of 6Sl#3. Two resistant recombinants, R43 (T6BS.6BL-6Sl#3L) and T27 (Ti6AS.6AL-6Sl#3L-6AL), contained segments harboring Pm6Sl with less than 8% of 6Sl#3 genomic length, and two markers were diagnostic for Pm6Sl. This study broadened powdery mildew resistance gene resources for wheat improvement and provided a fundamental basis for fine mapping and cloning of Pm6Sl to further understand its molecular mechanism of disease resistance.
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Affiliation(s)
- Xiubin Tian
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qifan Chen
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chao Ma
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqiang Men
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qianqian Liu
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yue Zhao
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jiajun Qian
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Ziwei Fan
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jingnan Miao
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jinqiu He
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Huanhuan Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenxuan Liu
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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21
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Yang G, Tong C, Li H, Li B, Li Z, Zheng Q. Cytogenetic identification and molecular marker development of a novel wheat-Thinopyrum ponticum translocation line with powdery mildew resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2041-2057. [PMID: 35451594 DOI: 10.1007/s00122-022-04092-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
A new wheat-Thinopyrum ponticum translocation line with excellent powdery mildew resistance was produced, and alien-specific PCR markers and FISH probes were developed by SLAF-seq. Powdery mildew is one of the most threatening diseases in wheat production. Thinopyrum ponticum (Podp.) Barkworth and D. R. Dewey, as a wild relative, has been used for wheat genetic improvement for the better part of a century. In view of the good powdery mildew resistance of Th. ponticum, we have been working to transfer the resistance genes from Th. ponticum to wheat by creating translocation lines. In this study, a new wheat-Th. ponticum translocation line with excellent resistance and agronomic performance was developed and through seedling disease evaluation, gene postulation and diagnostic marker analysis proved to carry a novel Pm gene derived from Th. ponticum. Cytogenetic analysis revealed that a small alien segment was translocated to the terminal of chromosome 1D to form new translocation TTh-1DS·1DL chromosome. The translocation breakpoint was determined to lie in 21.5 Mb region of chromosome 1D by using Wheat660K SNP array analysis. Based on specific-locus amplified fragment sequencing (SLAF-seq) technology, eight molecular markers and one repetitive sequence probe were developed, which were specific for Th. ponticum. Fortunately, the probe could be used in distinguishing six alien chromosome pairs in partial amphiploid Xiaoyan 7430 by fluorescence in situ hybridization (FISH). Furthermore, a Thinopyrum-specific oligonucleotide probe was designed depending on the sequence information of the FISH probe. The novel translocation line could be used in wheat disease resistance breeding, and these specific markers and probes will enable wheat breeders to rapidly trace the alien genome with the novel Pm gene(s).
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Affiliation(s)
- Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 010022, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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22
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Wang Q, He Z, Wang L, Qi Z. 染色体工程在杂交小麦育种中的应用进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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He J, Zhao Y, Zhang S, He Y, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. Uneven Levels of 5S and 45S rDNA Site Number and Loci Variations across Wild Chrysanthemum Accessions. Genes (Basel) 2022; 13:genes13050894. [PMID: 35627279 PMCID: PMC9141308 DOI: 10.3390/genes13050894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosomal DNA (rDNA) is an excellent cytogenetic marker owing to its tandem arrangement and high copy numbers. However, comparative studies have focused more on the number of rDNA site variations within the Chrysanthemum genus, and studies on the types of rDNA sites with the same experimental procedures at the species levels are lacking. To further explore the number and types of rDNA site variations, we combined related data to draw ideograms of the rDNA sites of Chrysanthemum accessions using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). Latent variations (such as polymorphisms of 45S rDNA sites and co-localized 5S-45S rDNA) also occurred among the investigated accessions. Meanwhile, a significant correlation was observed between the number of 5S rDNA sites and chromosome number. Additionally, the clumped and concentrated geographical distribution of different ploidy Chrysanthemum accessions may significantly promote the karyotype evolution. Based on the results above, we identified the formation mechanism of rDNA variations. Furthermore, these findings may provide a reliable method to examine the sites and number of rDNA variations among Chrysanthemum and its related accessions and allow researchers to further understand the evolutionary and phylogenetic relationships of the Chrysanthemum genus.
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24
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Luo J, Liao R, Duan Y, Fu S, Tang Z. Variations of subtelomeric tandem repeats and rDNA on chromosome 1RS arms in the genus Secale and 1BL.1RS translocations. BMC PLANT BIOLOGY 2022; 22:212. [PMID: 35468732 PMCID: PMC9036760 DOI: 10.1186/s12870-022-03598-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The wheat-rye 1BL.1RS translocations have played an important role in common wheat breeding programs. Subtelomeric tandem repeats have been often used to investigate polymorphisms of 1RS arms, but further research about their organizations on the 1RS chromosome is needed. RESULTS 162 1RS arms from a wild rye species (Secale strictum) and six cultivated rye accessions (Secale cereale L.) (81 plants), 102 1BL.1RS and one 1AL.1RS translocations were investigated using oligo probes Oligo-TaiI, Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250, which were derived from tandem repeats TaiI, pSc119.2, pTa71, pSc200 and pSc250, respectively. The variations of 1RS arms were revealed by signal intensity of probes Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250. Proliferation of rDNA sequences on the 1RS chromosomes was observed. According to the presence of probe signals, 34, 127 and 144 of the 162 1RS arms contained TaiI, pSc200 and pSc250, respectively, and all of them contained pSc119.2 and pTa71. Most of the 1RS arms in rye contained three kinds of subtelomeric tandem repeats, the combination of pSc119.2, pSc200 and pSc250 was most common, and only eight of them contained TaiI, pSc119.2, pSc200 and pSc250. All of the 1RS arms in 1BL.1RS and 1AL.1RS translocations contained pSc119.2, pTa71, pSc200 and pSc250, but the presence of the TaiI family was not observed. CONCLUSION New organizations of subtelomeric tandem repeats on 1RS were found, and they reflected new genetic variations of 1RS arms. These 1RS arms might contain abundant allelic diversity for agricultural traits. The narrow genetic base of 1RS arms in 1BL.1RS and 1AL.1RS translocations currently used in agriculture is seriously restricting their use in wheat breeding programs. This research has found new 1RS sources for the future restructuring of 1BL.1RS translocations. The allelic variations of these 1RS arms should be studied more intensely as they may enrich the genetic diversity of 1BL.1RS translocations.
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Affiliation(s)
- Jie Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Ruiying Liao
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yanling Duan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China.
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China.
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Yang Z, Wang Z, Wang W, Xie X, Chai L, Wang X, Feng X, Li J, Peng H, Su Z, You M, Yao Y, Xin M, Hu Z, Liu J, Liang R, Ni Z, Sun Q, Guo W. ggComp enables dissection of germplasm resources and construction of a multiscale germplasm network in wheat. PLANT PHYSIOLOGY 2022; 188:1950-1965. [PMID: 35088857 PMCID: PMC8968352 DOI: 10.1093/plphys/kiac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/10/2021] [Indexed: 05/31/2023]
Abstract
Accurate germplasm characterization is a vital step for accelerating crop genetic improvement, which remains largely infeasible for crops such as bread wheat (Triticum aestivum L.), which has a complex genome that undergoes frequent introgression and contains many structural variations. Here, we propose a genomic strategy called ggComp, which integrates resequencing data with copy number variations and stratified single-nucleotide polymorphism densities to enable unsupervised identification of pairwise germplasm resource-based Identity-By-Descent (gIBD) blocks. The reliability of ggComp was verified in wheat cultivar Nongda5181 by dissecting parental-descent patterns represented by inherited genomic blocks. With gIBD blocks identified among 212 wheat accessions, we constructed a multi-scale genomic-based germplasm network. At the whole-genome level, the network helps to clarify pedigree relationship, demonstrate genetic flow, and identify key founder lines. At the chromosome level, we were able to trace the utilization of 1RS introgression in modern wheat breeding by hitchhiked segments. At the single block scale, the dissected germplasm-based haplotypes nicely matched with previously identified alleles of "Green Revolution" genes and can guide allele mining and dissect the trajectory of beneficial alleles in wheat breeding. Our work presents a model-based framework for precisely evaluating germplasm resources with genomic data. A database, WheatCompDB (http://wheat.cau.edu.cn/WheatCompDB/), is available for researchers to exploit the identified gIBDs with a multi-scale network.
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Affiliation(s)
| | | | | | - Xiaoming Xie
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xibo Feng
- Tibet Key Experiments of Crop Cultivation and Farming/College of Plant Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China
| | - Jinghui Li
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Wheat Center, Henan Institute of Science and Technology/Henan Provincial Key Laboratory of Hybrid Wheat, Xinxiang 453003, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Rongqi Liang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Zhong YH, Zheng YF, Xue YX, Wang LJ, Zhang JW, Li DL, Wang J. Variation of Chromosome Composition in a Full-Sib Population Derived From 2x × 3x Interploidy Cross of Populus. FRONTIERS IN PLANT SCIENCE 2022; 12:816946. [PMID: 35154214 PMCID: PMC8825477 DOI: 10.3389/fpls.2021.816946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Interploidy cross commonly results in complex chromosome number and structural variations. In our previous study, a progeny with segregated ploidy levels was produced by an interploidy cross between diploid female parent Populus tomentosa × Populus bolleana clone TB03 and triploid male parent Populus alba × Populus berolinensis 'Yinzhong'. However, the chromosome compositions of aneuploid genotypes in the progeny were still unclear. In the present study, a microsatellite DNA allele counting-peak ratios (MAC-PR) method was employed to analyze allelic configurations of each genotype to clarify their chromosome compositions, while 45S rDNA fluorescence in situ hybridization (FISH) analysis was used to reveal the mechanism of chromosome number variation. Based on the MAC-PR analysis of 47 polymorphic simple sequence repeat (SSR) markers distributed across all 19 chromosomes of Populus, both chromosomal number and structural variations were detected for the progeny. In the progeny, 26 hypo-triploids, 1 hyper-triploid, 16 hypo-tetraploids, 10 tetraploids, and 5 hyper-tetraploids were found. A total of 13 putative structural variation events (duplications and/or deletions) were detected in 12 genotypes, involved in chromosomes 3, 6, 7, 14, 15, 16, and 18. The 46.2% (six events) structural variation events occurred on chromosome 6, suggesting that there probably is a chromosome breakpoint near the SSR loci of chromosome 6. Based on calculation of the allelic information, the transmission of paternal heterozygosity in the hypo-triploids, hyper-triploid, hypo-tetraploids, tetraploids, and hyper-tetraploids were 0.748, 0.887, 0.830, 0.833, and 0.836, respectively, indicating that the viable pollen gains of the male parent 'Yinzhong' were able to transmit high heterozygosity to progeny. Furthermore, 45S rDNA-FISH analysis showed that specific-chromosome segregation feature during meiosis and chromosome appointment in normal and fused daughter nuclei of telophase II of 'Yinzhong,' which explained that the formation of aneuploids and tetraploids in the progeny could be attributed to imbalanced meiotic chromosomal segregation and division restitution of 'Yinzhong,' The data of chromosomal composition and structural variation of each aneuploid in the full-sib progeny of TB03 × 'Yinzhong' lays a foundation for analyzing mechanisms of trait variation relying on chromosome or gene dosages in Populus.
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Affiliation(s)
- Yu-Hang Zhong
- National Engineering Research Center of Tree Breeding and Ecological Remediation, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun-Fei Zheng
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yin-Xuan Xue
- National Engineering Research Center of Tree Breeding and Ecological Remediation, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lv-Ji Wang
- National Engineering Research Center of Tree Breeding and Ecological Remediation, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jin-Wang Zhang
- Forestry and Grassland Research Institute of Tongliao City, Tongliao, China
| | - Dai-Li Li
- Beijing Institute of Landscape Architecture, Beijing, China
| | - Jun Wang
- National Engineering Research Center of Tree Breeding and Ecological Remediation, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, MOE, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Zhang S, Du P, Lu X, Fang J, Wang J, Chen X, Chen J, Wu H, Yang Y, Tsujimoto H, Chu C, Qi Z. Frequent numerical and structural chromosome changes in early generations of synthetic hexaploid wheat. Genome 2021; 65:205-217. [PMID: 34914567 DOI: 10.1139/gen-2021-0074] [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
Modern hexaploid wheat (Triticum aestivum L.; AABBDD) evolved from a hybrid of tetraploid wheat (closely related to Triticum turgidum L. ssp. durum (Desf.) Husn., AABB) and goatgrass (Aegilops tauschii Coss., DD). Variations in chromosome structure and ploidy played important roles in wheat evolution. How these variations occurred and their role in expanding the genetic diversity in modern wheat is mostly unknown. Synthetic hexaploid wheat (SHW) can be used to investigate chromosome variation that occurs during the early generations of existence. SHW lines derived by crossing durum wheat 'Langdon' with twelve Ae. tauschii accessions were analyzed using oligonucelotide probe multiplex fluorescence in situ hybridization (FISH) to metaphase chromosomes and SNP markers. Cluster analysis based on SNP markers categorized them into three groups. Among 702 plants from the S8 and S9 generations, 415 (59.12%) carried chromosome variations involving all 21 chromosomes but with different frequencies for each chromosome and sub-genome. Total chromosome variation frequencies varied between lines, but there was no significant difference among the three groups. The non-random chromosome variations in SHW lines detected in this research may be an indication that similar variations occurred in the early stages of wheat polyploidization and played important roles in wheat evolution.
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Affiliation(s)
- Siyu Zhang
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Pei Du
- Henan Academy of Agricultural Sciences, 74728, Henan Academy of Crop Molecular Breeding, Zhengzhou, Henan, China;
| | - Xueying Lu
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jiaxin Fang
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jiaqi Wang
- Nanjing Agricultural University, 70578, Weigang No.1, Nanjing, Jiangsu, China, 210095;
| | - Xuejun Chen
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Jianyong Chen
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Hao Wu
- Nanjing Agricultural University, 70578, Nanjing, Jiangsu, China;
| | - Yang Yang
- Zaozhuang University, 372543, Zaozhuang, Shandong, China;
| | - Hisashi Tsujimoto
- Tottori University, 13114, Arid Land Research Center, Hamasaka, Tottori, Japan;
| | - Chenggen Chu
- USDA ARS, 17123, Fargo, North Dakota, United States;
| | - Zengjun Qi
- Nanjing Agricultural University, 70578, Weigang 1,Nanjing, Nanjing, China, 210095;
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Wang Y, Cheng X, Yang X, Wang C, Zhang H, Deng P, Liu X, Chen C, Ji W, Wang Y. Molecular cytogenetics for a wheat-Aegilops geniculata 3M g alien addition line with resistance to stripe rust and powdery mildew. BMC PLANT BIOLOGY 2021; 21:575. [PMID: 34872505 PMCID: PMC8647465 DOI: 10.1186/s12870-021-03360-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Aegilops geniculata Roth is closely related to common wheat (Triticum aestivum L.) and is a valuable genetic resource for improvement of wheat. RESULTS In this study, the W19513 line was derived from the BC1F10 progeny of a cross between wheat 'Chinese Spring' and Ae. geniculata SY159. Cytological examination showed that W19513 contained 44 chromosomes. Twenty-two bivalents were formed at the first meiotic metaphase I in the pollen mother cellsand the chromosomes were evenly distributed to opposite poles at meiotic anaphase I. Genomic in situ hybridization demonstrated that W19513 carried a pair of alien chromosomes from the M genome. Fluorescence in situ hybridization confirmed detection of variation in chromosomes 4A and 6B. Functional molecular marker analysis using expressed sequence tag-sequence-tagged site and PCR-based landmark unique gene primers revealed that the alien gene belonged to the third homologous group. The marker analysis confirmed that the alien chromosome pair was 3Mg. In addition, to further explore the molecular marker specificity of chromosome 3Mg, based on the specific locus amplified fragment sequencing technique, molecular markers specific for W19513 were developed with efficiencies of up to 47.66%. The W19513 line was inoculated with the physiological race E09 of powdery mildew (Blumeria graminis f. sp. tritici) at the seedling stage and showed moderate resistance. Field inoculation with a mixture of the races CYR31, CYR32, CYR33, and CYR34 of the stripe rust fungus (Puccinia striiformis f. sp. triticii) revealed that the line W19513 showed strong resistance. CONCLUSIONS This study provides a foundation for use of the line W19513 in future genetic research and wheat improvement.
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Affiliation(s)
- Yongfu Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaofang Cheng
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoying Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Changyou Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China
| | - Hong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China
| | - Pingchuan Deng
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China
| | - Xinlun Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China
| | - Chunhuan Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China.
| | - Yajuan Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100, China.
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Li H, Tian X, Pei S, Men W, Ma C, Sehgal SK, Zhao Y, Chen Q, Wang B, Dong Z, Xiang Z, Friebe B, Liu W. Development of Novel Wheat- Aegilops longissima 3S 1 Translocations Conferring Powdery Mildew Resistance and Specific Molecular Markers for Chromosome 3S 1. PLANT DISEASE 2021; 105:2938-2945. [PMID: 33787309 DOI: 10.1094/pdis-12-20-2691-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Powdery mildew of wheat, caused by Blumeria graminis f. sp. tritici, is a destructive disease of common wheat. Cultivation of resistant varieties is the most cost-effective disease management strategy. Previous studies reported that chromosome 3Sl#2 present in Chinese Spring (CS)-Aegilops longissima 3Sl#2(3B) disomic substitution line TA3575 conferred resistance to powdery mildew. In this study, we further located the powdery mildew resistance gene(s) to the short arm of chromosome 3Sl#2 (3Sl#2S) by evaluating for B. graminis f. sp. tritici resistance of newly developed CS-Ae. longissima 3Sl#2 translocation lines. Meanwhile, TA7545, a previously designated CS-Ae. longissima 3Sl#3 disomic addition line, was reidentified as an isochromosome 3Sl#3S addition line and evaluated to confer resistance to powdery mildew, thus locating the resistance gene(s) to the short arm of chromosome 3Sl#3 (3Sl#3S). Based on transcriptome sequences of TA3575, 10 novel chromosome 3SlS-specific markers were developed, of which 5 could be used to distinguish between 3Sl#2S and 3Sl#3S derived from Ae. longissima accessions TL20 and TA1910 (TAM4) and the remaining 5 could identify both 3Sl#2S and 3Sl#3S. Also, CL897, one of five markers specific to both 3Sl#2S and 3Sl#3S, could be used to detect Pm13 located at chromosome 3Sl#1S from Ae. longissima accession TL01 in diverse wheat genetic backgrounds. The powdery mildew resistance genes on chromosomes 3Sl#2S and 3Sl#3S, the CS-Ae. longissima 3Sl#2 translocation lines, and the 3SlS-specific markers developed in this study will facilitate the transfer of B. graminis f. sp. tritici resistance genes into common wheat and provide new germplasm resources for powdery mildew resistance breeding.
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Affiliation(s)
- Huanhuan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiubin Tian
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Shaolong Pei
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenqiang Men
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007 U.S.A
| | - Yue Zhao
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Qifan Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Beilin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenjie Dong
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhiguo Xiang
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Bernd Friebe
- Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506 U.S.A
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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Li M, Wang Y, Liu X, Li X, Wang H, Bao Y. Molecular Cytogenetic Identification of a Novel Wheat- Thinopyrum ponticum 1J S (1B) Substitution Line Resistant to Powdery Mildew and Leaf Rust. FRONTIERS IN PLANT SCIENCE 2021; 12:727734. [PMID: 34659293 PMCID: PMC8519347 DOI: 10.3389/fpls.2021.727734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Thinopyrum ponticum (2n = 10x = 70) is a wild relative of wheat with high tolerance to both biotic and abiotic stresses; it has been wildly used in wheat genetic improvement. A disomic substitution line named SN19647 was derived from a cross between Triticum aestivum and the wheat-Th. ponticum partial amphiploid SNTE20 (2n = 8x = 56). It was evaluated for disease resistance and characterized via sequential fluorescence in situ hybridization (FISH)-genomic in situ hybridization (GISH) and molecular markers. The results showed that SN19647 carried resistance to both powdery mildew and leaf rust. It contained 42 chromosomes with a pair of wheat chromosome 1B replaced by a pair of JS chromosomes from Th. ponticum. In addition to chromosomal substitution events, structural variation also occurred on wheat chromosomes 2A, 5A, 6B, and 7B. Based on marker analysis, 19 markers specific to the JS chromosome were obtained, of which seventeen markers belonged to homoeologous group one. These results indicated that SN19647 was a 1JS (1B) substitution line. Compared with the known 1JS (1D) substitution line CH10A5, it was found that 17 markers generated different specific bands to Th. ponticum, confirming the novelty of the 1JS chromosome in SN19647. Therefore, SN19647, resistant to powdery mildew and leaf rust, was a novel 1JS (1B) substitution line that can be used in wheat genetic improvement.
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Affiliation(s)
- Mingzhu Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaojuan Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
- Agronomy College of Shandong Agricultural University, Tai'an, China
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Zou Y, Wan L, Luo J, Tang Z, Fu S. FISH landmarks reflecting meiotic recombination and structural alterations of chromosomes in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2021; 21:167. [PMID: 33823797 PMCID: PMC8025513 DOI: 10.1186/s12870-021-02947-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND DNA sequence composition affects meiotic recombination. However, the correlation between tandem repeat composition and meiotic recombination in common wheat (Triticum aestivum L.) is unclear. RESULTS Non-denaturing fluorescent in situ hybridization (ND-FISH) with oligonucleotide (oligo) probes derived from tandem repeats and single-copy FISH were used to investigate recombination in three kinds of the long arm of wheat 5A chromosome (5AL). 5AL535-18/275 arm carries the tandem repeats pTa-535, Oligo-18, and pTa-275, 5AL119.2-18/275 arm carries the tandem repeats pSc119.2, Oligo-18 and pTa-275, and 5AL119.2 arm carries the tandem repeats pSc119.2. In the progeny of 5AL535-18/275 × 5AL119.2, double recombination occurred between pSc119.2 and pTa-535 clusters (119-535 interval), and between pTa-535 and Oligo-18/pTa-275 clusters (535-18 interval). The recombination rate in the 119-535 interval in the progeny of 5AL535-18/275 × 5AL119.2-18/275 was higher than that in the progeny of 5AL535-18/275 × 5AL119.2. Recombination in the 119-535 interval produced 5AL119 + 535 segments with pTa-535 and pSc119.2 tandem repeats and 5ALNo segments without these repeats. The 5AL119 + 535 and 5ALNo segments were localized between the signal sites of the single-copy probes SC5A-479 and SC5A-527. The segment between SC5A-479 and SC5A-527 in the metaphase 5ALNo was significantly longer than that in the metaphase 5AL119 + 535. CONCLUSION The structural variations caused by tandem repeats might be one of the factors affecting meiotic recombination in wheat. Meiotic recombination aggregated two kinds of tandemly repeated clusters into the same chromosome, making the metaphase chromosome more condensed. To conclude, our study provides a robust tool to measure meiotic recombination and select parents for wheat breeding programs.
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Affiliation(s)
- Yang Zou
- College of Agronomy, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, 611130, Sichuan, China
| | - Linrong Wan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, 611130, Sichuan, China
| | - Jie Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, 611130, Sichuan, China
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
- Institute of Ecological Agriculture, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, 611130, Sichuan, China.
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, 611130, Sichuan, China.
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Wu N, Lei Y, Pei D, Wu H, Liu X, Fang J, Guo J, Wang C, Guo J, Zhang J, Liu A, Wen M, Qi Z, Yang X, Bie T, Chu C, Zhou B, Chen P. Predominant wheat-alien chromosome translocations in newly developed wheat of China. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:30. [PMID: 37309352 PMCID: PMC10236125 DOI: 10.1007/s11032-021-01206-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/15/2021] [Indexed: 06/14/2023]
Abstract
Founder wheat lines have played key role in Chinese wheat improvement. Wheat-Dasypyrum villosum translocation T6VS·6AL has been widely used in wheat breeding in recent years due to its high level of powdery mildew resistance and other beneficial genes. Reference oligo-nucleotide multiplex probe (ONMP)-FISH karyotypes of six T6VS·6AL donor lines were developed and used for characterizing 32 derivative cultivars and lines. T6VS·6AL was present in 27 cultivar/lines with 20 from southern China. Next, ONMP-FISH was used to study chromosome constitution of randomly collected wheat cultivars and advanced breeding lines from southern and northern regions of China: 123 lines from the regional test plots of southern China and 110 from northern China. In southern China, T6VS·6AL (35.8%) was the most predominant variation, while T1RS·1BL (27.3%) was the most predominant in northern China. The pericentric inversion perInv 6B derived from its founder wheat Funo and Abbondaza was the second most predominant chromosome variant in both regions. Other chromosome variants were present in very low frequencies. Additionally, 167 polymorphic chromosome types were identified. Based on these variations, 271 cultivars and lines were clustered into three groups, including southern, northern, and mixed groups that contained wheat from both regions. Different dominant chromosome variations were seen, indicating chromosome differentiation in the three groups of wheat. The clearly identified wheat lines with T6VS·6AL in different backgrounds and oligonucleotide probe set will facilitate their utilization in wheat breeding and in identifying other beneficial traits that may be linked to this translocation. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01206-3.
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Affiliation(s)
- Nan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yanhong Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dan Pei
- Horticulture College, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiaxin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiangtao Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Conglei Wang
- Tianjin Crops Research Institute, Tianjin, 300384 China
| | - Jie Guo
- Agriculture College, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Jinlong Zhang
- Henan Institute of Science and Technology, Xinxiang, 453003 China
| | - Aifeng Liu
- Crop Institute, Shandong Academy of Agriculture Science, Jinan, 2501000 China
| | - Mingxing Wen
- Zhenjiang Institute of Agricultural Sciences, Jurong, 212400 Jiangsu China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xueming Yang
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Tongde Bie
- Yangzhou Academy of Agricultural Sciences, Yangzhou, 225007 China
| | - Chenggen Chu
- USDA - ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Bo Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Peidu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Fu L, Wang Q, Li L, Lang T, Guo J, Wang S, Sun Z, Han S, Huang B, Dong W, Zhang X, Du P. Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut. BMC PLANT BIOLOGY 2021; 21:107. [PMID: 33610178 PMCID: PMC7896385 DOI: 10.1186/s12870-021-02875-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. RESULTS A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. CONCLUSIONS The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.
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Affiliation(s)
- Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Qian Wang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Lina Li
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Tao Lang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Junjia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Siyu Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Ziqi Sun
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Suoyi Han
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.
| | - Pei Du
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.
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Li G, Zhang T, Yu Z, Wang H, Yang E, Yang Z. An efficient Oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:978-993. [PMID: 33210785 DOI: 10.1111/tpj.15081] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/25/2020] [Accepted: 11/09/2020] [Indexed: 05/07/2023]
Abstract
A chromosome-specific painting technique has been developed which combines the most recent approaches of the companion disciplines of molecular cytogenetics and genome research. We developed seven oligonucleotide (oligo) pools derivd from single-copy sequences on chromosomes 1 to 7 of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The seven groups of pooled oligos comprised between 10 986 and 12 496 45-bp monomers, and these then produced stable fluorescence in situ hybridization (FISH) signals on chromosomes of each linkage group of wheat and barley. The pooled oligo probes were applied to high-throughput karyotyping of the chromosomes of other Triticeae species in the genera Secale, Aegilops, Thinopyrum, and Dasypyrum, and the study also extended to some wheat-alien amphiploids and derived lines. We demonstrated that a complete set of whole-chromosome oligo painting probes facilitated the study of inter-species chromosome homologous relationships and visualized non-homologous chromosomal rearrangements in Triticeae species and some wheat-alien species derivatives. When combined with other non-denaturing FISH procedures using tandem-repeat oligos, the newly developed oligo painting techniques provide an efficient tool for the study of chromosome structure, organization, and evolution among any wild Triticeae species with non-sequenced genomes.
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Affiliation(s)
- Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Zhihui Yu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Hongjin Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
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35
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Yu Z, Wang H, Jiang W, Jiang C, Yuan W, Li G, Yang Z. Karyotyping Dasypyrum breviaristatum chromosomes with multiple oligonucleotide probes reveals the genomic divergence in Dasypyrum. Genome 2021; 64:789-800. [PMID: 33513072 DOI: 10.1139/gen-2020-0147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The perennial species Dasypyrum breviaristatum (genome Vb) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of D. breviaristatum chromosomes will be useful for the detection of Dasypyrum chromatin in wheat background. We established the standard karyotype of 1Vb-7Vb chromosomes through nondenaturing fluorescence in situ hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat - D. breviaristatum partial amphiploid TDH-2 (AABBVbVb) and newly identified wheat - D. breviaristatum disomic translocation and addition lines D2138 (6VbS.2VbL), D2547 (4Vb), and D2532 (3VbS.6VbL) by comparative molecular marker analysis. The ND-FISH with multiple oligo probes was conducted on the durum wheat - D. villosum amphiploid TDV-1 and large karyotype differences between D. breviaristatum and D. villosum was revealed. These ND-FISH probes will be valuable for screening the wheat - Dasypyrum derivative lines for chromosome identification, and the newly developed wheat - D. breviaristatum addition lines may broaden the gene pool of wheat breeding. The differences between D. villosum and D. breviaristatum chromosomes revealed by ND-FISH will help us understand evolutionary divergence of repetitive sequences within the genus Dasypyrum.
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Affiliation(s)
- Zhihui Yu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
| | - Hongjin Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
| | - Wenxi Jiang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
| | - Chengzhi Jiang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
| | - Weiguang Yuan
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.,Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China
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He J, Lin S, Yu Z, Song A, Guan Z, Fang W, Chen S, Zhang F, Jiang J, Chen F, Wang H. Identification of 5S and 45S rDNA sites in Chrysanthemum species by using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). Mol Biol Rep 2021; 48:21-31. [PMID: 33454907 DOI: 10.1007/s11033-020-06102-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a conventional method used to visualize the distribution of DNA elements within a genome. To examine the relationships within the Chrysanthemum genus, ribosomal DNA (rDNA), a popular cytogenetic marker, was utilized as a probe for FISH within this genus. Based on the genome data of Chrysanthemum nankingense, C. seticuspe and its allied genera in the Compositae(Asteraceae), we explored rDNA sequences to design oligonucleotide probes and perform oligonucleotide fluorescence in situ hybridization (Oligo-FISH) in eight Chrysanthemum accessions. The results showed that the majority of 5S rDNA signals were located in subterminal chromosome regions and that the number of 5S rDNA sites might be tightly associated with ploidy. For 45S rDNA sites, the number and intensity of signals differed from those of previously investigated Chrysanthemum resources. These findings may provide an optimally reliable method of examining the chromosome composition and structural variation of Chrysanthemum and its related species and allow researchers to understand the evolutionary history and phylogenetic relationships of Chrysanthemum.
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Affiliation(s)
- Jun He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sisi Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhongyu Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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37
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Li J, Li J, Cheng X, Zhao L, Yang Z, Wu J, Yang Q, Chen X, Zhao J. Molecular Cytogenetic and Agronomic Characterization of the Similarities and Differences Between Wheat- Leymus mollis Trin. and Wheat- Psathyrostachys huashanica Keng 3Ns (3D) Substitution Lines. FRONTIERS IN PLANT SCIENCE 2021; 12:644896. [PMID: 33897735 PMCID: PMC8061751 DOI: 10.3389/fpls.2021.644896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/23/2021] [Indexed: 05/12/2023]
Abstract
Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) and Leymus mollis Trin. (2n = 4x = 28, NsNsXmXm) are valuable resources for wheat breeding improvement as they share the Ns genome, which contains diverse resistance genes. To explore the behaviors and traits of Ns chromosomes from the two species in wheat background, a series of wheat-P. huashanica and wheat-L. mollis substitution lines were developed. In the present study, line DH109 (F7 progeny of wheat-P. huashanica heptaploid line H8911 × durum wheat Trs-372) and line DM131 (F8 progeny of wheat-L. mollis octoploid line M842 × durum wheat Trs-372) were selected. Cytological observation combined with genomic in situ hybridization experiments showed that DH109 and DM131 each had 20 pairs of wheat chromosomes plus a pair of alien chromosomes (Ns chromosome), and the pair of alien chromosomes showed stable inheritance. Multiple molecular markers and wheat 55K SNP array demonstrated that a pair of wheat 3D chromosome in DH109 and in DM131 was substituted by a pair of P. huashanica 3Ns chromosome and a pair of L. mollis 3Ns chromosome, respectively. Fluorescence in situ hybridization (FISH) analysis confirmed that wheat 3D chromosomes were absent from DH109 and DM131, and chromosomal FISH karyotypes of wheat 3D, P. huashanica 3Ns, and L. mollis 3Ns were different. Moreover, the two lines had many differences in agronomic traits. Comparing with their wheat parents, DH109 expressed superior resistance to powdery mildew and fusarium head blight, whereas DM131 had powdery mildew resistance, longer spike, and more tiller number. Therefore, Ns genome from P. huashanica and L. mollis might have some different effects. The two novel wheat-alien substitution lines provide new ideas and resources for disease resistance and high-yield breeding on further utilization of 3Ns chromosomes of P. huashanica or L. mollis.
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Affiliation(s)
- Jiachuang Li
- Shaanxi Key Laboratory of Plant Genetic Engineering Breeding, College of Agronomy, Northwest A&F University, Xianyang, China
| | - Jiaojiao Li
- Shaanxi Key Laboratory of Plant Genetic Engineering Breeding, College of Agronomy, Northwest A&F University, Xianyang, China
| | - Xueni Cheng
- College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Li Zhao
- Shaanxi Key Laboratory of Plant Genetic Engineering Breeding, College of Agronomy, Northwest A&F University, Xianyang, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Wu
- Shaanxi Key Laboratory of Plant Genetic Engineering Breeding, College of Agronomy, Northwest A&F University, Xianyang, China
| | - Qunhui Yang
- Shaanxi Key Laboratory of Plant Genetic Engineering Breeding, College of Agronomy, Northwest A&F University, Xianyang, China
| | - Xinhong Chen
- Shaanxi Key Laboratory of Plant Genetic Engineering Breeding, College of Agronomy, Northwest A&F University, Xianyang, China
- *Correspondence: Xinhong Chen,
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Xianyang, China
- Jixin Zhao,
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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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Li H, Dong Z, Ma C, Xia Q, Tian X, Sehgal S, Koo DH, Friebe B, Ma P, Liu W. A spontaneous wheat-Aegilops longissima translocation carrying Pm66 confers resistance to powdery mildew. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1149-1159. [PMID: 31932954 DOI: 10.1007/s00122-020-03538-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 01/03/2020] [Indexed: 05/07/2023]
Abstract
A spontaneous Robertsonian T4SlS·4BL translocation chromosome carrying Pm66 for powdery mildew resistance was discovered and confirmed by RNA-seq, molecular marker, and in situ hybridization analyses. Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is a severe disease of bread wheat worldwide. Discovery and utilization of resistance genes to powdery mildew from wild relatives of wheat have played important roles in wheat improvement. Aegilops longissima, one of the S-genome diploid wild relatives of wheat, is a valuable source of disease and pest resistance for wheat. Chromosome 4Sl from Ae. longissima confers moderate resistance to powdery mildew. In this study, we conducted RNA-seq on a putative Chinese Spring (CS)-Ae. longissima 4Sl(4B) disomic substitution line (TA3465) to develop 4Sl-specific markers to assist the transfer of a Bgt resistance gene from 4Sl by induced homoeologous recombination. A pairwise comparison of genes between CS and TA3465 demonstrated that a number of genes on chromosome 4BS in CS were not expressed in TA3465. Analysis of 4B- and 4Sl-specific molecular markers showed that 4BS and 4SlL were both missing in TA3465, whereas 4BL and 4SlS were present. Further characterization by genomic and fluorescent in situ hybridization confirmed that TA3465 carried a spontaneous Robertsonian T4SlS·4BL translocation. Powdery mildew tests showed that TA3465 was resistant to 10 of 16 Bgt isolates collected from different regions of China, whereas CS was susceptible to all those Bgt isolates. The powdery mildew resistance gene(s) in TA3465 was further mapped to the short arm of 4Sl and designated as Pm66.
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Affiliation(s)
- Huanhuan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Zhenjie Dong
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Chao Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Qing Xia
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Xiubin Tian
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Sunish Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57006, USA
| | - Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, 264005, People's Republic of China.
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China.
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Luo J, Zhao L, Zheng J, Li Y, Zhang L, Liu D, Pu Z, Hao M. Karyotype mosaicism in early generation synthetic hexaploid wheats. Genome 2020; 63:329-336. [PMID: 32197055 DOI: 10.1139/gen-2019-0148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is known that both the number and the structure of somatic chromosomes can vary in early generation hexaploid wheats. The phenomenon is generally assumed to arise as a result of the meiotic instability characteristic of freshly created allopolyploids. Here, an analysis of the somatic karyotype of a set of 33 early generation synthetic hexaploid wheats has revealed that variation, taking the form of sub-chromosomal fragments and inter-chromosomal translocations, can also arise in somatic tissue. A possible explanation for the observations was that karyotypic instability in early generation hexaploid wheat probably occurs not just during sporogenesis, but also in somatic tissue. However, other factors such as the use of nitrous oxide during the experiments could also cause the chromosome variations, and additional experimentation would be required to determine the most likely.
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Affiliation(s)
- Jiangtao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, Sichuan 610066, P.R. China.,Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Ministry of Agriculture, Chengdu, Sichuan 610066, P.R. China
| | - Laibin Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China
| | - Jianmin Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, Sichuan 610066, P.R. China.,Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Ministry of Agriculture, Chengdu, Sichuan 610066, P.R. China
| | - Yazhou Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, P.R. China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, P.R. China
| | - Zongjun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, Sichuan 610066, P.R. China.,Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Ministry of Agriculture, Chengdu, Sichuan 610066, P.R. China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, P.R. China
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41
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Genome-wide impacts of alien chromatin introgression on wheat gene transcriptions. Sci Rep 2020; 10:4801. [PMID: 32179864 PMCID: PMC7076028 DOI: 10.1038/s41598-020-61888-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/04/2020] [Indexed: 01/29/2023] Open
Abstract
Agronomic characteristics and tolerance to biotic and abiotic stresses in hexaploid wheat can be drastically improved through wheat-alien introgression. However, the transcriptional level interactions of introduced alien genes in the wheat genetic background is rarely investigated. In this study, we report the genome-wide impacts of introgressed chromosomes derived from Ae. longissima on gene transcriptions of the wheat landrace Chinese Spring. RNA-seq analyses demonstrated 5.37% and 4.30% of the genes were significantly differentially expressed (DEGs) in CS-Ae. longissima disomic 3Sl#2(3B) substitution line TA3575 and disomic 6Sl#3 addition line TA7548, respectively when compared to CS. In addition, 561 DEGs, including 413 up-regulated and 148 down-regulated or not transcribed genes, were simultaneously impacted by introgressed chromosomes 3Sl#2 and 6Sl#3, which accounts for 41.25% of the DEGs in TA3575 and 38.79% in TA7548. Seventeen DEGs, annotated as R genes, were shared by both introgression lines carrying chromosomes 3Sl#2 and 6Sl#3, which confer resistance to powdery mildew. This study will benefit the understanding of the wheat gene responses as result of alien gene(s) or chromosome intogression and the plant defense response initiated by powdery mildew resistance genes in chromosomes 3Sl#2 and 6Sl#3.
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Zheng X, Tang C, Han R, Zhao J, Qiao L, Zhang S, Qiao L, Ge C, Zheng J, Liu C. Identification, Characterization, and Evaluation of Novel Stripe Rust-Resistant Wheat- Thinopyrum intermedium Chromosome Translocation Lines. PLANT DISEASE 2020; 104:875-881. [PMID: 31935342 DOI: 10.1094/pdis-01-19-0001-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Stripe rust is an important disease in wheat, and development of genetic resistance in cultivars is an effective approach to control the disease. Wild species of wheat, such as Thinopyrum intermedium, are an excellent gene source for wheat improvement. In this study, two stripe rust-resistant wheat-Th. intermedium chromosome translocation lines, CH4131 and CH4132, were characterized by cytogenetic and pathological methods. The introgressed chromosome fragment was tagged using amplified fragment-length polymorphism-derived sequence-characterized amplified region (SCAR) markers and intron targeting markers, indicating that CH4131 and CH4132 both possess a homologous group 3 chromatin of Th. intermedium. Genomic in situ hybridization results suggested that a very small Th. intermedium chromosome segment was translocated to the terminal region of wheat 1BS for both lines, forming a configuration of T3Ai-1BS.1BL. The two translocation lines were resistant to stripe rust, and the resistance gene, temporarily designated YrCH-1BS, was likely derived from Th. intermedium. The translocated chromosome fragments have no genetic linkage drag to agronomic performance. The grain quality indexes of these two translocations were higher than local wheat varieties. Therefore, CH4131 and CH4132 could be used as potential gene sources in wheat improvement programs. The SCAR markers are useful to select stripe rust resistance from Th. intermedium.
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Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Caiguo Tang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan 250100, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Shuwei Zhang
- Institute of Crop Science, Shanxi Agricultural University, Taiyuan 030031, China
| | - Linyi Qiao
- Institute of Crop Science, Shanxi Agricultural University, Taiyuan 030031, China
| | - Chuan Ge
- Institute of Crop Science, Shanxi Agricultural University, Taiyuan 030031, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan 250100, China
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Song X, Song R, Zhou J, Yan W, Zhang T, Sun H, Xiao J, Wu Y, Xi M, Lou Q, Wang H, Wang X. Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosome Res 2020; 28:171-182. [PMID: 32002727 DOI: 10.1007/s10577-020-09627-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/08/2023]
Abstract
Chromosome painting is a useful technique for distinguishing specific chromosomes (fragments), elucidating the genetic relationships of different genomes or chromosomes, and identifying chromosomal rearrangements. The development of chromosome- or genome-specific probes is fundamental for chromosome painting. The possibility for developing such probes specifically painting homoeologous chromosomes in allopolyploid species has been questioned since that chromosomes belonging to the same homoeologous group share highly conserved sequences. In the present study, we attempted to construct a wheat chromosome 4D-specific oligo probe library by selecting 4D-specific sequences in reference genome of common wheat cv. Chinese Spring (CS, 2n = 6x = 42, AABBDD). The synthesized library contains 27,392 oligos. Oligo painting using the probe library confirmed its specificity, shown by that only chromosome 4D could be painted in three wheat genotypes and CS nulli-tetrasomic line N4AT4D. Oligo painting was successfully used to define the 4D breakpoints in CS deletion lines involving 4D and two wheat-Haynaldia villosa 4D-4V translocation lines. Thirteen wheat relatives and a Triticum durum-H. villosa amphiploid were used for oligo painting. Except the 4D in two Aegilops tauschii accessions, the 4M in Ae. comosa and 4U in Ae. umbellulata could be painted. In tetraploid Ae. ventricosa, both 4D and 4M could be painted; however, the signal intensity of 4M was less compared with 4D. No painted chromosome was observed for the other alien species. This indicated that the relationship among D/M/U was closer than that among D/A/B as well as D with genomes H/R/Ss/Sc/Y/P/N/J. Our successful development of 4D-specific oligo probe library may serve as a model for developing oligo probes specific for other homoeologous chromosomes.
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Affiliation(s)
- Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Rongrong Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jiawen Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Wenkai Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China/Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
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Bariah I, Keidar-Friedman D, Kashkush K. Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome. FRONTIERS IN PLANT SCIENCE 2020; 11:585515. [PMID: 33072155 PMCID: PMC7530836 DOI: 10.3389/fpls.2020.585515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 05/16/2023]
Abstract
Transposable elements (TEs) are major contributors to genome plasticity and thus are likely to have a dramatic impact on genetic diversity and speciation. Recent technological developments facilitated the sequencing and assembly of the wheat genome, opening the gate for whole genome analysis of TEs in wheat, which occupy over 80% of the genome. Questions that have been long unanswered regarding TE dynamics throughout the evolution of wheat, are now being addressed more easily, while new questions are rising. In this review, we discuss recent advances in the field of TE dynamics in wheat and possible future directions.
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Wang Y, Cao Q, Zhang J, Wang S, Chen C, Wang C, Zhang H, Wang Y, Ji W. Cytogenetic Analysis and Molecular Marker Development for a New Wheat- Thinopyrum ponticum 1J s (1D) Disomic Substitution Line With Resistance to Stripe Rust and Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2020; 11:1282. [PMID: 32973841 PMCID: PMC7472378 DOI: 10.3389/fpls.2020.01282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/06/2020] [Indexed: 05/03/2023]
Abstract
Thinopyrum ponticum (2n = 10x = 70), a member of the tertiary gene pool of wheat (Triticum aestivum L.), harbors many biotic and abiotic stress resistance genes. CH10A5, a novel disomic substitution line from a cross of T. aestivum cv. 7182 and Th. ponticum, was characterized by cytogenetic identification, in situ hybridization, molecular marker analysis, and morphological investigation of agronomic traits and disease resistance. Cytological observations showed that CH10A5 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genome in situ hybridization (GISH) analysis indicated that two of its chromosomes came from the Js genome of Th. ponticum, and wheat 15K array mapping and fluorescence in situ hybridization (FISH) revealed that chromosome 1D was absent from CH10A5. Polymorphic analysis of molecular markers indicated that the pair of alien chromosomes belonged to homoeologous group one, designated as 1Js. Thus, CH10A5 was a wheat-Th. ponticum 1Js (1D) disomic substitution line. Field disease resistance trials demonstrated that the introduced Th. ponticum chromosome 1Js was probably responsible for resistance to both stripe rust and powdery mildew at the adult stage. Based on specific-locus amplified fragment sequencing (SLAF-seq), 507 STS molecular markers were developed to distinguish chromosome 1Js genetic material from that of wheat. Of these, 49 STS markers could be used to specifically identify the genetic material of Th. ponticum. CH10A5 will increase the resistance gene diversity of wheat breeding materials, and the markers developed here will permit further tracing of heterosomal chromosome fragments in the future.
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Affiliation(s)
- Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Qiang Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Siwen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, China
- *Correspondence: Wanquan Ji,
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Li J, Chen Q, Zhang P, Lang T, Hoxha S, Li G, Yang Z. Comparative FISH and molecular identification of new stripe rust resistant wheat-Thinopyrum intermedium ssp. trichophorum introgression lines. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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47
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Li H, Dong Z, Ma C, Tian X, Xiang Z, Xia Q, Ma P, Liu W. Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing. PLoS One 2019; 14:e0220089. [PMID: 31710598 PMCID: PMC6844473 DOI: 10.1371/journal.pone.0220089] [Citation(s) in RCA: 9] [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: 07/02/2019] [Accepted: 10/23/2019] [Indexed: 01/07/2023] Open
Abstract
Powdery mildew is one of the most widespread diseases of wheat. The development and deployment of resistant varieties are one of the most economical and effective methods to manage this disease. Our previous study showed that the gene(s) at 2Mb in Chinese Spring (CS)-Aegilops biuncialis 2Mb disomic addition line TA7733 conferred a high level of resistance to powdery mildew of wheat. In this study, resistance spectrum of TA7733 was assayed by using 15 Blumeria graminis f. sp. tritici (Bgt) isolates prevalent in different regions of China. The result indicated that TA7733 was highly resistant to all tested Bgt isolates and the gene(s) on chromosome 2Mb conferred broad-spectrum resistance to powdery mildew. In order to characterize mechanism of powdery mildew resistance by identifying candidates R-genes derived from Ae. biuncialis chromosome 2Mb and develop 2Mb-specific molecular markers, we performed RNA-seq analysis on TA7733 and CS. In total we identified 7,278 unigenes that showed specific expression in TA7733 pre and post Bgt-infection when compared to CS. Of these 7,278 unigenes, 295 were annotated as putative resistance (R) genes. Comparatively analysis of R-gene sequences from TA7733 and CS and integration CS Ref Seq v1.0 were used to develop R-gene specific primers. Of 295 R-genes we identified 53 R-genes were specific to 2Mb and could be involved in powdery mildew resistance. Functional annotation of majority of the 53 R-genes encoded nucleotide binding leucine rich repeat (NLR) protein. The broad-spectrum resistance to powdery mildew in TA7733 and availability of 2Mb-derived putative candidate R-gene specific molecular markers identified in this study will lay foundations for transferring powdery mildew resistance from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination. Our study also provides useful candidates for further isolation and cloning of powdery mildew resistance gene(s) from Ae. biuncialis chromosome 2Mb.
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Affiliation(s)
- Huanhuan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Zhenjie Dong
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Chao Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Xiubin Tian
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Zhiguo Xiang
- Wheat Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan Province, China
| | - Qing Xia
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, Shandong Province, China
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province, China
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Ma J, Ding P, Liu J, Li T, Zou Y, Habib A, Mu Y, Tang H, Jiang Q, Liu Y, Chen G, Wang J, Deng M, Qi P, Li W, Pu Z, Zheng Y, Wei Y, Lan X. Identification and validation of a major and stably expressed QTL for spikelet number per spike in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3155-3167. [PMID: 31435704 DOI: 10.1007/s00122-019-03415-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/14/2019] [Indexed: 05/19/2023]
Abstract
A major and stably expressed QTL for spikelet number per spike identified in a 2-cM interval on chromosome arm 2DS was validated using two populations with different genetic backgrounds. Spikelet number per spike (SNS) plays a key role in wheat yield improvement. Numerous genetic and environmental factors influencing SNS have been documented, but the number of major, stably expressed and validated loci underlying SNS is still limited. In this study, a recombinant inbred line (RIL) population derived from a normal spikelet cultivar and a multiple-spikelet wheat line (with a longer spike with more canonically oriented apical spikelets) was genotyped using a Wheat55K single-nucleotide polymorphism (SNP) array and simple sequence repeat (SSR) markers. SNS was measured for this RIL population in eight environments. Five QTL were each identified in two or more environments. One of them, QSns.sau-2D (LOD = 3.47-38.24, PVE = 10.16-45.68%), was detected in all the eight environments. The QTL was located in a 2-cM interval on chromosome arm 2DS flanked by the markers AX-109836946 and AX-111956072. This QTL, QSns.sau-2D, significantly increased SNS by up to 14.72%. Several genes associated with plant growth and development were identified in the physical interval of QSns.sau-2D. This QTL was further validated by the tightly linked Kompetitive Allele Specific PCR (KASP) marker, KASP-AX-94721936, in two other populations with different genetic backgrounds. The significant correlation between SNS and anthesis date, plant height, spike length, grain number per spike and thousand-grain weight were detected and discussed. These results lay the foundation for fine mapping and cloning gene(s) underlying QSns.sau-2D.
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Affiliation(s)
- Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Puyang Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaya Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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49
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Li H, Dong Z, Ma C, Tian X, Qi Z, Wu N, Friebe B, Xiang Z, Xia Q, Liu W, Li T. Physical Mapping of Stem Rust Resistance Gene Sr52 from Dasypyrum villosum Based on ph1b-Induced Homoeologous Recombination. Int J Mol Sci 2019; 20:ijms20194887. [PMID: 31581639 PMCID: PMC6801782 DOI: 10.3390/ijms20194887] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022] Open
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) had been a devastating foliar disease worldwide during the 20th century. With the emergence of Ug99 races, which are virulent to most stem rust resistance genes deployed in wheat varieties and advanced lines, stem rust has once again become a disease threatening global wheat production. Sr52, derived from Dasypyrum villosum and mapped to the long arm of 6V#3, is one of the few effective genes against Ug99 races. In this study, the wheat-D. villosum Robertsonian translocation T6AS·6V#3L, the only stock carrying Sr52 released to experimental and breeding programs so far, was crossed with a CS ph1b mutant to induce recombinants with shortened 6V#3L chromosome segments locating Sr52. Six independent homozygous recombinants with different segment sizes and breakpoints were developed and characterized using in situ hybridization and molecular markers analyses. Stem rust resistance evaluation showed that only three terminal recombinants (1381, 1380, and 1392) containing 8%, 22%, and 30% of the distal segment of 6V#3L, respectively, were resistant to stem rust. Thus, the gene Sr52 was mapped into 6V#3L bin FL 0.92-1.00. In addition, three molecular markers in the Sr52-located interval of 6V#3L were confirmed to be diagnostic markers for selection of Sr52 introgressed into common wheat. The newly developed small segment translocation lines with Sr52 and the identified molecular markers closely linked to Sr52 will be valuable for wheat disease breeding.
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Affiliation(s)
- Huanhuan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zhenjie Dong
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Chao Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Xiubin Tian
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Nan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Bernd Friebe
- Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506-5502, USA.
| | - Zhiguo Xiang
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| | - Qing Xia
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
| | - Tianya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110000, China.
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50
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Identification of P genome chromosomes in Agropyron cristatum and wheat-A. cristatum derivative lines by FISH. Sci Rep 2019; 9:9712. [PMID: 31273296 PMCID: PMC6609639 DOI: 10.1038/s41598-019-46197-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/24/2019] [Indexed: 11/08/2022] Open
Abstract
Agropyron cristatum (L.) Gaertn. (P genome) is cultivated as pasture fodder and can provide many desirable genes for wheat improvement. With the development of genomics and fluorescence in situ hybridization (FISH) technology, probes for identifying plant chromosomes were also developed. However, there are few reports on A. cristatum chromosomes. Here, FISH with the repeated sequences pAcTRT1 and pAcpCR2 enabled the identification of all diploid A. cristatum chromosomes. An integrated idiogram of A. cristatum chromosomes was constructed based on the FISH patterns of five diploid A. cristatum individuals. Structural polymorphisms of homologous chromosomes were observed not only among different individuals but also within individuals. Moreover, seventeen wheat-A. cristatum introgression lines containing different P genome chromosomes were identified with pAcTRT1 and pAcpCR2 probes. The arrangement of chromosomes in diploid A. cristatum was determined by identifying correspondence between the P chromosomes in these genetically identified introgression lines and diploid A. cristatum chromosomes. The two probes were also effective for discriminating all chromosomes of tetraploid A. cristatum, and the differences between two tetraploid A. cristatum accessions were similar to the polymorphisms among individuals of diploid A. cristatum. Collectively, the results provide an effective means for chromosome identification and phylogenetic studies of P genome chromosomes.
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