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Kroupin PY, Ulyanov DS, Karlov GI, Divashuk MG. The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae. Chromosoma 2023:10.1007/s00412-023-00789-4. [PMID: 36905415 DOI: 10.1007/s00412-023-00789-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/16/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023]
Abstract
Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for "classical" wheat probes (pSc119.2 and Afa family) and "universal" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.
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Affiliation(s)
- Pavel Yu Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia.
| | - Daniil S Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
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2
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Li G, Chen Q, Jiang W, Zhang A, Yang E, Yang Z. Molecular and Cytogenetic Identification of Wheat- Thinopyrum intermedium Double Substitution Line-Derived Progenies for Stripe Rust Resistance. PLANTS (BASEL, SWITZERLAND) 2022; 12:28. [PMID: 36616156 PMCID: PMC9823681 DOI: 10.3390/plants12010028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) has been hybridized extensively with common wheat and proven to be a valuable germplasm source for improving disease resistance and yield potential of wheat. A novel disease-resistant wheat-Th. intermedium double substitution line X479, carrying 1St(1B) and 4St-4JS (4B), was identified using multi-color non-denaturing fluorescence in situ hybridization (ND-FISH). With the aim of transferring Thinopyrum-specific chromatin to wheat, a total of 573 plants from F2 and F3 progenies of X479 crossed with wheat cultivar MY11 were developed and characterized using sequential ND-FISH with multiple probes. Fifteen types of wheat-Thinopyrum translocation chromosomes were preferentially transmitted in the progenies, and the homozygous wheat-1St, and wheat-4JSL translocation lines were identified using ND-FISH, Oligo-FISH painting and CENH3 immunostaining. The wheat-4JSL translocation lines exhibited high levels of resistance to stripe rust prevalent races in field screening. The gene for stripe rust resistance was found to be physically located on FL0-0.60 of the 4JSL, using deletion lines and specific DNA markers. The new wheat-Th. intermedium translocation lines can be exploited as useful germplasms for wheat improvement.
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Affiliation(s)
- Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qiheng Chen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wenxi Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ahui Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Zhang X, Li J, Ge Y, Guan H, Li G, Zhang S, Wang X, Li X, Chang Z, Zhang P, Jia J, Liu C. Molecular cytogenetic characterization of a new wheat- Thinopyrum intermedium homoeologous group-6 chromosome disomic substitution line with resistance to leaf rust and stripe rust. FRONTIERS IN PLANT SCIENCE 2022; 13:1006281. [PMID: 36147230 PMCID: PMC9486089 DOI: 10.3389/fpls.2022.1006281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
Thinopyrum intermedium (JJJsJsStSt, 2n = 6x = 42), a member of tertiary gene pool of hexaploid wheat (Triticum aestivum L., AABBDD, 2n = 6x = 42), provides several beneficial genes for wheat improvement. In this study, line CH51 was developed from the BC1F8 progeny of a partial wheat-Th. intermedium amphiploid TAI8335 (2n = 56) and wheat cultivar (cv.) Jintai 170. Somatic metaphase chromosome counting showed that CH51 had stable 42 chromosomes. Genomic in situ hybridization (GISH) analysis showed that CH51 had 40 wheat chromosomes and two Th. intermedium chromosomes involving translocation between Js- and St-genome chromosomes. Non-denaturing fluorescence in situ hybridization (ND-FISH) analysis revealed that CH51 lacked a pair of wheat chromosome 6B. Wheat 55K SNP array analysis verified that chromosome 6B had the highest percentage of missing SNP loci in both CH51 and Chinese Spring (CS) nullisomic 6B-tetrasomic 6D (CS-N6BT6D) and had the highest percentage of polymorphic SNP loci between CH51 and cv. Jintai 170. We identified that CH51 was a wheat-Th. intermedium T6StS.6JsL (6B) disomic substitution line. Disease resistance assessment showed that CH51 exhibited high levels of resistance to the prevalent Chinese leaf rust and stripe rust races in the field. Therefore, the newly developed line CH51 can be utilized as a potential germplasm in wheat disease resistance breeding.
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Affiliation(s)
- Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Jianbo Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yudi Ge
- School of Life Sciences, Shanxi University, Taiyuan, Shanxi, China
| | - Haixia Guan
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Guangrong Li
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Shuwei Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Zhijian Chang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Juqing Jia
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
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Li J, Bao Y, Han R, Wang X, Xu W, Li G, Yang Z, Zhang X, Li X, Liu A, Li H, Liu J, Zhang P, Liu C. Molecular and Cytogenetic Identification of Stem Rust Resistant Wheat- Thinopyrum intermedium Introgression Lines. PLANT DISEASE 2022; 106:2447-2454. [PMID: 35196099 DOI: 10.1094/pdis-10-21-2274-re] [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] [Indexed: 06/14/2023]
Abstract
Thinopyrum intermedium (JJJsJsStSt, 2n = 6x = 42), a wild relative of common wheat, possesses many desirable agronomic genes for wheat improvement. The production of wheat-Thinopyrum intermedium introgression lines is a key step for transferring these beneficial genes into wheat. In this study, we characterized three wheat-Thinopyrum intermedium introgression lines TA3681, TA5566, and TA5567 using non-denaturing fluorescence in situ hybridization, genomic in situ hybridization, PCR-based landmark unique gene, and intron targeting markers. Our results showed that TA3681 is a wheat-Thinopyrum intermedium 1St disomic addition line, TA5566 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying two pairs of 3A-7Js translocation chromosomes, and that TA5567 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying a pair of 3A-7Js translocation chromosomes. We developed 13, 36, and 15 Thinopyrum intermedium chromosome-specific markers for detecting the introgressed Thinopyrum chromosomes in TA3681, TA5566, and TA5567, respectively. Stem rust assessment revealed that TA3681 exhibited a high level of seedling resistance to Chinese-prevalent Puccinia graminis f. sp. tritici pathotypes, and both TA5566 and TA5567 were highly resistant to Australian P. graminis f. sp. tritici pathotypes, indicating that Thinopyrum intermedium chromosomes 1St and 7Js might carry new stem rust resistance genes. Therefore, the new identified introgression lines may be useful for improving wheat stem rust resistance.
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Affiliation(s)
- Jianbo Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2570, Australia
| | - Yinguang Bao
- Agronomy College, Shandong Agricultural University, Taian, Shandong 271002, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Wenjing Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030810, China
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030810, China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Haosheng Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Jianjun Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2570, Australia
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
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Yu Z, Wang H, Yang E, Li G, Yang Z. Precise Identification of Chromosome Constitution and Rearrangements in Wheat–Thinopyrum intermedium Derivatives by ND-FISH and Oligo-FISH Painting. PLANTS 2022; 11:plants11162109. [PMID: 36015412 PMCID: PMC9415406 DOI: 10.3390/plants11162109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
Abstract
Thinopyrum intermedium possesses many desirable agronomic traits that make it a valuable genetic source for wheat improvement. The precise identification of individual chromosomes of allohexaploid Th. intermedium is a challenge due to its three sub-genomic constitutions with complex evolutionary ancestries. The non-denaturing fluorescent in situ hybridization (ND-FISH) using tandem-repeat oligos, including Oligo-B11 and Oligo-pDb12H, effectively distinguished the St, J and JS genomes, while Oligo-FISH painting, based on seven oligonucleotide pools derived from collinear regions between barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.), was able to identify each linkage group of the Th. intermedium chromosomes. We subsequently established the first karyotype of Th. intermedium with individual chromosome recognition using sequential ND-FISH and Oligo-FISH painting. The chromosome constitutions of 14 wheat–Th. intermedium partial amphiploids and addition lines were characterized. Distinct intergenomic chromosome rearrangements were revealed among Th. intermedium chromosomes in these amphiploids and addition lines. The precisely defined karyotypes of these wheat–Th. intermedium derived lines may be helpful for further study on chromosome evolution, chromatin introgression and wheat breeding programs.
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Affiliation(s)
- Zhihui Yu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hongjin Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Correspondence: (G.L.); (Z.Y.)
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Correspondence: (G.L.); (Z.Y.)
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Wang S, Wang C, Feng X, Zhao J, Deng P, Wang Y, Zhang H, Liu X, Li T, Chen C, Wang B, Ji W. Molecular cytogenetics and development of St-chromosome-specific molecular markers of novel stripe rust resistant wheat-Thinopyrum intermedium and wheat-Thinopyrum ponticum substitution lines. BMC PLANT BIOLOGY 2022; 22:111. [PMID: 35279089 PMCID: PMC8917741 DOI: 10.1186/s12870-022-03496-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Owing to their excellent resistance to abiotic and biotic stress, Thinopyrum intermedium (2n = 6x = 42, JJJsJsStSt) and Th. ponticum (2n = 10x = 70) are both widely utilized in wheat germplasm innovation programs. Disomic substitution lines (DSLs) carrying one pair of alien chromosomes are valuable bridge materials for transmission of novel genes, fluorescence in situ hybridization (FISH) karyotype construction and specific molecular marker development. RESULTS Six wheat-Thinopyrum DSLs derived from crosses between Abbondanza nullisomic lines (2n = 40) and two octoploid Trititrigia lines (2n = 8x = 56), were characterized by sequential FISH-genome in situ hybridization (GISH), multicolor GISH (mc-GISH), and an analysis of the wheat 15 K SNP array combined with molecular marker selection. ES-9 (DS2St (2A)) and ES-10 (DS3St (3D)) are wheat-Th. ponticum DSLs, while ES-23 (DS2St (2A)), ES-24 (DS3St (3D)), ES-25(DS2St (2B)), and ES-26 (DS2St (2D)) are wheat-Th. intermedium DSLs. ES-9, ES-23, ES-25 and ES-26 conferred high thousand-kernel weight and stripe rust resistance at adult stages, while ES-10 and ES-24 were highly resistant to stripe rust at all stages. Furthermore, cytological analysis showed that the alien chromosomes belonging to the same homoeologous group (2 or 3) derived from different donors carried the same FISH karyotype and could form a bivalent. Based on specific-locus amplified fragment sequencing (SLAF-seq), two 2St-chromosome-specific markers (PTH-005 and PTH-013) and two 3St-chromosome-specific markers (PTH-113 and PTH-135) were developed. CONCLUSIONS The six wheat-Thinopyrum DSLs conferring stripe rust resistance can be used as bridging parents for transmission of valuable resistance genes. The utility of PTH-113 and PTH-135 in a BC1F2 population showed that the newly developed markers could be useful tools for efficient identification of St chromosomes in a common wheat background.
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Affiliation(s)
- Siwen Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Changyou Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Xianbo Feng
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Pingchuan Deng
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Yajuan Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Hong Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Xinlun Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Tingdong Li
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Chunhuan Chen
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, 712100 Shaanxi China
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Feng Z, Song L, Song W, Qi Z, Yuan J, Li R, Han H, Wang H, Chen Z, Guo W, Xin M, Liu J, Hu Z, Peng H, Yao Y, Sun Q, Ni Z, Xing J. The decreased expression of GW2 homologous genes contributed to the increased grain width and thousand‑grain weight in wheat-Dasypyrum villosum 6VS·6DL translocation lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3873-3894. [PMID: 34374829 DOI: 10.1007/s00122-021-03934-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/02/2021] [Indexed: 05/12/2023]
Abstract
This study demonstrated that the aberrant transcription of DvGW2 contributed to the increased grain width and thousand-grain weight in wheat-Dasypyrum villosum T6VS·6DL translocation lines. Due to the high immunity to powdery mildew, Dasypyrum villosum 6VS has been one of the most successful applications of the wild relatives in modern wheat breeding. Along with the desired traits, side-effects could be brought when large alien chromosome fragments are introduced into wheat, but little is known about effects of 6VS on agronomic traits. Here, we found that T6VS·6DL translocation had significantly positive effects on grain weight, plant heightand spike length, and small negative effects on total spikelet number and spikelet compactness using recipient and wheat-D. villosum T6VS·6DL allohexaploid wheats, Wan7107 and Pm97033. Further analysis showed that the 6VS segment might exert direct genetic effect on grain width, then driving the increase of thousand-grain weight. Furthermore, comparative transcriptome analysis identified 2549 and 1282 differentially expressed genes (DEGs) and 2220 and 1496 specifically expressed genes (SEGs) at 6 days after pollination (DAP) grains and 15 DAP endosperms, respectively. Enrichment analysis indicated that the process of cell proliferation category was over-represented in the DEGs. Notably, two homologous genes, TaGW2-D1 and DvGW2, were identified as putative candidate genes associated with grain weight and yield. The expression analysis showed that DvGW2 had an aberrant expression in Pm97033, resulting in significantly lower total expression level of GW2 than Wan7107, which drives the increase of grain weight and width in Pm97033. Collectively, our data indicated that the compromised expression of DvGW2 is critical for increased grain width and weight in T6VS·6DL translocation lines.
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Affiliation(s)
- Zhiyu Feng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Long Song
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongqi Qi
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jun Yuan
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Run Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Haiming Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Huifang Wang
- Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Qiao L, Liu S, Li J, Li S, Yu Z, Liu C, Li X, Liu J, Ren Y, Zhang P, Zhang X, Yang Z, Chang Z. Development of Sequence-Tagged Site Marker Set for Identification of J, J S, and St Sub-genomes of Thinopyrum intermedium in Wheat Background. FRONTIERS IN PLANT SCIENCE 2021; 12:685216. [PMID: 34249056 PMCID: PMC8261300 DOI: 10.3389/fpls.2021.685216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.
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Affiliation(s)
- Linyi Qiao
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Shujuan Liu
- Department of Plant Science, College of Agronomy, Northwest Agriculture & Forestry University, Yangling, China
| | - Jianbo Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Shijiao Li
- Department of Botany, College of Life Science, Shanxi University, Taiyuan, China
| | - Zhihui Yu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Liu
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Jing Liu
- Department of Botany, College of Life Science, Shanxi University, Taiyuan, China
| | - Yongkang Ren
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhijian Chang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
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9
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He H, Du H, Liu R, Liu T, Yang L, Gong S, Tang Z, Du H, Liu C, Han R, Sun W, Wang L, Zhu S. Characterization of a new gene for resistance to wheat powdery mildew on chromosome 1RL of wild rye Secale sylvestre. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:887-896. [PMID: 33388886 DOI: 10.1007/s00122-020-03739-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
PmSESY, a new wheat powdery mildew resistance gene was characterized and genetically mapped to the terminal region of chromosome 1RL of wild rye Secale sylvestre. The genus Secale is an important resource for wheat improvement. The Secale species are usually considered as non-adapted hosts of Blumeria graminis f. sp. tritici (Bgt) that causes wheat powdery mildew. However, as a wild species of cultivated rye, S. sylvestre is rarely studied. Here, we reported that 25 S. sylvestre accessions were susceptible to isolate BgtYZ01, whereas the other five confer effective resistance to all the tested isolates of Bgt. A population was then constructed by crossing the resistant accession SESY-01 with the susceptible accession SESY-11. Genetic analysis showed that the resistance in SESY-01 was controlled by a single dominant gene, temporarily designated as PmSESY. Subsequently, combining bulked segregant RNA-Seq (BSR-Seq) analysis with molecular analysis, PmSESY was mapped into a 1.88 cM genetic interval in the terminus of the long arm of 1R, which was closely flanked by markers Xss06 and Xss09 with genetic distances of 0.87 cM and 1.01 cM, respectively. Comparative mapping demonstrated that the corresponding physical region of the PmSESY locus was about 3.81 Mb in rye cv. Lo7 genome, where 30 disease resistance-related genes were annotated, including five NLR-type disease resistance genes, three kinase family protein genes, three leucine-rich repeat receptor-like protein kinase genes and so on. This study gives a new insight into S. sylvestre that shows divergence in response to Bgt and reports a new powdery mildew resistance gene that has potential to be used for resistance improvement in wheat.
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Affiliation(s)
- Huagang He
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
- School of Environment, Jiangsu University, Zhenjiang, 212013, China.
| | - Haonan Du
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Renkang Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Tianlei Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Lijun Yang
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Shuangjun Gong
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haimei Du
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cheng Liu
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ran Han
- Crop Research Institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Weihong Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Lei Wang
- INDEL Biological Technology Corporation, Nanjing, 210000, China
| | - Shanying Zhu
- School of Environment, Jiangsu University, Zhenjiang, 212013, China.
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10
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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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11
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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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12
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Nikitina E, Kuznetsova V, Kroupin P, Karlov GI, Divashuk MG. Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data. Int J Mol Sci 2020; 21:E4495. [PMID: 32599865 PMCID: PMC7349979 DOI: 10.3390/ijms21124495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 01/19/2023] Open
Abstract
The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae. The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs' abundance in the genomes of Triticum aestivum, Thinopyrum ponticum, Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs.
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Affiliation(s)
- Ekaterina Nikitina
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Victoria Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
- Kurchatov Genomics Center—ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia
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