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Structural and Functional Characterization at the Molecular Level of the MATE Gene Family in Wheat in Silico. CONTRAST MEDIA & MOLECULAR IMAGING 2022. [DOI: 10.1155/2022/9289007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A series of multidrug extransporters known as the multidrug and potentially toxic extrusion (MATE) genes are found in all living things and are crucial for the removal of heavy metal ions, metalloids, exogenous xenobiotics, endogenous secondary metabolites, and other toxic substances from the cells. However, there has only been a small amount of them in silico analysis of the MATE family of genes in plant species. In the current study, the MATE gene family was characterized in silico where two families and seven subfamilies based on their evolutionary relationships were proposed. Plant breeders may use TraesCS1D02G030400, TraesCS4B02G244400, and TraesCS1A02G029900 genes for marker-assisted or transgenic breeding to develop novel cultivars since these genes have been hypothesized from protein-protein interaction study to play a critical role in the transport of toxic chemicals across cells. The exon number varies from 01 to 14. One exon has TraesCS1A02G188100, TraesCS5B02G562500, TraesCS6A02G256400, and TraesCS6D02G384300 genes, while 14 exons have only two genes that are TraesCS6A02G418800 and TraesCS6D02G407900. Biological stress (infestations of disease) affects the expression of most of the MATE genes, with the gene TraesCS5D02G355500 having the highest expression level in the wheat expression browser tool. Using the Grain interpretation search engine tool, it is found that the vast bulk of MATE genes are voiced throughout biotic environmental stresses caused by disease pests, with the genotype TraesCS5B02G326600.1 from family 1 exhibiting the greatest level of expression throughout Fusarium head blight infection by Fusarium graminearum after 4 days of infection. The researchers constructed 39 ternary plots, each with a distinct degree of expression under biotic and abiotic stress settings, and observed that 44% of the triplets have imbalanced outputs (extreme values) due to their higher tissue specificity and increased intensity.
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Dong Y, Xu D, Xu X, Ren Y, Gao F, Song J, Jia A, Hao Y, He Z, Xia X. Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1083-1099. [PMID: 35006334 DOI: 10.1007/s00122-021-04019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431 kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene.
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Affiliation(s)
- Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xiaowan Xu
- College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yan Ren
- College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan, China
| | - Fengmei Gao
- Institute of Crop Germplasm Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Aolin Jia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Ye X, Hu H, Zhou H, Jiang Y, Gao S, Yuan Z, Stiller J, Li C, Chen G, Liu Y, Wei Y, Zheng YL, Wang YG, Liu C. Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids. Genome 2021; 64:847-856. [PMID: 33661713 DOI: 10.1139/gen-2020-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.
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Affiliation(s)
- Xueling Ye
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Haiyan Hu
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Hong Zhou
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yunfeng Jiang
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Shang Gao
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Zhongwei Yuan
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiri Stiller
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
| | - Chengwei Li
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Gan Wang
- Science and Engineering Facility, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, QLD 4067, Australia
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Xie J, Guo G, Wang Y, Hu T, Wang L, Li J, Qiu D, Li Y, Wu Q, Lu P, Chen Y, Dong L, Li M, Zhang H, Zhang P, Zhu K, Li B, Deal KR, Huo N, Zhang Y, Luo MC, Liu S, Gu YQ, Li H, Liu Z. A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat. THE NEW PHYTOLOGIST 2020; 228:1011-1026. [PMID: 32569398 DOI: 10.1111/nph.16762] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/02/2020] [Indexed: 05/18/2023]
Abstract
Powdery mildew poses severe threats to wheat production. The most sustainable way to control this disease is through planting resistant cultivars. We report the map-based cloning of the powdery mildew resistance allele Pm5e from a Chinese wheat landrace. We applied a two-step bulked segregant RNA sequencing (BSR-Seq) approach in developing tightly linked or co-segregating markers to Pm5e. The first BSR-Seq used phenotypically contrasting bulks of recombinant inbred lines (RILs) to identify Pm5e-linked markers. The second BSR-Seq utilized bulks of genetic recombinants screened from a fine-mapping population to precisely quantify the associated genomic variation in the mapping interval, and identified the Pm5e candidate genes. The function of Pm5e was validated by transgenic assay, loss-of-function mutants and haplotype association analysis. Pm5e encodes a nucleotide-binding domain leucine-rich-repeat-containing (NLR) protein. A rare nonsynonymous single nucleotide variant (SNV) within the C-terminal leucine rich repeat (LRR) domain is responsible for the gain of powdery mildew resistance function of Pm5e, an allele endemic to wheat landraces of Shaanxi province of China. Results from this study demonstrate the value of landraces in discovering useful genes for modern wheat breeding. The key SNV associated with powdery mildew resistance will be useful for marker-assisted selection of Pm5e in wheat breeding programs.
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Affiliation(s)
- Jingzhong Xie
- 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
| | - Guanghao Guo
- 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
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tiezhu Hu
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, 4530003, China
| | - Lili Wang
- China Agricultural University, Beijing, 100193, China
| | - Jingting Li
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China
| | - Dan Qiu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yahui Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiuhong Wu
- 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
| | - Ping Lu
- 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
| | - Yongxing Chen
- 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
| | - Lingli Dong
- 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
| | - Miaomiao 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
| | - Huaizhi Zhang
- 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
| | - Panpan Zhang
- 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
| | - Keyu Zhu
- 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
| | - Beibei 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, CA, 94710, USA
| | - Yan Zhang
- China Agricultural University, Beijing, 100193, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yong Qiang Gu
- USDA-ARS West Regional Research Center, Albany, CA, 94710, USA
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- 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
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5
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Dhariwal R, Henriquez MA, Hiebert C, McCartney CA, Randhawa HS. Mapping of Major Fusarium Head Blight Resistance from Canadian Wheat cv. AAC Tenacious. Int J Mol Sci 2020; 21:ijms21124497. [PMID: 32599868 PMCID: PMC7350018 DOI: 10.3390/ijms21124497] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
Fusarium head blight (FHB) is one of the most devastating wheat disease due to its direct detrimental effects on grain-yield, quality and marketability. Resistant cultivars offer the most effective approach to manage FHB; however, the lack of different resistance resources is still a major bottleneck for wheat breeding programs. To identify and dissect FHB resistance, a doubled haploid wheat population produced from the Canadian spring wheat cvs AAC Innova and AAC Tenacious was phenotyped for FHB response variables incidence and severity, visual rating index (VRI), deoxynivalenol (DON) content, and agronomic traits days to anthesis (DTA) and plant height (PHT), followed by single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker genotyping. A high-density map was constructed consisting of 10,328 markers, mapped on all 21 chromosomes with a map density of 0.35 cM/marker. Together, two major quantitative trait loci for FHB resistance were identified on chromosome 2D from AAC Tenacious; one of these loci on 2DS also colocated with loci for DTA and PHT. Another major locus for PHT, which cosegregates with locus for low DON, was also identified along with many minor and epistatic loci. QTL identified from AAC Tenacious may be useful to pyramid FHB resistance.
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Affiliation(s)
- Raman Dhariwal
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
| | - Maria A. Henriquez
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada; (M.A.H.); (C.H.); (C.A.M.)
| | - Colin Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada; (M.A.H.); (C.H.); (C.A.M.)
| | - Curt A. McCartney
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada; (M.A.H.); (C.H.); (C.A.M.)
| | - Harpinder S. Randhawa
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada;
- Correspondence: ; Tel.: +1-403-317-2238
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Yepuri V, Jalali S, Kancharla N, Reddy VB, Arockiasamy S. Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.). Mol Biol Rep 2020; 47:5091-5099. [PMID: 32562173 DOI: 10.1007/s11033-020-05579-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/10/2020] [Indexed: 11/29/2022]
Abstract
Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements' (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimers pipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.
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Affiliation(s)
- Vijay Yepuri
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Saakshi Jalali
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Nagesh Kancharla
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - V B Reddy
- AgriGenome Labs Private Limited, Hyderabad, 500078, India
| | - S Arockiasamy
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India.
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Zhang M, Zhang W, Zhu X, Sun Q, Chao S, Yan C, Xu SS, Fiedler J, Cai X. Partitioning and physical mapping of wheat chromosome 3B and its homoeologue 3E in Thinopyrum elongatum by inducing homoeologous recombination. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1277-1289. [PMID: 31970450 DOI: 10.1007/s00122-020-03547-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
We performed homoeologous recombination-based partitioning and physical mapping of wheat chromosome 3B and Th. elongatum chromosome 3E, providing a unique physical framework of this homoeologous pair for genome studies. The wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) and Thinopyrum elongatum (2n = 2x = 14, EE) genomes can be differentiated from each other by fluorescent genomic in situ hybridization (FGISH) as well as molecular markers. This has facilitated homoeologous recombination-based partitioning and engineering of their genomes for physical mapping and alien introgression. Here, we constructed a special wheat genotype, which was double monosomic for wheat chromosome 3B and Th. elongatum chromosome 3E and homozygous for the ph1b mutant, to induce 3B-3E homoeologous recombination. Totally, 81 3B-3E recombinants were recovered and detected in the primary, secondary, and tertiary homoeologous recombination cycles by FGISH. Comparing to the primary recombination, the secondary and tertiary recombination shifted toward the proximal regions due to the increase in homology between the pairing partners. The 3B-3E recombinants were genotyped by high-throughput wheat 90-K single nucleotide polymorphism (SNP) arrays and their recombination breakpoints physically mapped based on the FGISH patterns and SNP results. The 3B-3E recombination physically partitioned chromosome 3B into 38 bins, and 429 SNPs were assigned to the distinct bins. Integrative analysis of FGISH and SNP results led to the construction of a composite bin map for chromosome 3B. Additionally, we developed 22 SNP-derived semi-thermal asymmetric reverse PCR markers specific for chromosome 3E and constructed a comparative map of homoeologous chromosomes 3E, 3B, 3A, and 3D. In summary, this work provides a unique physical framework for further studies of the 3B-3E homoeologous pair and diversifies the wheat genome for wheat improvement.
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Affiliation(s)
- Mingyi Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Qing Sun
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Shiaoman Chao
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Jason Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
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8
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Pascual L, Ruiz M, López-Fernández M, Pérez-Peña H, Benavente E, Vázquez JF, Sansaloni C, Giraldo P. Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding. BMC Genomics 2020; 21:122. [PMID: 32019507 PMCID: PMC7001277 DOI: 10.1186/s12864-020-6536-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/24/2020] [Indexed: 02/08/2023] Open
Abstract
Background One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results The DArTseq GBS approach generated 10 K SNPs and 40 K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsp. durum, turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin. Conclusions The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties, and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.
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Affiliation(s)
- Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - Magdalena Ruiz
- National Plant Genetic Resources Centre, National Institute for Agricultural and Food Research and Technology, Alcalá de Henares, Spain
| | - Matilde López-Fernández
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - Helena Pérez-Peña
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - Elena Benavente
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - José Francisco Vázquez
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - Carolina Sansaloni
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Texcoco, Mexico
| | - Patricia Giraldo
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, Madrid, Spain.
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Tatineni S, Sato S, Nersesian N, Alexander J, Quach T, Graybosch RA, Clemente TE. Transgenic Wheat Harboring an RNAi Element Confers Dual Resistance Against Synergistically Interacting Wheat Streak Mosaic Virus and Triticum Mosaic Virus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:108-122. [PMID: 31687913 DOI: 10.1094/mpmi-10-19-0275-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wheat streak mosaic virus (WSMV) and triticum mosaic virus (TriMV) are economically important viruses of wheat (Triticum aestivum L.), causing significant yield losses in the Great Plains region of the United States. These two viruses are transmitted by wheat curl mites, which often leads to mixed infections with synergistic interaction in grower fields that exacerbates yield losses. Development of dual-resistant wheat lines would provide effective control of these two viruses. In this study, a genetic resistance strategy employing an RNA interference (RNAi) approach was implemented by assembling a hairpin element composed of a 202-bp (404-bp in total) stem sequence of the NIb (replicase) gene from each of WSMV and TriMV in tandem and of an intron sequence in the loop. The derived RNAi element was cloned into a binary vector and was used to transform spring wheat genotype CB037. Phenotyping of T1 lineages across eight independent transgenic events for resistance revealed that i) two of the transgenic events provided resistance to WSMV and TriMV, ii) four events provided resistance to either WSMV or TriMV, and iii) no resistance was found in two other events. T2 populations derived from the two events classified as dual-resistant were subsequently monitored for stability of the resistance phenotype through the T4 generation. The resistance phenotype in these events was temperature-dependent, with a complete dual resistance at temperatures ≥25°C and an increasingly susceptible response at temperatures below 25°C. Northern blot hybridization of total RNA from transgenic wheat revealed that virus-specific small RNAs (vsRNAs) accumulated progressively with an increase in temperature, with no detectable levels of vsRNA accumulation at 20°C. Thus, the resistance phenotype of wheat harboring an RNAi element was correlated with accumulation of vsRNAs, and the generation of vsRNAs can be used as a molecular marker for the prediction of resistant phenotypes of transgenic plants at a specific temperature.
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Affiliation(s)
- Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Shirley Sato
- Center for Biotechnology, University of Nebraska-Lincoln
| | | | | | - Truyen Quach
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln
| | | | - Tom Elmo Clemente
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln
- Center for Plant Science Innovation, University of Nebraska-Lincoln
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10
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Ma X, Xu Z, Wang J, Chen H, Ye X, Lin Z. Pairing and Exchanging between Daypyrum villosum Chromosomes 6V#2 and 6V#4 in the Hybrids of Two Different Wheat Alien Substitution Lines. Int J Mol Sci 2019; 20:ijms20236063. [PMID: 31805728 PMCID: PMC6929145 DOI: 10.3390/ijms20236063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/21/2019] [Accepted: 11/27/2019] [Indexed: 11/16/2022] Open
Abstract
Normal pairing and exchanging is an important basis to evaluate the genetic relationship between homologous chromosomes in a wheat background. The pairing behavior between 6V#2 and 6V#4, two chromosomes from different Dasypyrum villosum accessions, is still not clear. In this study, two wheat alien substitution lines, 6V#2 (6A) and 6V#4 (6D), were crossed to obtain the F1 hybrids and F2 segregating populations, and the testcross populations were obtained by using the F1 as a parent crossed with wheat variety Wan7107. The chromosomal behavior at meiosis in pollen mother cells (PMCs) of the F1 hybrids was observed using a genomic in situ hybridization (GISH) technique. Exchange events of two alien chromosomes were investigated in the F2 populations using nine polymerase chain reaction (PCR) markers located on the 6V short arm. The results showed that the two alien chromosomes could pair with each other to form ring- or rod-shaped bivalent chromosomes in 79.76% of the total PMCs, and most were pulled to two poles evenly at anaphase I. Investigation of the F2 populations showed that the segregation ratios of seven markers were consistent with the theoretical values 3:1 or 1:2:1, and recombinants among markers were detected. A genetic linkage map of nine PCR markers for 6VS was accordingly constructed based on the exchange frequencies and compared with the physical maps of wheat and barley based on homologous sequences of the markers, which showed that conservation of sequence order compared to 6V was 6H and 6B > 6A > 6D. In the testcross populations with 482 plants, seven showed susceptibility to powdery mildew (PM) and lacked amplification of alien chromosomal bands. Six other plants had amplification of specific bands of both the alien chromosomes at multiple sites, which suggested that the alien chromosomes had abnormal separation behavior in about 1.5% of the PMCs in F1, which resulted in some gametes containing two alien chromosomes. In addition, three new types of chromosome substitution were developed. This study lays a foundation for alien allelism tests and further assessment of the genetic relationship among 6V#2, 6V#4, and their wheat homoeologous chromosomes.
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Affiliation(s)
- Xiaolan Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.M.); (Z.X.); (J.W.); (H.C.); (X.Y.)
| | - Zhiying Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.M.); (Z.X.); (J.W.); (H.C.); (X.Y.)
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jing Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.M.); (Z.X.); (J.W.); (H.C.); (X.Y.)
| | - Haiqiang Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.M.); (Z.X.); (J.W.); (H.C.); (X.Y.)
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.M.); (Z.X.); (J.W.); (H.C.); (X.Y.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhishan Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.M.); (Z.X.); (J.W.); (H.C.); (X.Y.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence:
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11
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Danilova TV, Poland J, Friebe B. Production of a complete set of wheat-barley group-7 chromosome recombinants with increased grain β-glucan content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3129-3141. [PMID: 31535163 DOI: 10.1007/s00122-019-03411-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Wheat-barley group-7 recombinant chromosomes were selected using molecular cytogenetics and SNP markers; increased grain β-glucan content was observed in wheat plants with two and four copies of HvCslF6. The soluble dietary fiber (1-3)(1-4) mixed linked β-D-glucan from cereal grains is a valuable component of a healthy diet, which reduces risks of coronary disease and diabetes. Although wheat is an important cereal crop providing a substantial portion of daily calories and protein intake in the human diet, it has a low level of β-glucan. Owing to the plasticity of the polyploid wheat genome, agronomically important traits absent in the wheat primary gene pool can be introgressed from distant relatives. Barley (Hordeum vulgare L.) has a high grain β-glucan content. Earlier, we introgressed this trait into wheat in the form of whole arm compensating Robertsonian translocations (RobT) involving group-7 chromosomes of barley and all three sub-genomes of hexaploid wheat (Triticum aestivum L). In the presented research, we shortened the barley 7HL arms in these RobTs to small pericentromeric segments, using induced wheat-barley homoeologous recombination. The recombinants were selected using SNP markers and molecular cytogenetics. Plants, comprising barley cellulose synthase-like F6 gene (HvCslF6), responsible for β-glucan synthesis, had a higher grain β-glucan content than the wheat control. Three wheat-barley group-7 recombinant chromosomes involving the A, B and D sub-genomes laid the basis for a multiple-copy gene introgression to hexaploid wheat. It is hypothesized that further increases in the β-glucan content in wheat grain can be obtained by increasing the number of HvCslF6 copies through combining several recombinant chromosomes in one line. The wheat lines with four copies of HvCslF6 exceeded the β-glucan content of the lines with two copies.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jesse Poland
- 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.
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12
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Danilova TV, Poland J, Friebe B. Production of a complete set of wheat-barley group-7 chromosome recombinants with increased grain β-glucan content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3129-3141. [PMID: 31535163 DOI: 10.1007/s00122-019-03411-3413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/29/2019] [Indexed: 05/20/2023]
Abstract
Wheat-barley group-7 recombinant chromosomes were selected using molecular cytogenetics and SNP markers; increased grain β-glucan content was observed in wheat plants with two and four copies of HvCslF6. The soluble dietary fiber (1-3)(1-4) mixed linked β-D-glucan from cereal grains is a valuable component of a healthy diet, which reduces risks of coronary disease and diabetes. Although wheat is an important cereal crop providing a substantial portion of daily calories and protein intake in the human diet, it has a low level of β-glucan. Owing to the plasticity of the polyploid wheat genome, agronomically important traits absent in the wheat primary gene pool can be introgressed from distant relatives. Barley (Hordeum vulgare L.) has a high grain β-glucan content. Earlier, we introgressed this trait into wheat in the form of whole arm compensating Robertsonian translocations (RobT) involving group-7 chromosomes of barley and all three sub-genomes of hexaploid wheat (Triticum aestivum L). In the presented research, we shortened the barley 7HL arms in these RobTs to small pericentromeric segments, using induced wheat-barley homoeologous recombination. The recombinants were selected using SNP markers and molecular cytogenetics. Plants, comprising barley cellulose synthase-like F6 gene (HvCslF6), responsible for β-glucan synthesis, had a higher grain β-glucan content than the wheat control. Three wheat-barley group-7 recombinant chromosomes involving the A, B and D sub-genomes laid the basis for a multiple-copy gene introgression to hexaploid wheat. It is hypothesized that further increases in the β-glucan content in wheat grain can be obtained by increasing the number of HvCslF6 copies through combining several recombinant chromosomes in one line. The wheat lines with four copies of HvCslF6 exceeded the β-glucan content of the lines with two copies.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jesse Poland
- 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.
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13
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Mu J, Wu J, Liu S, Dai M, Sun D, Huang S, Wang Q, Zeng Q, Yu S, Chen L, Kang Z, Han D. Genome-Wide Linkage Mapping Reveals Stripe Rust Resistance in Common Wheat ( Triticum aestivum) Xinong1376. PLANT DISEASE 2019; 103:2742-2750. [PMID: 31509495 DOI: 10.1094/pdis-12-18-2264-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust, also known as yellow rust, is a significant threat to wheat yield worldwide. Adult plant resistance (APR) is the preferred way to obtain durable protection. Chinese winter wheat cultivar Xinong1376 has maintained acceptable APR to stripe rust in field environments. To characterize APR in this cultivar, 190 F10 recombinant inbred lines (RILs) developed from Xiaoyan81 × Xinong1376 were evaluated for infection type and disease severity in fields either artificially or naturally inoculated. The population along with parents were genotyped using the Illumina 90K single-nucleotide polymorphism arrays. Six quantitative trait loci (QTL) were detected using the inclusive composite interval mapping method. QYr.nwafu-4AL and QYr.nwafu-6BL.3 conferred stable resistance in all environments, and likely corresponded to a gene-rich region on the long arm of chromosomes 4A and 6B. QYr.nwafu-5AL, QYr.nwafu-5BL, QYr.nwafu-3BL.1, and QYr.nwafu-3BL.2 were detected only in some environments but enhanced the level of resistance conferred by QYr.nwafu-4AL and QYr.nwafu-6BL.3. Kompetitive allele-specific PCR (KASP) markers developed for QYr.nwafu-4AL and QYr.nwafu-6BL.3 were confirmed in a subset of RILs and 133 wheat genotypes. The QTL on 4AL and 6BL with their linked KASP markers would be useful for marker-assisted selection to improve stripe rust resistance in breeding programs.
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Affiliation(s)
- Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Miaofei Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Daojie Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Li Chen
- Extension Center for Agriculture Technology, Agriculture Department of Tibetan Autonomous Region, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
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14
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Zhao C, Sun H, Guan C, Cui J, Zhang Q, Liu M, Zhang M, Guo Q, Hou Y, Xiang M, Jiang X, Luo X, Han D, Wu Y, Cui F. Physical information of 2705 PCR-based molecular markers and the evaluation of their potential use in wheat. J Genet 2019; 98:69. [PMID: 31544776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Genetic information of polymerase chain reaction (PCR)-based markers, one of the main tools of genetics and genomics research in wheat, have been well documented in wheat. However, the physical position in relation to these markers has not yet been systematically characterized. Aim of this study was to characterize the physical information of thousands of widely used molecular markers.We first assigned 2705 molecular markers to wheat physical map, of which 86.1% and 84.7% were the best hits to chromosome survey sequencing (CSS) project (CSS-contigs) and International Wheat Genome Sequencing Consortium Reference Sequence v1.0 (IWGSC RefSeq v1.0), respectively. Physical position of 96.2% markers were predicated based on BLAST analysis, were in accordance with that of the previous nullisomic/aneuploidy/linkage analysis. A suggestive high-density physical map with 4643 loci was constructed, spanning 14.01 Gb (82.4%) of the wheat genome, with 3.02 Mb between adjacent markers. Both forward and reverse primer sequences of 1166 markers had consistent best hits to IWGSC RefSeq v1.0 based on BLAST analysis, and the corresponding allele sizes were characterized. A detailed physical map with 1532 loci was released, spanning 13.93 Gb (81.9%) of the wheat genome, with 9.09 Mb between adjacent markers. Characteristic of recombination rates in different chromosomal regions was discussed. In addition, markers with multiple sites were aligned to homoeologous sites with a consistent order, confirming that a collinearity existed among A, B and D subgenomes. This study facilitates the integration of physical and genetical information of molecular markers, which could be of value for use in genetics and genomics research such as gene/QTL map-based cloning and marker-assisted selection.
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Affiliation(s)
- Chunhua Zhao
- College of Agriculture, Ludong University, Yantai 264025, Shandong, People's Republic of China. ,
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15
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Physical information of 2705 PCR-based molecular markers and the evaluation of their potential use in wheat. J Genet 2019. [DOI: 10.1007/s12041-019-1114-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Zeng Q, Wu J, Liu S, Huang S, Wang Q, Mu J, Yu S, Han D, Kang Z. A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1409-1424. [PMID: 30707240 DOI: 10.1007/s00122-019-03288-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/16/2019] [Indexed: 05/27/2023]
Abstract
Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Ran Y, Patron N, Kay P, Wong D, Buchanan M, Cao Y, Sawbridge T, Davies JP, Mason J, Webb SR, Spangenberg G, Ainley WM, Walsh TA, Hayden MJ. Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2088-2101. [PMID: 29734518 PMCID: PMC6230953 DOI: 10.1111/pbi.12941] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 05/07/2023]
Abstract
Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides. We recovered edited wheat plants having the targeted amino acid modification in one or more AHAS homoalleles via direct selection for resistance to imazamox, an AHAS-inhibiting imidazolinone herbicide. Using a cotransformation strategy based on chemical selection for an exogenous marker, we achieved a 1.2% recovery rate of edited plants having the desired amino acid change and a 2.9% recovery of plants with targeted mutations at the AHAS locus resulting in a loss-of-function gene knockout. The latter results demonstrate a broadly applicable approach to introduce targeted modifications into native genes for nonselectable traits. All ZFN-mediated changes were faithfully transmitted to the next generation.
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Affiliation(s)
- Yidong Ran
- Genovo Biotechnology Co. LtdTianjinChina
| | | | - Pippa Kay
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Debbie Wong
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Margaret Buchanan
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Ying‐Ying Cao
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Tim Sawbridge
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | - John Mason
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | - German Spangenberg
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | | | - Matthew J. Hayden
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
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18
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Zhang W, Zhu X, Zhang M, Chao S, Xu S, Cai X. Meiotic homoeologous recombination-based mapping of wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2381-2395. [PMID: 30109393 DOI: 10.1007/s00122-018-3160-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/03/2018] [Indexed: 05/09/2023]
Abstract
We physically dissected and mapped wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum based on meiotic homoeologous recombination, providing a unique physical framework for genome studies. Common wheat has a large and complex genome with narrow genetic diversity and various degrees of recombination between the A, B, and D subgenomes. This has limited the homologous recombination-based genome studies in wheat. Here, we exploited meiotic homoeologous recombination for molecular mapping of wheat chromosome 2B and its homoeologue 2S from Aegilops speltoides and 2E from Thinopyrum elongatum. The 2B-2S and 2B-2E recombination was induced by the ph1b mutant, and recovered using molecular markers and fluorescent genomic in situ hybridization (FGISH). A total of 112 2B-2S and 87 2B-2E recombinants involving different chromosome regions were developed and physically delineated by FGISH. The 2B-2S and 2B-2E recombination hotspots mapped to the subterminal regions on both arms. Recombination hotspots with the highest recombination rates mapped to the short arms. Eighty-three 2B-2S and 67 2B-2E recombinants were genotyped using the wheat 90 K SNP arrays. Based on the genotyping results and FGISH patterns of the recombinants, chromosomes 2B, 2S, and 2E were partitioned into 93, 66, and 46 bins, respectively. In total, 1037 SNPs physically mapped onto distinct bins of these three homoeologous chromosomes. A homoeologous recombination-based bin map was constructed for chromosome 2B, providing a unique physical framework for genome studies in wheat and its relatives. Meiotic homoeologous recombination also facilitates gene introgression to diversify the wheat genome for germplasm development. Therefore, homoeologous recombination-based studies enhance understanding of the wheat genome and its homoeologous counterparts from wild grasses, and expand the genetic variability of the wheat genome.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Mingyi Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Shiaoman Chao
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND, 58102, USA
| | - Steven Xu
- USDA-ARS, Red River Valley Agricultural Research Center, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
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19
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Sun H, Hu J, Song W, Qiu D, Cui L, Wu P, Zhang H, Liu H, Yang L, Qu Y, Li Y, Li T, Cheng W, Zhou Y, Liu Z, Li J, Li H. Pm61: a recessive gene for resistance to powdery mildew in wheat landrace Xuxusanyuehuang identified by comparative genomics analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2085-2097. [PMID: 29967989 DOI: 10.1007/s00122-018-3135-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/21/2018] [Indexed: 05/23/2023]
Abstract
A single recessive powdery mildew resistance gene Pm61 from wheat landrace Xuxusanyuehuang was mapped within a 0.46-cM genetic interval spanning a 1.3-Mb interval of the genomic region of chromosome arm 4AL. Epidemics of powdery mildew incited by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt) have caused significant yield reductions in many wheat (Triticum aestivum)-producing regions. Identification of powdery mildew resistance genes is required for sustainable improvement of wheat for disease resistance. Chinese wheat landrace Xuxusanyuehuang was resistant to several Bgt isolates at the seedling stage. Genetic analysis based on the inoculation of Bgt isolate E09 on the F1, F2, and F2:3 populations produced by crossing Xuxusanyuehuang to susceptible cultivar Mingxian 169 revealed that the resistance of Xuxusanyuehuang was controlled by a single recessive gene. Bulked segregant analysis and simple sequence repeat (SSR) mapping placed the gene on chromosome bin 4AL-4-0.80-1.00. Comparative genomics analysis was performed to detect the collinear genomic regions of Brachypodium distachyon, rice, sorghum, Aegilops tauschii, T. urartu, and T. turgidum ssp. dicoccoides. Based on the use of 454 contig sequences and the International Wheat Genome Sequence Consortium survey sequence of Chinese Spring wheat, four EST-SSR and seven SSR markers were linked to the gene. An F5 recombinant inbred line population derived from Xuxusanyuehuang × Mingxian 169 cross was used to develop the genetic linkage map. The gene was localized in a 0.46-cM genetic interval between Xgwm160 and Xicsx79 corresponding to 1.3-Mb interval of the genomic region in wheat genome. This is a new locus for powdery mildew resistance on chromosome arm 4AL and is designated Pm61.
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Affiliation(s)
- Huigai Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life and Environmental Science, Minzu University of China, Beijing, 100081, China
| | - Jinghuang Hu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Song
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Biology, Hunan University, Changsha, 410082, China
| | - Dan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Cui
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China
| | - Peipei Wu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongjun Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunfeng Qu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Harbin Normal University, Harbin, 150080, China
| | - Yahui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Teng Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Cheng
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China
| | - Yang Zhou
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jingting Li
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
| | - Hongjie Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Milner MJ, Howells RM, Craze M, Bowden S, Graham N, Wallington EJ. A PSTOL-like gene, TaPSTOL, controls a number of agronomically important traits in wheat. BMC PLANT BIOLOGY 2018; 18:115. [PMID: 29884124 PMCID: PMC5994007 DOI: 10.1186/s12870-018-1331-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/24/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Phosphorus (P) is an essential macronutrient for plant growth, and is required in large quantities by elite varieties of crops to maintain yields. Approximately 70% of global cultivated land suffers from P deficiency, and it has recently been estimated that worldwide P resources will be exhausted by the end of this century, increasing the demand for crops more efficient in their P usage. A greater understanding of how plants are able to maintain yield with lower P inputs is, therefore, highly desirable to both breeders and farmers. Here, we clone the wheat (Triticum aestivum L.) homologue of the rice PSTOL gene (OsPSTOL), and characterize its role in phosphate nutrition plus other agronomically important traits. RESULTS TaPSTOL is a single copy gene located on the short arm of chromosome 5A, encoding a putative kinase protein, and shares a high level of sequence similarity to OsPSTOL. We re-sequenced TaPSTOL from 24 different wheat accessions and (3) three T. durum varieties. No sequence differences were detected in 26 of the accessions, whereas two indels were identified in the promoter region of one of the durum wheats. We characterised the expression of TaPSTOL under different P concentrations and demonstrated that the promoter was induced in root tips and hairs under P limiting conditions. Overexpression and RNAi silencing of TaPSTOL in transgenic wheat lines showed that there was a significant effect upon root biomass, flowering time independent of P treatment, tiller number and seed yield, correlating with the expression of TaPSTOL. However this did not increase PUE as elevated P concentration in the grain did not correspond to increased yields. CONCLUSIONS Manipulation of TaPSTOL expression in wheat shows it is responsible for many of the previously described phenotypic advantages as OsPSTOL except yield. Furthermore, we show TaPSTOL contributes to additional agronomically important traits including flowering time and grain size. Analysis of TaPSTOL sequences from a broad selection of wheat varieties, encompassing 91% of the genetic diversity in UK bread wheat, showed that there is very little genetic variation in this gene, which would suggest that this locus may have been under high selection pressure.
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Affiliation(s)
- Matthew J. Milner
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
| | - Rhian M. Howells
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
| | - Melanie Craze
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
| | - Sarah Bowden
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
| | - Neil Graham
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Emma J. Wallington
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
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21
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Yi X, Cheng J, Jiang Z, Hu W, Bie T, Gao D, Li D, Wu R, Li Y, Chen S, Cheng X, Liu J, Zhang Y, Cheng S. Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:573. [PMID: 29780395 PMCID: PMC5946024 DOI: 10.3389/fpls.2018.00573] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/11/2018] [Indexed: 05/21/2023]
Abstract
Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL (QFhbs-jaas.2AL, QFhbp-jaas.2DS, and QFhbp-jaas.2DL) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding.
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Affiliation(s)
- Xin Yi
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jingye Cheng
- College of Agronomy, Yangzhou University, Yangzhou, China
| | - Zhengning Jiang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Wenjing Hu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Tongde Bie
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Derong Gao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Dongsheng Li
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Ronglin Wu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Yuling Li
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shulin Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoming Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Jian Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Yong Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
| | - Shunhe Cheng
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley Ministry of Agriculture, Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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22
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Ishikawa G, Saito M, Tanaka T, Katayose Y, Kanamori H, Kurita K, Nakamura T. An efficient approach for the development of genome-specific markers in allohexaploid wheat (Triticum aestivum L.) and its application in the construction of high-density linkage maps of the D genome. DNA Res 2018; 25:4898127. [PMID: 29481583 PMCID: PMC6014326 DOI: 10.1093/dnares/dsy004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/16/2018] [Indexed: 12/20/2022] Open
Abstract
In common wheat, the development of genotyping platforms has been hampered by the large size of the genome, its highly repetitive elements and its allohexaploid nature. However, recent advances in sequencing technology provide opportunities to resolve these difficulties. Using next-generation sequencing and gene-targeting sequence capture, 12,551 nucleotide polymorphisms were detected in the common wheat varieties 'Hatsumochi' and 'Kitahonami' and were assigned to chromosome arms using International Wheat Genome Sequencing Consortium survey sequences. Because the number of markers for D genome chromosomes in commercially available wheat single nucleotide polymorphism arrays is insufficient, we developed markers using a genome-specific amplicon sequencing strategy. Approximately 80% of the designed primers successfully amplified D genome-specific products, suggesting that by concentrating on a specific subgenome, we were able to design successful markers as efficiently as could be done in a diploid species. The newly developed markers were uniformly distributed across the D genome and greatly extended the total coverage. Polymorphisms were surveyed in six varieties, and 31,542 polymorphic sites and 5,986 potential marker sites were detected in the D genome. The marker development and genotyping strategies are cost effective, robust and flexible and may enhance multi-sample studies in the post-genomic era in wheat.
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Affiliation(s)
- Goro Ishikawa
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Morioka, Iwate 020-0198, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Mika Saito
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Morioka, Iwate 020-0198, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Yuichi Katayose
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Kanako Kurita
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiki Nakamura
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Morioka, Iwate 020-0198, Japan
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23
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Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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24
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Yan J, Su P, Wei Z, Nevo E, Kong L. Genome-wide identification, classification, evolutionary analysis and gene expression patterns of the protein kinase gene family in wheat and Aegilops tauschii. PLANT MOLECULAR BIOLOGY 2017; 95:227-242. [PMID: 28918554 DOI: 10.1007/s11103-017-0637-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/16/2017] [Indexed: 05/19/2023]
Abstract
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes. QRT-PCR of 15 selected PKs were performed under drought treatment and with infection of Fusarium graminearum to validate the prediction of microarray. The protein kinase (PK) gene superfamily is one of the largest families in plants and participates in various plant processes, including growth, development, and stress response. To better understand wheat PKs, we conducted genome-wide identification, classification, evolutionary analysis and expression profiles of wheat and Ae. tauschii PKs. We identified 3269, 1213 and 1448 typical PK genes in T. aestivum, T. urartu and Ae. tauschii, respectively, and classified them into major groups and subfamilies. Domain distributions and gene structures were analyzed and visualized. Some conserved intron-exon structures within the conserved kinase domain were found in T. aestivum, T. urartu and Ae. tauschii, as well as the primitive land plants Selaginella moellendorffii and Physcomitrella patens, revealing the important roles and conserved evolutionary history of these PKs. We analyzed the collinearity events of T. aestivum PKs and identified PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed tissue-specific and stress-specific expression profiles, hinting that some wheat PKs may regulate abiotic and biotic stress response signaling pathways. QRT-PCR of 15 selected PKs were performed under drought treatment and with infection of F. graminearum to validate the prediction of microarray. Our results will provide the foundational information for further studies on the molecular functions of wheat PKs.
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Affiliation(s)
- Jun Yan
- College of Information Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Peisen Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhaoran Wei
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, 3498838, Haifa, Israel.
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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25
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Niranjana M. Gametocidal genes of Aegilops: segregation distorters in wheat-Aegilops wide hybridization. Genome 2017; 60:639-647. [PMID: 28654760 DOI: 10.1139/gen-2017-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aegilops is a genus belonging to the family Poaceace, which have played an indispensible role in the evolution of bread wheat and continues to do so by transferring genes by wide hybridization. Being the secondary gene pool of wheat, gene transfer from Aegilops poses difficulties and segregation distortion is common. Gametocidal genes are the most well characterized class of segregation distorters reported in interspecific crosses of wheat with Aegilops. These "selfish" genetic elements ensure their preferential transmission to progeny at the cost of gametes lacking them without providing any phenotypic benefits to the plant, thereby causing a proportional reduction in fertility. Gametocidal genes (Gc) have been reported in different species of Aegilops belonging to the sections Aegilops (Ae. geniculata and Ae. triuncialis), Cylindropyrum (Ae. caudata and Ae. cylindrica), and Sitopsis (Ae. longissima, Ae. sharonensis, and Ae. speltoides). Gametocidal activity is mostly confined to 2, 3, and 4 homeologous groups of C, S, S1, Ssh, and Mg genomes. Removal of such genes is necessary for successful alien gene introgression and can be achieved by mutagenesis or allosyndetic pairing. However, there are some instances where Gc genes are constructively utilized for development of deletion stocks in wheat, improving genetic variability and chromosome engineering.
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Affiliation(s)
- M Niranjana
- Indian Agricultural Research Institute, New Delhi, India.,Indian Agricultural Research Institute, New Delhi, India
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26
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Mutti JS, Bhullar RK, Gill KS. Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids. G3 (BETHESDA, MD.) 2017; 7:1225-1237. [PMID: 28193629 PMCID: PMC5386871 DOI: 10.1534/g3.116.038711] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/11/2017] [Indexed: 11/18/2022]
Abstract
Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homeologs in natural polyploids is largely unknown. To study this expression balance, the expression patterns of 2180 structurally well-characterized genes of wheat were studied, of which 813 had the expected three copies and 375 had less than three. Copy numbers of the remaining 992 ranged from 4 to 14, including homeologs, orthologs, and paralogs. Of the genes with three structural copies corresponding to homeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies. Homeologs of 76-87% of the genes showed differential expression patterns in different tissues, thus have evolved different gene expression controls, possibly resulting in novel functions. Homeologs of 55% of the genes showed tissue-specific expression, with the largest percentage (14%) in the anthers and the smallest (7%) in the pistils. The highest number (1.72/3) of homeologs/gene expression was in the roots and the lowest (1.03/3) in the anthers. As the expression of homeologs changed with changes in structural copy number, about 30% of the genes showed dosage dependence. Chromosomal location also impacted expression pattern as a significantly higher proportion of genes in the proximal regions showed expression from all three copies compared to that present in the distal regions.
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Affiliation(s)
- Jasdeep S Mutti
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Ramanjot K Bhullar
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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Pont C, Salse J. Wheat paleohistory created asymmetrical genomic evolution. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:29-37. [PMID: 28182971 DOI: 10.1016/j.pbi.2017.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/12/2016] [Accepted: 01/04/2017] [Indexed: 05/26/2023]
Abstract
Following the triplication reported in Brassiceae ∼10million years ago, and at the basis of rosids ∼100million years ago, bias in organization and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestors of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic control between the A, B and D subgenomes.
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Affiliation(s)
- Caroline Pont
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Jérôme Salse
- INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France*.
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28
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Danilova TV, Zhang G, Liu W, Friebe B, Gill BS. Homoeologous recombination-based transfer and molecular cytogenetic mapping of a wheat streak mosaic virus and Triticum mosaic virus resistance gene Wsm3 from Thinopyrum intermedium to wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:549-556. [PMID: 27900400 DOI: 10.1007/s00122-016-2834-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 05/07/2023]
Abstract
Here, we report the production of a wheat- Thinopyrum intermedium recombinant stock conferring resistance to wheat streak mosaic virus and Triticum mosaic virus. Wheat streak mosaic caused by the wheat streak mosaic virus (WSMV) is an important disease of bread wheat (Triticum aestivum) worldwide. To date, only three genes conferring resistance to WSMV have been named and two, Wsm1 and Wsm3, were derived from the distantly related wild relative Thinopyrum intermedium. Wsm3 is only available in the form of a compensating wheat-Th. intermedium whole-arm Robertsonian translocation T7BS·7S#3L. Whole-arm alien transfers usually suffer from linkage drag, which prevents their use in cultivar improvement. Here, we report ph1b-induced homoeologous recombination to shorten the Th. intermedium segment and recover a recombinant chromosome consisting of the short arm of wheat chromosome 7B, part of the long arm of 7B, and the distal 43% of the long arm derived from the Th. intermedium chromosome arm 7S#3L. The recombinant chromosome T7BS·7BL-7S#3L confers resistance to WSMV at 18 and 24 °C and also confers resistance to Triticum mosaic virus, but only at 18 °C. Wsm3 is the only gene conferring resistance to WSMV at a high temperature level of 24 °C. We also developed a user-friendly molecular marker that will allow to monitor the transfer of Wsm3 in breeding programs. Wsm3 is presently being transferred to adapted hard red winter wheat cultivars and can be used directly in wheat improvement.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Guorong Zhang
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, 67601, USA
| | - Wenxuan Liu
- Laboratory of Cell and Chromosome Engineering, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, Henan, People's Republic of China
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA.
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
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29
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Balcárková B, Frenkel Z, Škopová M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Doležel J, Valárik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. FRONTIERS IN PLANT SCIENCE 2017; 7:2063. [PMID: 28119729 PMCID: PMC5222868 DOI: 10.3389/fpls.2016.02063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
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Affiliation(s)
- Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Zeev Frenkel
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Monika Škopová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, FargoND, USA
| | - Shiaoman Chao
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, University of Minnesota, St. PaulMN, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
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30
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Wen W, He Z, Gao F, Liu J, Jin H, Zhai S, Qu Y, Xia X. A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array. FRONTIERS IN PLANT SCIENCE 2017; 8:1389. [PMID: 28848588 PMCID: PMC5552701 DOI: 10.3389/fpls.2017.01389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/25/2017] [Indexed: 05/04/2023]
Abstract
A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.
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Affiliation(s)
- Weie Wen
- College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT)Beijing, China
| | - Fengmei Gao
- Crop Breeding Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Jin
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shengnan Zhai
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China
- *Correspondence: Yanying Qu, Xianchun Xia,
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Yanying Qu, Xianchun Xia,
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31
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Liu J, He Z, Wu L, Bai B, Wen W, Xie C, Xia X. Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2179-2190. [PMID: 27531362 DOI: 10.1007/s00122-016-2766-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/30/2016] [Indexed: 05/23/2023]
Abstract
Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas-2AL, QBp.caas-2BL, QBp.caas-3AL, QBp.caas-3BL, QBp.caas-5AS, QBp.caas-6A, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS, respectively. All resistance alleles, except for QBp.caas-7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas-3BL, QBp.caas-5AS, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance.
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Affiliation(s)
- Jindong Liu
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Plant Genetics and Breeding, State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 20 Jingjusi Road, Chengdu, 610066, Sichuan, China
| | - Bin Bai
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Weie Wen
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Chaojie Xie
- Department of Plant Genetics and Breeding, State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Zhong S, Ma L, Fatima SA, Yang J, Chen W, Liu T, Hu Y, Li Q, Guo J, Zhang M, Lei L, Li X, Tang S, Luo P. Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538. PLoS One 2016; 11:e0164815. [PMID: 27755575 PMCID: PMC5068701 DOI: 10.1371/journal.pone.0164815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/01/2016] [Indexed: 11/18/2022] Open
Abstract
The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs.
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Affiliation(s)
- Shengfu Zhong
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lixia Ma
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Syeda Akash Fatima
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiezhi Yang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuting Hu
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Li
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
- Department of Biology and Chemistry, Chongqing Industry and Trade Polytechnic Institute, Fuling District of Chongqing, China
| | - Jingwei Guo
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Zhang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Lei
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States of America
| | - Xin Li
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengwen Tang
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peigao Luo
- State Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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33
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Majka J, Majka M, Kwiatek M, Wiśniewska H. Similarities and differences in the nuclear genome organization within Pooideae species revealed by comparative genomic in situ hybridization (GISH). J Appl Genet 2016; 58:151-161. [PMID: 27743251 PMCID: PMC5391381 DOI: 10.1007/s13353-016-0369-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 01/29/2023]
Abstract
In this paper, we highlight the affinity between the genomes of key representatives of the Pooideae subfamily, revealed at the chromosomal level by genomic in situ hybridization (GISH). The analyses were conducted using labeled probes from each species to hybridize with chromosomes of every species used in this study based on a “round robin” rule. As a result, the whole chromosomes or chromosome regions were distinguished or variable types of signals were visualized to prove the different levels of the relationships between genomes used in this study. We observed the unexpected lack of signals in secondary constrictions of rye (RR) chromosomes probed by triticale (AABBRR) genomic DNA. We have also identified unlabeled chromosome regions, which point to species-specific sequences connected with disparate pathways of chromosome differentiation. Our results revealed a conservative character of coding sequence of 35S rDNA among selected species of the genera Aegilops, Brachypodium, Festuca, Hordeum, Lolium, Secale, and Triticum. In summary, we showed strong relationships in genomic DNA sequences between species which have been previously reported to be phylogenetically distant.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Maciej Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Halina Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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34
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Lou X, Li X, Li A, Pu M, Shoaib M, Liu D, Sun J, Zhang A, Yang W. Molecular Characterization of Three GIBBERELLIN-INSENSITIVE DWARF2 Homologous Genes in Common Wheat. PLoS One 2016; 11:e0157642. [PMID: 27327160 PMCID: PMC4915692 DOI: 10.1371/journal.pone.0157642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/02/2016] [Indexed: 01/01/2023] Open
Abstract
F-box protein is a core component of the ubiquitin E3 ligase SCF complex and is involved in the gibberellin (GA) signaling pathway. To elucidate the molecular mechanism of GA signaling in wheat, three homologous GIBBERELLIN-INSENSITIVE DWARF2 genes, TaGID2s, were isolated from the Chinese Spring wheat variety. A subcellular localization assay in onion epidermal cells and Arabidopsis mesophyll protoplasts showed that TaGID2s are localized in the nuclei. The expression profiles using quantitative real-time polymerase chain reaction showed that TaGID2s were downregulated by GA3. The interaction between TaGID2s and TSK1 (homologous to ASK1) in yeast indicated that TaGID2s might function as a component of an E3 ubiquitin-ligase SCF complex. Yeast two-hybrid assays showed that a GA-independent interaction occurred between three TaGID2s and RHT-A1a, RHT-B1a, and RHT-D1a. Furthermore, TaGID2s interact with most RHT-1s, such as RHT-B1h, RHT-B1i, RHT-D1e, RHT-D1f, etc., but cannot interact with RHT-B1b or RHT-B1e, which have a stop codon in the DELLA motif, resulting in a lack of a GRAS domain. In addition, RHT-B1k has a frame-shift mutation in the VHIID motif leading to loss of the LHRII motif in the GRAS domain and RHT-D1h has a missense mutation in the LHRII motif. These results indicate that TaGID2s, novel positive regulators of the GA response, recognize RHT-1s in the LHRII motif resulting in poly-ubiquitination and degradation of the DELLA protein.
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Affiliation(s)
- XueYuan Lou
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - AiXia Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - MingYu Pu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Shoaib
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - DongCheng Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - JiaZhu Sun
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - AiMin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Collaborative Innovation Center for Grain crops in Henan, Henan Agricultural University, Zhengzhou, 450002, China
| | - WenLong Yang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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35
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Song L, Lu Y, Zhang J, Pan C, Yang X, Li X, Liu W, Li L. Physical mapping of Agropyron cristatum chromosome 6P using deletion lines in common wheat background. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1023-34. [PMID: 26920547 DOI: 10.1007/s00122-016-2680-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 01/23/2016] [Indexed: 05/21/2023]
Abstract
Genetically stable deletion lines of Agropyron cristatum chromosome 6P in common wheat background were generated, which allowed for physical mapping of 255 6P-specific STS markers and leaf rust resistance gene(s). Chromosomal deletion lines are valuable tools for gene discovery and localization. The chromosome 6P of Agropyron cristatum (2n = 4x = 28, PPPP) confers many desirable agronomic traits to common wheat, such as higher grain number per spike, multiple fertile tiller number, and enhanced resistance to certain diseases. Although many elite genes from A. cristatum have been identified, their chromosomal locations were largely undetermined due to the lack of A. cristatum 6P deletion lines. In this study, various A. cristatum 6P deletion lines were developed using a wheat-A. cristatum 6P disomic addition line 4844-12 subjected to (60)Co-γ irradiation as well as an Aegilops cylindrica gametocidal chromosome. Twenty-six genetically stable A. cristatum 6P deletion lines in the genetic background of common wheat were obtained, and their genetic constitutions were elucidated by genomic in situ hybridization (GISH) and sequence-tagged site (STS) markers specific to A. cristatum chromosome 6P. Moreover, 255 novel chromosome 6P-specific STS markers were physically mapped to 14 regions of chromosome 6P. Field evaluation of leaf rust resistance of various deletion lines and BC1F2 populations indicated that the A.cristatum chromosome 6P-originated leaf rust resistance gene(s) was located in the region 6PS-0.81-1.00. This study will provide not only useful tools for characterization and utilization of wheat materials with alien chromosomal segments, but also novel wheat germplasms potentially valuable in wheat breeding and improvement.
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Affiliation(s)
- Liqiang Song
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cuili Pan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A, Luo MC, Lazo G, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian S, Leonard JM. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:195-207. [PMID: 26945524 DOI: 10.1111/tpj.13153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.
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Affiliation(s)
- Vijay K Tiwari
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Adam Heesacker
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | | | - Hilary Gunn
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Shichen Wang
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yi Wang
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Young Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Etienne Paux
- Diversité et Ecophysiologie des Céréales, INRA, UMR 1095 Génétique, 5 chemin de Beaulieu, F-63039, Clermont-Ferrand, France
- Diversité et Ecophysiologie des Céréales, UMR 1095 Génétique, Université Blaise Pascal, F-63177, Aubière Cedex, France
| | - Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Gerard Lazo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Robert Zemetra
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Shahryar Kianian
- Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
| | - Jeffrey M Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
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Hu MJ, Zhang HP, Liu K, Cao JJ, Wang SX, Jiang H, Wu ZY, Lu J, Zhu XF, Xia XC, Sun GL, Ma CX, Chang C. Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA. FRONTIERS IN PLANT SCIENCE 2016; 7:1902. [PMID: 28066462 PMCID: PMC5167734 DOI: 10.3389/fpls.2016.01902] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/01/2016] [Indexed: 05/18/2023]
Abstract
Thousand-grain weight (TGW) of wheat (Triticum aestivum L.) contributes significantly to grain yield. In the present study, a candidate gene associated with TGW was identified through specific-locus amplified fragment sequencing (SLAF-seq) of DNA bulks of recombinant inbred lines (RIL) derived from the cross between Jing 411 and Hongmangchun 21. The gene was located on chromosome 7A, designated as TaTGW-7A with a complete genome sequence and an open reading frame (ORF). A single nucleotide polymorphism (SNP) was present in the first exon between two alleles at TaTGW-7A locus, resulting in a Val to Ala substitution, corresponding to a change from higher to lower TGW. Cleaved amplified polymorphic sequence (CAPS) (TGW7A) and InDel (TG9) markers were developed to discriminate the two alleles TaTGW-7Aa and TaTGW-7Ab for higher and lower TGW, respectively. A major QTL co-segregating with TaTGW-7A explained 21.7-27.1% of phenotypic variance for TGW in the RIL population across five environments. The association of TaTGW-7A with TGW was further validated in a natural population and Chinese mini-core collections. Quantitative real-time PCR revealed higher transcript levels of TaTGW-7Aa than those of TaTGW-7Ab during grain development. High frequencies of the superior allele TaTGW-7Aa for higher TGW in Chinese mini-core collections (65.0%) and 501 wheat varieties (86.0%) indicated a strong and positive selection of this allele in wheat breeding. The molecular markers TGW7A and TG9 can be used for improvement of TGW in breeding programs.
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Affiliation(s)
- Ming-Jian Hu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Hai-Ping Zhang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Kai Liu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Jia-Jia Cao
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Sheng-Xing Wang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Zeng-Yun Wu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Xiao F. Zhu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Xian-Chun Xia
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Gen-Lou Sun
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- Department of Biology, Saint Mary’s University, HalifaxNS, Canada
| | - Chuan-Xi Ma
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- *Correspondence: Cheng Chang,
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Sidhu G, Mohan A, Zheng P, Dhaliwal AK, Main D, Gill KS. Sequencing-based high throughput mutation detection in bread wheat. BMC Genomics 2015; 16:962. [PMID: 26578187 PMCID: PMC4650848 DOI: 10.1186/s12864-015-2112-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Background Forward genetic approaches have limited use for agronomic traits that can’t be reliably scored on a single plant basis. Thus, mutants in wheat and other crops are more useful for gene function studies by reverse genetic approach. With a long-term goal to develop a sequence-based mutation detection resource in hexaploid wheat, we conducted a feasibility study to accurately differentiate induced mutations from the homoeologs’ sequence variations present among the three wheat genomes. Results A reduced representation ApeKI library consisting of 21 Ethylmethane Sulfonate (EMS) induced mutants and two wild type cv. Indian plants was developed using individual barcode adapters and sequenced. A novel bioinformatics pipeline was developed to identify sequence variants using 178,464 wheat unigenes as a reference wheat transcriptome. In total, 14,130 mutational changes [Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (INDELs)] and 150,511 homoeologous sequence changes were detected. On an average, 662 SNPs (ranging from 46 to 1,330) and 10 small INDELs (ranging from 0 to 23) were identified for each of the mutants. A mutation frequency of one per 5 Kb was observed with 70 % being transitions and 30 % transversions. The pipeline was tested using the known sequence changes in the three wheat genes. Genes present in the distal regions of the chromosomes were found to be more prone to EMS compared to genes present in the proximal regions. Redefined parameters identified a total of 28,348 mutational changes (1,349/plant). Conclusions We conclude that sequencing based mutation detection is a valuable method to identify induced mutations at large. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2112-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaganjot Sidhu
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman 99164-6420, WA, USA.
| | - Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman 99164-6420, WA, USA.
| | - Ping Zheng
- Department of Horticulture, Washington State University, PO Box 646414, Pullman 99164-6414, WA, USA.
| | - Amandeep Kaur Dhaliwal
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman 99164-6420, WA, USA.
| | - Dorrie Main
- Department of Horticulture, Washington State University, PO Box 646414, Pullman 99164-6414, WA, USA.
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, PO Box 646420, Pullman 99164-6420, WA, USA.
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Barabaschi D, Magni F, Volante A, Gadaleta A, Šimková H, Scalabrin S, Prazzoli ML, Bagnaresi P, Lacrima K, Michelotti V, Desiderio F, Orrù L, Mazzamurro V, Fricano A, Mastrangelo A, Tononi P, Vitulo N, Jurman I, Frenkel Z, Cattonaro F, Morgante M, Blanco A, Doležel J, Delledonne M, Stanca AM, Cattivelli L, Valè G. Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach. THE PLANT GENOME 2015; 8:eplantgenome2015.03.0011. [PMID: 33228274 DOI: 10.3835/plantgenome2015.03.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/21/2015] [Indexed: 06/11/2023]
Abstract
The huge size, redundancy, and highly repetitive nature of the bread wheat [Triticum aestivum (L.)] genome, makes it among the most difficult species to be sequenced. To overcome these limitations, a strategy based on the separation of individual chromosomes or chromosome arms and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium (IWGSC). A total of 95,812 bacterial artificial chromosome (BAC) clones of short-arm chromosome 5A (5AS) and long-arm chromosome 5A (5AL) arm-specific BAC libraries were fingerprinted and assembled into contigs by complementary analytical approaches based on the FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) tools. Combined anchoring approaches based on polymerase chain reaction (PCR) marker screening, microarray, and sequence homology searches applied to several genomic tools (i.e., genetic maps, deletion bin map, neighbor maps, BAC end sequences (BESs), genome zipper, and chromosome survey sequences) allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively) of contigs ordered along the chromosome. In the genome of grasses, Brachypodium [Brachypodium distachyon (L.) Beauv.], rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] homologs of genes on wheat chromosome 5A were separated into syntenic blocks on different chromosomes as a result of translocations and inversions during evolution. The physical map presented represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits and a reference for the 5A sequencing projects.
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Affiliation(s)
- Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | | | - Andrea Volante
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Agata Gadaleta
- Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
| | | | - Maria Lucia Prazzoli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Katia Lacrima
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Vania Michelotti
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Luigi Orrù
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Valentina Mazzamurro
- Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
| | | | - AnnaMaria Mastrangelo
- Council for Agricultural Research and Economics (CREA)-Cereal Research Centre, Foggia, I-71122
| | - Paola Tononi
- Dep. of Biotechnology, Univ. of Verona, Verona, I-37129
| | - Nicola Vitulo
- CRIBI Biotechnology Center, Univ. of Padova, Padova, I-35121
| | | | - Zeev Frenkel
- Institute of Evolution and Dep. of Evolutionary and Environmental Biology, Univ. of Haifa, Haifa, IL-3498838
| | | | | | - Antonio Blanco
- Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
| | | | - Antonio M Stanca
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
- Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
- Council for Agricultural Research and Economics (CREA)-Rice Research Unit, Vercelli, I-13100
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40
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Koo DH, Sehgal SK, Friebe B, Gill BS. Structure and Stability of Telocentric Chromosomes in Wheat. PLoS One 2015; 10:e0137747. [PMID: 26381743 PMCID: PMC4575054 DOI: 10.1371/journal.pone.0137747] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/21/2015] [Indexed: 01/04/2023] Open
Abstract
In most eukaryotes, centromeres assemble at a single location per chromosome. Naturally occurring telocentric chromosomes (telosomes) with a terminal centromere are rare but do exist. Telosomes arise through misdivision of centromeres in normal chromosomes, and their cytological stability depends on the structure of their kinetochores. The instability of telosomes may be attributed to the relative centromere size and the degree of completeness of their kinetochore. Here we test this hypothesis by analyzing the cytogenetic structure of wheat telosomes. We used a population of 80 telosomes arising from the misdivision of the 21 chromosomes of wheat that have shown stable inheritance over many generations. We analyzed centromere size by probing with the centromere-specific histone H3 variant, CENH3. Comparing the signal intensity for CENH3 between the intact chromosome and derived telosomes showed that the telosomes had approximately half the signal intensity compared to that of normal chromosomes. Immunofluorescence of CENH3 in a wheat stock with 28 telosomes revealed that none of the telosomes received a complete CENH3 domain. Some of the telosomes lacked centromere specific retrotransposons of wheat in the CENH3 domain, indicating that the stability of telosomes depends on the presence of CENH3 chromatin and not on the presence of CRW repeats. In addition to providing evidence for centromere shift, we also observed chromosomal aberrations including inversions and deletions in the short arm telosomes of double ditelosomic 1D and 6D stocks. The role of centromere-flanking, pericentromeric heterochromatin in mitosis is discussed with respect to genome/chromosome integrity.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506–5502, United States of America
| | - Sunish K. Sehgal
- Department of Plant Science, South Dakota State University, Brookings, SD, 57007, United States of America
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506–5502, United States of America
- * E-mail:
| | - Bikram S. Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506–5502, United States of America
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41
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Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J, Gill BS, Kianian SF, Luo MC, Gu YQ. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 2015; 16:646. [PMID: 26315263 PMCID: PMC4552153 DOI: 10.1186/s12864-015-1852-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
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Affiliation(s)
- Yi Wang
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Thomas Drader
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Vijay K Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. .,Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Lingli Dong
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu
| | - Naxin Huo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.,Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA
| | - M Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Jeff Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
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42
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Shi G, Zhang Z, Friesen TL, Bansal U, Cloutier S, Wicker T, Rasmussen JB, Faris JD. Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Mol Genet Genomics 2015; 291:107-19. [PMID: 26187026 DOI: 10.1007/s00438-015-1091-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/01/2015] [Indexed: 12/29/2022]
Abstract
Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a severe foliar and glume disease on durum and common wheat. Pathogen-produced necrotrophic effectors (NEs) are the major determinants for SNB on leaves. One such NE is SnTox3, which evokes programmed cell death and leads to disease when recognized by the wheat Snn3-B1 gene. Here, we developed saturated genetic linkage maps of the Snn3-B1 region using two F2 populations derived from the SnTox3-sensitive line Sumai 3 crossed with different SnTox3-insensitive lines. Markers were identified and/or developed from various resources including previously mapped simple sequence repeats, bin-mapped expressed sequence tags, single nucleotide polymorphisms, and whole genome survey sequences. Subsequent high-resolution mapping of the Snn3-B1 locus in 5600 gametes delineated the gene to a 1.5 cM interval. Analysis of micro-colinearity of the Snn3-B1 region indicated that it was highly disrupted compared to rice and Brachypodium distachyon. The screening of a collection of durum and common wheat cultivars with tightly linked markers indicated they are not diagnostic for the presence of Snn3-B1, but can be useful for marker-assisted selection if the SnTox3 reactions of lines are first determined. Finally, we developed an ethyl methanesulfonate-induced mutant population of Sumai 3 where the screening of 408 M2 families led to the identification of 17 SnTox3-insensitive mutants. These mutants along with the markers and high-resolution map developed in this research provide a strong foundation for the map-based cloning of Snn3-B1, which will broaden our understanding of the wheat-P. nodorum system and plant-necrotrophic pathogen interactions in general.
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Affiliation(s)
- Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58102, USA
| | - Zengcui Zhang
- USDA-ARS Cereal Crops Research Unit, USDA-ARS NPA NCSL, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA
| | - Timothy L Friesen
- USDA-ARS Cereal Crops Research Unit, USDA-ARS NPA NCSL, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA
| | - Urmil Bansal
- The University of Sydney PBI-Cobbity, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Sylvie Cloutier
- Eastern Cereal and Oil Research Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, USDA-ARS NPA NCSL, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA.
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Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
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Jo KM, Jo Y, Chu H, Lian S, Cho WK. Development of EST-derived SSR markers using next-generation sequencing to reveal the genetic diversity of 50 chrysanthemum cultivars. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Maciąga M, Szkop M, Paszkowski A. Chromosomal Localization and Contribution of Three Homoeologous Genes to Biosynthesis of Cytosolic Aspartate Aminotransferase in Common Wheat. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, INDIA. SECTION B 2015; 86:945-951. [PMID: 27881898 PMCID: PMC5102977 DOI: 10.1007/s40011-015-0536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 02/23/2015] [Accepted: 04/23/2015] [Indexed: 11/27/2022]
Abstract
Chromosomal localization of the three homoeologous genes encoding cytosolic aspartate aminotransferase in common wheat (Triticum aestivum cv. Chinese Spring, 2n = 6x = 42, AABBDD) was specified to: 3AL (0.42÷0.61), 3BL (0.38÷0.41) and 3DL (0.23÷0.81) by a comparative zymographic analysis of the enzymatic activities in deletion lines. It was also attempted to precisely explain the nature of the relationship between a number of genes encoding α and β subunits and a distribution of staining intensity of cytosolic aspartate aminotransferase allozyme activity bands using aneuploid lines of common wheat with modified third pair of homoeologous chromosomes from genomes A, B and D, on which the genes encoding subunit α (genome A) and β (genome B and D) are localized. The highest consistency between the experimental results and the theoretical distributions was achieved by substituting values of α = 0.57 and β = 0.43 in a theoretical model. These results demonstrate that the individual participation of the diploid genome A in the biosynthesis of the cytosolic aspartate aminotransferase allozymes subunits is greater than the individual participation of the diploid genomes B and D.
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Affiliation(s)
- Marcin Maciąga
- Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michał Szkop
- Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Andrzej Paszkowski
- Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences – SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
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Gao Y, Faris JD, Liu Z, Kim YM, Syme RA, Oliver RP, Xu SS, Friesen TL. Identification and Characterization of the SnTox6-Snn6 Interaction in the Parastagonospora nodorum-Wheat Pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:615-25. [PMID: 25608181 DOI: 10.1094/mpmi-12-14-0396-r] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Parastagonospora nodorum is a necrotrophic fungal pathogen that causes Septoria nodorum blotch (SNB) (formerly Stagonospora nodorum blotch) on wheat. P. nodorum produces necrotrophic effectors (NE) that are recognized by dominant host sensitivity gene products resulting in disease development. The NE-host interaction is critical to inducing NE-triggered susceptibility (NETS). To date, seven NE-host sensitivity gene interactions, following an inverse gene-for-gene model, have been identified in the P. nodorum-wheat pathosystem. Here, we used a wheat mapping population that segregated for sensitivity to two previously characterized interactions (SnTox1-Snn1 and SnTox3-Snn3-B1) to identify and characterize a new interaction involving the NE designated SnTox6 and the host sensitivity gene designated Snn6. SnTox6 is a small secreted protein that induces necrosis on wheat lines harboring Snn6. Sensitivity to SnTox6, conferred by Snn6, was light-dependent and was shown to underlie a major disease susceptibility quantitative trait locus (QTL). No other QTL were identified, even though the P. nodorum isolate used in this study harbored both the SnTox1 and SnTox3 genes. Reverse transcription-polymerase chain reaction showed that the expression of SnTox1 was not detectable, whereas SnTox3 was expressed and, yet, did not play a significant role in disease development. This work expands our knowledge of the wheat-P. nodorum interaction and further establishes this system as a model for necrotrophic specialist pathosystems.
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Affiliation(s)
- Y Gao
- 1Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - J D Faris
- 2USDA-ARS, Northern Crop Science Lab, Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
| | - Z Liu
- 1Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Y M Kim
- 1Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - R A Syme
- 3Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Western Australia, Australia
| | - R P Oliver
- 3Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Western Australia, Australia
| | - S S Xu
- 2USDA-ARS, Northern Crop Science Lab, Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
| | - T L Friesen
- 1Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- 2USDA-ARS, Northern Crop Science Lab, Cereal Crops Research Unit, Fargo, ND 58102, U.S.A
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Cviková K, Cattonaro F, Alaux M, Stein N, Mayer KF, Doležel J, Bartoš J. High-throughput physical map anchoring via BAC-pool sequencing. BMC PLANT BIOLOGY 2015; 15:99. [PMID: 25887276 PMCID: PMC4407875 DOI: 10.1186/s12870-015-0429-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/20/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers. Here we present a novel approach for anchoring physical maps, based on sequencing three-dimensional pools of BAC clones from minimum tilling path. RESULTS We used physical map of wheat chromosome arm 3DS to validate the method with two different DNA sequence datasets. The first comprised 567 genes ordered along the chromosome arm based on syntenic relationship of wheat with the sequenced genomes of Brachypodium, rice and sorghum. The second dataset consisted of 7,136 SNP-containing sequences, which were mapped genetically in Aegilops tauschii, the donor of the wheat D genome. Mapping of sequence reads from individual BAC pools to the first and the second datasets enabled unambiguous anchoring 447 and 311 3DS-specific sequences, respectively, or 758 in total. CONCLUSIONS We demonstrate the utility of the novel approach for BAC contig anchoring based on mass parallel sequencing of three-dimensional pools prepared from minimum tilling path of physical map. The existing genetic markers as well as any other DNA sequence could be mapped to BAC clones in a single in silico experiment. The approach reduces significantly the cost and time needed for anchoring and is applicable to any genomic project involving the construction of anchored physical map.
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Affiliation(s)
- Kateřina Cviková
- Institute of Experimental Botany, Centre of Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc-Holice, Czech Republic.
| | - Federica Cattonaro
- Istituto di Genomica Applicata, Via J. Linussio 51, 33100, Udine, Italy.
| | - Michael Alaux
- INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026, Versailles, France.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, OT Gatersleben, Germany.
| | - Klaus Fx Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc-Holice, Czech Republic.
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc-Holice, Czech Republic.
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48
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Zhang Z, Zhu H, Gill BS, Li W. Fine mapping of shattering locus Br2 reveals a putative chromosomal inversion polymorphism between the two lineages of Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:745-755. [PMID: 25656150 DOI: 10.1007/s00122-015-2469-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
This work laid the foundation for cloning of shattering gene Br2 and provided first line of evidence that two major Aegilops tauschii lineages are differentiated by an inversion polymorphism. Chromosome inversions often accompany population differentiation and capture local adaptation during speciation. Aegilops tauschii, the D-genome donor species of hexaploid wheat, consists of two genetically isolated lineages, L1 and L2, but little is known about the genetic mechanisms underlying the population differentiation in this diploid species. During fine mapping of the shattering gene Br2 using a large F2 population derived from a cross between TA1604 (an L1 accession) and AL8/78 (an L2 accession), we found contrasting patterns of crossover distribution in the Br2 interval and neighboring regions despite the high local gene synteny with Brachypodium distachyon and rice. Br2 was localized in a 0.08-cM interval, and 13 marker loci formed a block, where single-crossovers were completely suppressed, but double-crossovers were enriched with a recombination rate of ~11 cM/Mb. In contrast, in a neighboring region no double-crossover was recovered, but single-crossover rate reached 24 cM/Mb, which is much higher than the genome-wide average. This result suggests a putative inversion polymorphism between the parental lines in the Br2 region. Genotyping using the markers from the Br2 region divided a collection of 55 randomly sampled A. tauschii accessions into two major groups, and they are largely genetically isolated. The two groups correspond to the L1 and L2 lineages based on their geographic distribution patterns. This provides first evidence that inversions may underlie the evolution of A. tauschii lineages. The presence of inter-lineage inversions may complicate map-based cloning in A. tauschii and transfer of useful traits to wheat.
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Affiliation(s)
- Zhengzhi Zhang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
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49
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Shen XK, Ma LX, Zhong SF, Liu N, Zhang M, Chen WQ, Zhou YL, Li HJ, Chang ZJ, Li X, Bai GH, Zhang HY, Tan FQ, Ren ZL, Luo PG. Identification and genetic mapping of the putative Thinopyrum intermedium-derived dominant powdery mildew resistance gene PmL962 on wheat chromosome arm 2BS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:517-528. [PMID: 25556931 DOI: 10.1007/s00122-014-2449-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Powdery resistance putatively derived from Thinopyrum intermedium in the wheat line L962 is controlled by a single dominant gene designated PmL962 and mapped to chromosome arm 2BS. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease affecting the production of wheat (Triticum aestivum). Powdery mildew resistance was putatively transferred from Thinopyrum intermedium to the common wheat line L962, which conferred resistance to multiple Chinese Bgt isolates. Genetic analysis of the powdery mildew response was conducted by crossing the resistant line L962 with the susceptible line L983. Disease assessments of the F1, F2, and F2:3 populations from the cross L983/L962 indicated that resistance was controlled by a single dominant gene. A total of 373 F2:3 lines and 781 pairs of genomic simple sequence repeat (SSR) primers were employed to determine the chromosomal location of the resistance gene. The gene was linked to four publicly available and recently developed wheat genomic SSR markers and seven EST-STS markers. The resistance gene was mapped to chromosome arm 2BS based on the locations of the linked markers. Pedigree, molecular marker and resistance response data indicated that the powdery mildew resistance gene in L962 is novel. It was temporarily designated PmL962. It is flanked by Xwmc314 and BE443737at genetic distances of 2.09 and 3.74 cM, respectively, and located in a 20.77 cM interval that is co-linear with a 269.4 kb genomic region on chromosome 5 in Brachypodium distachyon and a 223.5 kb genomic region on rice (Oryza sativa) chromosome 4. The markers that are closely linked to this gene have potential applications in marker-assisted breeding.
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Affiliation(s)
- X K Shen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
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50
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Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol 2015; 16:48. [PMID: 25886949 PMCID: PMC4389885 DOI: 10.1186/s13059-015-0606-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0606-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine W Jordan
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shichen Wang
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Yanni Lun
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Ron MacLachlan
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Pierre Hucl
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Krysta Wiebe
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Debbie Wong
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Kerrie L Forrest
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | | | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Timothy Close
- Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Jorge Dubcovsky
- Department Plant Sciences, University of California, Davis, CA, 95616, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Alina Akhunova
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. .,Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
| | - Luther Talbert
- Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
| | - Urmil K Bansal
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Harbans S Bariana
- Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia.
| | - Curtis Pozniak
- Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | | | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Eduard Akhunov
- Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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