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Man-Yu Y, Fang-Jie Y, Zu-Jun Y, En-Nian Y. Investigation of chromosomal genetic characteristics and identification of structural variation in the offspring of hexaploid triticale× hexaploid wheat. Yi Chuan 2024; 46:63-77. [PMID: 38230457 DOI: 10.16288/j.yczz.23-212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Hexaploid triticale is an important genetic resource for genetic improvement of common wheat, which can broaden the genetic basis of wheat. In order to lay a foundation for the subsequent research and utilization of triticale germplasm materials, the chromosomal genetic characteristics of cross and backcross offspring of hexaploid triticale×hexaploid wheat were investigated in the process of transferring rye chromatin from hexaploid triticale to hexaploid wheat. Hybrid and backcross combinations were prepared with hexaploid triticale 16yin171 as the maternal parent and hexaploid wheat Chuanmai62 as the paternal parent. The chromosomes in root tip cells of F1, BC1F1 and BC1F2 plants were traced and identified non-denaturing florescence in situ hybridization (ND-FISH). The results indicated that the backcross setting rate of hybrid F1 was 2.61%. The transmission frequency of 2R chromosome was the highest in BC1F1 plants while the transmissibility of rye chromosome in BC1F2 plant was 6R>4R>2R, and the 5B-7B wheat translocation in BC1F2 plants showed severe segregation. A total of 24 structural variant chromosomes were observed both in BC1F1 and BC1F2 plants, including chromosome fragments, isochromosomes, translocations, and dicentric chromosomes. In addition, the seed length and 1000-grain weight of some BC1F2 plants were better than that of the hexaploid wheat parent Chuanmai 62. Therefore, multiple backcrosses should be adopted as far as possible to make the rapid recovery of group D chromosomes, ensuring the recovery of fertility in offspring, when hexaploid tritriale is used as a bridge to introduce rye genetic material into common wheat. At the same time, the potential application value of chromosomal structural variation materials should be also concerned.
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Affiliation(s)
- Yang Man-Yu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Key Laboratory of Tianfu Seed Industry Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Yao Fang-Jie
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Key Laboratory of Tianfu Seed Industry Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Yang Zu-Jun
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yang En-Nian
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Key Laboratory of Tianfu Seed Industry Innovation (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
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Draeger TN, Rey MD, Hayta S, Smedley M, Martin AC, Moore G. DMC1 stabilizes crossovers at high and low temperatures during wheat meiosis. Front Plant Sci 2023; 14:1208285. [PMID: 37615022 PMCID: PMC10442654 DOI: 10.3389/fpls.2023.1208285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023]
Abstract
Effective chromosome synapsis and crossover formation during meiosis are essential for fertility, especially in grain crops such as wheat. These processes function most efficiently in wheat at temperatures between 17-23 °C, although the genetic mechanisms for such temperature dependence are unknown. In a previously identified mutant of the hexaploid wheat reference variety 'Chinese Spring' lacking the long arm of chromosome 5D, exposure to low temperatures during meiosis resulted in asynapsis and crossover failure. In a second mutant (ttmei1), containing a 4 Mb deletion in chromosome 5DL, exposure to 13 °C led to similarly high levels of asynapsis and univalence. Moreover, exposure to 30 °C led to a significant, but less extreme effect on crossovers. Previously, we proposed that, of 41 genes deleted in this 4 Mb region, the major meiotic gene TaDMC1-D1 was the most likely candidate for preservation of synapsis and crossovers at low (and possibly high) temperatures. In the current study, using RNA-guided Cas9, we developed a new Chinese Spring CRISPR mutant, containing a 39 bp deletion in the 5D copy of DMC1, representing the first reported CRISPR-Cas9 targeted mutagenesis in Chinese Spring, and the first CRISPR mutant for DMC1 in wheat. In controlled environment experiments, wild-type Chinese Spring, CRISPR dmc1-D1 and backcrossed ttmei1 mutants were exposed to either high or low temperatures during the temperature-sensitive period from premeiotic interphase to early meiosis I. After 6-7 days at 13 °C, crossovers decreased by over 95% in the dmc1-D1 mutants, when compared with wild-type plants grown under the same conditions. After 24 hours at 30 °C, dmc1-D1 mutants exhibited a reduced number of crossovers and increased univalence, although these differences were less marked than at 13 °C. Similar results were obtained for ttmei1 mutants, although their scores were more variable, possibly reflecting higher levels of background mutation. These experiments confirm our previous hypothesis that DMC1-D1 is responsible for preservation of normal crossover formation at low and, to a certain extent, high temperatures. Given that reductions in crossovers have significant effects on grain yield, these results have important implications for wheat breeding, particularly in the face of climate change.
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Affiliation(s)
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Azahara C. Martin
- Department of Plant Genetic Improvement, Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Lee MH, Choi C, Kim KH, Son JH, Lee GE, Choi JY, Kang CS, Shon J, Ko JM, Kim KM. Generation of Wheat Near-Isogenic Lines Overexpressing 1Bx7 Glutenin with Increased Protein Contents and SDS-Sedimentation Values. Plants (Basel) 2023; 12:1244. [PMID: 36986938 PMCID: PMC10051937 DOI: 10.3390/plants12061244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Overexpression of Glu-1Bx7 via allele 1Bx7OE significantly contributes to high dough strength in some wheat varieties and is useful for improving wheat quality. However, the proportion of wheat varieties containing Bx7OE is quite low. In this study, four cultivars containing 1Bx7OE were selected, and among the selected varieties, Chisholm (1Ax2*, 1Bx7OE + 1By8*, and 1Dx5 + 1Dx10) was crossed with Keumkang, a wheat variety that contains 1Bx7 (1Ax2*, 1Bx7 + 1By8, and 1Dx5 + 1Dx10). SDS-PAGE and UPLC analyses showed that the expression of the high-molecular-weight glutenin subunit (HMW-GS) 1Bx7 was significantly higher in NILs (1Ax2*, 1Bx7OE + 1By8*, and 1Dx5 + 1Dx10) compared with that in Keumkang. Wheat quality was analyzed with near infrared reflectance spectroscopy by measuring the protein content and SDS-sedimentation of NILs. The protein content of NILs (12.94%) was 21.65% higher than that of Chisholm (10.63%) and 4.54% higher than that of Keumkang (12.37%). In addition, the SDS-sedimentation value of NILs (44.29 mL) was 14.97% and 16.44% higher than that of Keumkang (38.52 mL) and Chisholm (38.03 mL), respectively. This study predicts that the quality of domestic wheat can be improved by crossbreeding with 1Bx7OE-containing cultivars.
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Wu N, He Z, Fang J, Liu X, Shen X, Zhang J, Lei Y, Xia Y, He H, Liu W, Chu C, Wang C, Qi Z. Chromosome diversity in Dasypyrum villosum, an important genetic and trait resource for hexaploid wheat engineering. Ann Bot 2023; 131:185-198. [PMID: 35451455 PMCID: PMC9904354 DOI: 10.1093/aob/mcac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/20/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Dasypyrum villosum (2n = 2x = 14) harbours potentially beneficial genes for hexaploid and tetraploid wheat improvement. Highly diversified chromosome variation exists among and within accessions due to its open-pollination nature. The wheat-D. villosum T6VS·6AL translocation was widely used in breeding mainly because gene Pm21 in the 6VS segment conferred high and lasting powdery mildew resistance. However, the widespread use of this translocation may narrow the genetic base of wheat. A better solution is to utilize diversified D. villosum accessions as the genetic source for wheat breeding. Analysis of cytological and genetic polymorphisms among D. villosum accessions also provides genetic evolution information on the species. Using cytogenetic and molecular tools we analysed genetic polymorphisms among D. villosum accessions and developed consensus karyotypes to assist the introgression of beneficial genes from D. villosum into wheat. METHODS A multiplex probe of repeats for FISH, GISH and molecular markers were used to detect chromosome polymorphisms among D. villosum accessions. Polymorphic signal block types, chromosome heterogeneity and heterozygosity, and chromosome polymorphic information content were used in genetic diversity analysis. KEY RESULTS Consensus karyotypes of D. villosum were developed, and the homoeologous statuses of individual D. villosum chromosomes relative to wheat were determined. Tandem repeat probes of pSc119.2, (GAA)10 and the AFA family produced high-resolution signals and not only showed different signal patterns in D. villosum chromosomes but also revealed the varied distribution of tandem repeats among chromosomes and accessions. A total of 106 polymorphic chromosomes were identified from 13 D. villosum accessions and high levels of chromosomal heterozygosity and heterogeneity were observed. A subset of 56 polymorphic chromosomes was transferred into durum wheat through wide crosses, and seven polymorphic chromosomes are described in two newly developed durum-D. villosum amphidiploids. CONCLUSIONS Consensus karyotypes of D. villosum and oligonucleotide FISH facilitated identification of polymorphic signal blocks and a high level of chromosomal heterozygosity and heterogeneity among D. villosum accessions, seen in newly developed amphiploids. The abundant genetic diversity of D. villosum and range of alleles, exploitable through interploid crosses, backcrosses and recombination (chromosome engineering), allow introduction of biotic and abiotic stress resistances into wheat, translating into increasing yield, end-use quality and crop sustainability.
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Affiliation(s)
- Nan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziming He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaxin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xia Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhong Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yating Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Huagang He
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wenxuan Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Chenggen Chu
- USDA-ARS, Sugarbeet & Potato Research Unit, Fargo, ND 58102, USA
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Lu Y, Ha M, Li X, Wang J, Mo R, Zhang A. Distribution, expression of hexaploid wheat Fes1s and functional characterization of two TaFes1As in Arabidopsis. Front Plant Sci 2022; 13:1037989. [PMID: 36325559 PMCID: PMC9621618 DOI: 10.3389/fpls.2022.1037989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Hexaploid wheat is a major food crop and is sensitive to heat stress. It is necessary to discover genes related to thermotolerance in wheat. Fes1s is a class of nucleotide exchange factor of heat shock protein 70s, proven to be participated in heat response in human, yeast, and Arabidopsis. However, little is known about Fes1s in hexaploid wheat. In this study, we identified nine Fes1s in hexaploid wheat (TaFes1s) and found that they present as three triads. A phylogenetic relationship analysis revealed that these Fes1s grouped into Fes1A, Fes1B and Fes1C subclades, and Fes1As and Fes1Bs were divergent in monocots, but possibly not in dicots. The sequences, gene structures and protein motifs of TaFes1s homoeologues within a triad were highly conserved. Through cis-elements analysis including heat shock elements, and miRNA targets prediction, we found that regulation of three TaFes1s homoeologues may be different, while the expression patterns of three homoeologues were similar. The expression levels of TaFes1As were higher than those of TaFes1Bs and TaFes1Cs, and based on these expressions, TaFes1As were chosen for functional characterization. Intriguingly, neither TaFes1A-5A nor TaFes1A-5D could not rescue the thermotolerance defect of Arabidopsis fes1a mutants at seedling stage, but in the transgenic plants seed germination was accelerated under normal and heat stress condition. The functional characterization indicated that roles of Fes1As would be different in Arabidopsis and hexaploid wheat, and function retention of TaFes1As may occur during wheat evolution. In conclusion, our study comprehensively characterized the distribution and expression of Fes1s in hexaploid wheat and found that two TaFes1As could accelerate seed germination under normal and heat stress condition.
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Affiliation(s)
- Yunze Lu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Mingran Ha
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Xinming Li
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Junzhe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Ruirui Mo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Aihua Zhang
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
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Lee MH, Kim KM, Sang WG, Kang CS, Choi C. Comparison of Gene Expression Changes in Three Wheat Varieties with Different Susceptibilities to Heat Stress Using RNA-Seq Analysis. Int J Mol Sci 2022; 23:ijms231810734. [PMID: 36142649 PMCID: PMC9505106 DOI: 10.3390/ijms231810734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 12/04/2022] Open
Abstract
Wheat is highly susceptible to heat stress, which significantly reduces grain yield. In this study, we used RNA-seq technology to analyze the transcript expression at three different time-points after heat treatment in three cultivars differing in their susceptibility to heat stress: Jopum, Keumkang, and Olgeuru. A total of 11,751, 8850, and 14,711; 10,959, 7946, and 14,205; and 22,895, 13,060, and 19,408 differentially-expressed genes (log2 fold-change > 1 and FDR (padj) < 0.05) were identified in Jopum, Keumkang, and Olgeuru in the control vs. 6-h, in the control vs. 12-h, and in the 6-h vs. 12-h heat treatment, respectively. Functional enrichment analysis showed that the biological processes for DEGs, such as the cellular response to heat and oxidative stress—and including the removal of superoxide radicals and the positive regulation of superoxide dismutase activity—were significantly enriched among the three comparisons in all three cultivars. Furthermore, we investigated the differential expression patterns of reactive oxygen species (ROS)-scavenging enzymes, heat shock proteins, and heat-stress transcription factors using qRT-PCR to confirm the differences in gene expression among the three varieties under heat stress. This study contributes to a better understanding of the wheat heat-stress response at the early growth stage and the varietal differences in heat tolerance.
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Wang X, Yan X, Hu Y, Qin L, Wang D, Jia J, Jiao Y. A recent burst of gene duplications in Triticeae. Plant Commun 2022; 3:100268. [PMID: 35529951 PMCID: PMC9073319 DOI: 10.1016/j.xplc.2021.100268] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 11/09/2021] [Accepted: 12/09/2021] [Indexed: 06/13/2023]
Abstract
Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement. The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years, but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated. Here, we found that a recent burst of gene duplications (hereafter abbreviated as the RBGD) has probably occurred in all sequenced Triticeae species. Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element (TE) activity may have been involved in generating the RBGD. We also characterized the duplication timing, retention pattern, diversification, and expression of the duplicates following the evolution of Triticeae. Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat. Moreover, several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat. Our results provide insights into a unique source of gene duplicates in Triticeae species, which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.
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Affiliation(s)
- Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daowen Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Jizeng Jia
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, Henan 450046, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Othmeni M, Grewal S, Walker J, Yang CY, King IP, King J. Assessing the Potential of Using the Langdon 5D(5B) Substitution Line for the Introgression of Aegilops tauschii Into Durum Wheat. Front Plant Sci 2022; 13:927728. [PMID: 35873983 PMCID: PMC9302120 DOI: 10.3389/fpls.2022.927728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/07/2022] [Indexed: 05/17/2023]
Abstract
Aegilops tauschii, the D-genome donor of hexaploid wheat, provides a source of genetic variation that could be used for tetraploid (durum) wheat improvement. In addition to the genes for wheat quality on the D-genome, which differentiate between bread and durum wheats in terms of end-use properties, genes coding for resistances to biotic and abiotic stresses are also present on the D-genome which would be useful in durum wheat. The introgression of Ae. tauschii into durum wheat, however, requires cytogenetic manipulation to induce homoeologous chromosome pairing to promote recombination. For this purpose, the introgression of Ae. tauschii into durum wheat was performed through a bridge cross of the wild species to the Langdon 5D(5B) disomic substitution line that lacks the Ph1 locus present on chromosome 5B, followed by a cross of the F1 to the durum wheat cultivar Om Rabi 5. Subsequent generations were self-fertilized, and these were screened for D-genome introgressions using (i) D-genome-specific Kompetitive Allele-Specific PCR (KASP) markers and (ii) KASP markers polymorphic between the 5D chromosomes of wheat, present in the Langdon 5D(5B) substitution line, and of Ae. tauschii. Homozygous introgression lines were confirmed using genomic and fluorescence in situ hybridization. The results showed that the use of the Langdon 5D(5B) disomic substitution line did not promote D-genome introgression across all linkage groups with only a limited success in the introgression of Ae. tauschii 5D segments into durum wheat.
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Nyine M, Adhikari E, Clinesmith M, Jordan KW, Fritz AK, Akhunov E. Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative. G3 (Bethesda) 2020; 10:3651-61. [PMID: 32737066 DOI: 10.1534/g3.120.401479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.
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Takenaka S, Nitta M, Nasuda S. Population structure and association analyses of the core collection of hexaploid accessions conserved ex situ in the Japanese gene bank NBRP-Wheat. Genes Genet Syst 2018; 93:237-254. [PMID: 30555105 DOI: 10.1266/ggs.18-00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this study, we investigated the genetic diversity and population structure of the core collection of hexaploid wheat accessions in the Japanese wheat gene bank NBRP-Wheat. The core collection, consisting of 188 accessions of Triticum aestivum, T. spelta, T. compactum, T. sphaerococcum, T. macha and T. vavilovii, was intensively genotyped by DArTseq markers and consisted of 20,186 SNPs and 60,077 present and absent variations (PAVs). Polymorphic markers were distributed in all chromosomes, with a tendency for smaller numbers on the D-genome chromosomes. We examined the population structure by Bayesian clustering and principal component analysis with a general linear model. Overall, the core collection was divided into seven clusters. Non-admixture accessions in each cluster indicated that the clusters reflect the geographic distribution of the accessions. Both structure analyses strongly suggested that the cluster consisting of T. spelta and T. macha is out-grouped from other hexaploid wheat accessions. We performed genome-wide association analysis pilot studies for nine quantitative and seven qualitative traits and found marker-trait associations for all traits but one, indicating that the current core collection will be useful for detecting uncharacterized QTLs associated with phenotypes of interest.
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Affiliation(s)
- Shotaro Takenaka
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University.,Department of Plant Life Science, Faculty of Agriculture, Ryukoku University
| | - Miyuki Nitta
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
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Liang Z, Chen K, Yan Y, Zhang Y, Gao C. Genotyping genome-edited mutations in plants using CRISPR ribonucleoprotein complexes. Plant Biotechnol J 2018; 16:2053-2062. [PMID: 29723918 PMCID: PMC6230946 DOI: 10.1111/pbi.12938] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 05/04/2023]
Abstract
Despite the great achievements in genome editing, accurately detecting mutations induced by sequence-specific nucleases is still a challenge in plants, especially in polyploidy plants. An efficient detection method is particularly vital when the mutation frequency is low or when a large population needs to be screened. Here, we applied purified CRISPR ribonucleoprotein complexes to cleave PCR products for genome-edited mutation detection in hexaploid wheat and diploid rice. We show that this mutation detection method is more sensitive than Sanger sequencing and more applicable than PCR/RE method without the requirement for restriction enzyme site. We also demonstrate that this detection method is especially useful for genome editing in wheat, because target sites are often surrounded by single nucleotide polymorphisms. Using this screening method, we were also able to detect foreign DNA-free tagw2 mutations induced by purified TALEN protein. Finally, we show that partial base editing mutations can also be detected using high-fidelity SpCas9 variants or FnCpf1. The PCR/RNP method is low-cost and widely applicable for rapid detection of genome-edited mutation in plants.
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Affiliation(s)
- Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yan Yan
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yi Zhang
- Key Laboratory of Plant Stress ResearchCollege of Life ScienceShandong Normal UniversityJinanChina
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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12
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Abstract
Despite the great achievements in genome editing, accurately detecting mutations induced by sequence-specific nucleases is still a challenge in plants, especially in polyploidy plants. An efficient detection method is particularly vital when the mutation frequency is low or when a large population needs to be screened. Here, we applied purified CRISPR ribonucleoprotein complexes to cleave PCR products for genome-edited mutation detection in hexaploid wheat and diploid rice. We show that this mutation detection method is more sensitive than Sanger sequencing and more applicable than PCR/RE method without the requirement for restriction enzyme site. We also demonstrate that this detection method is especially useful for genome editing in wheat, because target sites are often surrounded by single nucleotide polymorphisms. Using this screening method, we were also able to detect foreign DNA-free tagw2 mutations induced by purified TALEN protein. Finally, we show that partial base editing mutations can also be detected using high-fidelity SpCas9 variants or FnCpf1. The PCR/RNP method is low-cost and widely applicable for rapid detection of genome-edited mutation in plants.
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Affiliation(s)
- Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Yan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Zhang
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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13
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Akpinar BA, Biyiklioglu S, Alptekin B, Havránková M, Vrána J, Doležel J, Distelfeld A, Hernandez P, Budak H. Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides. Plant Biotechnol J 2018; 16:2077-2087. [PMID: 29729062 PMCID: PMC6230948 DOI: 10.1111/pbi.12940] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.
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Affiliation(s)
- Bala Ani Akpinar
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Sezgi Biyiklioglu
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Burcu Alptekin
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Miroslava Havránková
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Assaf Distelfeld
- Department of Molecular Biology and Ecology of PlantsFaculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS)Consejo Superior de Investigaciones Científicas (CSIC)CordobaSpain
| | - The IWGSC
- International Wheat Genome Sequencing ConsortiumBethesdaMDUSA
| | - Hikmet Budak
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
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14
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Ullah S, Bramley H, Daetwyler H, He S, Mahmood T, Thistlethwaite R, Trethowan R. Genetic Contribution of Emmer Wheat ( Triticum dicoccon Schrank) to Heat Tolerance of Bread Wheat. Front Plant Sci 2018; 9:1529. [PMID: 30524452 PMCID: PMC6257323 DOI: 10.3389/fpls.2018.01529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/28/2018] [Indexed: 05/16/2023]
Abstract
Rising global temperatures cause substantial yield losses in many wheat growing environments. Emmer wheat (Triticum dicoccon Schrank), one of the first wheat species domesticated, carries significant variation for tolerance to abiotic stresses. This study identified new genetic variability for high-temperature tolerance in hexaploid progeny derived from crosses with emmer wheat. Eight hexaploid and 11 tetraploid parents were recombined in 43 backcross combinations using the hexaploid as the recurrent parent. A total of 537 emmer-based hexaploid lines were developed by producing approximately 10 doubled haploids on hexaploid like BC1F1 progeny and subsequent selection for hexaploid morphology. These materials and 17 commercial cultivars and hexaploid recurrent parents were evaluated under two times of sowing in the field, in 2014-2016. The materials were genotyped using a 90K SNP platform and these data were used to estimate the contribution of emmer wheat to the progeny. Significant phenotypic and genetic variation for key agronomical traits including grain yield, TKW and screenings was observed. Many of the emmer derived lines showed improved performance under heat stress (delayed sowing) compared with parents and commercial cultivars. Emmer derived lines were the highest yielding material in both sowing dates. The emmer wheat parent contributed between 1 and 44% of the genome of the derived lines. Emmer derived lines with superior kernel weight and yield generally had a greater genetic contribution from the emmer parent compared to those with lower trait values. The study showed that new genetic variation for key traits such as yield, kernel weight and screenings can be introduced to hexaploid wheat from emmer wheat. These genetic resources should be explored more systematically to stabilize grain yield and quality in a changing climate.
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Affiliation(s)
- Smi Ullah
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Melbourne, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia
| | - Sang He
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Melbourne, VIC, Australia
| | - Tariq Mahmood
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
| | - Rebecca Thistlethwaite
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, Australia
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, The University of Sydney, Cobbitty, NSW, Australia
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Takahagi K, Inoue K, Mochida K. Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat. Front Plant Sci 2018; 9:1163. [PMID: 30135697 PMCID: PMC6092485 DOI: 10.3389/fpls.2018.01163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/23/2018] [Indexed: 05/20/2023]
Abstract
Genome duplications aid in the formation of novel molecular networks through regulatory differentiation of the duplicated genes and facilitate adaptation to environmental change. Hexaploid wheat, Triticum aestivum, contains three homoeologous chromosome sets, the A-, B-, and D-subgenomes, which evolved through interspecific hybridization and subsequent whole-genome duplication. The divergent expression patterns of the homoeologs in hexaploid wheat suggest that they have undergone transcriptional and/or functional differentiation during wheat evolution. However, the distribution of transcriptionally differentiated homoeologs in gene regulatory networks and their related biological functions in hexaploid wheat are still largely unexplored. Therefore, we retrieved 727 publicly available wheat RNA-sequencing (RNA-seq) datasets from various tissues, developmental stages, and conditions, and identified 10,415 expressed homoeologous triplets. Examining the co-expression modules in the wheat transcriptome, we found that 66% of the expressed homoeologous triplets possess all three homoeologs grouped in the same co-expression modules. Among these, 15 triplets contain co-expressed homoeologs with differential expression levels between homoeoalleles across ≥ 95% of the 727 RNA-seq datasets, suggesting a consistent trend of homoeolog expression bias. In addition, we identified 2,831 differentiated homoeologs that showed gene expression patterns that deviated from those of the other two homoeologs. We found that seven co-expression modules contained a high proportion of such differentiated homoeologs, which accounted for ≥ 20% of the genes in each module. We also found that five of the co-expression modules are abundantly composed of genes involved in biological processes such as chloroplast biogenesis, RNA metabolism, putative defense response, putative posttranscriptional modification, and lipid metabolism, thereby suggesting that, the differentiated homoeologs might highly contribute to these biological functions in the gene network of hexaploid wheat.
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Affiliation(s)
- Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- *Correspondence: Keiichi Mochida,
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16
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Ayalew H, Liu H, Börner A, Kobiljski B, Liu C, Yan G. Genome-Wide Association Mapping of Major Root Length QTLs Under PEG Induced Water Stress in Wheat. Front Plant Sci 2018; 9:1759. [PMID: 30555498 PMCID: PMC6281995 DOI: 10.3389/fpls.2018.01759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/12/2018] [Indexed: 05/18/2023]
Abstract
Roots are vital plant organs that determine adaptation to various soil conditions. The present study evaluated a core winter wheat collection for rooting depth under PEG induced early stage water stress and non-stress growing conditions. Analysis of phenotypic data indicated highly significant (p < 0.01) variation among genotypes. Broad sense heritability of 59 and 73% with corresponding genetic gains of 7.6 and 9.7 (5% selection intensity) were found under non-stress and stress conditions, respectively. The test genotypes were grouped in to three distinct clusters using unweighted pair group method with arithmetic mean (UPGMA) clustering based on maximum Euclidian distance. The first three principal components gave optimum mixed linear model for genome wide association study (GWAS). Linkage disequilibrium (LD) analysis showed significant LD (p < 0.05) amongst 15% of total marker pairs (25,125). Nearly 16% of the significant LDs were among inter chromosomal marker pairs. GWAS revealed five significant root length QTLs spread across four chromosomes. None of the identified QTLs were common between the two growing conditions. Stress specific QTLs, combined explaining 31% of phenotypic variation were located on chromosomes 2B (wPt6278) and 3B (wPt1159). Similarly, two of the three QTLs (wPt0021 and wPt8890) identified under the non-stress condition were found on chromosomes 3B and 5B, respectively. The B genome showed significant importance in controlling root growth both under stress and non-stress conditions. The identified markers can potentially be validated and used for marker assisted selection.
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Affiliation(s)
- Habtamu Ayalew
- School of Agriculture and Environment, Faculty of Science, The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Hui Liu
- School of Agriculture and Environment, Faculty of Science, The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Chunji Liu
- CSIRO Agriculture Flagship, Townsville, QLD, Australia
| | - Guijun Yan
- School of Agriculture and Environment, Faculty of Science, The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- *Correspondence: Guijun Yan,
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Zhang Y, Bai Y, Wu G, Zou S, Chen Y, Gao C, Tang D. Simultaneous modification of three homoeologs of TaEDR1 by genome editing enhances powdery mildew resistance in wheat. Plant J 2017; 91:714-724. [PMID: 28502081 DOI: 10.1111/tpj.13599] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/23/2017] [Accepted: 05/03/2017] [Indexed: 05/18/2023]
Abstract
Wheat (Triticum aestivum L.) incurs significant yield losses from powdery mildew, a major fungal disease caused by Blumeria graminis f. sp. tritici (Bgt). enhanced disease resistance1 (EDR1) plays a negative role in the defense response against powdery mildew in Arabidopsis thaliana; however, the edr1 mutant does not show constitutively activated defense responses. This makes EDR1 an ideal target for approaches using new genome-editing tools to improve resistance to powdery mildew. We cloned TaEDR1 from hexaploid wheat and found high similarity among the three homoeologs of EDR1. Knock-down of TaEDR1 by virus-induced gene silencing or RNA interference enhanced resistance to powdery mildew, indicating that TaEDR1 negatively regulates powdery mildew resistance in wheat. We used CRISPR/Cas9 technology to generate Taedr1 wheat plants by simultaneous modification of the three homoeologs of wheat EDR1. No off-target mutations were detected in the Taedr1 mutant plants. The Taedr1 plants were resistant to powdery mildew and did not show mildew-induced cell death. Our study represents the successful generation of a potentially valuable trait using genome-editing technology in wheat and provides germplasm for disease resistance breeding.
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Affiliation(s)
- Yunwei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Bai
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangheng Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resources Engineering, Wuyi University, Wuyishan, 354300, Fujian, China
| | - Shenghao Zou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongfang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dingzhong Tang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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18
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Wang K, Liu H, Du L, Ye X. Generation of marker-free transgenic hexaploid wheat via an Agrobacterium-mediated co-transformation strategy in commercial Chinese wheat varieties. Plant Biotechnol J 2017; 15:614-623. [PMID: 27862820 PMCID: PMC5399001 DOI: 10.1111/pbi.12660] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 05/02/2023]
Abstract
Genotype specificity is a big problem lagging the development of efficient hexaploid wheat transformation system. Increasingly, the biosecurity of genetically modified organisms is garnering public attention, so the generation of marker-free transgenic plants is very important to the eventual potential commercial release of transgenic wheat. In this study, 15 commercial Chinese hexaploid wheat varieties were successfully transformed via an Agrobacterium-mediated method, with efficiency of up to 37.7%, as confirmed by the use of Quickstix strips, histochemical staining, PCR analysis and Southern blotting. Of particular interest, marker-free transgenic wheat plants from various commercial Chinese varieties and their F1 hybrids were successfully obtained for the first time, with a frequency of 4.3%, using a plasmid harbouring two independent T-DNA regions. The average co-integration frequency of the gus and the bar genes located on the two independent T-DNA regions was 49.0% in T0 plants. We further found that the efficiency of generating marker-free plants was related to the number of bar gene copies integrated in the genome. Marker-free transgenic wheat plants were identified in the progeny of three transgenic lines that had only one or two bar gene copies. Moreover, silencing of the bar gene was detected in 30.7% of T1 positive plants, but the gus gene was never found to be silenced in T1 plants. Bisulphite genomic sequencing suggested that DNA methylation in the 35S promoter of the bar gene regulatory region might be the main reason for bar gene silencing in the transgenic plants.
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Affiliation(s)
- Ke Wang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Huiyun Liu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Lipu Du
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xingguo Ye
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
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19
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Bulli P, Zhang J, Chao S, Chen X, Pumphrey M. Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection. G3 (Bethesda) 2016; 6:2237-53. [PMID: 27226168 PMCID: PMC4978880 DOI: 10.1534/g3.116.028407] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/16/2016] [Indexed: 12/30/2022]
Abstract
Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs.
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Affiliation(s)
- Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Shiaoman Chao
- USDA-ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, North Dakota 58102
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, Washington 99164 Department of Plant Pathology, Washington State University, Pullman, Washington 99164
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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20
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Prins R, Dreisigacker S, Pretorius Z, van Schalkwyk H, Wessels E, Smit C, Bender C, Singh D, Boyd LA. Stem Rust Resistance in a Geographically Diverse Collection of Spring Wheat Lines Collected from Across Africa. Front Plant Sci 2016; 7:973. [PMID: 27462322 PMCID: PMC4939729 DOI: 10.3389/fpls.2016.00973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/20/2016] [Indexed: 05/08/2023]
Abstract
Following the emergence of the Ug99 lineage of Puccinia graminis f. sp. tritici (Pgt) a collective international effort has been undertaken to identify new sources of wheat stem rust resistance effective against these races. Analyses were undertaken in a collection of wheat genotypes gathered from across Africa to identify stem rust resistance effective against the Pgt races found in Eastern and Southern Africa. The African wheat collection consisted of historic genotypes collected in Kenya, South Africa, Ethiopia, Sudan, Zambia, Morocco, and Tunisia, and current South African breeding lines. Both Bayesian cluster and principal coordinate analyses placed the wheat lines from Sudan in a distinct group, but indicated a degree of genetic relatedness among the other wheat lines despite originating from countries across Africa. Seedling screens with Pgt race PTKST, pedigree information and marker haplotype analysis confirmed the presence of Sr2, Sr36, Sr24, Sr31, and Lr34/Yr18/Sr57 in a number of the lines. A genome-wide association study (GWAS) undertaken with Diversiry Arrays Technology (DArT) and stem rust (Sr) gene associated markers and Stem Area Infected (SAI) and Reaction Type (RT) field phenotypes, collected from trials carried out across two seasons in Kenya in 2009 and in South Africa in 2011, identified 29 marker-trait associations (MTA). Three MTA were in common between SAI and RT, with the biggest effect MTA being found on chromosome 6AS. Two wheat lines, W1406 and W6979 that exhibited high levels of adult plant stem rust resistance were selected to generate bi-parental mapping populations. Only the MTA on chromosomes 6AS and 3BS, and the locus Lr34/Yr18/Sr57 were confirmed following QTL mapping. Additional stem rust resistance QTL, not detected by the GWAS, were found on chromosomes 2BS, 2DL, 3DL, and 4D.
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Affiliation(s)
- Renée Prins
- CenGen (Pty) Ltd.Worcester, South Africa
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | | | - Zakkie Pretorius
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | - Hester van Schalkwyk
- CenGen (Pty) Ltd.Worcester, South Africa
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | | | | | - Cornel Bender
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | - Davinder Singh
- Faculty of Agriculture and Environment, Plant Breeding Institute Cobbitty, University of SydneyNarellan, NSW, Australia
| | - Lesley A. Boyd
- Department of Genetics and Breeding, National Institute of Agricultural BotanyCambridge, UK
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Rong W, Luo M, Shan T, Wei X, Du L, Xu H, Zhang Z. A Wheat Cinnamyl Alcohol Dehydrogenase TaCAD12 Contributes to Host Resistance to the Sharp Eyespot Disease. Front Plant Sci 2016; 7:1723. [PMID: 27899932 PMCID: PMC5110560 DOI: 10.3389/fpls.2016.01723] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/02/2016] [Indexed: 05/18/2023]
Abstract
Sharp eyespot, caused mainly by the necrotrophic fungus Rhizoctonia cerealis, is a destructive disease in hexaploid wheat (Triticum aestivum L.). In Arabidopsis, certain cinnamyl alcohol dehydrogenases (CADs) have been implicated in monolignol biosynthesis and in defense response to bacterial pathogen infection. However, little is known about CADs in wheat defense responses to necrotrophic or soil-borne pathogens. In this study, we isolate a wheat CAD gene TaCAD12 in response to R. cerealis infection through microarray-based comparative transcriptomics, and study the enzyme activity and defense role of TaCAD12 in wheat. The transcriptional levels of TaCAD12 in sharp eyespot-resistant wheat lines were significantly higher compared with those in susceptible wheat lines. The sequence and phylogenetic analyses revealed that TaCAD12 belongs to IV group in CAD family. The biochemical assay proved that TaCAD12 protein is an authentic CAD enzyme and possesses catalytic efficiencies toward both coniferyl aldehyde and sinapyl aldehyde. Knock-down of TaCAD12 transcript significantly repressed resistance of the gene-silenced wheat plants to sharp eyespot caused by R. cerealis, whereas TaCAD12 overexpression markedly enhanced resistance of the transgenic wheat lines to sharp eyespot. Furthermore, certain defense genes (Defensin, PR10, PR17c, and Chitinase1) and monolignol biosynthesis-related genes (TaCAD1, TaCCR, and TaCOMT1) were up-regulated in the TaCAD12-overexpressing wheat plants but down-regulated in TaCAD12-silencing plants. These results suggest that TaCAD12 positively contributes to resistance against sharp eyespot through regulation of the expression of certain defense genes and monolignol biosynthesis-related genes in wheat.
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22
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Zheng Z, Ma J, Stiller J, Zhao Q, Feng Q, Choulet F, Feuillet C, Zheng YL, Wei Y, Han B, Yan G, Manners JM, Liu C. Fine mapping of a large-effect QTL conferring Fusarium crown rot resistance on the long arm of chromosome 3B in hexaploid wheat. BMC Genomics 2015; 16:850. [PMID: 26493707 PMCID: PMC4618961 DOI: 10.1186/s12864-015-2105-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Fusarium crown rot (FCR) is a major cereal disease in semi-arid areas worldwide. Of the various QTL reported, the one on chromosome arm 3BL (Qcrs.cpi-3B) has the largest effect that can be consistently detected in different genetic backgrounds. Nine sets of near isogenic lines (NILs) for this locus were made available in a previous study. To identify markers that could be reliably used in tagging the Qcrs.cpi-3B locus, a NIL-derived population consisting of 774 F10 lines were generated and exploited to assess markers selected from the existing linkage map and generated from sequences of the 3B pseudomolecule. RESULTS This is the first report on fine mapping a QTL conferring FCR resistance in wheat. By three rounds of linkage mapping using the NILs and the NIL-derived population, the Qcrs.cpi-3B locus was mapped to an interval of 0.7 cM covering a physical distance of about 1.5 Mb. Seven markers co-segregating with the locus were developed. This interval contains a total of 63 gene-coding sequences based on the 3B pseudomolecule, and six of them were known to encode disease resistance proteins. Several of the genes in this interval were among those responsive to FCR infection detected in an earlier study. CONCLUSIONS The accurate localization of the Qcrs.cpi-3B locus and the development of the markers co-segregating with it should facilitate the incorporation of this large-effect QTL conferring FCR resistance into breeding programs as well as the cloning of the gene(s) underlying the QTL.
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Affiliation(s)
- Zhi Zheng
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
- National Foxtail Millet Improvement Centre, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
| | - Jian Ma
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jiri Stiller
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Qiang Zhao
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Qi Feng
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Frédéric Choulet
- INRA-UBP Joint Research Unit 1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, Clermont-Ferrand, F-63100, France.
| | - Catherine Feuillet
- INRA-UBP Joint Research Unit 1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, Clermont-Ferrand, F-63100, France.
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Bin Han
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Guijun Yan
- National Foxtail Millet Improvement Centre, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
| | - John M Manners
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Chunji Liu
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Šimková H, Šafář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KFX, Korol A, Bergès H, Doležel J, Feuillet C. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013; 14:R64. [PMID: 23800011 PMCID: PMC4054855 DOI: 10.1186/gb-2013-14-6-r64] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. RESULTS Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. CONCLUSIONS Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
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Affiliation(s)
- Romain Philippe
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Etienne Paux
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Isabelle Bertin
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Fréderic Choulet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Christel Laugier
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Sonia Vautrin
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Federica Magni
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Simone Scalabrin
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | | | - Klaus FX Mayer
- MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Abraham Korol
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Catherine Feuillet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
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