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Gong B, Gao J, Xie Y, Zhang H, Zhu W, Xu L, Cheng Y, Wang Y, Zeng J, Fan X, Sha L, Zhang H, Zhou Y, Wu D, Li Y, Kang H. Development of wheat-tetraploid Thinopyrum elongatum 4EL small fragment translocation lines with stripe rust resistance gene Yr4EL. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:246. [PMID: 39365463 DOI: 10.1007/s00122-024-04756-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 09/25/2024] [Indexed: 10/05/2024]
Abstract
KEY MESSAGE Two small fragment translocation lines (T4DS·4DL-4EL and T5AS·5AL-4EL) showed high resistance to stripe rust and resistance gene Yr4EL was localized to an about 35 Mb region at the end of chr arm 4EL. Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a devastating wheat disease worldwide. Deployment of disease resistance (R) genes in wheat cultivars is the most effective way to control the disease. Previously, the all-stage stripe rust R gene Yr4EL from tetraploid Thinopyrum elongatum was introduced into common wheat as 4E(4D) substitution and T4DS·4EL translocation lines. To further map and utilize Yr4EL, Chinese Spring (CS) mutant pairing homoeologous gene ph1b was used in crossing to induce recombination between chromosome (chr) 4EL and wheat chromosomes. Two small fragment translocation lines T4DS·4DL-4EL and T5AS·5AL-4EL with Yr4EL resistance were selected using molecular markers and confirmed by genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and Wheat 660 K SNP array analyses. We mapped Yr4EL to an about 35 Mb region at the end of chr 4EL, corresponding to 577.76-612.97 Mb based on the diploid Th. elongatum reference genome. In addition, two competitive allele-specific PCR (KASP) markers co-segregating with Yr4EL were developed to facilitate molecular marker-assisted selection in breeding. The T4DS·4DL-4EL lines were crossed and backcrossed with wheat cultivars SM482 and CM42, and the resulting pre-breeding lines showed high stripe rust resistance and potential for wheat breeding with good agronomic traits. These lines represent new germplasm for wheat stripe rust resistance breeding, as well as providing a solid foundation for Yr4EL fine mapping and cloning.
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Affiliation(s)
- Biran Gong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yangqiu Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lili Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiran Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Haiqin Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yinghui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Chen L, Zhang J, Ma P, Miao Y, Wu L, Zhou K, Yang J, Zhang M, Liu X, Jiang B, Hao M, Huang L, Ning S, Chen X, Chen X, Liu D, Wan H, Zhang L. Identification of a recessive gene RgM4G52 conferring red glume, stem, and rachis in a Triticum boeoticum mutant. FRONTIERS IN PLANT SCIENCE 2024; 15:1459505. [PMID: 39253576 PMCID: PMC11381283 DOI: 10.3389/fpls.2024.1459505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/01/2024] [Indexed: 09/11/2024]
Abstract
Anthocyanins are plant secondary metabolites belonging to the polyphenol class of natural water-soluble phytopigments. The accumulation of anthocyanins in different plant tissues can improve plant survival under adverse conditions. In addition, plants with the resulting colorful morphology can be utilized as landscape plants. Triticum boeoticum (syn. Triticum monococcum ssp. aegilopoides, 2n=2x=14, AbAb) serves as a valuable genetic resource for the improvement of its close relative common wheat in terms of enhancing resilience to various biotic and abiotic stresses. In our previous study, the EMS-mutagenized mutant Z2921 with a red glume, stem, and rachis was generated from T. boeoticum G52, which has a green glume, stem, and rachis. In this study, the F1, F2, and F2:3 generations of a cross between mutant-type Z2921 and wild-type G52 were developed. A single recessive gene, tentatively designated RgM4G52, was identified in Z2921 via genetic analysis. Using bulked segregant exome capture sequencing (BSE-Seq) analysis, RgM4G52 was mapped to chromosome 6AL and was flanked by the markers KASP-58 and KASP-26 within a 3.40-cM genetic interval corresponding to 1.71-Mb and 1.61-Mb physical regions in the Chinese Spring (IWGSC RefSeq v1.1) and Triticum boeoticum (TA299) reference genomes, respectively, in which seven and four genes related to anthocyanin synthesis development were annotated. Unlike previously reported color morphology-related genes, RgM4G52 is a recessive gene that can simultaneously control the color of glumes, stems, and rachis in wild einkorn. In addition, a synthetic Triticum dicoccum-T. boeoticum amphiploid Syn-ABAb-34, derived from the colchicine treatment of F1 hybrids between tetraploid wheat PI 352367 (T. dicoccum, AABB) and Z2921, expressed the red stems of Z2921. The flanking markers of RgM4G52 developed in this study could be useful for developing additional common wheat lines with red stems, laying the foundation for marker-assisted breeding and the fine mapping of RgM4G52.
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Affiliation(s)
- Longyu Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Junqing Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pan Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yongping Miao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lei Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiaru Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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Song Z, Zuo Y, Li W, Dai S, Liu G, Pu Z, Yan Z. Chromosome stability of synthetic Triticum turgidum-Aegilops umbellulata hybrids. BMC PLANT BIOLOGY 2024; 24:391. [PMID: 38735929 PMCID: PMC11089697 DOI: 10.1186/s12870-024-05110-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND Unreduced gamete formation during meiosis plays a critical role in natural polyploidization. However, the unreduced gamete formation mechanisms in Triticum turgidum-Aegilops umbellulata triploid F1 hybrid crosses and the chromsome numbers and compostions in T. turgidum-Ae. umbellulata F2 still not known. RESULTS In this study, 11 T.turgidum-Ae. umbellulata triploid F1 hybrid crosses were produced by distant hybridization. All of the triploid F1 hybrids had 21 chromosomes and two basic pathways of meiotic restitution, namely first-division restitution (FDR) and single-division meiosis (SDM). Only FDR was found in six of the 11 crosses, while both FDR and SDM occurred in the remaining five crosses. The chromosome numbers in the 127 selfed F2 seeds from the triploid F1 hybrid plants of 10 crosses (no F2 seeds for STU 16) varied from 35 to 43, and the proportions of euploid and aneuploid F2 plants were 49.61% and 50.39%, respectively. In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes. The chromosome loss of the U genome was the highest (26.77%) among the three genomes, followed by that of the B (22.83%) and A (11.81%) genomes, and the chromosome gain for the A, B, and U genomes was 3.94%, 3.94%, and 1.57%, respectively. Of the 21 chromosomes, 7U (16.54%), 5 A (3.94%), and 1B (9.45%) had the highest loss frequency among the U, A, and B genomes. In addition to chromosome loss, seven chromosomes, namely 1 A, 3 A, 5 A, 6 A, 1B, 1U, and 6U, were gained in the aneuploids. CONCLUSION In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes, chromsomes, and crosses. In addition to variations in chromosome numbers, three types of chromosome translocations including 3UL·2AS, 6UL·1AL, and 4US·6AL were identified in the F2 plants. Furthermore, polymorphic fluorescence in situ hybridization karyotypes for all the U chromosomes were also identified in the F2 plants when compared with the Ae. umbellulata parents. These results provide useful information for our understanding the naturally occurred T. turgidum-Ae. umbellulata amphidiploids.
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Affiliation(s)
- Zhongping Song
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, P. R. China
- Neijiang Normal University, Neijiang, 641000, P. R. China
| | - Yuanyuan Zuo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Wenjia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Gang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, P. R. China
| | - Zongjun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, 610066, P. R. China
- Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, P. R. China
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, P. R. China.
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4
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Li H, Zhu L, Fan R, Li Z, Liu Y, Shaheen A, Nie F, Li C, Liu X, Li Y, Liu W, Yang Y, Guo T, Zhu Y, Bu M, Li C, Liang H, Bai S, Ma F, Guo G, Zhang Z, Huang J, Zhou Y, Song CP. A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops. Nat Protoc 2024; 19:281-312. [PMID: 38017137 DOI: 10.1038/s41596-023-00922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/28/2023] [Indexed: 11/30/2023]
Abstract
Breeding new and sustainable crop cultivars of high yields and desirable traits has been a major challenge for ensuring food security for the growing global human population. For polyploid crops such as wheat, introducing genetic variation from wild relatives of its subgenomes is a key strategy to improve the quality of their breeding pools. Over the past decades, considerable progress has been made in speed breeding, genome sequencing, high-throughput phenotyping and genomics-assisted breeding, which now allows us to realize whole-genome introgression from wild relatives to modern crops. Here, we present a standardized protocol to rapidly introgress the entire genome of Aegilops tauschii, the progenitor of the D subgenome of bread wheat, into elite wheat backgrounds. This protocol integrates multiple modern high-throughput technologies and includes three major phases: development of synthetic octaploid wheat, generation of hexaploid A. tauschii-wheat introgression lines (A-WIs) and homozygosis of the generated A-WIs. Our approach readily generates stable introgression lines in 2 y, thus greatly accelerating the generation of A-WIs and the introduction of desirable genes from A. tauschii to wheat cultivars. These A-WIs are valuable for wheat-breeding programs and functional gene discovery. The current protocol can be easily modified and used for introgressing the genomes of wild relatives to other polyploid crops.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, China
| | - Lele Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ruixiao Fan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Zheng Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yifan Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Aaqib Shaheen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Fang Nie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Can Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Xuqin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yuanyuan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Wenjuan Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yingying Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Tutu Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yu Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Mengchen Bu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chenglin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Huihui Liang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Feifei Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Guanghui Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, China
| | - Zhen Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, China
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
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Gong B, Chen L, Zhang H, Zhu W, Xu L, Cheng Y, Wang Y, Zeng J, Fan X, Sha L, Zhang H, Chen G, Zhou Y, Kang H, Wu D. Development, identification, and utilization of wheat-tetraploid Thinopyrum elongatum 4EL translocation lines resistant to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:17. [PMID: 38198011 DOI: 10.1007/s00122-023-04525-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
KEY MESSAGE The new stripe rust resistance gene Yr4EL in tetraploid Th. elongatum was identified and transferred into common wheat via 4EL translocation lines. Tetraploid Thinopyrum elongatum is a valuable genetic resource for improving the resistance of wheat to diseases such as stripe rust, powdery mildew, and Fusarium head blight. We previously reported that chromosome 4E of the 4E (4D) substitution line carries all-stage stripe rust resistance genes. To optimize the utility of these genes in wheat breeding programs, we developed translocation lines by inducing chromosomal structural changes through 60Co-γ irradiation and developing monosomic substitution lines. In total, 53 plants with different 4E chromosomal structural changes were identified. Three homozygous translocation lines (T4DS·4EL, T5AL·4EL, and T3BL·4EL) and an addition translocation line (T5DS·4EL) were confirmed by the genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), FISH-painting, and wheat 55 K SNP array analyses. These four translocation lines, which contained chromosome arm 4EL, exhibited high stripe rust resistance. Thus, a resistance gene (tentatively named Yr4EL) was localized to the chromosome arm 4EL of tetraploid Th. elongatum. For the application of marker-assisted selection (MAS), 32 simple sequence repeat (SSR) markers were developed, showing specific amplification on the chromosome arm 4EL and co-segregation with Yr4EL. Furthermore, the 4DS·4EL line could be selected as a good pre-breeding line that better agronomic traits than other translocation lines. We transferred Yr4EL into three wheat cultivars SM482, CM42, and SM51, and their progenies were all resistant to stripe rust, which can be used in future wheat resistance breeding programs.
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Affiliation(s)
- Biran Gong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Linfeng Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lili Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Haiqin Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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6
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Li H, Liu X, Zhang J, Chen L, Zhang M, Miao Y, Ma P, Hao M, Jiang B, Ning S, Huang L, Yuan Z, Chen X, Chen X, Liu D, Wan H, Zhang L. Identification of the Solid Stem Suppressor Gene Su-TdDof in Synthetic Hexaploid Wheat Syn-SAU-117. Int J Mol Sci 2023; 24:12845. [PMID: 37629026 PMCID: PMC10454891 DOI: 10.3390/ijms241612845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Lodging is one of the most important factors affecting the high and stable yield of wheat worldwide. Solid-stemmed wheat has higher stem strength and lodging resistance than hollow-stemmed wheat does. There are many solid-stemmed varieties, landraces, and old varieties of durum wheat. However, the transfer of solid stem genes from durum wheat is suppressed by a suppressor gene located on chromosome 3D in common wheat, and only hollow-stemmed lines have been created. However, synthetic hexaploid wheat can serve as a bridge for transferring solid stem genes from tetraploid wheat to common wheat. In this study, the F1, F2, and F2:3 generations of a cross between solid-stemmed Syn-SAU-119 and semisolid-stemmed Syn-SAU-117 were developed. A single dominant gene, which was tentatively designated Su-TdDof and suppresses stem solidity, was identified in synthetic hexaploid wheat Syn-SAU-117 by using genetic analysis. By using bulked segregant RNA-seq (BSR-seq) analysis, Su-TdDof was mapped to chromosome 7DS and flanked by markers KASP-669 and KASP-1055 within a 4.53 cM genetic interval corresponding to 3.86 Mb and 2.29 Mb physical regions in the Chinese Spring (IWGSC RefSeq v1.1) and Ae. tauschii (AL8/78 v4.0) genomes, respectively, in which three genes related to solid stem development were annotated. Su-TdDof differed from a previously reported solid stem suppressor gene based on its origin and position. Su-TdDof would provide a valuable example for research on the suppression phenomenon. The flanking markers developed in this study might be useful for screening Ae. tauschii accessions with no suppressor gene (Su-TdDof) to develop more synthetic hexaploid wheat lines for the breeding of lodging resistance in wheat and further cloning the suppressor gene Su-TdDof.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Junqing Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Longyu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yongping Miao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Pan Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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7
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Ning S, Li S, Xu K, Liu D, Ma L, Ma C, Hao M, Zhang L, Chen W, Zhang B, Jiang Y, Huang L, Chen X, Jiang B, Yuan Z, Liu D. Development and Characterization of Near-Isogenic Lines Derived from Synthetic Wheat Revealing the 2 kb Insertion in the PPD-D1 Gene Responsible for Heading Delay and Grain Number Improvement. Int J Mol Sci 2023; 24:10834. [PMID: 37446014 DOI: 10.3390/ijms241310834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Spikelet number and grain number per spike are two crucial and correlated traits for grain yield in wheat. Photoperiod-1 (Ppd-1) is a key regulator of inflorescence architecture and spikelet formation in wheat. In this study, near-isogenic lines derived from the cross of a synthetic hexaploid wheat and commercial cultivars generated by double top-cross and two-phase selection were evaluated for the number of days to heading and other agronomic traits. The results showed that heading time segregation was conferred by a single incomplete dominant gene PPD-D1, and the 2 kb insertion in the promoter region was responsible for the delay in heading. Meanwhile, slightly delayed heading plants and later heading plants obviously have advantages in grain number and spikelet number of the main spike compared with early heading plants. Utilization of PPD-D1 photoperiod sensitivity phenotype as a potential means to increase wheat yield potential.
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Affiliation(s)
- Shunzong Ning
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dongmei Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunfang Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Yun Jiang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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8
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Xie D, Hao M, Zhao L, Chen X, Chen X, Jiang B, Ning S, Yuan Z, Zhang L, Shu K, Zhang Y, Liu D, Wu P. Transcriptomic analysis provides insight into the genetic regulation of shade avoidance in Aegilops tauschii. BMC PLANT BIOLOGY 2023; 23:336. [PMID: 37353759 DOI: 10.1186/s12870-023-04348-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/14/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND Weeds are not only economically important but also fascinating models for studying the adaptation of species in human-mediated environments. Aegilops tauschii is the D-genome donor species of common wheat but is also a weed that influences wheat production. How shading stress caused by adjacent wheat plants affects Ae. tauschii growth is a fundamental scientific question but is also important in agriculture, such as for weed control and wheat breeding. RESULT The present study indicated that shade avoidance is a strategy of Ae. tauschii in response to shading stress. Ae. tauschii plants exhibited growth increases in specific organs, such as stem and leaf elongation, to avoid shading. However, these changes were accompanied by sacrificing the growth of other parts of the plants, such as a reduction in tiller number. The two reverse phenotype responses seem to be formed by systemically regulating the expression of different genes. Fifty-six genes involved in the regulation of cell division and cell expansion were found to be downregulated, and one key upstream negative regulator (RPK2) of cell division was upregulated under shading stress. On the other hand, the upregulated genes under shading stress were mainly enriched in protein serine/threonine kinase activity and carbon metabolism, which are associated with cell enlargement, signal transduction and energy supply. The transcription factor WRKY72 may be important in regulating genes in response to shading stress, which can be used as a prior candidate gene for further study on the genetic regulation of shade avoidance. CONCLUSIONS This study sheds new light on the gene expression changes and molecular processes involved in the response and avoidance of Ae. tauschii to shading stress, which may aid more effective development of shading stress avoidance or cultivars in wheat and other crops in the future.
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Affiliation(s)
- Die Xie
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Laibin Zhao
- Henan Provincial Key Laboratory of Hybrid Wheat, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710012, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
| | - Peipei Wu
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
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9
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Ali I, Anwar S, Ali A, Ullah Z, Binjawhar DN, Sher H, Abdel-Hameed UK, Khan MA, Majeed K, Jaremko M. Biochemical and phenological characterization of diverse wheats and their association with drought tolerance genes. BMC PLANT BIOLOGY 2023; 23:326. [PMID: 37331960 DOI: 10.1186/s12870-023-04278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/11/2023] [Indexed: 06/20/2023]
Abstract
Drought is one of the most important wheat production limiting factor, and can lead to severe yield losses. This study was designed to examine the effect of drought stress on wheat physiology and morphology under three different field capacities (FC) viz. 80% (control), 50% (moderate) and 30% (severe drought stress) in a diverse collection of wheat germplasm including cultivars, landraces, synthetic hexaploid and their derivatives. Traits like grain weight, thousand grain weight and biomass were reduced by 38.23%, 18.91% and 26.47% respectively at 30% FC, whereas the reduction rate for these traits at 50% FC were 19.57%, 8.88% and 18.68%. In principal component analysis (PCA), the first two components PC1 and PC2 accounted for 58.63% of the total variation and separated the cultivars and landraces from synthetic-based germplasm. Landraces showed wide range of phenotypic variations at 30% FC compared to synthetic-based germplasm and improved cultivars. However, least reduction in grain weight was observed in improved cultivars which indicated the progress in developing drought resilient cultivars. Allelic variations of the drought-related genes including TaSnRK2.9-5A, TaLTPs-11, TaLTPs-12, TaSAP-7B-, TaPPH-13, Dreb-B1 and 1fehw3 were significantly associated with the phenological traits under drought stress in all 91 wheats including 40 landraces, 9 varieties, 34 synthetic hexaploids and 8 synthetic derivatives. The favorable haplotypes of 1fehw3, Dreb-B1, TaLTPs-11 and TaLTPs-12 increased grain weight, and biomass. Our results iterated the fact that landraces could be promising source to deploy drought adaptability in wheat breeding. The study further identified drought tolerant wheat genetic resources across various backgrounds and identified favourable haplotypes of water-saving genes which should be considered to develop drought tolerant varieties.
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Affiliation(s)
- Iftikhar Ali
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- School of Life Sciences & Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong, 999077, Hong Kong.
| | - Saeed Anwar
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan
| | - Ahmad Ali
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan.
| | - Zahid Ullah
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan
| | - Dalal Nasser Binjawhar
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11671, Saudi Arabia.
| | - Hassan Sher
- Center for Plant Science and Biodiversity, University of Swat, Charbagh Swat, 19120, Pakistan
| | - Usama K Abdel-Hameed
- Biology Department, College of Science, Taibah University, Al-Madinah Al-Munawarah, 42353, Saudi Arabia
- Botany Department, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | | | - Khawar Majeed
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 329555-6900, Saudi Arabia
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10
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Wang F, Zhang M, Hu Y, Gan M, Jiang B, Hao M, Ning S, Yuan Z, Chen X, Chen X, Zhang L, Wu B, Liu D, Huang L. Pyramiding of Adult-Plant Resistance Genes Enhances All-Stage Resistance to Wheat Stripe Rust. PLANT DISEASE 2023; 107:879-885. [PMID: 36044366 DOI: 10.1094/pdis-07-22-1716-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases in wheat production. Pyramiding of adult-plant resistance (APR) genes is a promising strategy to increase durability of resistance. The stripe rust resistance (R) genes Yr18, Yr28, and Yr36 encode different protein families which confer partial resistance to a broad array of P. striiformis f. sp. tritici races. Here, we developed BC3F5 wheat lines representing all possible combinations of Yr18, Yr28, and Yr36 in a genetic background of the highly P. striiformis f. sp. tritici-susceptible wheat line SY95-71 that is widely used in stripe rust analysis. These lines enabled us to accurately evaluate these genes singly and in combination in a common genetic background. The adult plant resistance experiments were analyzed in the field, where stripe rust epidemics occurred frequently. The field results indicated that these partial R genes act additively in enhancing the levels of resistance, and a minimum of two-gene combinations can generate adequate stripe rust resistance. The Yr28 + Yr36 and Yr18 + Yr28 + Yr36 combinations also showed adequate resistance at the seedling stage, implying that APR gene pyramiding can achieve all-stage resistance. Meanwhile, the three genes were simultaneously introduced into elite wheat lines through gene-based marker selection. Elite lines exhibited strong all-stage resistance to stripe rust. This work provides valuable insights and resources for developing durable P. striiformis f. sp. tritici-resistant varieties and for elucidating the regulation mechanism of partial R gene pyramiding.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yanling Hu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Meijuan Gan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Bihua Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
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11
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Wan H, Yang F, Li J, Wang Q, Liu Z, Tang Y, Yang W. Genetic Improvement and Application Practices of Synthetic Hexaploid Wheat. Genes (Basel) 2023; 14:283. [PMID: 36833210 PMCID: PMC9956247 DOI: 10.3390/genes14020283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Synthetic hexaploid wheat (SHW) is a useful genetic resource that can be used to improve the performance of common wheat by transferring favorable genes from a wide range of tetraploid or diploid donors. From the perspectives of physiology, cultivation, and molecular genetics, the use of SHW has the potential to increase wheat yield. Moreover, genomic variation and recombination were enhanced in newly formed SHW, which could generate more genovariation or new gene combinations compared to ancestral genomes. Accordingly, we presented a breeding strategy for the application of SHW-the 'large population with limited backcrossing method'-and we pyramided stripe rust resistance and big-spike-related QTLs/genes from SHW into new high-yield cultivars, which represents an important genetic basis of big-spike wheat in southwestern China. For further breeding applications of SHW-derived cultivars, we used the 'recombinant inbred line-based breeding method' that combines both phenotypic and genotypic evaluations to pyramid multi-spike and pre-harvest sprouting resistance QTLs/genes from other germplasms to SHW-derived cultivars; consequently, we created record-breaking high-yield wheat in southwestern China. To meet upcoming environmental challenges and continuous global demand for wheat production, SHW with broad genetic resources from wild donor species will play a major role in wheat breeding.
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Affiliation(s)
- Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Fan Yang
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Yonglu Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu 610066, China
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12
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Liu X, Chen L, Zhang M, Li H, Jiang X, Zhang J, Jia Z, Ma P, Hao M, Jiang B, Huang L, Ning S, Yuan Z, Chen X, Chen X, Liu D, Zhang L. Cytogenetic Characterization and Molecular Marker Development for a Wheat- T. boeoticum 4A b (4B) Disomic Substitution Line with Stripe Rust Resistance. PLANT DISEASE 2023; 107:125-130. [PMID: 35698253 DOI: 10.1094/pdis-04-22-0865-re] [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: 06/15/2023]
Abstract
Triticum boeoticum (2n = 2x = 14, AbAb) is an important relative of wheat. This species tolerates many different types of environmental stresses, including drought, salt, and pathogenic infection, and is lower in dietary fiber and higher in antioxidants, protein (15 to 18%), lipids, and trace elements than common wheat. However, the gene transfer rate from this species to common wheat is low, and few species-specific molecular markers are available. In this study, the wheat-T. boeoticum substitution line Z1889, derived from a cross between the common wheat cultivar Crocus and T. boeoticum line G52, was identified using multicolor fluorescence in situ hybridization, multicolor genomic in situ hybridization, and a 55K single-nucleotide polymorphism array. Z1889 was revealed to be a 4Ab (4B) substitution line with a high degree of resistance to stripe rust pathogen strains prevalent in China. In addition, 22 4Ab chromosome-specific molecular markers and 11 T. boeoticum genome-specific molecular markers were developed from 1,145 4Ab chromosome-specific fragments by comparing the sequences generated by specific-length amplified fragment sequencing, with an efficiency of up to 55.0%. Furthermore, the specificity of these markers was verified in four species containing the Ab genome. These markers not only can be used for the detection of the 4Ab chromosome but also provide a basis for molecular marker-assisted, selection-based breeding in wheat.
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Affiliation(s)
- Xin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Longyu Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Hui Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xiaomei Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Junqing Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Zhenjiao Jia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Pan Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
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13
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Li S, Li X, Li S, Liu Y, Zang T, Hao M, Zhang L, Huang L, Jiang B, Yuan Z, Chen X, Chen X, Liu D, Ning S. Variation in the tonoplast cadmium transporter heavy metal ATPase 3 (HMA3) homolog gene in Aegilops tauschii. PLoS One 2023; 18:e0279707. [PMID: 36867624 PMCID: PMC9983875 DOI: 10.1371/journal.pone.0279707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/13/2022] [Indexed: 03/04/2023] Open
Abstract
The functionality of HMA3 is a key determinant controlling Cd accumulation in the shoots and grains of plants. Wild relatives of modern crop plants can serve as sources of valuable genetic variation for various traits. Here, resequencing of HMA3 homoeologous genes from Aegilops tauschii (the donor of the wheat D genome) was carried out to identify natural variation at both the nucleotide and polypeptide levels. HMA3 homoeologs are highly conserved, and 10 haplotypes were revealed based on 19 single nucleotide polymorphisms (eight induced single amino acid residue substitutions, including 2 altered amino acids in transmembrane domains) in 80 widely distributed Ae. tauschii accessions. The results provide genetic resources for low/no Cd concentration wheat improvement.
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Affiliation(s)
- Shengke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiao Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shijie Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu’e Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tianqing Zang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail:
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14
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Zuo Y, Dai S, Song Z, Xiang Q, Li W, Liu G, Li J, Xu D, Yan Z. Identification and Characterization of Wheat- Aegilops comosa 7M (7A) Disomic Substitution Lines with Stripe Rust and Powdery Mildew Resistance. PLANT DISEASE 2022; 106:2663-2671. [PMID: 35253481 DOI: 10.1094/pdis-11-21-2485-re] [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: 06/14/2023]
Abstract
Aegilops comosa (MM, 2n = 2x = 14), an important diploid species from the wheat tertiary gene pool, contains many unique genes/traits of potential use for wheat breeding, such as disease resistance. In this study, three sister lines, NAL-32, NAL-33, and NAL-34, were identified from a wheat-A. comosa distant cross using fluorescence in situ hybridization, simple sequence repeat markers, and PCR-based unique gene markers combined with single nucleotide polymorphism (SNP) array analysis. Genetically, NAL-32 contained neither an alien nor translocation chromosome, whereas NAL-33 and NAL-34 had disomic 7M (7A) substitution chromosomes but differed in the absence or presence of the 1BL/1RS translocation chromosomes, respectively. The absence of 7A in NAL-33 and NAL-34 and the unusual 1B in the latter were verified by wheat 55K SNP arrays. The two 7M (7A) substitution lines had similar levels of resistance to stripe rust and powdery mildew, but better than that of NAL-32 and their common wheat parents, suggesting that the stripe rust and powdery mildew resistance of NAL-33 and NAL-34 were derived from the 7M of A. comosa. This research provides important bridge materials that can potentially be used for transferring stripe rust and powdery mildew resistance.
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Affiliation(s)
- Yuanyuan Zuo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, P.R. China
| | - Zhongping Song
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Qin Xiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Wenjia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Gang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
| | - Donghe Xu
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, P.R. China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, Sichuan 611130, P.R. China
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15
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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16
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Hao M, Zhang L, Huang L, Ning S, Yuan Z, Jiang B, Yan Z, Wu B, Zheng Y, Liu D. 渗入杂交与小麦杂种优势. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Development and identification of four new synthetic hexaploid wheat lines with solid stems. Sci Rep 2022; 12:4898. [PMID: 35318389 PMCID: PMC8941074 DOI: 10.1038/s41598-022-08866-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
Stem solidness is an important agronomic trait for increasing the ability of wheat to resist lodging. In this study, four new synthetic hexaploid wheat with solid stems were developed from natural chromosome doubling of F1 hybrids between a solid-stemmed durum wheat (Triticum turgidum ssp. durum, 2n = 4x = 28, AABB) and four Aegilops tauschii (2n = 2x = 14, DD) accessions. The solid expression of the second internode at the base of the stem was stable for two synthetic hexalpoid wheat Syn-SAU-117 and Syn-SAU-119 grown in both the greenhouse and field. The lodging resistance of four synthetic solid-stem wheats is stronger than that of CS, and Syn-SAU-116 has the strongest lodging resistance, followed by Syn-SAU-119. The paraffin sections of the second internode showed that four synthetic wheat lines had large outer diameters, well-developed mechanical tissues, large number of vascular bundles, and similar anatomical characteristics with solid-stemmed durum wheat. The chromosomal composition of four synthetic hexaploid wheat was identified by FISH (fluorescence in situ hybridization) using Oligo-pSc119.2-1 and Oligo-pTa535-1. At adult stage, all four synthetic hexaploid wheat showed high resistance to mixed physiological races of stripe rust pathogen (CYR31, CYR32, CYR33, CYR34). These synthetic hexaploid wheat lines provide new materials for the improvement of common wheat.
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18
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Gong F, Qi T, Zhang T, Lu Y, Liu J, Zhong X, He J, Li Y, Zheng Y, Liu D, Huang L, Wu B. Comparison of the Agronomic, Cytological, Grain Protein Characteristics, as Well as Transcriptomic Profile of Two Wheat Lines Derived From Wild Emmer. Front Genet 2022; 12:804481. [PMID: 35154252 PMCID: PMC8831750 DOI: 10.3389/fgene.2021.804481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Two advanced wheat lines BAd7-209 and BAd23-1 without the functional gene GPC-B1 were obtained from a cross between common wheat cultivar Chuannong 16 (CN16) and wild emmer wheat accession D97 (D97). BAd7-209 showed superior quality parameters than those of BAd23-1 and CN16. We found that the components of glutenins and gliadins in BAd7-209 and BAd23-1 were similar, whereas BAd7-209 had higher amount of glutenins and gliadins than those of BAd23-1. RNA sequencing analysis on developing grains of BAd7-209 and BAd23-1 as well as their parents revealed 382 differentially expressed genes (DEGs) between the high–grain protein content (GPC) (D97 + BAd7-209) and the low-GPC (CN16 + BAd23-1) groups. DEGs were mainly associated with transcriptional regulation of the storage protein genes, protein processing in endoplasmic reticulum, and protein export pathways. The upregulated gluten genes and transcription factors (e.g., NAC, MYB, and bZIP) may contribute to the high GPC in BAd7-209. Our results provide insights into the potential regulation pathways underlying wheat grain protein accumulation and contribute to make use of wild emmer for wheat quality improvement.
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Affiliation(s)
- Fangyi Gong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Tiangang Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Tian Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yusen Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jia Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoying Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jingshu He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfang Li
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Chengdu, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Chengdu, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Lin Huang, ; Bihua Wu,
| | - Bihua Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Lin Huang, ; Bihua Wu,
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19
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Ma X, Zhang Z, Li G, Gou X, Bian Y, Zhao Y, Wang B, Lang M, Wang T, Xie K, Liu X, Liu B, Gong L. Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD). FRONTIERS IN PLANT SCIENCE 2022; 13:887133. [PMID: 35651770 PMCID: PMC9150853 DOI: 10.3389/fpls.2022.887133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/08/2022] [Indexed: 05/15/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to "transcriptome shock. " However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors Triticum urartu and Aegilops tauschii. We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the cis-only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in cis elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T. urartu may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.
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Affiliation(s)
- Xintong Ma
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yao Bian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Yue Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Man Lang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Kun Xie
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaoming Liu
- Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang, China
- *Correspondence: Xiaoming Liu
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Bao Liu
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Lei Gong
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20
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Zhang M, Liu X, Peng T, Wang D, Liang D, Li H, Hao M, Ning S, Yuan Z, Jiang B, Chen X, Chen X, Huang L, Zhang L, Liu D. Identification of a recessive gene YrZ15-1370 conferring adult plant resistance to stripe rust in wheat-Triticum boeoticum introgression line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2891-2900. [PMID: 34089337 DOI: 10.1007/s00122-021-03866-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
A novel recessive gene YrZ15-1370 derived from Triticum boeoticum confers adult-plant resistance to wheat stripe rust. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most damaging diseases of wheat globally and resistance is the effectively control strategy. Triticum boeoticum Boiss (T. monococcum L. ssp. aegilopoides, 2n = 2x = 14, AbAb) accession G52 confers a high level of adult-plant resistance against a mixture of the Chinese prevalent Pst races. To transfer the resistance to common wheat, a cross was made between G52 and susceptible common wheat genotype Crocus. A highly resistant wheat-T. boeoticum introgression line Z15-1370 (F5 generation) with 42 chromosomes was selected cytologically and by testing with Pst races. F1, F2, and F2:3 generations of the cross between Z15-1370 and stripe rust susceptible common wheat Mingxian169 were developed. Genetic analysis revealed that the resistance in Z15-1370 was controlled by a single recessive gene, tentatively designated YrZ15-1370. Using the bulked segregant RNA-Seq (BSR-Seq) analysis, YrZ15-1370 was mapped to chromosome 6AL and flanked by markers KASP1370-3 and KASP-1370-5 within a 4.3 cM genetic interval corresponding to 1.8 Mb physical region in the Chinese Spring genome, in which a number of disease resistance-related genes were annotated. YrZ15-1370 differed from previously Yr genes identified on chromosome 6A based on its position and/or origin. The YrZ15-1370 would be a valuable resource for wheat resistance improvement and the flanking markers developed here could be useful tools for marker-assisted selection (MAS) in breeding and further cloning the gene.
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Affiliation(s)
- Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Xin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Ting Peng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Dinghao Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Dongyu Liang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Hongyu Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China.
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China.
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, China
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21
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Wang Q, Yan N, Chen H, Li S, Hu H, Lin Y, Shi H, Zhou K, Jiang X, Yu S, Li C, Chen G, Yang Z, Liu Y. Genome-Wide Association Study of Kernel Traits in Aegilops tauschii. Front Genet 2021; 12:651785. [PMID: 34122506 PMCID: PMC8194309 DOI: 10.3389/fgene.2021.651785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Aegilops tauschii is the diploid progenitor of the D subgenome of hexaploid wheat (Triticum aestivum L.). Here, the phenotypic data of kernel length (KL), kernel width (KW), kernel volume (KV), kernel surface area (KSA), kernel width to length ratio (KWL), and hundred-kernel weight (HKW) for 223 A. tauschii accessions were gathered across three continuous years. Based on population structure analysis, 223 A. tauschii were divided into two subpopulations, namely T-group (mainly included A. tauschii ssp. tauschii accessions) and S-group (mainly included A. tauschii ssp. strangulata). Classifications based on cluster analysis were highly consistent with the population structure results. Meanwhile, the extent of linkage disequilibrium decay distance (r2 = 0.5) was about 110 kb and 290 kb for T-group and S-group, respectively. Furthermore, a genome-wide association analysis was performed on these kernel traits using 6,723 single nucleotide polymorphism (SNP) markers. Sixty-six significant markers, distributed on all seven chromosomes, were identified using a mixed linear model explaining 4.82–13.36% of the phenotypic variations. Among them, 15, 28, 22, 14, 21, and 13 SNPs were identified for KL, KW, KV, KSA, KWL, and HKW, respectively. Moreover, six candidate genes that may control kernel traits were identified (AET2Gv20774800, AET4Gv20799000, AET5Gv20005900, AET5Gv20084100, AET7Gv20644900, and AET5Gv21111700). The transfer of beneficial genes from A. tauschii to wheat using marker-assisted selection will broaden the wheat D subgenome improve the efficiency of breeding.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ning Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hao Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Sirui Li
- Chengdu Foreign Language School, Chengdu, China
| | - Haiyan Hu
- School of Life Sciences and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haoran Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojun Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shifan Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zisong Yang
- College of Resources and Environment, Aba Teachers University, Wenchuan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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22
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Schaart JG, Salentijn EMJ, Goryunova SV, Chidzanga C, Esselink DG, Gosman N, Bentley AR, Gilissen LJWJ, Smulders MJM. Exploring the alpha-gliadin locus: the 33-mer peptide with six overlapping coeliac disease epitopes in Triticum aestivum is derived from a subgroup of Aegilops tauschii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:86-94. [PMID: 33369792 PMCID: PMC8248119 DOI: 10.1111/tpj.15147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 05/28/2023]
Abstract
Most alpha-gliadin genes of the Gli-D2 locus on the D genome of hexaploid bread wheat (Triticum aestivum) encode for proteins with epitopes that can trigger coeliac disease (CD), and several contain a 33-mer peptide with six partly overlapping copies of three epitopes, which is regarded as a remarkably potent T-cell stimulator. To increase genetic diversity in the D genome, synthetic hexaploid wheat lines are being made by hybridising accessions of Triticum turgidum (AB genome) and Aegilops tauschii (the progenitor of the D genome). The diversity of alpha-gliadins in A. tauschii has not been studied extensively. We analysed the alpha-gliadin transcriptome of 51 A. tauschii accessions representative of the diversity in A. tauschii. We extracted RNA from developing seeds and performed 454 amplicon sequencing of the first part of the alpha-gliadin genes. The expression profile of allelic variants of the alpha-gliadins was different between accessions, and also between accessions of the Western and Eastern clades of A. tauschii. Generally, both clades expressed many allelic variants not found in bread wheat. In contrast to earlier studies, we detected the 33-mer peptide in some A. tauschii accessions, indicating that it was introduced along with the D genome into bread wheat. In these accessions, transcripts with the 33-mer peptide were present at lower frequencies than in bread wheat varieties. In most A. tauschii accessions, however, the alpha-gliadins do not contain the epitope, and this may be exploited, through synthetic hexaploid wheats, to breed bread wheat varieties with fewer or no coeliac disease epitopes.
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Affiliation(s)
- Jan G. Schaart
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Elma M. J. Salentijn
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Svetlana V. Goryunova
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Present address:
FSBSI Lorch Potato Research InstituteKraskovo140051Russia
- Present address:
Institute of General GeneticsRussian Academy of ScienceMoscow119333Russia
| | - Charity Chidzanga
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Present address:
University of AdelaideSchool of Agriculture, Food and WineWaite CampusUrrbraeSouth Australia5064Australia
| | - Danny G. Esselink
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Nick Gosman
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
- Present address:
Gosman AssociatesAg‐Biotech Consultingthe StreetBressingham, DissIP22 2BLUK
| | - Alison R. Bentley
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
- Present address:
International Maize and Wheat Improvement Center (CIMMYT)TexcocoMexico
| | - Luud J. W. J. Gilissen
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Allergy Consortium WageningenDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
| | - Marinus J. M. Smulders
- Plant BreedingWageningen University and ResearchDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
- Allergy Consortium WageningenDroevendaalsesteeg 1NL‐6708 PB Wageningenthe Netherlands
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23
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Pototskaya IV, Shamanin VP, Shepelev SS, Bhatta M, Morgounov AI. Analysis of the Genome D Polymorphism of Synthetic Wheat Obtained on the Basis of Ae. tauschii L. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421020083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Zhao L, Xie D, Fan C, Zhang S, Huang L, Ning S, Jiang B, Zhang L, Yuan Z, Liu D, Hao M. Chromosome Stability of Synthetic-Natural Wheat Hybrids. FRONTIERS IN PLANT SCIENCE 2021; 12:654382. [PMID: 33815455 PMCID: PMC8010257 DOI: 10.3389/fpls.2021.654382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Primary allopolyploids are not only ideal materials to study species evolution, but also important bridges in incorporating genetic diversity of wild species into crops. Primary allopolyploids typically exhibit chromosome instability that a disadvantage trait in crop breeding. Newly synthesized hexaploid wheat has been widely used in wheat genetics and breeding studies. To better understand the cytological and genetic basis of chromosome instability, this study investigated the chromosomes of a large number of seeds derived from the synthetic wheat SHW-L1 and its hybrids with natural wheat. SHW-L1 exhibited persistent chromosome instability since we observed a high frequent chromosome variation de novo generated from euploid SHW-L1 plants at the 14th generation of selfing (F14). High frequent chromosome variations were also observed in the F2 hybrids and most of the analyzed recombinant inbred lines (RILs) at F14, derived from the cross of SHW-L1 with common wheat variety Chuanmai 32. Chromosome instability was associated with frequent univalency during meiotic metaphase I. The experiment on reciprocal crosses between SHW-L1 and Chuanmai 32 indicated that cytoplasm has not obvious effects on chromosome instability. An analysis on 48 F14 RILs revealed chromosome variation frequency was not associated with the Ph1 alleles from either SHW-L1 or Chuanmai 32, rejecting the hypothesis that chromosome instability was due to the Ph1 role of synthetic wheat. In the analyzed RILs, chromosome instability influences the phenotype uniformity, showing as obvious trait differences among plants within a RIL. However, the analyzed commercial varieties only containing ∼12.5% genomic components of synthetic wheat were chromosomally stable, indicating that chromosome instability caused by synthetic wheat can be effectively overcome by increasing the genetic background of common wheat.
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Affiliation(s)
- Laibin Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Wheat Center, Henan Institute of Science and Technology, Xinxiang, China
| | - Die Xie
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaolan Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shujie Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lei Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ming Hao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
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25
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Przewieslik-Allen AM, Wilkinson PA, Burridge AJ, Winfield MO, Dai X, Beaumont M, King J, Yang CY, Griffiths S, Wingen LU, Horsnell R, Bentley AR, Shewry P, Barker GLA, Edwards KJ. The role of gene flow and chromosomal instability in shaping the bread wheat genome. NATURE PLANTS 2021; 7:172-183. [PMID: 33526912 DOI: 10.1038/s41477-020-00845-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/18/2020] [Indexed: 05/02/2023]
Abstract
Bread wheat (Triticum aestivum) is one of the world's most important crops; however, a low level of genetic diversity within commercial breeding accessions can significantly limit breeding potential. In contrast, wheat relatives exhibit considerable genetic variation and so potentially provide a valuable source of novel alleles for use in breeding new cultivars. Historically, gene flow between wheat and its relatives may have contributed novel alleles to the bread wheat pangenome. To assess the contribution made by wheat relatives to genetic diversity in bread wheat, we used markers based on single nucleotide polymorphisms to compare bread wheat accessions, created in the past 150 years, with 45 related species. We show that many bread wheat accessions share near-identical haplotype blocks with close relatives of wheat's diploid and tetraploid progenitors, while some show evidence of introgressions from more distant species and structural variation between accessions. Hence, introgressions and chromosomal rearrangements appear to have made a major contribution to genetic diversity in cultivar collections. As gene flow from relatives to bread wheat is an ongoing process, we assess the impact that introgressions might have on future breeding strategies.
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Affiliation(s)
| | - Paul A Wilkinson
- Life Sciences, University of Bristol, Bristol, UK
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | - Xiaoyang Dai
- Life Sciences, University of Bristol, Bristol, UK
| | | | - Julie King
- Plant Sciences Building, School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | - Cai-Yun Yang
- Plant Sciences Building, School of Biosciences, The University of Nottingham, Sutton Bonington, UK
| | | | | | | | - Alison R Bentley
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Mexico
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26
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Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny. G3-GENES GENOMES GENETICS 2020; 10:2445-2455. [PMID: 32430306 PMCID: PMC7341124 DOI: 10.1534/g3.120.401132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population derived from a bi-parental cross, we isolate alleles originating from the elite and exotic parents, which then allows us to separate out the predicted marker effects based on the allele origins. We validated the usefulness of OSGS using two nested association mapping (NAM) datasets: barley NAM (elite-exotic) and maize NAM (elite-elite), as well as by computer simulation. Our results suggest that OSGS works well in its goal to increase the contribution of favorable exotic alleles in bi-parental crosses, and it is possible to extend the approach to broader multi-parental populations.
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27
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Luo J, Zhao L, Zheng J, Li Y, Zhang L, Liu D, Pu Z, Hao M. Karyotype mosaicism in early generation synthetic hexaploid wheats. Genome 2020; 63:329-336. [PMID: 32197055 DOI: 10.1139/gen-2019-0148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is known that both the number and the structure of somatic chromosomes can vary in early generation hexaploid wheats. The phenomenon is generally assumed to arise as a result of the meiotic instability characteristic of freshly created allopolyploids. Here, an analysis of the somatic karyotype of a set of 33 early generation synthetic hexaploid wheats has revealed that variation, taking the form of sub-chromosomal fragments and inter-chromosomal translocations, can also arise in somatic tissue. A possible explanation for the observations was that karyotypic instability in early generation hexaploid wheat probably occurs not just during sporogenesis, but also in somatic tissue. However, other factors such as the use of nitrous oxide during the experiments could also cause the chromosome variations, and additional experimentation would be required to determine the most likely.
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Affiliation(s)
- Jiangtao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, Sichuan 610066, P.R. China.,Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Ministry of Agriculture, Chengdu, Sichuan 610066, P.R. China
| | - Laibin Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China
| | - Jianmin Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, Sichuan 610066, P.R. China.,Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Ministry of Agriculture, Chengdu, Sichuan 610066, P.R. China
| | - Yazhou Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, P.R. China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, P.R. China
| | - Zongjun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, Sichuan 610066, P.R. China.,Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Ministry of Agriculture, Chengdu, Sichuan 610066, P.R. China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, P.R. China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, P.R. China
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28
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Hao M, Zhang L, Ning S, Huang L, Yuan Z, Wu B, Yan Z, Dai S, Jiang B, Zheng Y, Liu D. The Resurgence of Introgression Breeding, as Exemplified in Wheat Improvement. FRONTIERS IN PLANT SCIENCE 2020; 11:252. [PMID: 32211007 PMCID: PMC7067975 DOI: 10.3389/fpls.2020.00252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/18/2020] [Indexed: 05/21/2023]
Abstract
Breeding progress in most crops has relied heavily on the exploitation of variation within the species' primary gene pool, a process which is destined to fail once the supply of novel variants has been exhausted. Accessing a crop's secondary gene pool, as represented by its wild relatives, has the potential to greatly expand the supply of usable genetic variation. The crop in which this approach has been most strongly championed is bread wheat (Triticum aestivum), a species which is particularly tolerant of the introduction of chromosomal segments of exotic origin thanks to the genetic buffering afforded by its polyploid status. While the process of introgression can be in itself cumbersome, a larger problem is that linkage drag and/or imperfect complementation frequently impose a yield and/or quality penalty, which explains the reluctance of breeders to introduce such materials into their breeding populations. Thanks to the development of novel strategies to induce introgression and of genomic tools to facilitate the selection of desirable genotypes, introgression breeding is returning as a mainstream activity, at least in wheat. Accessing variation present in progenitor species has even been able to drive genetic advance in grain yield. The current resurgence of interest in introgression breeding can be expected to result in an increased deployment of exotic genes in commercial wheat cultivars.
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Affiliation(s)
- Ming Hao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Ya’an, China
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Ya’an, China
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Bihua Wu
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Ya’an, China
- Triticeae Research Institute, Sichuan Agricultural University, Ya’an, China
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29
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Zeng D, Guan J, Luo J, Zhao L, Li Y, Chen W, Zhang L, Ning S, Yuan Z, Li A, Zheng Y, Mao L, Liu D, Hao M. A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy. BMC PLANT BIOLOGY 2020; 20:97. [PMID: 32131739 PMCID: PMC7057484 DOI: 10.1186/s12870-020-2309-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/24/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND In contrast to most animal species, polyploid plant species are quite tolerant of aneuploidy. Here, the global transcriptome of four aneuploid derivatives of a synthetic hexaploid wheat line was acquired, with the goal of characterizing the relationship between gene copy number and transcript abundance. RESULTS For most of the genes mapped to the chromosome involved in aneuploidy, the abundance of transcripts reflected the gene copy number. Aneuploidy had a greater effect on the strength of transcription of genes mapped to the chromosome present in a noneuploid dose than on that of genes mapped elsewhere in the genome. Overall, changing the copy number of one member of a homeologous set had little effect on the abundance of transcripts generated from the set of homeologs as a whole, consistent with the tolerance of aneuploidy exhibited by allopolyploids, whether in the form of a chromosomal deficit (monosomy) or chromosomal excess (trisomy). CONCLUSIONS Our findings shed new light on the genetic regulation of homeoallele transcription and contribute to a deeper understanding of allopolyploid genome evolution, with implications for the breeding of polyploid crops.
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Affiliation(s)
- Deying Zeng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Jiantao Guan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiangtao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu, 610066, Sichuan, China
| | - Laibin Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Yazhou Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Wenshuai Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Shunzong Ning
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Zhongwei Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Aili Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Long Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, 611130, Sichuan, China.
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30
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Liu X, Feng Z, Liang D, Zhang M, Liu X, Hao M, Liu D, Ning S, Yuan Z, Jiang B, Chen X, Chen X, Zhang L. Development, identification, and characterization of blue-grained wheat-Triticum boeoticum substitution lines. J Appl Genet 2020; 61:169-177. [PMID: 32072449 DOI: 10.1007/s13353-020-00553-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
Diploid wild einkorn wheat, Triticum boeoticum Boiss (AbAb, 2n = 2x = 14), is a wheat-related species with a blue aleurone layer. In this study, six blue-grained wheat lines were developed from F8 progeny of crosses between common wheat and T. boeoticum. The chromosome constitutions of these lines were characterized by fluorescence in situ hybridization (FISH) using the oligonucleotide probes Oligo-pTa535-1, Oligo-pSc119.2-1, Oligo-pTa71-2, and (AAC)7. Multicolor FISH using Oligo-pTa535-1, Oligo-pSc119.2-1, and Oligo-pTa71-2 identified all 42 common wheat chromosomes, while Oligo-pTa535-1 and (AAC)7 discriminated the 14 chromosomes of T. boeoticum. FISH revealed that all six blue-grained lines were wheat-T. boeoticum 4Ab (4B) disomic substitution lines. The substitution lines were validated by genotyping using the wheat 55 K single nucleotide polymorphism (SNP) array containing 53,063 markers. These 4Ab (4B) substitution lines represent novel germplasm for blue-grained wheat breeding. The FISH probes and SNP markers used here can be applied in the development of blue-grained wheat-Triticum boeoticum translocation lines.
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Affiliation(s)
- Xin Liu
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Zhen Feng
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Dongyu Liang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Minghu Zhang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Xiaojuan Liu
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. .,Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, China.
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31
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Takumi S, Mitta S, Komura S, Ikeda TM, Matsunaka H, Sato K, Yoshida K, Murai K. Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars. PLoS One 2020; 15:e0228397. [PMID: 31986184 PMCID: PMC6984701 DOI: 10.1371/journal.pone.0228397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/14/2020] [Indexed: 12/03/2022] Open
Abstract
The breeding of agriculturally useful genes from wild crop relatives must take into account recent and future climate change. In Japan, the development of early heading wheat cultivars without the use of any major gene controlling the heading date is desired to avoid overlap of the harvesting time before the rainy season. Here, we backcrossed two early heading lines of a synthetic hexaploid wheat, derived from a crossing between durum wheat and the wild wheat progenitor Aegilops tauschii, with four Japanese elite cultivars to develop early heading lines of bread wheat. In total, nine early heading lines that showed a heading date two to eight days earlier than their parental cultivars in field conditions were selected and established from the selfed progenies of the two- or three-times backcrossed populations. The whole appearance and spike shape of the selected early heading lines looked like their parental wheat cultivars. The mature grains of the selected lines had the parental cultivars’ characteristics, although the grains exhibited longer and narrower shapes. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines. The introgression regions could shorten wheat heading date, and their chromosomal positions were dependent on the backcrossed wheat cultivars. Therefore, early heading synthetic hexaploid wheat is useful for fine-tuning of the heading date through introgression of Ae. tauschii chromosomal regions.
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Affiliation(s)
- Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
- * E-mail: (ST); (KM)
| | - Seito Mitta
- Fukui Prefectural University, Eiheiji, Yoshida, Fukui, Japan
| | - Shoya Komura
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Tatsuya M. Ikeda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Hiroshima, Japan
| | - Hitoshi Matsunaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Koji Murai
- Fukui Prefectural University, Eiheiji, Yoshida, Fukui, Japan
- * E-mail: (ST); (KM)
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