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Wu L, Xie Z, Li D, Chen Y, Xia C, Kong X, Liu X, Zhang L. TaMYB72 directly activates the expression of TaFT to promote heading and enhance grain yield traits in wheat (Triticum aestivum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1266-1269. [PMID: 38888244 DOI: 10.1111/jipb.13716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Heading date, grain number per spike, and grain weight are crucial traits affecting yield and adaptability in wheat. The transcription factor TaMYB72 is an important regulator of wheat grain yield and its knock-out mutants can be used as germplasm resources for wheat improvement.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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2
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Fu M, Liu S, Che Y, Cui D, Deng Z, Li Y, Zou X, Kong X, Chen G, Zhang M, Liu Y, Wang X, Liu W, Liu D, Geng S, Li A, Mao L. Genome-editing of a circadian clock gene TaPRR95 facilitates wheat peduncle growth and heading date. J Genet Genomics 2024:S1673-8527(24)00124-3. [PMID: 38849110 DOI: 10.1016/j.jgg.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024]
Abstract
Plant height and heading date are important agronomic traits in wheat (Triticum aestivum L.) that affect final grain yield. In wheat, knowledge of pseudo-response regulator (PRR) genes on agronomic traits is limited. Here, we identify a wheat TaPRR95 gene by genome-wide association study to be associated with plant height. Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height, particularly the peduncle, with an earlier heading date. The longer peduncle is mainly caused by the increased cell elongation at its upper section, whilst the early heading date is accompanied by elevated expression of flowering genes, such as TaFT and TaCO1. A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAA/Aux genes for auxin signaling in prr95aabbdd plants that may act as a regulatory mechanism to promote robust plant growth. A haplotype analysis identifies a TaPRR95-B haplotype (Hap2) to be closely associated with reduced plant height and increased thousand-grain weight. Moreover, the Hap2 frequency is higher in cultivars than that in landraces, suggesting the artificial selection on the allele during wheat breeding. These findings suggest that TaPRR95 is a regulator for plant height and heading date, thereby providing an important target for wheat yield improvement.
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Affiliation(s)
- Mingxue Fu
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoshuai Liu
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuqing Che
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dada Cui
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongyin Deng
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Li
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinyu Zou
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingchen Kong
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, China
| | - Guoliang Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 610106, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 610106, China
| | - Yifan Liu
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xiang Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Wei Liu
- School of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Danmei Liu
- School of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Shuaifeng Geng
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Aili Li
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Long Mao
- State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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3
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Ma M, Wu L, Li M, Li L, Guo L, Ka D, Zhang T, Zhou M, Wu B, Peng H, Hu Z, Liu X, Jing R, Zhao H. Pleiotropic phenotypic effects of the TaCYP78A family on multiple yield-related traits in wheat. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38783571 DOI: 10.1111/pbi.14385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Increasing crop yield depends on selecting and utilizing pleiotropic genes/alleles to improve multiple yield-related traits (YRTs) during crop breeding. However, synergistic improvement of YRTs is challenging due to the trade-offs between YRTs in breeding practices. Here, the favourable haplotypes of the TaCYP78A family are identified by analysing allelic variations in 1571 wheat accessions worldwide, demonstrating the selection and utilization of pleiotropic genes to improve yield and related traits during wheat breeding. The TaCYP78A family members, including TaCYP78A3, TaCYP78A5, TaCYP78A16, and TaCYP78A17, are organ size regulators expressed in multiple organs, and their allelic variations associated with various YRTs. However, due to the trade-offs between YRTs, knockdown or overexpression of TaCYP78A family members does not directly increase yield. Favourable haplotypes of the TaCYP78A family, namely A3/5/16/17Ap-Hap II, optimize the expression levels of TaCYP78A3/5/16/17-A across different wheat organs to overcome trade-offs and improve multiple YRTs. Different favourable haplotypes have both complementary and specific functions in improving YRTs, and their aggregation in cultivars under strong artificial selection greatly increase yield, even under various planting environments and densities. These findings provide new support and valuable genetic resources for molecular breeding of wheat and other crops in the era of Breeding 4.0.
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Affiliation(s)
- Meng Ma
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi, China
| | - Linnan Wu
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Mengyao Li
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Long Li
- State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijian Guo
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Deyan Ka
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Tianxing Zhang
- College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Mengdie Zhou
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Baowei Wu
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Haixia Peng
- College of Landscape Architecture and Art, Northwest A & F University, Yangling, Shaanxi, China
| | - Zhaoxin Hu
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Xiangli Liu
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Ruilian Jing
- State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A & F University, Yangling, Shaanxi, China
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4
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Ai G, He C, Bi S, Zhou Z, Liu A, Hu X, Liu Y, Jin L, Zhou J, Zhang H, Du D, Chen H, Gong X, Saeed S, Su H, Lan C, Chen W, Li Q, Mao H, Li L, Liu H, Chen D, Kaufmann K, Alazab KF, Yan W. Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat. PLANT COMMUNICATIONS 2024; 5:100879. [PMID: 38486454 PMCID: PMC11121755 DOI: 10.1016/j.xplc.2024.100879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 04/30/2024]
Abstract
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
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Affiliation(s)
- Guo Ai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Siteng Bi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanyan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liujie Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - JiaCheng Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Heping Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sulaiman Saeed
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome, Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115 Berlin, Germany
| | - Khaled F Alazab
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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5
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Fan C, Xu D, Wang C, Chen Z, Dou T, Qin D, Guo A, Zhao M, Pei H, Zhao M, Zhang R, Wang K, Zhang J, Ni Z, Guo G. Natural variations of HvSRN1 modulate the spike rachis node number in barley. PLANT COMMUNICATIONS 2024; 5:100670. [PMID: 37563835 PMCID: PMC10811343 DOI: 10.1016/j.xplc.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Grain number, one of the major determinants of yield in Triticeae crops, is largely determined by spikelet number and spike rachis node number (SRN). Here, we identified three quantitative trait loci (QTLs) for SRN using 145 recombinant inbred lines derived from a barley R90/1815D cross. qSRN1, the major-effect QTL, was mapped to chromosome 2H and explained up to 38.77% of SRN variation. Map-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein HvSRN1. Further analysis revealed that two key SNPs in the HvSRN1 promoter region (∼2 kb upstream of the transcription start site) affect the transcript level of HvSRN1 and contribute to variation in SRN. Similar to its orthologous proteins OsLAX2 and ZmBA2, HvSRN1 showed protein-protein interactions with HvLAX1, suggesting that the LAX2-LAX1 model for spike morphology regulation may be conserved in Poaceae crops. CRISPR-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight, demonstrating a trade-off effect. Our results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.
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Affiliation(s)
- Chaofeng Fan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhaoyan Chen
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Tingyu Dou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Dandan Qin
- Key Laboratory for Crop Molecular Breeding of Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Aikui Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Meng Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Honghong Pei
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Mengwei Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Renxu Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Ke Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China.
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6
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [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: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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7
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Jia J, Zhao G, Li D, Wang K, Kong C, Deng P, Yan X, Zhang X, Lu Z, Xu S, Jiao Y, Chong K, Liu X, Cui D, Li G, Zhang Y, Du C, Wu L, Li T, Yan D, Zhan K, Chen F, Wang Z, Zhang L, Kong X, Ru Z, Wang D, Gao L. Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement. MOLECULAR PLANT 2023; 16:1893-1910. [PMID: 37897037 DOI: 10.1016/j.molp.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 07/12/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.
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Affiliation(s)
- Jizeng Jia
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- Xi'An Shansheng Biosciences Co., Ltd., Xi'an 710000, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pingchuan Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 612100, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shujuan Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Chong
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dangqun Cui
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Guangwei Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, 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
| | - Chunguang Du
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan 562000, China
| | - Tianbao Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Yan
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kehui Zhan
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Feng Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Zhiyong Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Daowen Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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8
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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9
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Si Y, Tian S, Niu J, Yu Z, Ma S, Lu Q, Wu H, Ling HQ, Zheng S. Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:240. [PMID: 37930446 DOI: 10.1007/s00122-023-04488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments. Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.
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Affiliation(s)
- Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Zhou X, Zhao Y, Ni P, Ni Z, Sun Q, Zong Y. CRISPR-mediated acceleration of wheat improvement: advances and perspectives. J Genet Genomics 2023; 50:815-834. [PMID: 37741566 DOI: 10.1016/j.jgg.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.
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Affiliation(s)
- Ximeng Zhou
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Pei Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuan Zong
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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11
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Luo X, Yang Y, Lin X, Xiao J. Deciphering spike architecture formation towards yield improvement in wheat. J Genet Genomics 2023; 50:835-845. [PMID: 36907353 DOI: 10.1016/j.jgg.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of the daily consumed calories and protein content around the world. With the growing global population and frequent occurrence of extreme weather caused by climate change, ensuring adequate wheat production is essential for food security. The architecture of the inflorescence plays a crucial role in determining the grain number and size, which is a key trait for improving yield. Recent advances in wheat genomics and gene cloning techniques have improved our understanding of wheat spike development and its applications in breeding practices. Here, we summarize the genetic regulation network governing wheat spike formation, the strategies used for identifying and studying the key factors affecting spike architecture, and the progress made in breeding applications. Additionally, we highlight future directions that will aid in the regulatory mechanistic study of wheat spike determination and targeted breeding for grain yield improvement.
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Affiliation(s)
- Xumei Luo
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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12
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Zhao C, Zhou J, Li C, You J, Liu Y, Tang H, Deng M, Xu Q, Zhang Y, Jiang Q, Chen G, Qi P, Jiang Y, Wang J, Li W, Pu Z, Chen G, Jiang Y, Zheng Z, Liu C, Zheng Y, Wei Y, Ma J. A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:213. [PMID: 37740730 DOI: 10.1007/s00122-023-04459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023]
Abstract
KEY MESSAGE A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86-15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the 'Chinese Spring' wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.
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Affiliation(s)
- Conghao Zhao
- 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
| | - Jieguang 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
| | - Cong Li
- 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
| | - Jianing You
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yanling 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
| | - Huaping Tang
- 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
| | - Mei Deng
- 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
| | - Qiang Xu
- 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
| | - Yazhou 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
| | - Qiantao Jiang
- 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
| | - Guoyue 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
| | - Pengfei Qi
- 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
| | - Yunfeng Jiang
- 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
| | - Jirui Wang
- 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
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy ofAgricultural Sciences, Chengdu, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Youliang Zheng
- 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
| | - Yuming Wei
- 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.
| | - Jian 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.
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13
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Qin R, Ma T, Cai Y, Shi X, Cheng J, Dong J, Wang C, Li S, Pan G, Guan Y, Zhang L, Yang S, Xu H, Zhao C, Sun H, Li X, Wu Y, Li J, Cui F. Characterization and fine mapping analysis of a major stable QTL qKnps-4A for kernel number per spike in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:211. [PMID: 37737910 DOI: 10.1007/s00122-023-04456-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023]
Abstract
KEY MESSAGE A major stable QTL for kernel number per spike was narrowed down to a 2.19-Mb region containing two potential candidate genes, and its effects on yield-related traits were characterized. Kernel number per spike (KNPS) in wheat is a key yield component. Dissection and characterization of major stable quantitative trait loci (QTLs) for KNPS would be of considerable value for the genetic improvement of yield potential using molecular breeding technology. We had previously reported a major stable QTL controlling KNPS, qKnps-4A. In the current study, primary fine-mapping analysis, based on the primary mapping population, located qKnps-4A to an interval of approximately 6.8-Mb from 649.0 to 655.8 Mb on chromosome 4A refering to 'Kenong 9204' genome. Further fine-mapping analysis based on a secondary mapping population narrowed qKnps-4A to an approximately 2.19-Mb interval from 653.72 to 655.91 Mb. Transcriptome sequencing, gene function annotation analysis and homologous gene related reports showed that TraesKN4A01HG38570 and TraesKN4A01HG38590 were most likely to be candidate genes of qKnps-4A. Phenotypic analysis based on paired near-isogenic lines in the target region showed that qKnps-4A increased KNPS mainly by increasing the number of central florets per spike. We also evaluated the effects of qKnps-4A on other yield-related traits. Moreover, we dissected the QTL cluster of qKnps-4A and qTkw-4A and proved that the phenotypic effects were probably due to close linkage of two or more genes rather than pleiotropic effects of a single gene. This study provides molecular marker resource for wheat molecular breeding designed to improve yield potential, and lay the foundation for gene functional analysis of qKnps-4A.
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Affiliation(s)
- Ran Qin
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Tianhang Ma
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yibiao Cai
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Xinyao Shi
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jiajia Cheng
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jizi Dong
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Chenyang Wang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Shihui Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Guoqing Pan
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yuxiang Guan
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Lei Zhang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Shuang Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Huiyuan Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Chunhua Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Han Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Ximei Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
- Shandong Key Laboratory of Dryland Farming Technology, Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yongzhen Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China.
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
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Yang H, Luo L, Li Y, Li H, Zhang X, Zhang K, Zhu S, Li X, Li Y, Wan Y, Liu F. Fine mapping of qAHPS07 and functional studies of AhRUVBL2 controlling pod size in peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1785-1798. [PMID: 37256840 PMCID: PMC10440995 DOI: 10.1111/pbi.14076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/18/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important oil and cash crop. Pod size is one of the major traits determining yield and commodity characteristic of peanut. Fine mapping of quantitative trait locus (QTL) and identification of candidate genes associated with pod size are essential for genetic improvement and molecular breeding of peanut varieties. In this study, a major QTL related to pod size, qAHPS07, was fine mapped to a 36.46 kb interval on chromosome A07 using F2 , recombinant inbred line (RIL) and secondary F2 populations. qAHPS07 explained 38.6%, 23.35%, 37.48%, 25.94% of the phenotypic variation for single pod weight (SPW), pod length (PL), pod width (PW) and pod shell thickness (PST), respectively. Whole genome resequencing and gene expression analysis revealed that a RuvB-like 2 protein coding gene AhRUVBL2 was the most likely candidate for qAHPS07. Overexpression of AhRUVBL2 in Arabidopsis led to larger seeds and plants than the wild type. AhRUVBL2-silenced peanut seedlings represented small leaves and shorter main stems. Three haplotypes were identified according to three SNPs in the promoter of AhRUVBL2 among 119 peanut accessions. Among them, SPW, PW and PST of accessions carrying Hap_ATT represent 17.6%, 11.2% and 26.3% higher than those carrying Hap_GAC,respectively. In addition, a functional marker of AhRUVBL2 was developed. Taken together, our study identified a key functional gene of peanut pod size, which provides new insights into peanut pod size regulation mechanism and offers practicable markers for the genetic improvement of pod size-related traits in peanut breeding.
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Affiliation(s)
- Hui Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Lu Luo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yuying Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Huadong Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Xiurong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Kun Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Suqing Zhu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Xuanlin Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yingjie Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
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15
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Tang Q, Wang X, Jin X, Peng J, Zhang H, Wang Y. CRISPR/Cas Technology Revolutionizes Crop Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:3119. [PMID: 37687368 PMCID: PMC10489799 DOI: 10.3390/plants12173119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.
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Affiliation(s)
- Qiaoling Tang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soi-Borne Diseases, Baoding University, Baoding 071000, China;
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
| | - Haiwen Zhang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Youhua Wang
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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16
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Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Yigider E, Taspinar MS, Agar G. Advances in bread wheat production through CRISPR/Cas9 technology: a comprehensive review of quality and other aspects. PLANTA 2023; 258:55. [PMID: 37522927 DOI: 10.1007/s00425-023-04199-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
MAIN CONCLUSION This review provides a comprehensive overview of the CRISPR/Cas9 technique and the research areas of this gene editing tool in improving wheat quality. Wheat (Triticum aestivum L.), the basic nutrition for most of the human population, contributes 20% of the daily energy needed because of its, carbohydrate, essential amino acids, minerals, protein, and vitamin content. Wheat varieties that produce high yields and have enhanced nutritional quality will be required to fulfill future demands. Hexaploid wheat has A, B, and D genomes and includes three like but not identical copies of genes that influence important yield and quality. CRISPR/Cas9, which allows multiplex genome editing provides major opportunities in genome editing studies of plants, especially complicated genomes such as wheat. In this overview, we discuss the CRISPR/Cas9 technique, which is credited with bringing about a paradigm shift in genome editing studies. We also provide a summary of recent research utilizing CRISPR/Cas9 to investigate yield, quality, resistance to biotic/abiotic stress, and hybrid seed production. In addition, we provide a synopsis of the laboratory experience-based solution alternatives as well as the potential obstacles for wheat CRISPR studies. Although wheat's extensive genome and complicated polyploid structure previously slowed wheat genetic engineering and breeding progress, effective CRISPR/Cas9 systems are now successfully used to boost wheat development.
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Affiliation(s)
- Esma Yigider
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey
| | - Mahmut Sinan Taspinar
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey.
| | - Guleray Agar
- Faculty of Science, Department of Biology, Atatürk University, 25240, Erzurum, Turkey
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18
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Li Y, Xiong H, Guo H, Zhou C, Fu M, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Wang C, Irshad A, Liu L, Fang Z. Fine mapping and genetic analysis identified a C 2H 2-type zinc finger as a candidate gene for heading date regulation in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:140. [PMID: 37243757 DOI: 10.1007/s00122-023-04363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/08/2023] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C2H2-type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS. Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41 cM, corresponding to a genomic region spanning 1.70 Mb (from 138.87 to 140.57 Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C2H2-type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2-4 days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants.
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Affiliation(s)
- Yuting Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyun Zhou
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiyu Fu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaojie Wang
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahsan Irshad
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luxiang Liu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China.
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19
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Mizuno N, Matsunaka H, Yanaka M, Ishikawa G, Kobayashi F, Nakamura K. Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:139. [PMID: 37233781 DOI: 10.1007/s00122-023-04386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-Minami, Memuro, Kasai, Hokkaido, 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8517, Japan
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20
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Zhang F, Neik TX, Thomas WJW, Batley J. CRISPR-Based Genome Editing Tools: An Accelerator in Crop Breeding for a Changing Future. Int J Mol Sci 2023; 24:ijms24108623. [PMID: 37239967 DOI: 10.3390/ijms24108623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Genome editing is an important strategy to maintain global food security and achieve sustainable agricultural development. Among all genome editing tools, CRISPR-Cas is currently the most prevalent and offers the most promise. In this review, we summarize the development of CRISPR-Cas systems, outline their classification and distinctive features, delineate their natural mechanisms in plant genome editing and exemplify the applications in plant research. Both classical and recently discovered CRISPR-Cas systems are included, detailing the class, type, structures and functions of each. We conclude by highlighting the challenges that come with CRISPR-Cas and offer suggestions on how to tackle them. We believe the gene editing toolbox will be greatly enriched, providing new avenues for a more efficient and precise breeding of climate-resilient crops.
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Affiliation(s)
- Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Ting Xiang Neik
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Malaysia
| | - William J W Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
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21
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Wang Z, Dhakal S, Cerit M, Wang S, Rauf Y, Yu S, Maulana F, Huang W, Anderson JD, Ma XF, Rudd JC, Ibrahim AMH, Xue Q, Hays DB, Bernardo A, St. Amand P, Bai G, Baker J, Baker S, Liu S. QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster. FRONTIERS IN PLANT SCIENCE 2022; 13:1057701. [PMID: 36570880 PMCID: PMC9768232 DOI: 10.3389/fpls.2022.1057701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.
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Affiliation(s)
- Zhen Wang
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Smit Dhakal
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Mustafa Cerit
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States
| | - Yahya Rauf
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shuhao Yu
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Frank Maulana
- Noble Research Institute, Ardmore, OK, United States
| | - Wangqi Huang
- Noble Research Institute, Ardmore, OK, United States
| | | | - Xue-Feng Ma
- Noble Research Institute, Ardmore, OK, United States
| | - Jackie C. Rudd
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Amir M. H. Ibrahim
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, United States
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Dirk B. Hays
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, United States
| | - Amy Bernardo
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Paul St. Amand
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Guihua Bai
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Jason Baker
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shannon Baker
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
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22
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Miroshnichenko D, Timerbaev V, Klementyeva A, Pushin A, Sidorova T, Litvinov D, Nazarova L, Shulga O, Divashuk M, Karlov G, Salina E, Dolgov S. CRISPR/Cas9-induced modification of the conservative promoter region of VRN-A1 alters the heading time of hexaploid bread wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1048695. [PMID: 36544871 PMCID: PMC9760837 DOI: 10.3389/fpls.2022.1048695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
In cereals, the vernalization-related gene network plays an important role in regulating the transition from the vegetative to the reproductive phase to ensure optimal reproduction in a temperate climate. In hexaploid bread wheat (Triticum aestivum L.), the spring growth habit is associated with the presence of at least one dominant locus of VERNALIZATION 1 gene (VRN-1), which usually differs from recessive alleles due to mutations in the regulatory sequences of the promoter or/and the first intron. VRN-1 gene is a key regulator of floral initiation; various combinations of dominant and recessive alleles, especially VRN-A1 homeologs, determine the differences in the timing of wheat heading/flowering. In the present study, we attempt to expand the types of VRN-A1 alleles using CRISPR/Cas9 targeted modification of the promoter sequence. Several mono- and biallelic changes were achieved within the 125-117 bp upstream sequence of the start codon of the recessive vrn-A1 gene in plants of semi-winter cv. 'Chinese Spring'. New mutations stably inherited in subsequent progenies and transgene-free homozygous plants carrying novel VRN-A1 variants were generated. Minor changes in the promoter sequence, such as 1-4 nucleotide insertions/deletions, had no effect on the heading time of plants, whereas the CRISPR/Cas9-mediated 8 bp deletion between -125 and -117 bp of the vrn-A1 promoter shortened the time of head emergence by up to 2-3 days. Such a growth habit was consistently observed in homozygous mutant plants under nonvernalized cultivation using different long day regimes (16, 18, or 22 h), whereas the cold treatment (from two weeks and more) completely leveled the effect of the 8 bp deletion. Importantly, comparison with wild-type plants showed that the implemented alteration has no negative effects on main yield characteristics. Our results demonstrate the potential to manipulate the heading time of wheat through targeted editing of the VRN-A1 gene promoter sequence on an otherwise unchanged genetic background.
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Affiliation(s)
- Dmitry Miroshnichenko
- Kurchatov Genomic Center — All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Branch of Institute of Bioorganic Chemistry RAS, Pushchino, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Vadim Timerbaev
- Kurchatov Genomic Center — All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Branch of Institute of Bioorganic Chemistry RAS, Pushchino, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Anna Klementyeva
- Branch of Institute of Bioorganic Chemistry RAS, Pushchino, Russia
| | - Alexander Pushin
- Branch of Institute of Bioorganic Chemistry RAS, Pushchino, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Tatiana Sidorova
- Branch of Institute of Bioorganic Chemistry RAS, Pushchino, Russia
| | - Dmitry Litvinov
- Kurchatov Genomic Center — All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Lubov Nazarova
- Kurchatov Genomic Center — All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Olga Shulga
- Kurchatov Genomic Center — All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Mikhail Divashuk
- Kurchatov Genomic Center — All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Elena Salina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
| | - Sergey Dolgov
- Branch of Institute of Bioorganic Chemistry RAS, Pushchino, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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23
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Kuluev BR, Mikhailova EV, Kuluev AR, Galimova AA, Zaikina EA, Khlestkina EK. Genome Editing in Species of the Tribe Triticeae with the CRISPR/Cas System. Mol Biol 2022. [DOI: 10.1134/s0026893322060127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Liu X, Zhao D, Ou C, Hao W, Zhao Z, Zhuang F. Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot. Front Genet 2022; 13:1047890. [PMID: 36437940 PMCID: PMC9696379 DOI: 10.3389/fgene.2022.1047890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2023] Open
Abstract
Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.
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Affiliation(s)
| | | | | | | | | | - Feiyun Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, China
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25
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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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26
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Liu X, Xu Z, Feng B, Zhou Q, Ji G, Guo S, Liao S, Lin D, Fan X, Wang T. Quantitative trait loci identification and breeding value estimation of grain weight-related traits based on a new wheat 50K single nucleotide polymorphism array-derived genetic map. FRONTIERS IN PLANT SCIENCE 2022; 13:967432. [PMID: 36110352 PMCID: PMC9468616 DOI: 10.3389/fpls.2022.967432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
Mining novel and less utilized thousand grain weight (TGW) related genes are useful for improving wheat yield. In this study, a recombinant inbred line population from a cross between Zhongkemai 138 (ZKM138, high TGW) and Chuanmai 44 (CM44, low TGW) was used to construct a new Wheat 50K SNP array-derived genetic map that spanned 1,936.59 cM and contained 4, 139 markers. Based on this map, ninety-one quantitative trait loci (QTL) were detected for eight grain-related traits in six environments. Among 58 QTLs, whose superior alleles were contributed by ZKM138, QTgw.cib-6A was a noticeable major stable QTL and was also highlighted by bulked segregant analysis with RNA sequencing (BSR-Seq). It had a pyramiding effect on TGW enhancement but no significant trade-off effect on grain number per spike or tiller number, with two other QTLs (QTgw.cib-2A.2 and QTgw.cib-6D), possibly explaining the excellent grain performance of ZKM138. After comparison with known loci, QTgw.cib-6A was deduced to be a novel locus that differed from nearby TaGW2 and TaBT1. Seven simple sequence repeat (SSR) and thirty-nine kompetitive allele-specific PCR (KASP) markers were finally developed to narrow the candidate interval of QTgw.cib-6A to 4.1 Mb. Only six genes in this interval were regarded as the most likely candidate genes. QTgw.cib-6A was further validated in different genetic backgrounds and presented 88.6% transmissibility of the ZKM138-genotype and a 16.4% increase of TGW in ZKM138 derivatives. And the geographic pattern of this locus revealed that its superior allele is present in only 6.47% of 433 Chinese modern wheat varieties, indicating its potential contribution to further high-yield breeding.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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27
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Awan MJA, Pervaiz K, Rasheed A, Amin I, Saeed NA, Dhugga KS, Mansoor S. Genome edited wheat- current advances for the second green revolution. Biotechnol Adv 2022; 60:108006. [PMID: 35732256 DOI: 10.1016/j.biotechadv.2022.108006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/21/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022]
Abstract
Common wheat is a major source of nutrition around the globe, but unlike maize and rice hybrids, no breakthrough has been made to enhance wheat yield since Green Revolution. With the availability of reference genome sequence of wheat and advancement of allied genomics technologies, understanding of genes involved in grain yield components and disease resistance/susceptibility has opened new avenues for crop improvement. Wheat has a huge hexaploidy genome of approximately 17 GB with 85% repetition, and it is a daunting task to induce any mutation across three homeologues that can be helpful for the enhancement of agronomic traits. The CRISPR-Cas9 system provides a promising platform for genome editing in a site-specific manner. In wheat, CRISPR-Cas9 is being used in the improvement of yield, grain quality, biofortification, resistance against diseases, and tolerance against abiotic factors. The promising outcomes of the CRISPR-based multiplexing approach circumvent the constraint of targeting merely one gene at a time. Deployment of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) 9 endonuclease (CRISPR-Cas9) and Cas9 variant systems such as cytidine base editing, adenosine base editing, and prime editing in wheat has been used to induce point mutations more precisely. Scientists have acquired major events such as induction of male sterility, fertility restoration, and alteration of seed dormancy through Cas9 in wheat that can facilitate breeding programs for elite variety development. Furthermore, a recent discovery in tissue culturing enables scientists to significantly enhance regeneration efficiency in wheat by transforming the GRF4-GIF1 cassette. Rapid generation advancement by speed breeding technology provides the opportunity for the generation advancement of the desired plants to segregate out unwanted transgenes and allows rapid integration of gene-edited wheat into the breeding pipeline. The combination of these novel technologies addresses some of the most important limiting factors for sustainable and climate-smart wheat that should lead to the second "Green Revolution" for global food security.
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Affiliation(s)
- Muhammad Jawad Akbar Awan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Komal Pervaiz
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS) & CIMMYT-China office, 12 Zhongguanccun South Street, Beijing 100081, China
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Nasir A Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan
| | - Kanwarpal S Dhugga
- Corteva Agriscience, Johnston, IA, USA; International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, Pakistan.
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