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Zhang C, Wang H, Tian X, Lin X, Han Y, Han Z, Sha H, Liu J, Liu J, Zhang J, Bu Q, Fang J. A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination. Nat Commun 2024; 15:2211. [PMID: 38480722 PMCID: PMC10937917 DOI: 10.1038/s41467-024-46420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.
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Affiliation(s)
- Chuanzhong Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Xinyan Lin
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, 136000, China
| | - Yunfei Han
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Zhongmin Han
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Hanjing Sha
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jianfeng Liu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping, Jilin Province, 136000, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Jun Fang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China.
- Yazhouwan National Laboratory, Sanya, 572024, China.
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2
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Sun Z, Peng J, Lv Q, Ding J, Chen S, Duan M, He Q, Wu J, Tian Y, Yu D, Tan Y, Sheng X, Chen J, Sun X, Liu L, Peng R, Liu H, Zhou T, Xu N, Lou J, Yuan L, Wang B, Yuan D. Dissecting the genetic basis of heterosis in elite super-hybrid rice. PLANT PHYSIOLOGY 2023; 192:307-325. [PMID: 36755501 PMCID: PMC10152689 DOI: 10.1093/plphys/kiad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/06/2023] [Accepted: 01/18/2023] [Indexed: 05/03/2023]
Abstract
Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm-2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.
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Affiliation(s)
- Zhizhong Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | | | - Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Jia Ding
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Siyang Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Meijuan Duan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yan Tian
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Dong Yu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xiabing Sheng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jin Chen
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xuewu Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ling Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Rui Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Tianshun Zhou
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
| | - Na Xu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jianhang Lou
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Longping Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Bingbing Wang
- Biobin Data Sciences Co., Ltd., Changsha 410221, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Longping Branch, College of Biology, Hunan University, Changsha 410125, China
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3
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Wang Y, Li F, Zhang F, Wu L, Xu N, Sun Q, Chen H, Yu Z, Lu J, Jiang K, Wang X, Wen S, Zhou Y, Zhao H, Jiang Q, Wang J, Jia R, Sun J, Tang L, Xu H, Hu W, Xu Z, Chen W, Guo A, Xu Q. Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:202-218. [PMID: 36196761 PMCID: PMC9829401 DOI: 10.1111/pbi.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Temperate japonica/geng (GJ) rice yield has significantly improved due to intensive breeding efforts, dramatically enhancing global food security. However, little is known about the underlying genomic structural variations (SVs) responsible for this improvement. We compared 58 long-read assemblies comprising cultivated and wild rice species in the present study, revealing 156 319 SVs. The phylogenomic analysis based on the SV dataset detected the putatively selected region of GJ sub-populations. A significant portion of the detected SVs overlapped with genic regions were found to influence the expression of involved genes inside GJ assemblies. Integrating the SVs and causal genetic variants underlying agronomic traits into the analysis enables the precise identification of breeding signatures resulting from complex breeding histories aimed at stress tolerance, yield potential and quality improvement. Further, the results demonstrated genomic and genetic evidence that the SV in the promoter of LTG1 is accounting for chilling sensitivity, and the increased copy numbers of GNP1 were associated with positive effects on grain number. In summary, the current study provides genomic resources for retracing the properties of SVs-shaped agronomic traits during previous breeding procedures, which will assist future genetic, genomic and breeding research on rice.
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Affiliation(s)
- Yu Wang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Fengcheng Li
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Fan Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Lian Wu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Na Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Qi Sun
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Hao Chen
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Zhiwen Yu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Jiahao Lu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Kai Jiang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Xiaoche Wang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Siyu Wen
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Yao Zhou
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Hui Zhao
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Qian Jiang
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | | | - Ruizong Jia
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jian Sun
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Liang Tang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Hai Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Wei Hu
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Wenfu Chen
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Anping Guo
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
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4
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Xu N, Xu H, Xu Z, Li F, Xu Q. Introgression of a Complex Genomic Structural Variation Causes Hybrid Male Sterility in GJ Rice ( Oryza sativa L.) Subspecies. Int J Mol Sci 2022; 23:ijms232112804. [PMID: 36361593 PMCID: PMC9656383 DOI: 10.3390/ijms232112804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 11/26/2022] Open
Abstract
Hybrids between different subspecies of rice Oryza sativa L. commonly show hybrid sterility. Here we show that a widely planted commercial japonica/GJ variety, DHX2, exhibited hybrid sterility when crossing with other GJ varieties. Using the high-quality genome assembly, we identified three copies of the Sc gene in DHX2, whereas Nipponbare (Nip) had only one copy of Sc. Knocking out the extra copies of Sc in DHX2 significantly improved the pollen fertility of the F1 plant of DHX2/Nip cross. The population structure analysis revealed that a slight introgression from Basmati1 might occur in the genome of DHX2. We demonstrated that both DHX2 and Basmati1 harbored three copies of Sc. Moreover, the introgression of GS3 and BADH2/fgr from Basmati1 confers the slender and fragrance grain of DHX2. These results add to our understanding of the hybrid sterility of inter-subspecies and intra-subspecies and may provide a novel strategy for hybrid breeding.
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Affiliation(s)
| | | | | | | | - Quan Xu
- Correspondence: (F.L.); (Q.X.)
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5
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Gong H, Han B. Genetic introgression between different groups reveals the differential process of Asian cultivated rice. Sci Rep 2022; 12:17662. [PMID: 36271113 PMCID: PMC9587041 DOI: 10.1038/s41598-022-22674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/18/2022] [Indexed: 01/18/2023] Open
Abstract
The Asian cultivated rice consists of two major subspecies: indica and japonica. There are already many reports about the existence of genetic introgression between the two subspecies. They propose some possible introgression-related genes from the comparison of population parameters. This study uses the genome-wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica populations. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions, they generally get consistent results. Some previously known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays a vital role in the determination of both the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and the domestication process.
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Affiliation(s)
- Hao Gong
- grid.411411.00000 0004 0644 5457School of Life Science, Huizhou University, Huizhou, 516007 China
| | - Bin Han
- grid.9227.e0000000119573309National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233 China
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6
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Yang G, Deng P, Guo Q, Shi T, Pan W, Cui L, Liu X, Nie X. Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:450. [PMID: 36127641 PMCID: PMC9490906 DOI: 10.1186/s12870-022-03828-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are emerging as the important regulators involving in growth and development as well as stress response in plants. However, current lncRNA studies were mainly performed at the individual level and the significance of it is not well understood in wheat. RESULTS In this study, the lncRNA landscape of wheat spike was characterized through analysing a total of 186 spike RNA-seq datasets from 93 wheat genotypes. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. Compared to coding genes, these lncRNAs displayed rather low conservation among wheat and other gramineous species. Based on re-sequencing data, the genetic variations of these lncRNA were investigated and obvious genetic bottleneck were found on them during wheat domestication process. Furthermore, 122 lncRNAs were found to act as ceRNA to regulate endogenous competition. Finally, association and co-localization analysis of the candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target mRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) associated with heading date and spike length, respectively. CONCLUSIONS This study reported the lncRNA landscape of wheat spike through the population transcriptome analysis, which not only contribute to better understand the wheat evolution from the perspective of lncRNA, but also lay the foundation for revealing roles of lncRNA playing in spike development.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qifan Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingrui Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Xiaoqin Liu
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China.
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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7
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Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. PLANT COMMUNICATIONS 2022; 3:100325. [PMID: 35576158 PMCID: PMC9251437 DOI: 10.1016/j.xplc.2022.100325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maomao Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jianchang Sun
- Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China
| | - Xianju Wang
- Rice Research Institute of Liaoning Province, Shenyang 110161, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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8
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Su Q, Zhang F, Xiao Y, Zhang P, Xing H, Chen F. An efficient screening system to identify protein-protein or protein-DNA interaction partners of rice transcription factors. J Genet Genomics 2022; 49:979-981. [PMID: 35218975 DOI: 10.1016/j.jgg.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 02/06/2022] [Indexed: 10/19/2022]
Affiliation(s)
- Qingmei Su
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; OE biotech Co., Ltd. Shanghai, China
| | | | | | | | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Huang H, Ye Y, Song W, Li Q, Han R, Wu C, Wang S, Yu J, Liu X, Fu X, Liu Q, Wu K. Modulating the C-terminus of DEP1 synergistically enhances grain quality and yield in rice. J Genet Genomics 2022; 49:506-509. [PMID: 35182790 DOI: 10.1016/j.jgg.2022.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Haixiang Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Jiaxing Academy of Agricultural Sciences, Jiaxing 314024, Zhejiang, China
| | - Yafeng Ye
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China
| | - Wenzhen Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruixi Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenchen Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuoxun Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianping Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xueying Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Kun Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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10
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Li J, Zhang Z, Chong K, Xu Y. Chilling tolerance in rice: Past and present. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153576. [PMID: 34875419 DOI: 10.1016/j.jplph.2021.153576] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.
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Affiliation(s)
- Junhua Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zeyong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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11
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Chen J, Zhang H, Dai D, Li X, Ma L, Liang C, Zhang R, Liang C, Du H, Chen Z, Zhao Y, Deng S. A backbone parent contributes key genomic architecture to pedigree breeding of early-season indica rice. J Genet Genomics 2021; 48:1040-1043. [PMID: 34365020 DOI: 10.1016/j.jgg.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Junyu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dongqing Dai
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ximing Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Liangyong Ma
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhui Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuhan Deng
- Novogene Bioinformatics Institute, Beijing, 100083, China
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12
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Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, He Q, Ou S, Zhang H, Li X, Li X, Li Y, Liao Y, Gao Q, Tu B, Yuan H, Ma B, Wang Y, Qian Y, Fan S, Li W, Wang J, He M, Yin J, Li T, Jiang N, Chen X, Liang C, Li S. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 2021; 184:3542-3558.e16. [PMID: 34051138 DOI: 10.1016/j.cell.2021.04.046] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/31/2021] [Accepted: 04/24/2021] [Indexed: 12/30/2022]
Abstract
Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.
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Affiliation(s)
- Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Hao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weilan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiang He
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Hongyu Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xuanzhao Li
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bingtian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yangwen Qian
- Biogle Genome Editing Center, Changzhou, Jiangsu, China
| | - Shijun Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
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