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Wang P, Ma L, Li D, Zhang B, Zhou T, Zhou X, Xing Y. Fine mapping of the panicle length QTL qPL5 in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:6. [PMID: 38261843 PMCID: PMC10794681 DOI: 10.1007/s11032-024-01443-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/02/2023] [Indexed: 01/25/2024]
Abstract
Panicle length is a crucial trait tightly associated with spikelets per panicle and grain yield in rice. To dissect the genetic basis of panicle length, a population of 161 recombinant inbred lines (RILs) was developed from the cross between an aus variety Chuan 7 (C7) and a tropical Geng variety Haoboka (HBK). C7 has a panicle length of 30 cm, 7 cm longer than that of HBK, and the panicle length was normally distributed in the RIL population. A total of six quantitative trait loci (QTLs) for panicle length were identified, and single QTLs explained the phenotypic variance from 4.9 to 18.1%. Among them, three QTLs were mapped to the regions harbored sd1, DLT, and Ehd1, respectively. To validate the genetic effect of a minor QTL qPL5, a near-isogenic F2 (NIF2) population segregated at qPL5 was developed. Interestingly, panicle length displayed bimodal distribution, and heading date also exhibited significant variation in the NIF2 population. qPL5 accounted for 66.5% of the panicle length variance. The C7 allele at qPL5 increased panicle length by 2.4 cm and promoted heading date by 5 days. Finally, qPL5 was narrowed down to an 80-kb region flanked by markers M2197 and M2205 using a large NIF2 population of 7600 plants. LOC_Os05g37540, encoding a phytochrome signal protein whose homolog in Arabidopsis enlarges panicle length, is regarded as the candidate gene because a single-nucleotide mutation (C1099T) caused a premature stop codon in HBK. The characterization of qPL5 with enlarging panicle length but promoting heading date makes its great value in breeding early mature varieties without yield penalty in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01443-2.
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Affiliation(s)
- Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Daoyang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tianhao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
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Li S, Luo Y, Wei G, Zong W, Zeng W, Xiao D, Zhang H, Song Y, Hao Y, Sun K, Lei C, Guo X, Xu B, Li W, Wu Z, Liu Y, Xie X, Guo J. Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:239. [PMID: 37930441 DOI: 10.1007/s00122-023-04489-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE We developed an efficient promoter editing method to create different weak Ehd1 alleles in elite japonica rice variety ZJ8 with slightly delayed heading and improved yield for use in breeding. Heading date is an important agronomic trait of rice (Oryza sativa) that determines the planting areas and cultivation seasons of different varieties, thus affecting final yield. Early heading date 1 (Ehd1) is a major rice integrator gene in the regulatory network of heading date whose expression level is negatively correlated with heading date and grain yield. Some elite japonica varieties such as Zhongjia 8 (ZJ8) show very early heading with poor agronomic traits when planted in South China. This problem can be addressed by downregulating the expression of Ehd1. In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be created to expand the planting area of rice and improve grain yields.
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Affiliation(s)
- Shengting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Guangliang Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanyong Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongdong Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Han Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kangli Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chen Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Bingqun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weitao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zeqiang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangdong Laboratory for Lingnan Modern AgricultureCollege of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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3
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Li S, Hu Y, An C, Wen Q, Fan X, Zhang Z, Sherif A, Liu H, Xing Y. The amino acid residue E96 of Ghd8 is crucial for the formation of the flowering repression complex Ghd7-Ghd8-OsHAP5C in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1012-1025. [PMID: 36479821 DOI: 10.1111/jipb.13426] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Ghd7 is an important gene involved in the photoperiod flowering pathway in rice. A Ghd7-involved transcriptional regulatory network has been established, but its translational regulatory pathway is poorly understood. The mutant suppressor of overexpression of Ghd7 (sog7) was identified from EMS-induced mutagenesis on the background of ZH11 overexpressing Ghd7. MutMap analysis revealed that SOG7 is allelic to Ghd8 and delayed flowering under long-day (LD) conditions. Biochemical assays showed that Ghd8 interacts with OsHAP5C and Ghd7 both in vivo and in vitro. Surprisingly, a point mutation E96K in the α2 helix of the Ghd8 histone fold domain (HFD) destroyed its ability to interact with Ghd7. The prediction of the structure shows that mutated amino acid is located in the interaction region of CCT/NF-YB/YC complexes, which alter the structure of α4 of Ghd8. This structural difference prevents the formation of complex NF-YB/YC. The triple complex of Ghd8-OsHAP5C-Ghd7 directly bound to the promotor of Hd3a and downregulated the expression of Ehd1, Hd3a and RFT1, and finally resulted in a delayed heading. These findings are helpful in deeply understanding the Ghd7-involved photoperiod flowering pathway and promote the elucidation of rice heading.
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Affiliation(s)
- Shuangle Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Chen An
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Qingli Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Ahmed Sherif
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Hongshan Laboratory, Wuhan, 430070, China
- Hongshan Laboratory, Wuhan, 430070, China
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4
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Li B, Liu X, Guo Y, Deng L, Qu L, Yan M, Li M, Wang T. BnaC01.BIN2, a GSK3-like kinase, modulates plant height and yield potential in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:29. [PMID: 36867248 DOI: 10.1007/s00122-023-04325-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Using map-based cloning and transgenic transformation, we revealed that glycogen kinase synthase 3-like kinase, BnaC01.BIN2, modulates plant height and yield in rapeseed. The modification of plant height is one of the most important goals in rapeseed breeding. Although several genes that regulate rapeseed plant height have been identified, the genetics mechanisms underlying rapeseed plant height regulation remain poorly understood, and desirable genetic resources for rapeseed ideotype breeding are scarce. Here, we map-based cloned and functionally verified that the rapeseed semi-dominant gene, BnDF4, greatly affects rapeseed plant height. Specifically, BnDF4 encodes brassinosteroid (BR)-insensitive 2, a glycogen synthase kinase 3 primarily expressed in the lower internodes to modulate rapeseed plant height by blocking basal internode-cell elongation. Transcriptome data showed that several cell expansion-related genes involving auxin and BRs pathways were significantly downregulated in the semi-dwarf mutant. Heterozygosity in the BnDF4 allele results in small stature with no marked differences in other agronomic traits. Using BnDF4 in the heterozygous condition, the hybrid displayed strong yield heterosis through optimum intermediate plant height. Our results provide a desirable genetic resource for breeding semi-dwarf rapeseed phenotypes and support an effective strategy for breeding rapeseed hybrid varieties with strong yield heterosis.
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Affiliation(s)
- Bao Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China
| | - Xinhong Liu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China
| | - Yiming Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China
| | - Lichao Deng
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China
| | - Liang Qu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China.
| | - Tonghua Wang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- Hunan Hybrid Rapeseed Engineering and Technology Research Center, Changsha, 410125, China.
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5
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Hu Z, Yang Z, Zhang Y, Zhang A, Lu Q, Fang Y, Lu C. Autophagy targets Hd1 for vacuolar degradation to regulate rice flowering. MOLECULAR PLANT 2022; 15:1137-1156. [PMID: 35591785 DOI: 10.1016/j.molp.2022.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/03/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
Flowering time (heading date) is a critical agronomic trait that determines the yield and regional adaptability of crops. Heading date 1 (Hd1) is a central regulator of photoperiodic flowering in rice (Oryza sativa). However, how the homeostasis of Hd1 protein is achieved is poorly understood. Here, we report that the nuclear autophagy pathway mediates Hd1 degradation in the dark to regulate flowering. Loss of autophagy function results in an accumulation of Hd1 and delays flowering under both short-day and long-day conditions. In the dark, nucleus-localized Hd1 is recognized as a substrate for autophagy and is subjected to vacuolar degradation via the autophagy protein OsATG8. The Hd1-OsATG8 interaction is required for autophagic degradation of Hd1 in the dark. Our study reveals a new mechanism by which Hd1 protein homeostasis is regulated by autophagy to control rice flowering. Our study also indicates that the regulation of flowering by autophagic degradation of Hd1 orthologs may have arisen over the course of mesangiosperm evolution, which would have increased their flexibility and adaptability to the environment by modulating flowering time.
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Affiliation(s)
- Zhi Hu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhipan Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Aihong Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Qingtao Lu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ying Fang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong 271018, China.
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6
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Fujino K, Kawahara Y, Shirasawa K. Artificial selection in the expansion of rice cultivation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:291-299. [PMID: 34731272 DOI: 10.1007/s00122-021-03966-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Gene distributions and population genomics suggest artificial selection of ghd7 osprr37, for extremely early heading date of rice, in the Tohoku region of Japan. The ranges of cultivated crops expanded into various environmental conditions around the world after their domestication. Hokkaido, Japan, lies at the northern limit of cultivation of rice, which originated in the tropics. Novel genotypes for extremely early heading date in Hokkaido are controlled by loss-of-function of both Grain number, plant height and heading date 7 (Ghd7) and Oryza sativa Pseudo-Response Regulator 37 (OsPRR37). We traced genotypes for extremely early heading date and analyzed the phylogeny of rice varieties grown historically in Japan. The mutations in Ghd7 and OsPRR37 had distinct local distributions. Population genomics revealed that varieties collected from the Tohoku region of northern Japan formed three clusters. Mutant alleles of Ghd7 and OsPRR37 appear to have allowed rice cultivation to spread into Hokkaido. Our results show that the mutations of two genes might be occurred in the process of artificial selection during early rice cultivation in the Tohoku region.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization (NARO), Sapporo, 062-8555, Japan.
- Institute of Crop Science, National Agricultural Research Organization, Tsukuba, 305-8518, Japan.
| | - Yoshihiro Kawahara
- Institute of Crop Science, NARO, Tsukuba, 305-8518, Japan
- Advanced Analysis Center, NARO, Tsukuba, 305-8602, Japan
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7
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Zhou X, Nong C, Wu B, Zhou T, Zhang B, Liu X, Gao G, Mi J, Zhang Q, Liu H, Liu S, Li Z, He Y, Mou T, Guo S, Li S, Yang Y, Zhang Q, Xing Y. Combinations of Ghd7, Ghd8, and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6963-6976. [PMID: 34283218 DOI: 10.1093/jxb/erab344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Heterosis of grain yield is closely associated with heading date in crops. Gene combinations of the major heading date genes Ghd7, Ghd8, and Hd1 play important roles in enhancing grain yield and adaptation to ecological regions in rice. However, the predominant three-gene combinations for a specific ecological region remain unclear in both three-line and two-line hybrids. In this study, we sequenced these three genes of 50 cytoplasmic male sterile/maintainer lines, 31 photo-thermo-sensitive genic male sterile lines, and 109 restorer lines. Sequence analysis showed that hybrids carrying strong functional alleles of Ghd7 and Hd1 and non-functional Ghd8 are predominant in three-line hybrids and are recommended for rice production in the subtropics around 30°N/S. Hybrids carrying strong functional Ghd7 and Ghd8 and non-functional Hd1 are predominant in two-line hybrids and are recommended for low latitude areas around 23.5°N/S rich in photothermal resources. Hybrids carrying strong functional Ghd7 and Ghd8 and functional Hd1 were not identified in commercial hybrids in the middle and lower reaches of the Yangtze River, but they have high yield potential in tropical regions because they have the strongest photoperiod sensitivity. Based on these findings, two genic sterile lines, Xiangling 628S and C815S, whose hybrids often head very late, were diagnosed with these three genes, and Hd1 was targeted to be knocked out in Xiangling 628S and replaced with hd1 in C815S. The hybrids developed from both modified sterile lines in turn had appropriate heading dates and significantly improved grain yield. This study provides new insights for breeding design to develop hybrids for various regions.
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Affiliation(s)
- Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Chunxiao Nong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Tianhao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Xingshao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou 434023,China
| | - Shisheng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Zhixin Li
- College of Agriculture, Yangtze University, Jingzhou 434023,China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Sibin Guo
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Naning 530007,China
| | - Shaoqing Li
- College of Life Science, Wuhan University, Wuhan 430072,China
| | - Yuanzhu Yang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha 410128,China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
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8
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Li B, Du X, Fei Y, Wang F, Xu Y, LI X, Li W, Chen Z, Fan F, Wang J, Tao Y, Jiang Y, Zhu QH, Yang J. Efficient Breeding of Early-Maturing Rice Cultivar by Editing PHYC via CRISPR/Cas9. RICE (NEW YORK, N.Y.) 2021; 14:86. [PMID: 34643821 PMCID: PMC8514591 DOI: 10.1186/s12284-021-00527-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Bin Li
- Institute of Life Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
| | - Xi Du
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yunyan Fei
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xia LI
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wenqi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Zhihui Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yajun Tao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yanjie Jiang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT Australia
| | - Jie Yang
- Institute of Life Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
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9
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Zhou S, Zhu S, Cui S, Hou H, Wu H, Hao B, Cai L, Xu Z, Liu L, Jiang L, Wang H, Wan J. Transcriptional and post-transcriptional regulation of heading date in rice. THE NEW PHYTOLOGIST 2021; 230:943-956. [PMID: 33341945 PMCID: PMC8048436 DOI: 10.1111/nph.17158] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/15/2020] [Indexed: 05/04/2023]
Abstract
Rice is a facultative short day (SD) plant. In addition to serving as a model plant for molecular genetic studies of monocots, rice is a staple crop for about half of the world's population. Heading date is a critical agronomic trait, and many genes controlling heading date have been cloned over the last 2 decades. The mechanism of flowering in rice from recognition of day length by leaves to floral activation in the shoot apical meristem has been extensively studied. In this review, we summarise current progress on transcriptional and post-transcriptional regulation of heading date in rice, with emphasis on post-translational modifications of key regulators, including Heading date 1 (Hd1), Early heading date 1 (Ehd1), Grain number, plant height, and heading date7 (Ghd7). The contribution of heading date genes to heterosis and the expansion of rice cultivation areas from low-latitude to high-latitude regions are also discussed. To overcome the limitations of diverse genetic backgrounds used in heading date studies and to gain a clearer understanding of flowering in rice, we propose a systematic collection of genetic resources in a common genetic background. Strategies in breeding adapted cultivars by rational design are also discussed.
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Affiliation(s)
- Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haigang Hou
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haoqin Wu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Benyuan Hao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Liang Cai
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Zhuang Xu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing210095China
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
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10
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Zhang J, Fan X, Hu Y, Zhou X, He Q, Liang L, Xing Y. Global analysis of CCT family knockout mutants identifies four genes involved in regulating heading date in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:913-923. [PMID: 32889758 DOI: 10.1111/jipb.13013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Many genes encoding CCT domain-containing proteins regulate flowering time. In rice (Oryza sativa), 41 such genes have been identified, but only a few have been shown to regulate heading date. Here, to test whether and how additional CCT family genes regulate heading date in rice, we classified these genes into five groups based on their diurnal expression patterns. The expression patterns of genes in the same subfamily or in close phylogenetic clades tended to be similar. We generated knockout mutants of the entire gene family via CRISPR/Cas9. The heading dates of knockout mutants of only 4 of 14 genes previously shown to regulate heading date were altered, pointing to functional redundancy of CCT family genes in regulating this trait. Analysis of mutants of four other genes showed that OsCCT22, OsCCT38, and OsCCT41 suppress heading under long-day conditions and promote heading under short-day conditions. OsCCT03 promotes heading under both conditions and upregulates the expression of Hd1 and Ehd1, a phenomenon not previously reported for other such genes. To date, at least 18 CCT domain-containing genes involved in regulating heading have been identified, providing diverse, flexible gene combinations for generating rice varieties with a given heading date.
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Affiliation(s)
- Jia Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liwen Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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11
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Hu Y, Zhou X, Zhang B, Li S, Fan X, Zhao H, Zhang J, Liu H, He Q, Li Q, Ayaad M, You A, Xing Y. OsPRR37 Alternatively Promotes Heading Date Through Suppressing the Expression of Ghd7 in the Japonica Variety Zhonghua 11 under Natural Long-Day Conditions. RICE (NEW YORK, N.Y.) 2021; 14:20. [PMID: 33630174 PMCID: PMC7907330 DOI: 10.1186/s12284-021-00464-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/12/2021] [Indexed: 05/24/2023]
Abstract
Heading date is an important agronomic trait of rice (Oryza sativa L.) and is regulated by numerous genes, some of which exhibit functional divergence in a genetic background-dependent manner. Here, we identified a late heading date 7 (lhd7) mutant that flowered later than wild-type Zhonghua 11 (ZH11) under natural long-day (NLD) conditions. Map-based cloning facilitated by the MutMap strategy revealed that LHD7 was on the same locus as OsPRR37 but exhibited a novel function as a promoter of heading date. A single-nucleotide mutation of G-to-A in the coding region caused a substitution of aspartic acid for glycine at site 159 within the pseudo-receiver (PR) domain of OsPRR37. Transcriptional analysis revealed that OsPRR37 suppressed Ghd7 expression in both ZH11 background under NLD conditions and the Zhenshan 97 background under natural short-day conditions. Consistently, the expression of Ehd1, Hd3a and RFT1 was enhanced by OsPRR37 in the ZH11 background. Genetic analysis indicated that the promotion of heading date and reduction in grain yield by OsPRR37 were partially dependent on Ghd7. Further investigation showed that the alternative function of OsPRR37 required an intact Ghd7-related regulatory pathway involving not only its upstream regulators OsGI and PhyB but also its interacting partner Hd1. Our study revealed the distinct role of OsPRR37 in the ZH11 background, which provides a more comprehensive understanding of OsPRR37 function and enriches the theoretical bases for improvement of rice heading date in the future.
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Affiliation(s)
- Yong Hu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiuping Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal, 13759, Egypt
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
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12
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Fujino K. Days to heading, controlled by the heading date genes, Hd1 and DTH8, limits rice yield-related traits in Hokkaido, Japan. BREEDING SCIENCE 2020; 70:277-282. [PMID: 32714049 PMCID: PMC7372023 DOI: 10.1270/jsbbs.19151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/05/2019] [Indexed: 06/11/2023]
Abstract
A key aspect of rice breeding programs is the optimization of days to heading (DTH) for maximizing grain productivity in cultivation areas. Here, the effects of genotypes for heading date on yield-related traits in rice (culm and panicle length (CL and PL), panicle number (PN), and total number of seeds) were investigated. Heading date 1 (Hd1) and Days to heading 8 (DTH8) are the main controllers of the variation in heading date in the rice population of Hokkaido, Japan. Thus, an F2 population (n = 192) derived from a cross between Kitaibuki (Hd1dth8) and Akage (hd1DTH8) was developed. Significant differences in DTH were found among all combinations. Each genotype for heading date showed variations in the yield-related traits without a significant difference. However, DTH exhibited high positive coefficient values (more than 0.709) with the yield-related traits except for PN, which had a negative coefficient value of -0.431. A later heading date resulted in a longer growth duration and a higher yield with a combination of longer PL and CL and lower PN. These results suggest that DTH limits the yield-related traits rather than the genotype for heading date.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
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13
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Fujino K, Yamanouchi U. Genetic effect of a new allele for the flowering time locus Ghd7 in rice. BREEDING SCIENCE 2020; 70:342-346. [PMID: 32714056 PMCID: PMC7372035 DOI: 10.1270/jsbbs.19112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/02/2020] [Indexed: 06/11/2023]
Abstract
The optimization of flowering time is a key aspect in maximizing grain productivity in rice. Allelic variations in genes for flowering time are major drivers in the wide adaptability of cultivated rice around the world. Here, we identified a novel allele of flowering time gene Grain number, plant height and heading date 7 (Ghd7). Loss-of-function ghd7, Ghd7-0a, is important for extremely early flowering time for adaptability to cultivation in Hokkaido, Japan. However, the rice variety Sorachi lacks a key functional nucleotide polymorphism of Ghd7, which results in a loss of function of the gene. Based on the sequence of Ghd7 allele in Sorachi, we identified the insertion of a transposon-like sequence at an upstream site of Ghd7. Segregation analysis using an F2 population derived from the cross between Hoshinoyume and Sorachi demonstrated that the Ghd7 locus contributed to extremely early flowering time in Sorachi. This Ghd7 allele in Sorachi showed a weak function in terms of delay of flowering time, compared with loss-of-function allele, and a distinct distribution in northern Japan.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
| | - Utako Yamanouchi
- Institute of Crop Science, National Agricultural Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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14
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Liu H, Zhou X, Li Q, Wang L, Xing Y. CCT domain-containing genes in cereal crops: flowering time and beyond. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1385-1396. [PMID: 32006055 DOI: 10.1007/s00122-020-03554-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/23/2020] [Indexed: 05/04/2023]
Abstract
The review summarizes the functions of the plant special transcription factors CCT family genes in multiple traits and discusses the molecular breeding strategies with CCT family genes in the future. Plants integrate circadian clock and external signals such as temperature and photoperiod to synchronize flowering with seasonal environmental changes. This process makes cereal crops including short-day crops, such as rice and maize, and long-day crops, such as wheat and barley, better adapt to varied growth zones from temperate to tropical regions. CCT family genes involve circadian clock and photoperiodic flowering pathways and help plants set a suitable flowering time to produce offspring. Beyond the flowering time, CCT family genes in cereal crops are associated with biomass and grain yield. Moreover, recent studies showed that they also associate with photosynthesis, nutrition use efficiency and stress tolerance. Here, we systematically review the progress in functional characterization of CCT family genes in flowering, geographical adaptation and grain yield formation, raise the core questions related to their molecular mechanisms and discuss how to practice them in genetic improvement in cereal crops by combining gene diagnosis and top-level design.
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Affiliation(s)
- Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Qiuping Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070, China.
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15
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Fujino K, Ikegaya T. A novel genotype DATTO5 developed using the five genes exhibits the fastest heading date designed in rice. BREEDING SCIENCE 2020; 70:193-199. [PMID: 32523401 PMCID: PMC7272244 DOI: 10.1270/jsbbs.19113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 06/11/2023]
Abstract
The optimization of heading date is a key aspect for maximizing grain productivity in cereal crops including rice. The combinations of genes for heading date, a quantitative trait, are a major driver in the wide adaptability of cultivated rice worldwide. Here, we identified a novel QTL, qDTH3 (quantitative trait locus for days-to-heading on chromosome 3), for early flowering time in the F2 population derived from a cross between Hoshinoyume (HS) and Daichinohoshi (DH) among local rice populations with extremely early heading date. The DH allele at qDTH3, qDTH3DH , headed 2.7 days earlier than the HS allele at qDTH3, qDTH3HS . We sought to design a genotype for earlier heading date by pyramiding of five heading date genes. We designated this aggregate of the five genes as DATTO5. Plants with DATTO5 were selected from the F2 population derived from a cross between DH and HShd5, which is a near-isogenic line carrying a loss-of-function of days to heading 8 in a genetic background of HS. Plants with DATTO5 exhibited earlier heading date but reduced fitness, including shorter culm and panicle length and fewer seeds compared with HS, as a representative local rice variety with extremely early heading date.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
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16
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Zhang ZH, Zhu YJ, Wang SL, Fan YY, Zhuang JY. Importance of the Interaction between Heading Date Genes Hd1 and Ghd7 for Controlling Yield Traits in Rice. Int J Mol Sci 2019; 20:ijms20030516. [PMID: 30691093 PMCID: PMC6387254 DOI: 10.3390/ijms20030516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 12/29/2022] Open
Abstract
Appropriate flowering time is crucial for successful grain production, which relies on not only the action of individual heading date genes, but also the gene-by-gene interactions. In this study, influences of interaction between Hd1 and Ghd7 on flowering time and yield traits were analyzed using near isogenic lines derived from a cross between indica rice cultivars ZS97 and MY46. In the non-functional ghd7ZS97 background, the functional Hd1ZS97 allele promoted flowering under both the natural short-day (NSD) conditions and natural long-day (NLD) conditions. In the functional Ghd7MY46 background, Hd1ZS97 remained to promote flowering under NSD conditions, but repressed flowering under NLD conditions. For Ghd7, the functional Ghd7MY46 allele repressed flowering under both conditions, which was enhanced in the functional Hd1ZS97 background under NLD conditions. With delayed flowering, spikelet number and grain weight increased under both conditions, but spikelet fertility and panicle number fluctuated. Rice lines carrying non-functional hd1MY46 and functional Ghd7MY46 alleles had the highest grain yield under both conditions. These results indicate that longer growth duration for a larger use of available temperature and light does not always result in higher grain production. An optimum heading date gene combination needs to be carefully selected for maximizing grain yield in rice.
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Affiliation(s)
- Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shi-Lin Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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17
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Desai SV, Balasubramanian VN, Fukatsu T, Ninomiya S, Guo W. Automatic estimation of heading date of paddy rice using deep learning. PLANT METHODS 2019; 15:76. [PMID: 31338116 PMCID: PMC6626381 DOI: 10.1186/s13007-019-0457-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 07/02/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Accurate estimation of heading date of paddy rice greatly helps the breeders to understand the adaptability of different crop varieties in a given location. The heading date also plays a vital role in determining grain yield for research experiments. Visual examination of the crop is laborious and time consuming. Therefore, quick and precise estimation of heading date of paddy rice is highly essential. RESULTS In this work, we propose a simple pipeline to detect regions containing flowering panicles from ground level RGB images of paddy rice. Given a fixed region size for an image, the number of regions containing flowering panicles is directly proportional to the number of flowering panicles present. Consequently, we use the flowering panicle region counts to estimate the heading date of the crop. The method is based on image classification using Convolutional Neural Networks. We evaluated the performance of our algorithm on five time series image sequences of three different varieties of rice crops. When compared to the previous work on this dataset, the accuracy and general versatility of the method has been improved and heading date has been estimated with a mean absolute error of less than 1 day. CONCLUSION An efficient heading date estimation method has been described for rice crops using time series RGB images of crop under natural field conditions. This study demonstrated that our method can reliably be used as a replacement of manual observation to detect the heading date of rice crops.
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Affiliation(s)
- Sai Vikas Desai
- Department of Computer Science and Engineering, Indian Institute of Technology - Hyderabad, Kandi, Hyderabad, 502285 India
| | - Vineeth N. Balasubramanian
- Department of Computer Science and Engineering, Indian Institute of Technology - Hyderabad, Kandi, Hyderabad, 502285 India
| | - Tokihiro Fukatsu
- Institute of Agricultural Machinery, National Agriculture and Food Research Organization, 1-31-1 Kannondai, Tsukuba, Ibaraki 3050856 Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 3058572 Japan
| | - Seishi Ninomiya
- International Field Phenomics Research Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishi-Tokyo, Tokyo 1880002 Japan
| | - Wei Guo
- International Field Phenomics Research Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Nishi-Tokyo, Tokyo 1880002 Japan
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