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Tiwari K, Tiwari S, Kumar N, Sinha S, Krishnamurthy SL, Singh R, Kalia S, Singh NK, Rai V. QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued. PLANTS (BASEL, SWITZERLAND) 2024; 13:1099. [PMID: 38674508 PMCID: PMC11054697 DOI: 10.3390/plants13081099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 04/28/2024]
Abstract
Rice (Oryza sativa L.) is a crucial crop contributing to global food security; however, its production is susceptible to salinity, a significant abiotic stressor that negatively impacts plant germination, vigour, and yield, degrading crop production. Due to the presence of exchangeable sodium ions (Na+), the affected plants sustain two-way damage resulting in initial osmotic stress and subsequent ion toxicity in the plants, which alters the cell's ionic homeostasis and physiological status. To adapt to salt stress, plants sense and transfer osmotic and ionic signals into their respective cells, which results in alterations of their cellular properties. No specific Na+ sensor or receptor has been identified in plants for salt stress other than the SOS pathway. Increasing productivity under salt-affected soils necessitates conventional breeding supplemented with biotechnological interventions. However, knowledge of the genetic basis of salinity stress tolerance in the breeding pool is somewhat limited because of the complicated architecture of salinity stress tolerance, which needs to be expanded to create salt-tolerant variants with better adaptability. A comprehensive study that emphasizes the QTLs, genes and governing mechanisms for salt stress tolerance is discussed in the present study for future research in crop improvement.
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Affiliation(s)
- Keshav Tiwari
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sushma Tiwari
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Nivesh Kumar
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Shikha Sinha
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | | | - Renu Singh
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, New Delhi 110003, India
| | - Nagendra Kumar Singh
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Vandna Rai
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
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Somsri A, Chu SH, Nawade B, Lee CY, Park YJ. Harnessing γ-TMT Genetic Variations and Haplotypes for Vitamin E Diversity in the Korean Rice Collection. Antioxidants (Basel) 2024; 13:234. [PMID: 38397832 PMCID: PMC10886147 DOI: 10.3390/antiox13020234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Gamma-tocopherol methyltransferase (γ-TMT), a key gene in the vitamin E biosynthesis pathway, significantly influences the accumulation of tocochromanols, thereby determining rice nutritional quality. In our study, we analyzed the γ-TMT gene in 475 Korean rice accessions, uncovering 177 genetic variants, including 138 SNPs and 39 InDels. Notably, two functional SNPs, tmt-E2-28,895,665-G/A and tmt-E4-28,896,689-A/G, were identified, causing substitutions from valine to isoleucine and arginine to glycine, respectively, across 93 accessions. A positive Tajima's D value in the indica group suggests a signature of balancing selection. Haplotype analysis revealed 27 haplotypes, with two shared between cultivated and wild accessions, seven specific to cultivated accessions, and 18 unique to wild types. Further, profiling of vitamin E isomers in 240 accessions and their association with haplotypes revealed that Hap_2, distinguished by an SNP in the 3' UTR (tmt-3UTR-28,897,360-T/A) exhibited significantly lower α-tocopherol (AT), α-tocotrienol (AT3), total tocopherol, and total tocotrienol, but higher γ-tocopherol (GT) in the japonica group. Additionally, in the indica group, Hap_2 showed significantly higher AT, AT3, and total tocopherol, along with lower GT and γ-tocotrienol, compared to Hap_19, Hap_20, and Hap_21. Overall, this study highlights the genetic landscape of γ-TMT and provides a valuable genetic resource for haplotype-based breeding programs aimed at enhancing nutritional profiles.
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Affiliation(s)
- Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Sang-Ho Chu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Bhagwat Nawade
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan 31080, Republic of Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
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Guo N, Tang S, Wang Y, Chen W, An R, Ren Z, Hu S, Tang S, Wei X, Shao G, Jiao G, Xie L, Wang L, Chen Y, Zhao F, Sheng Z, Hu P. A mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice. Nat Commun 2024; 15:1134. [PMID: 38326370 PMCID: PMC10850359 DOI: 10.1038/s41467-024-45402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Preharvest sprouting (PHS) is a deleterious phenotype that occurs frequently in rice-growing regions where the temperature and precipitation are high. It negatively affects yield, quality, and downstream grain processing. Seed dormancy is a trait related to PHS. Longer seed dormancy is preferred for rice production as it can prevent PHS. Here, we map QTLs associated with rice seed dormancy and clone Seed Dormancy 3.1 (SDR3.1) underlying one major QTL. SDR3.1 encodes a mediator of OsbZIP46 deactivation and degradation (MODD). We show that SDR3.1 negatively regulates seed dormancy by inhibiting the transcriptional activity of ABIs. In addition, we reveal two critical amino acids of SDR3.1 that are critical for the differences in seed dormancy between the Xian/indica and Geng/japonica cultivars. Further, SDR3.1 has been artificially selected during rice domestication. We propose a two-line model for the process of rice seed dormancy domestication from wild rice to modern cultivars. We believe the candidate gene and germplasm studied in this study would be beneficial for the genetic improvement of rice seed dormancy.
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Affiliation(s)
- Naihui Guo
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
- National Nanfan Research Academy (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, P. R. China
| | - Wei Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ruihu An
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zongliang Ren
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ling Wang
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Ying Chen
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Fengli Zhao
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Jiangxi Early-season Rice Research Center, Pingxiang, Jiangxi Province, 337000, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biological Breeding/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Improvement Centre/China National Rice Research Institute, Hangzhou, 310006, P. R. China.
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, P. R. China.
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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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Zuo G, Huo J, Yang X, Mei W, Zhang R, Khan A, Feng N, Zheng D. Photosynthetic mechanisms underlying NaCl-induced salinity tolerance in rice (Oryza sativa). BMC PLANT BIOLOGY 2024; 24:41. [PMID: 38195408 PMCID: PMC10777521 DOI: 10.1186/s12870-024-04723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/01/2024] [Indexed: 01/11/2024]
Abstract
BACKGROUND Salinity stress is an environmental constraint that normally develops concurrently under field conditions, resulting in drastic limitation of rice plant growth and grain productivity. The objective of this study was to explore the alleviating effects of NaCl pre-treatment on rice seedlings as well as the salt tolerance mechanisms by evaluating morph-physiological traits. RESULTS Variety Huanghuazhan, either soaked in distilled water or 25 mg/L Prohexadione calcium (Pro-Ca), were first hardened with varying concentrations of NaCl solutions (0 and 50 mM NaCl), and then subjected to varying degrees of salt stress (0 and 100 mM NaCl), indicated by S0, S1, S2 and S3, respectively. Growth analysis suggested that NaCl-pretreatment improved the root/shoot ratio in water-soaked rice plant at DAP 0. Data related to the reaction center density, photosynthetic electron transport efficiency, trapping efficiency were compared before (CK) using performance Index (PIabs). Compared to S2 (Pro-Ca-S2) treatment, PIabs did not show any difference with plants pre-treated with NaCl (S3 or Pro-Ca-S3). Rather than PIabs, significant difference was found in photosynthetic electron transport efficiency (ΨEo). The ΨEo value in Pro-S2 was significantly lowered as compared to Pro-S3 treatment at DAP 7, and the decrease rate was about 6.5%. Correlation analysis indicated leaf PIabs was weak correlated with plant biomass while the quantum yield for reduction of the PSI end electron acceptors, trapped energy flux per reaction center and PSII antenna size displayed strong positive correlation with biomass. Additional analysis revealed that 100 mM NaCl significantly reduced leaf linear electron flux under low-light conditions, regardless of whether seedlings had been pre-treated with 50 mM NaCl or not. CONCLUSIONS NaCl-induced salt tolerance was related to the robust photosynthetic machinery.
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Affiliation(s)
- Guanqiang Zuo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
- College of Natural Resources and Environment, Northwest A&F University, Xianyang, 712100, China
| | - Jingxin Huo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
| | - Xiaohui Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
| | - Wanqi Mei
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
| | - Rui Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
| | - Aaqil Khan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China
- National Saline-tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524008, China.
- National Saline-tolerant Rice Technology Innovation Center, South China, Zhanjiang, 524008, China.
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518108, China.
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Deng XL, Li JQ, Yi JM, Lian RJ, Zhang ZY, Li JH, He S, Bai LY. A pH-responsive MOF-functionalized hollow mesoporous silica controlled herbicide delivery system exhibits enhanced activity against ACCase-herbicide-resistant weeds. PEST MANAGEMENT SCIENCE 2023; 79:5237-5249. [PMID: 37595063 DOI: 10.1002/ps.7729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Weeds grow aggressively in agricultural fields, leading to reduced crop yields and an inability to meet the growing demand for food. Herbicides are currently the most effective method for weed control. However, the overuse of herbicides has resulted in the evolution of resistance mutants and has caused environmental pollution. Therefore, new technologies are urgently required to address this global challenge. RESULTS We report a copper-benzene-1,4-dicarboxylate metal organic framework (Cu-BDC MOF)-functionalized carboxyl hollow mesoporous silica (HMS-COOH) delivery system for the pH-controlled release of the acetyl-CoA carboxylase (ACCase)-inhibiting herbicide quizalofop-p-ethyl (QE). The delivery system (QE@HMS@Cu-BDC) enabled the efficient control of barnyard grasses that are susceptible and resistant to ACCase-inhibiting herbicides, which showed 93.33% and 88.33% FW control efficacy at 67.5 g ha-1 , respectively. With the lowest pH value (3), QE and copper ion were released slowly to total 70.30% and 78.55% levels (respectively) from QE@HMS@Cu-BDC after 89 h. QE@HMS@Cu-BDC showed better absorption, conduction, transportation and ACCase activity inhibition performance than that of QE emulsifiable concentrate (EC) in both susceptible and ACCase-herbicide resistant barnyard grasses. In addition, with the safener effect of carrier HMS@Cu-BDC and the aid of the safener fenchlorazole-ethyl (FE), the application of QE@HMS@Cu-BDC was shown to mitigate the damage caused by QE to rice plants. CONCLUSION This work found that the new material HMS-COOH@Cu-BDC can be used to mitigate herbicide-induced oxidative stress and improve rice plant safety. Futhermore, the QE@HMS-COOH@Cu-BDC constructed in this research might be used as an efficient nanopesticide formulation for weed controls in paddy rice fields. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xi-le Deng
- Key Laboratory for Biology and Control of Weeds, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jia-Qing Li
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ji-Ming Yi
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Ren-Jie Lian
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhao-Yang Zhang
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian-Hong Li
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shun He
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lian-Yang Bai
- Key Laboratory for Biology and Control of Weeds, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
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Gu S, Zhang Z, Li J, Sun J, Cui Z, Li F, Zhuang J, Chen W, Su C, Wu L, Wang X, Guo Z, Xu H, Zhao M, Ma D, Chen W. Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice. PLANT PHYSIOLOGY 2023; 193:2180-2196. [PMID: 37471276 DOI: 10.1093/plphys/kiad420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/17/2023] [Accepted: 06/05/2023] [Indexed: 07/22/2023]
Abstract
Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.
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Affiliation(s)
- Shuang Gu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhe Zhang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Strube Research GmbH & Co. KG, Söllingen 38387, Germany
| | - Jian Sun
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhibo Cui
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Fengcheng Li
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Jia Zhuang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Wanchun Chen
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Chang Su
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Lian Wu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoliang Wang
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhifu Guo
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Hai Xu
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | - Minghui Zhao
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
| | | | - Wenfu Chen
- Rice Research Institute/Collaborative Innovation Center for Genetic Improvement and High Quality and Efficiency Production of Northeast Japonica Rice in China, Shenyang Agricultural University, Shenyang 110866, China
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Marti-Jerez K, Català-Forner M, Tomàs N, Murillo G, Ortiz C, Sánchez-Torres MJ, Vitali A, Lopes MS. Agronomic performance and remote sensing assessment of organic and mineral fertilization in rice fields. FRONTIERS IN PLANT SCIENCE 2023; 14:1230012. [PMID: 37860263 PMCID: PMC10582757 DOI: 10.3389/fpls.2023.1230012] [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: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Introduction Rice heavily relies on nitrogen fertilizers, posing environmental, resource, and geopolitical challenges. This study explores sustainable alternatives like animal manure and remote sensing for resource-efficient rice cultivation. It aims to assess the long-term impact of organic fertilization and remote sensing monitoring on agronomic traits, yield, and nutrition. Methods A six-year experiment in rice fields evaluated fertilization strategies, including pig slurry (PS) and chicken manure (CM) with mineral fertilizers (MIN), MIN-only, and zero-fertilization. Traits, yield, spectral responses, and nutrient content were measured. Sentinel-2 remote sensing tracked crop development. Results Cost-effective organic fertilizers (PS and CM) caused a 13% and 15% yield reduction but still doubled zero-fertilization yield. PS reduced nitrogen leaching. Heavy metals in rice grains were present at safe amounts. Organic-fertilized crops showed nitrogen deficiency at the late vegetative stages, affecting yield. Sentinel-2 detected nutrient deficiencies through NDVI. Discussion Organic fertilizers, especially PS, reduce nitrogen loss, benefiting the environment. However, they come with yield trade-offs and nutrient management challenges that can be managed and balanced with reduced additional mineral applications. Sentinel-2 remote sensing helps manage nutrient deficiencies. In summary, this research favors cost-effective organic fertilizers with improved nutrient management for sustainable rice production.
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Affiliation(s)
- Karen Marti-Jerez
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Amposta, Spain
| | - Mar Català-Forner
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Amposta, Spain
| | - Núria Tomàs
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Amposta, Spain
| | - Gemma Murillo
- Ministry of Climate Action, Food and Rural Agenda, Lleida, Spain
| | - Carlos Ortiz
- Ministry of Climate Action, Food and Rural Agenda, Lleida, Spain
| | | | - Andrea Vitali
- Ente Nazionale Risi, Rice Research Centre, Castello d’Agogna, Italy
| | - Marta S. Lopes
- Sustainable Field Crops, Institute of Agrifood Research and Technology, Lleida, Spain
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Yang S, Zhou J, Li Y, Wu J, Ma C, Chen Y, Sun X, Wu L, Liang X, Fu Q, Xu Z, Li L, Huang Z, Zhu J, Jia X, Ye X, Chen R. AP2/EREBP Pathway Plays an Important Role in Chaling Wild Rice Tolerance to Cold Stress. Int J Mol Sci 2023; 24:14441. [PMID: 37833888 PMCID: PMC10572191 DOI: 10.3390/ijms241914441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Cold stress is the main factor limiting rice production and distribution. Chaling wild rice can survive in cold winters. AP2/EREBP is a known transcription factor family associated with abiotic stress. We identified the members of the AP2/EREBP transcription factor family in rice, maize, and Arabidopsis, and conducted collinearity analysis and gene family analysis. We used Affymetrix array technology to analyze the expression of AP2/EREBP family genes in Chaling wild rice and cultivated rice cultivar Pei'ai64S, which is sensitive to cold. According to the GeneChip results, the expression levels of AP2/EREBP genes in Chaling wild rice were different from those in Pei'ai64S; and the increase rate of 36 AP2/EREBP genes in Chaling wild rice was higher than that in Pei'ai64S. Meanwhile, the MYC elements in cultivated rice and Chaling wild rice for the Os01g49830, Os03g08470, and Os03g64260 genes had different promoter sequences, resulting in the high expression of these genes in Chaling wild rice under low-temperature conditions. Furthermore, we analyzed the upstream and downstream genes of the AP2/EREBP transcription factor family and studied the conservation of these genes. We found that the upstream transcription factors were more conserved, indicating that these upstream transcription factors may be more important in regulating cold stress. Meanwhile, we found the expression of AP2/EREBP pathway genes was significantly increased in recombinant inbred lines from Nipponbare crossing with Chaling wild rice, These results suggest that the AP2/EREBP signaling pathway plays an important role in Chaling wild rice tolerance to cold stress.
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Affiliation(s)
- Songjin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jingming Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Yaqi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jiacheng Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Chuan Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Yulin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Xingzhuo Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Lingli Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Xin Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Qiuping Fu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Zhengjun Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Lihua Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Zhengjian Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
| | - Jianqing Zhu
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Xiaomei Jia
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Xiaoying Ye
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
| | - Rongjun Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China; (S.Y.); (J.Z.); (Y.L.); (J.W.); (C.M.); (Y.C.); (X.S.); (L.W.); (X.L.); (Q.F.); (Z.X.); (L.L.); (Z.H.)
- Demonstration Base for International Science & Technology Cooperation of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.Z.); (X.J.); (X.Y.)
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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10
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Jing CY, Zhang FM, Wang XH, Wang MX, Zhou L, Cai Z, Han JD, Geng MF, Yu WH, Jiao ZH, Huang L, Liu R, Zheng XM, Meng QL, Ren NN, Zhang HX, Du YS, Wang X, Qiang CG, Zou XH, Gaut BS, Ge S. Multiple domestications of Asian rice. NATURE PLANTS 2023; 9:1221-1235. [PMID: 37550371 DOI: 10.1038/s41477-023-01476-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
Abstract
The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.
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Affiliation(s)
- Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing-Dan Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Xiang Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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11
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Wang D, Wang H, Xu X, Wang M, Wang Y, Chen H, Ping F, Zhong H, Mu Z, Xie W, Li X, Feng J, Zhang M, Fan Z, Yang T, Zhao J, Liu B, Ruan Y, Zhang G, Liu C, Liu Z. Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice. Nat Commun 2023; 14:4531. [PMID: 37507369 PMCID: PMC10382596 DOI: 10.1038/s41467-023-40189-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Understanding the evolutionary forces in speciation is a central goal in evolutionary biology. Asian cultivated rice has two subspecies, indica and japonica, but the underlying mechanism of the partial reproductive isolation between them remains obscure. Here we show a presence-absence variation (PAV) at the Se locus functions as an indica-japonica reproductive barrier by causing hybrid sterility (HS) in indica-japonica crosses. The locus comprises two adjacent genes: ORF3 encodes a sporophytic pollen killer, whereas ORF4 protects pollen in a gametophytic manner. In F1 of indica-japonica crosses, pollen with the japonica haplotype, which lacks the sequence containing the protective ORF4, is aborted due to the pollen-killing effect of ORF3 from indica. Evolutionary analysis suggests ORF3 is a gene associated with the Asian cultivated rice species complex, and the PAV has contributed to the reproductive isolation between the two subspecies of Asian cultivated rice. Our analyses provide perspectives on rice inter-subspecies post-zygotic isolation, and will promote efforts to overcome reproductive barriers in indica-japonica hybrid rice breeding.
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Affiliation(s)
- Daiqi Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomic Insitute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Xiaomei Xu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Man Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yahuan Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Hong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Fei Ping
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huanhuan Zhong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhengkun Mu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Wantong Xie
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xiangyu Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jingbin Feng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Milan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhilan Fan
- National Field Genebank for Wild Rice (Guangzhou), Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Tifeng Yang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Junliang Zhao
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Bin Liu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Ying Ruan
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Chunlin Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Ziqiang Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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12
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Lu Y. Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication. Genes (Basel) 2023; 14:1412. [PMID: 37510316 PMCID: PMC10379336 DOI: 10.3390/genes14071412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica and japonica and five subgroups (aus, indica (sensu stricto), japonica (sensu stricto), tropical japonica, and aromatic) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 Oryza genomes (two parental and ten O. sativa (Os)) in parallel to allow gene genealogy-based mutation (GGM) analysis. From the sample, 361 Os mutations were shared by two or more subgroups (referred to here as trans mutations) from 549 mutations identified at 51 Os loci. The GGM analysis and related tests indicates that aus diverged from indica at a time significantly earlier than when tropical japonica split from japonica. The results also indicate that aromatic was selected from hybrid progeny of aus and tropical japonica and that all five subgroups share a significant number of the early mutations identified previously. The results suggest that aus, tropical japonica, and aromatic emerged sequentially within the most recent 4-5 millennia of rice domestication after the split of indica and japonica.
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Affiliation(s)
- Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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He S, Liang S, Meng L, Cao L, Ye G. Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice. RICE (NEW YORK, N.Y.) 2023; 16:27. [PMID: 37284992 DOI: 10.1186/s12284-023-00643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/20/2023] [Indexed: 06/08/2023]
Abstract
The multi-environment genomic selection enables plant breeders to select varieties resilient to diverse environments or particularly adapted to specific environments, which holds a great potential to be used in rice breeding. To realize the multi-environment genomic selection, a robust training set with multi-environment phenotypic data is of necessity. Considering the huge potential of genomic prediction enhanced sparse phenotyping on the cost saving of multi-environment trials (MET), the establishment of a multi-environment training set could also benefit from it. Optimizing the genomic prediction methods is also crucial to enhance the multi-environment genomic selection. Using haplotype-based genomic prediction models is able to capture local epistatic effects which could be conserved and accumulated across generations much like additive effects thereby benefitting breeding. However, previous studies often used fixed length haplotypes composed by a few adjacent molecular markers disregarding the linkage disequilibrium (LD) which is of essential role in determining the haplotype length. In our study, based on three rice populations with different sizes and compositions, we investigated the usefulness and effectiveness of multi-environment training sets with varying phenotyping intensities and different haplotype-based genomic prediction models based on LD-derived haplotype blocks for two agronomic traits, i.e., days to heading (DTH) and plant height (PH). Results showed that phenotyping merely 30% records in multi-environment training set is able to provide a comparable prediction accuracy to high phenotyping intensities; the local epistatic effects are much likely existent in DTH; dividing the LD-derived haplotype blocks into small segments with two or three single nucleotide polymorphisms (SNPs) helps to maintain the predictive ability of haplotype-based models in large populations; modelling the covariances between environments improves genomic prediction accuracy. Our study provides means to improve the efficiency of multi-environment genomic selection in rice.
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Affiliation(s)
- Sang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Shanshan Liang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Lijun Meng
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- Rice Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines.
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14
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Pan YH, Nong BX, Chen L, Yang XH, Xia XZ, Zhang ZQ, Qing DJ, Gao J, Huang CC, Li DT, Deng GF. QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice. Genes Genomics 2023:10.1007/s13258-023-01394-6. [PMID: 37209287 DOI: 10.1007/s13258-023-01394-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/01/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe. OBJECTIVE This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment. METHODS A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage. RESULTS A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11. CONCLUSIONS This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.
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Affiliation(s)
- Ying-Hua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Bao-Xuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xing-Hai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xiu-Zhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zong-Qiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Dong-Jin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Cheng-Cui Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Dan-Ting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Guo-Fu Deng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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15
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Wang W, Cheng M, Wei X, Wang R, Fan F, Wang Z, Tian Z, Li S, Yuan H. Comprehensive evolutionary analysis of growth-regulating factor gene family revealing the potential molecular basis under multiple hormonal stress in Gramineae crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1174955. [PMID: 37063175 PMCID: PMC10102486 DOI: 10.3389/fpls.2023.1174955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/20/2023] [Indexed: 06/17/2023]
Abstract
Growth-regulating factors (GRFs) are plant-specific transcription factors that contain two highly conserved QLQ and WRC domains, which control a range of biological functions, including leaf growth, floral organ development, and phytohormone signaling. However, knowledge of the evolutionary patterns and driving forces of GRFs in Gramineae crops is limited and poorly characterized. In this study, a total of 96 GRFs were identified from eight crops of Brachypodium distachyon, Hordeum vulgare, Oryza sativa L. ssp. indica, Oryza rufipogon, Oryza sativa L. ssp. japonica, Setaria italic, Sorghum bicolor and Zea mays. Based on their protein sequences, the GRFs were classified into three groups. Evolutionary analysis indicated that the whole-genome or segmental duplication plays an essential role in the GRFs expansion, and the GRFs were negatively selected during the evolution of Gramineae crops. The GRFs protein function as transcriptional activators with distinctive structural motifs in different groups. In addition, the expression of GRFs was induced under multiple hormonal stress, including IAA, BR, GA3, 6BA, ABA, and MeJ treatments. Specifically, OjGRF11 was significantly induced by IAA at 6 h after phytohormone treatment. Transgenic experiments showed that roots overexpressing OjGRF11 were more sensitive to IAA and affect root elongation. This study will broaden our insights into the origin and evolution of the GRF family in Gramineae crops and will facilitate further research on GRF function.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiao Wei
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zhikai Wang
- College of Life Science, Yangtze University, Jingzhou, China
| | - Zhihong Tian
- College of Life Science, Yangtze University, Jingzhou, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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16
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Parida M, Gouda G, Chidambaranathan P, Umakanta N, Katara JL, Sai CB, Samantaray S, Patra BC, Mohapatra T. Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight. J Genet 2023. [DOI: 10.1007/s12041-023-01422-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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17
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Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [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: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
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Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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18
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Lu S, Huo Z, Niu T, Zhu W, Wang J, Wu D, He C, Wang Y, Zou L, Sheng L. Molecular mechanisms of toxicity and detoxification in rice (Oryza sativa L.) exposed to polystyrene nanoplastics. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107605. [PMID: 37119549 DOI: 10.1016/j.plaphy.2023.02.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 05/01/2023]
Abstract
Nanoplastics (NPs) are an emerging threat to higher plants in terrestrial ecosystems. However, the molecular of NP-related phytotoxicity remains unclear. In the present study, rice seedlings were exposed to polystyrene (PS, 50 nm) NPs at 0, 50, 100, and 200 mg/L under hydroponic conditions to investigate the induced physiological indices and transcriptional mechanisms. We found that 50, 100, and 200 mg/L PS significantly reduced root (53.05%, 49.61%, and 57.58%, respectively) and shoot (54.63%, 61.56%, and 62.64%, respectively) biomass as compared with the control seedlings. The activities of antioxidant enzymes, including catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX), were significantly activated in all PS treatment groups, indicating that PS inhibited plant growth and induced oxidative stress. Transcriptome analyses showed that PS modulated the expression of the genes involved in cell detoxification, active oxygen metabolism, mitogen-activated protein kinase (MAPK), and plant hormone transduction pathways. Our study provides new insights into phytotoxicity by demonstrating the potential underlying toxicity of PS NPs in higher plants.
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Affiliation(s)
- Siyuan Lu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Zhongqi Huo
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Tingting Niu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Weize Zhu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Junyuan Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Donghui Wu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Chunguang He
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
| | - Yong Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China.
| | - Lifang Zou
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China.
| | - Lianxi Sheng
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun, Jilin, 130117, China
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19
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Deng X, Zhao P, Xie Y, Bai L. Self-Assembled Sphere Covalent Organic Framework with Enhanced Herbicidal Activity by Loading Cyhalofop-butyl. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1417-1425. [PMID: 36629331 DOI: 10.1021/acs.jafc.2c07616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nanopesticides are considered to be a novel and efficient kind of tool for controlling pests in modern agriculture. Covalent organic frameworks (COFs), with high surface areas, ordered structures, and rich functional groups for loading pesticides, are a class of promising carrier materials that can be used to develop efficient nanopesticide delivery systems. However, until now, only a strong ionic interaction between the pesticide and COF can be utilized to achieve the combination between the pesticide and COF. On the basis of this method, charged pesticide molecules are the only choice for COF-based nanopesticides, which limits the exploitation. The way to load the uncharged pesticide molecules into COF still needs to be explored. Herein, in this research, we provided a commonly mild and high-efficacy strategy for loading an uncharged pesticide molecule into COF. The herbicide cyhalofop-butyl (CB), as a neutral model pesticide molecule, was loaded into the sphere COF (SCOF, a model COF synthesized at room temperature) without any ionic interaction via the host-guest strategy. The loading capacity of CB into SCOF (CB@SCOF) was determined at 57% (w/w). Smaller CB@SCOF particles (150-200 nm) can efficiently enter the weed leaves and stems, enhancing the accumulation of the effective concentration in weeds, thus increasing herbicidal activity, in comparison to CB emulsifiable (EC, micrometer scale). Furthermore, CB@SCOF had a solubilization effect for CB in water and can improve the photostability of CB. Thus, the CB-loaded COF nanosphere showed excellent herbicidal activities against the target weeds Echinochloa crus-galli and Leptochloa chinensis compared to commercial CB EC. In conclusion, this study also provides a mild and high-efficacy pesticide loading strategy for COFs. The constructed efficient delivery system and pesticide formulation containing herbicidal COF nanospheres exhibit great potential applications for controlling weeds in sustainable agriculture.
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Affiliation(s)
- Xile Deng
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan410125, People's Republic of China
| | - Pengyue Zhao
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, People's Republic of China
| | - Yong Xie
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing100193, People's Republic of China
| | - Lianyang Bai
- Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, Hunan410125, People's Republic of China
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20
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Hasan S, Furtado A, Henry R. Analysis of Domestication Loci in Wild Rice Populations. PLANTS (BASEL, SWITZERLAND) 2023; 12:489. [PMID: 36771574 PMCID: PMC9919211 DOI: 10.3390/plants12030489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication.
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Affiliation(s)
- Sharmin Hasan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Brisbane 4072, Australia
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21
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Gautam RK, Singh PK, Venkatesan K, Rakesh B, Sakthivel K, Swain S, Srikumar M, Zamir Ahmed SK, Devakumar K, Rao SS, Vijayan J, Ali S, Langyan S. Harnessing intra-varietal variation for agro-morphological and nutritional traits in a popular rice landrace for sustainable food security in tropical islands. Front Nutr 2023; 10:1088208. [PMID: 36908925 PMCID: PMC9995847 DOI: 10.3389/fnut.2023.1088208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Rice crop meets the calorie and nutritional requirements of a larger segment of the global population. Here, we report the occurrence of intra-varietal variation in a popular rice landrace C14-8 traditionally grown under the geographical isolation of the Andaman Islands. Methods Based on grain husk color, four groups were formed, wherein the extent of intra-varietal variation was studied by employing 22 agro-morphological and biochemical traits. Results Among the traits studied, flavonoid and anthocyanin contents and grain yield exhibited a wider spectrum of variability due to more coefficients of variation (>25%). The first five principal components (PCs) of principal components analysis explained a significant proportion of the variation (91%) and the first two PCs explained 63.3% of the total variation, with PC1 and PC2 explaining 35.44 and 27.91%, respectively. A total of 50 highly variable SSR (HvSSR) markers spanning over 12 chromosomes produced 314 alleles, which ranged from 1 to 15 alleles per marker, with an average of 6.28. Of the 314 alleles, 64 alleles were found to be rare among the C14-8 selections. While 62% of HvSSR markers exhibited polymorphism among the C14-8 population, chromosomes 2, 7, 9, and 11 harbored the most polymorphic loci. The group clustering of the selections through HvSSR markers conformed to the grouping based on grain husk coloration. Discussion Our studies on the existence and pertinence of intra-varietal variations are expected to be of significance in the realms of evolutionary biology and sustainable food and nutritional security under the changing climate.
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Affiliation(s)
- Raj Kumar Gautam
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
| | - Pankaj Kumar Singh
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Kannan Venkatesan
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Bandol Rakesh
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Krishnan Sakthivel
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-Indian Institute of Oilseed Research, Hyderabad, Telangana, India
| | - Sachidananda Swain
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Muthulingam Srikumar
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - S K Zamir Ahmed
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Kishnamoorthy Devakumar
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Shyam Sunder Rao
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Joshitha Vijayan
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-National Institute of Plant Biotechnology, Pusa, New Delhi, India
| | - Sharik Ali
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
| | - Sapna Langyan
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
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22
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Mmbando GS. Challenges and prospects in using biotechnological interventions in O. glaberrima, an African cultivated rice. GM CROPS & FOOD 2022; 13:372-387. [DOI: 10.1080/21645698.2022.2149212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma (Udom), Dodoma, Tanzania
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23
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Shahidi F, Danielski R, Rhein SO, Meisel LA, Fuentes J, Speisky H, Schwember AR, de Camargo AC. Wheat and Rice beyond Phenolic Acids: Genetics, Identification Database, Antioxidant Properties, and Potential Health Effects. PLANTS (BASEL, SWITZERLAND) 2022; 11:3283. [PMID: 36501323 PMCID: PMC9739071 DOI: 10.3390/plants11233283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Wheat and rice play a vital role in human nutrition and food security. A better understanding of the potential health benefits associated with consuming these cereals, combined with studies by plant scientists and food chemists to view the entire food value chain from the field, pre and post-harvest processing, and subsequent "fork" consumption, may provide the necessary tools to optimize wheat and rice production towards the goal of better human health improvement and food security, providing tools to better adapt to the challenges associated with climate change. Since the available literature usually focuses on only one food chain segment, this narrative review was designed to address the identities and concentration of phenolics of these cereal crops from a farm-to-fork perspective. Wheat and rice genetics, phenolic databases, antioxidant properties, and potential health effects are summarized. These cereals contain much more than phenolic acids, having significant concentrations of flavonoids (including anthocyanins) and proanthocyanidins in a cultivar-dependent manner. Their potential health benefits in vitro have been extensively studied. According to a number of in vivo studies, consumption of whole wheat, wheat bran, whole rice, and rice bran may be strategies to improve health. Likewise, anthocyanin-rich cultivars have shown to be very promising as functional foods.
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Affiliation(s)
- Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Renan Danielski
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Samantha Ottani Rhein
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Lee A. Meisel
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Jocelyn Fuentes
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Hernan Speisky
- Nutrition and Food Technology Institute, University of Chile, Santiago 7830490, Chile
| | - Andrés R. Schwember
- Departament of Plant Sciences, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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24
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Wang X, Zhao Y, Jiang C, Wang L, Chen L, Li F, Zhang Y, Pan Y, Zhang T. Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS. BMC PLANT BIOLOGY 2022; 22:526. [PMID: 36376791 PMCID: PMC9661789 DOI: 10.1186/s12870-022-03924-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rice is the world's second largest food crop and accelerated global climate change due to the intensification of human activities has a huge impact on rice. Research on the evolution of different rice ecotypes is essential for enhancing the adaptation of rice to the unpredictable environments. RESULTS The sequencing data of 868 cultivated and 140 wild rice accessions were used to study the domestication history and signatures of adaptation in the distinct rice ecotypes genome. The different populations had formed distinct rice ecotypes by phylogenetic analyses and were domesticated independently in the two subspecies of rice, especially deepwater and upland rice. The domestication history of distinct rice ecotypes was confirmed and the four predicted admixture events mainly involved gene flow between wild rice and cultivated rice. Importantly, we identified numerous selective sweeps that have occurred during the domestication of different rice ecotypes and one candidate gene (LOC_Os11g21804) for deepwater based on transcriptomic evidence. In addition, many regions of genomic differentiation between the different rice ecotypes were identified. Furthermore, the main reason for the increase in genetic diversity in the ecotypes of xian (indica) rice was the high proportion of alternative allele frequency in new mutations. Genome-wide association analysis revealed 28 QTLs associated with flood tolerance which contained 12 related cloned genes, and 20 candidate genes within 13 deepwater QTLs were identified by transcriptomic and haplotype analyses. CONCLUSIONS These results enhanced our understanding of domestication history in different rice ecotypes and provided valuable insights for genetic improvement and breeding of rice in the current changing environments.
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Affiliation(s)
- Xueqiang Wang
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China
- Hainan Institute of Zhejiang University, Sanya, Hainan, 572025, People's Republic of China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Conghui Jiang
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Libing Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China
| | - Lei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, Guangxi, China
| | - Fengmei Li
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China
| | - Yanhong Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, Guangxi, China.
| | - Tianzhen Zhang
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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25
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Xiong L, Huang Y, Liu Z, Li C, Yu H, Shahid MQ, Lin Y, Qiao X, Xiao J, Gray JE, Jin J. Small EPIDERMAL PATTERNING FACTOR-LIKE2 peptides regulate awn development in rice. PLANT PHYSIOLOGY 2022; 190:516-531. [PMID: 35689635 PMCID: PMC9434303 DOI: 10.1093/plphys/kiac278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/16/2022] [Indexed: 05/06/2023]
Abstract
The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) family of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rice (Oryza sativa). Here, we used clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology to individually knockout each of 11 EPF/EPFL genes in the rice cultivar Kasalath. Loss of function of most OsEPF/EPFL genes generated no obvious phenotype alteration, while disruption of OsEPFL2 in Kasalath caused a short or no awn phenotype and reduced grain size. OsEPFL2 is strongly expressed in the young panicle, consistent with a role in regulating awn and grain development. Haplotype analysis indicated that OsEPFL2 can be classified into six major haplotypes. Nucleotide diversity and genetic differentiation analyses suggested that OsEPFL2 was positively selected during the domestication of rice. Our work to systematically investigate the function of EPF/EPFL peptides demonstrates that different members of the same gene family have been independently selected for their ability to regulate a similar biological function and provides perspective on rice domestication.
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Affiliation(s)
| | | | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Muhammad Qasim Shahid
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Hainan Key Laboratory of Crop Genetics and Breeding, Hainan Scientific Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Haikou 571100, China
| | - Xiaoyi Qiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Junyi Xiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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Lee SJ, Kang K, Lim JH, Paek NC. Natural alleles of CIRCADIAN CLOCK ASSOCIATED1 contribute to rice cultivation by fine-tuning flowering time. PLANT PHYSIOLOGY 2022; 190:640-656. [PMID: 35723564 PMCID: PMC9434239 DOI: 10.1093/plphys/kiac296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/26/2022] [Indexed: 05/11/2023]
Abstract
The timing of flowering is a crucial factor for successful grain production at a wide range of latitudes. Domestication of rice (Oryza sativa) included selection for natural alleles of flowering-time genes that allow rice plants to adapt to broad geographic areas. Here, we describe the role of natural alleles of CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1) in cultivated rice based on analysis of single-nucleotide polymorphisms deposited in the International Rice Genebank Collection Information System database. Rice varieties harboring japonica-type OsCCA1 alleles (OsCCA1a haplotype) flowered earlier than those harboring indica-type OsCCA1 alleles (OsCCA1d haplotype). In the japonica cultivar "Dongjin", a T-DNA insertion in OsCCA1a resulted in late flowering under long-day and short-day conditions, indicating that OsCCA1 is a floral inducer. Reverse transcription quantitative PCR analysis showed that the loss of OsCCA1a function induces the expression of the floral repressors PSEUDO-RESPONSE REGULATOR 37 (OsPRR37) and Days to Heading 8 (DTH8), followed by repression of the Early heading date 1 (Ehd1)-Heading date 3a (Hd3a)-RICE FLOWERING LOCUS T 1 (RFT1) pathway. Binding affinity assays indicated that OsCCA1 binds to the promoter regions of OsPRR37 and DTH8. Naturally occurring OsCCA1 alleles are evolutionarily conserved in cultivated rice (O. sativa). Oryza rufipogon-I (Or-I) and Or-III type accessions, representing the ancestors of O. sativa indica and japonica, harbored indica- and japonica-type OsCCA1 alleles, respectively. Taken together, our results demonstrate that OsCCA1 is a likely domestication locus that has contributed to the geographic adaptation and expansion of cultivated rice.
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Affiliation(s)
| | | | - Jung-Hyun Lim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
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Wang X, Wang W, Tai S, Li M, Gao Q, Hu Z, Hu W, Wu Z, Zhu X, Xie J, Li F, Zhang Z, Zhi L, Zhang F, Ma X, Yang M, Xu J, Li Y, Zhang W, Yang X, Chen Y, Zhao Y, Fu B, Zhao X, Li J, Wang M, Yue Z, Fang X, Zeng W, Yin Y, Zhang G, Xu J, Zhang H, Li Z, Li Z. Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding. J Adv Res 2022; 42:1-16. [PMID: 35988902 PMCID: PMC9788959 DOI: 10.1016/j.jare.2022.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/28/2022] [Accepted: 08/07/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Rice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding. OBJECTIVES How rice was domesticated and impacted by modern breeding. METHODS We performed comprehensive analyses of genomic sequences of 504 accessions of Os and 456 accessions of O. rufipogon/O. nivara (Or). RESULTS The natural selection on Or before domestication and the natural and artificial selection during domestication together shaped the well-differentiated genomes of two subspecies, geng(j) (japonica) and xian(i) (indica), while breeding has made apparent genomic imprints between landrace and modern varieties of each subspecies, and also between primary modern and advanced modern varieties of xian(i). Selection during domestication and breeding left genome-wide selective signals covering ∼ 22.8 % and ∼ 8.6 % of the Os genome, significantly reduced within-population genomic diversity by ∼ 22 % in xian(i) and ∼ 53 % in geng(j) plus more pronounced subspecific differentiation. Only ∼ 10 % reduction in the total genomic diversity was observed between the Os and Or populations, indicating domestication did not suffer severe genetic bottleneck. CONCLUSION Our results revealed clear differentiation of the Or accessions into three large populations, two of which correspond to the well-differentiated Os subspecies, geng(j) and xian(i). Improved productivity and common changes in the same suit of adaptive traits in xian(i) and geng(j) during domestication and breeding resulted apparently from compensatory and convergent selections for different genes/alleles acting in the common KEGG terms and/or same gene families, and thus maintaining or even increasing the within population diversity and subspecific differentiation of Os, while more genes/alleles of novel function were selected during domestication than modern breeding. Our results supported the multiple independent domestication of Os in Asia and suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement.
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Affiliation(s)
- Xueqiang Wang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Institute of Crop Science, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China
| | | | - Min Li
- The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiqiang Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wushu Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhichao Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jianyin Xie
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fengmei Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhifang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Linran Zhi
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xiaoqian Ma
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ming Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenzhuo Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiyu Yang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ying Chen
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100193, China
| | - Yan Zhao
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Binying Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Miao Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Wei Zeng
- The College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Gengyun Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China,The College of Agronomy, Anhui Agricultural University, Hefei, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,Corresponding authors at: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Z. Li).
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Bates J. The Fits and Starts of Indian Rice Domestication: How the Movement of Rice Across Northwest India Impacted Domestication Pathways and Agricultural Stories. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.924977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rice is currently the staple food for over 3.5 billion people and is arguably the most important crop exploited by humans. Understanding how we came to the point where a single crop dominates the lives of almost half of the Earth’s population has major significance for our future, even more so given the climatic instability we face today, as rice is a cereal that is dependent on water to an extreme degree. In this study, the nature of early rice agriculture in South Asia is explored, looking at how this critical crop may have begun to be exploited, cultivated, and then brought under agricultural regimes during the long span between c.6500 and 1500 BC. There is now clear evidence for early Holocene cultivation of rice in the Middle Gangetic plains of northern India, but there is still considerable debate about the timing of when this cultivation began and whether it involved domestication of rice. By 3200 BC, however, rice agriculture was present outside the Ganges in the Indus Civilization. The data show accelerated domestication in the Indus environment and agricultural systems that played a part in later hybridization with the arrival of Chinese rice. Understanding how this move from its place of origin to a new environment may have become entangled in the domestication pathways of South Asia rice prior to the arrival of Chinese rice c.1500 BC are important to the overall rice story, as they play into modern concerns relating to biodiversity and different ways of growing and watering rice.
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Eizenga GC, Kim H, Jung JKH, Greenberg AJ, Edwards JD, Naredo MEB, Banaticla-Hilario MCN, Harrington SE, Shi Y, Kimball JA, Harper LA, McNally KL, McCouch SR. Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex ( ORSC). FRONTIERS IN PLANT SCIENCE 2022; 13:787703. [PMID: 35769295 PMCID: PMC9235872 DOI: 10.3389/fpls.2022.787703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as characterization data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions characterized as annual and largely inbreeding. From these groups, 42 "core" O. rufipogon and 25 "core" O. nivara accessions were identified for domestication studies. The third group, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a "pre-breeding" pool for breeders attempting to incorporate novel variation into elite breeding lines.
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Affiliation(s)
- Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Janelle K. H. Jung
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | | | | | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Jennifer A. Kimball
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Lisa A. Harper
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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30
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Genetic Diversity and Environmental Influence on Yield and Yield-Related Traits of Adzuki Bean (Vigna angularis L.). PLANTS 2022; 11:plants11091132. [PMID: 35567132 PMCID: PMC9103669 DOI: 10.3390/plants11091132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/17/2022]
Abstract
Adzuki beans are an important food legume crop in East Asia. A large number of adzuki bean accessions are maintained in the Chinese national seed genebank. A collection of 59 elite cultivars, 389 landraces, and 27 wild adzuki beans were selected and phenotyped extensively for yield and yield-related traits at two different locations (Nanning and Nanyang, China). Ten agronomic and yield-related traits were scored, and the data were subjected to analysis of variance (ANOVA), principal component analysis (PCA), correlation, and cluster analysis. Significant variation was observed for genotypes, locations, and genotype x environment interaction for most traits. Also, there were significant differences in the phenotypes among accessions of different germplasm types. The broad-sense heritability of traits studied ranged from 4.4% to 77.8%. The number of seeds per pod (77.8%), 100-seed weight (68.0%), and number of plant branches (63.9%) had a high heritability. A total of 10 traits were transformed into 3 comprehensive factors by principal component analysis, and the first three principal component factors contributed 72.31% of the total variability. Cluster analysis categorized the 475 adzuki bean accessions into five distinct groups. The results described in this study will be useful for adzuki bean breeders for the development of varieties with high end-use quality.
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Liu C, Cui D, Jiao A, Ma X, Li X, Han B, Chen H, Ruan R, Wang Y, Han L. Kam Sweet Rice ( Oryza sativa L.) Is a Special Ecotypic Rice in Southeast Guizhou, China as Revealed by Genetic Diversity Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:830556. [PMID: 35330871 PMCID: PMC8940365 DOI: 10.3389/fpls.2022.830556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Kam Sweet Rice (KSR) is a special kind of rice landrace that has been domesticated for thousands of years by the local Dong people in southeast Guizhou province, China. KSR has many distinguishing characteristics including strong fragrance; high resistance to diseases, pests, and adverse abiotic conditions; difficulty of threshing; and glutinous texture. There is a lack of systematic research on its genetic diversity. In this study, we analyzed the levels and patterns of genetic diversity and nucleotide variation in 1,481 rice germplasm using simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The accessions included 315 KSR resources from southeast Guizhou, 578 rice landraces from six rice-growing ecological zones in Guizhou, 546 rice landraces from nine provinces around Guizhou, and 42 wild rice sources. Genetic diversity and heterozygosity of KSR were both low, and thus KSR might be close to a pure rice line. Population structure analysis showed that KSR was isolated into a single type of rice, which had a large genetic distance and a unique genetic background compared to the local varieties in Guizhou province, indicating that KSR is a special rice ecotype. Haplotype analysis of the target genes showed that the population of KSR was rich in haplotypes for resistance to bacterial blight (Xa23) and rice blast (Pid3), and identified unique haplotypes that were different from those of the six rice ecotypes in Guizhou. This study shows that KSR is an excellent rice germplasm resource, provides important information for the improvement and utilization of rice landraces, and serves as a reference for formulating effective rice conservation measures.
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Affiliation(s)
- Chunhui Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aixia Jiao
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaobing Li
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huicha Chen
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Renchao Ruan
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanjie Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Kuo WH, Liu SH, Chang CC, Hsieh CL, Li YH, Ito T, Won H, Kokubugata G, Chung KF. Plastome phylogenomics of Allaeanthus, Broussonetia and Malaisia (Dorstenieae, Moraceae) and the origin of B. × kazinoki. JOURNAL OF PLANT RESEARCH 2022; 135:203-220. [PMID: 35080694 DOI: 10.1007/s10265-022-01369-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Species of Broussonetia have been essential in the development of papermaking technology. In Japan and Korea, a hybrid between B. monoica and B. papyrifera (= B. × kazinoki) known as kōzo and daknamu is still the major source of raw materials for making traditional paper washi and hanji, respectively. Despite their cultural and practical significance, however, the origin and taxonomy of kōzo and daknamu remain controversial. Additionally, the long-held generic concept of Broussonetia s.l., which included Sect. Allaeanthus and Sect. Broussonetia, was challenged as phylogenetic analyses showed Malaisia is sister to the latter section. To re-examine the taxonomic proposition that recognizes Allaeanthus, Broussonetia, and Malaisia (i.e., Broussonetia alliance), plastome and nuclear ribosomal DNA (nrDNA) sequences of six species of the alliance were assembled. Characterized by the canonical quadripartite structure, genome alignments and contents of the six plastomes (160,121-162,594 bp) are highly conserved, except for the pseudogenization and/or loss of the rpl22 gene. Relationships of the Broussonetia alliance are identical between plastome and nrDNA trees, supporting the maintenance of Malaisia and the resurrection of Allaeanthus. The phylogenomic relationships also indicate that the monoecy in B. monoica is a derived state, possibly resulting from hybridization between the dioecious B. kaempferi (♀) and B. papyrifera (♂). Based on the hypervariable ndhF-rpl32 intergenic spacer selected by sliding window analysis, phylogeographic analysis indicates that B. monoica is the sole maternal parent of B. × kazinoki and that daknamu carries multiple haplotypes, while only one haplotype was detected in kōzo. Because hybridizations between B. monoica and B. papyrifera are unidirectional and have occurred rarely in nature, our data suggest that daknamu might have originated via deliberate hybrid breeding selected for making hanji in Korea. On the contrary, kōzo appears to have a single origin and the possibility of a Korean origin cannot be ruled out.
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Affiliation(s)
- Wen-Hsi Kuo
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat- sen University, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Chia-Lun Hsieh
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Yi-Hsuan Li
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Takuro Ito
- The Center for Academic Resources and Archives/Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Hyosig Won
- Department of Biological Science and Institute of Natural Sciences, Daegu University, Gyungsan, Gyungbuk, South Korea
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Kuo-Fang Chung
- Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
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Huang L, Geng FD, Fan JJ, Zhai W, Xue C, Zhang XH, Ren Y, Kang JQ. Evidence for two types of Aquilegia ecalcarata and its implications for adaptation to new environments. PLANT DIVERSITY 2022; 44:153-162. [PMID: 35505982 PMCID: PMC9043306 DOI: 10.1016/j.pld.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 06/14/2023]
Abstract
Spurs have played an important role in the radiation of the genus Aquilegia, but little is known about how the spurless state arose in A. ecalcarata. Here we aim to characterize the genetic divergence within A. ecalcarata and gain insights into the origin of this species. A total of 19 populations from A. ecalcarata and 23 populations from three of its closest relatives (Aquilegia kansuensis, Aquilegia rockii and Aquilegia yabeana) were sampled in this study. We sequenced fifteen nuclear gene fragments across the genome and three chloroplast loci to conduct phylogenetic, PCoA and STRUCTURE analyses. Our analyses indicate that A. ecalcarata may not be monophyletic and can be divided into two distinct lineages (A. ecalcarata I and A. ecalcarata II). A. ecalcarata I is genetically close to A. kansuensis, whereas A. ecalcarata II is close to A. rockii. Isolation-with-migration analysis suggested that historical gene flow was low between A. ecalcarata I and A. rockii, as well as between A. ecalcarata II and A. kansuensis. The two distinct lineages of A. ecalcarata show significant divergence in 13 floral traits and also have distinct distributions. In addition, both A. ecalcarata I and II are adapted to a stony environment that differs from that of their closest relatives, indicating a habitat shift may have driven new adaptations. Our findings enrich the understanding of how floral evolution contributes to species diversification.
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Affiliation(s)
| | | | | | | | | | | | - Yi Ren
- Corresponding author. Fax: +86 29 85310270.
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Lu Y, Xu Y, Li N. Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies. RICE (NEW YORK, N.Y.) 2022; 15:11. [PMID: 35166949 PMCID: PMC8847465 DOI: 10.1186/s12284-022-00556-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/22/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. RESULTS Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5' regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. CONCLUSIONS Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5' regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.
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Affiliation(s)
- Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Present Address: College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016 China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Dang X, Zhang Y, Li Y, Chen S, Liu E, Fang B, Liu Q, She D, Dong Z, Fan Z, Li D, Wang H, Zhu S, Hu X, Li Y, Jiang J, Hong D. SYL3-k increases style length and yield of F 1 seeds via enhancement of endogenous GA 4 content in Oryza sativa L. pistils. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:321-336. [PMID: 34657161 PMCID: PMC8741667 DOI: 10.1007/s00122-021-03968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
SYL3-k allele increases the outcrossing rate of male sterile line and the yield of hybrid F1 seeds via enhancement of endogenous GA4 content in Oryza sativa L. pistils. The change in style length might be an adaptation of rice cultivation from south to north in the northern hemisphere. The style length (SYL) in rice is one of the major factors influencing the stigma exertion, which affects the outcross rate of male sterile line and the yield of hybrid F1 seeds. However, the biological mechanisms underlying SYL elongation remain elusive. Here, we report a map-based cloning and characterisation of the allele qSYL3-k. The qSYL3-k allele encodes a MADS-box family transcription factor, and it is expressed in various rice organs. The qSYL3-k allele increases SYL via the elongation of cell length in the style, which is associated with a higher GA4 content in the pistil. The expression level of OsGA3ox2 in pistils with qSYL3-k alleles is significantly higher than that in pistils with qSYL3-n allele on the same genome background of Nipponbare. The yield of F1 seeds harvested from plants with 7001SSYL3-k alleles was 16% higher than that from plants with 7001SSYL3-n allele. The sequence data at the qSYL3 locus in 136 accessions showed that alleles containing the haplotypes qSYL3AA, qSYL3AG, and qSYL3GA increased SYL, whereas those containing the haplotype qSYL3GG decreased it. The frequency of the haplotype qSYL3GG increases gradually from the south to north in the northern hemisphere. These findings will facilitate improvement in SYL and yield of F1 seeds henceforward.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Yuanqing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yulong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Siqi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingjie Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiangming Liu
- Special Crop Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, China
| | - Dong She
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyao Dong
- Department of Student Affairs, Jilin Normal University, Siping, 136000, Jilin, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dalu Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shangshang Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoxiao Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanhui Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume. DIVERSITY 2021. [DOI: 10.3390/d13120654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.
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Miao X, Miao Y, Tao S, Liu D, Chen Z, Wang J, Huang W, Yu Y. Classification of rice based on storage time by using near infrared spectroscopy and chemometric methods. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Li F, Han Z, Qiao W, Wang J, Song Y, Cui Y, Li J, Ge J, Lou D, Fan W, Li D, Nong B, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:775051. [PMID: 34868173 PMCID: PMC8639688 DOI: 10.3389/fpls.2021.775051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
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Affiliation(s)
- Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Little Berry Research Room, Liaoning Institute of Fruit Science, Yingkou, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Genetic Structure and Geographical Differentiation of Traditional Rice ( Oryza sativa L.) from Northern Vietnam. PLANTS 2021; 10:plants10102094. [PMID: 34685903 PMCID: PMC8540186 DOI: 10.3390/plants10102094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/24/2022]
Abstract
Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.
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40
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Li JT, Wang Q, Huang Yang MD, Li QS, Cui MS, Dong ZJ, Wang HW, Yu JH, Zhao YJ, Yang CR, Wang YX, Sun XQ, Zhang Y, Zhao R, Jia ZY, Wang XY. Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. Nat Genet 2021; 53:1493-1503. [PMID: 34594040 PMCID: PMC8492472 DOI: 10.1038/s41588-021-00933-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.
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Affiliation(s)
- Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China.
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Mei-Di Huang Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qing-Song Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming-Shu Cui
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zai-Jie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ju-Hua Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Yu-Jie Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chen-Ru Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ya-Xin Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zhi-Ying Jia
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Xi-Yin Wang
- North China University of Science and Technology, Tangshan, China
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Lee JS, Chebotarov D, McNally KL, Pede V, Setiyono TD, Raquid R, Hyun WJ, Jeung JU, Kohli A, Mo Y. Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement. PLANTS (BASEL, SWITZERLAND) 2021; 10:1709. [PMID: 34451754 PMCID: PMC8401653 DOI: 10.3390/plants10081709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/04/2022]
Abstract
Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8-10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.
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Affiliation(s)
- Jae-Sung Lee
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Dmytro Chebotarov
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Kenneth L. McNally
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Valerien Pede
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Tri Deri Setiyono
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Rency Raquid
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Woong-Jo Hyun
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
| | - Ajay Kohli
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
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Huang J, Zhang Q, He Y, Liu W, Xu Y, Liu K, Xian F, Li J, Hu J. Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops. Int J Mol Sci 2021; 22:ijms22168758. [PMID: 34445464 PMCID: PMC8395763 DOI: 10.3390/ijms22168758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.
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Affiliation(s)
- Jishuai Huang
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
| | - Qiannan Zhang
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
| | - Yurong He
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
| | - Wei Liu
- School of Biological Science, University of Bristol, Bristol BS8 1TQ, UK;
| | - Yanghong Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200000, China;
| | - Kejia Liu
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
| | - Fengjun Xian
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
| | - Junde Li
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China; (J.H.); (Q.Z.); (Y.H.); (K.L.); (F.X.); (J.L.)
- Correspondence:
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Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice. Int J Mol Sci 2021; 22:ijms22094742. [PMID: 33947059 PMCID: PMC8124408 DOI: 10.3390/ijms22094742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
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45
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Feng Q, Song WC, Zhang YJ, Shi C. The complete chloroplast genome sequence of Oryza sativa Temperate japonica. Mitochondrial DNA B Resour 2021; 6:927-928. [PMID: 33796685 PMCID: PMC7971287 DOI: 10.1080/23802359.2021.1888331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, the complete chloroplast genome of O. sativa Temperate Japonica YunJing-24 was assembled using Illumina sequencing data. The complete chloroplast (cp) genome is 134,556 bp in length, including a pair of invert repeats (IRA and IRB) regions of 20,797 bp, large single-copy (LSC) region of 80,615 bp, and small single-copy (SSC) region of 12,347 bp. A total of 129 genes were predicted in the genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between O. sativa Temperate Japonica and other representative species.
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Affiliation(s)
- Qi Feng
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Wei-Cai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Yun-Jiao Zhang
- Kunming Medical University Haiyuan College, Kunming, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
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46
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Sharma R, Upadhyay S, Bhattacharya S, Singh A. Abiotic Stress-Responsive miRNA and Transcription Factor-Mediated Gene Regulatory Network in Oryza sativa: Construction and Structural Measure Study. Front Genet 2021; 12:618089. [PMID: 33643383 PMCID: PMC7907651 DOI: 10.3389/fgene.2021.618089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Climate changes and environmental stresses have a consequential association with crop plant growth and yield, meaning it is necessary to cultivate crops that have tolerance toward the changing climate and environmental disturbances such as water stress, temperature fluctuation, and salt toxicity. Recent studies have shown that trans-acting regulatory elements, including microRNAs (miRNAs) and transcription factors (TFs), are emerging as promising tools for engineering naive improved crop varieties with tolerance for multiple environmental stresses and enhanced quality as well as yield. However, the interwoven complex regulatory function of TFs and miRNAs at transcriptional and post-transcriptional levels is unexplored in Oryza sativa. To this end, we have constructed a multiple abiotic stress responsive TF-miRNA-gene regulatory network for O. sativa using a transcriptome and degradome sequencing data meta-analysis approach. The theoretical network approach has shown the networks to be dense, scale-free, and small-world, which makes the network stable. They are also invariant to scale change where an efficient, quick transmission of biological signals occurs within the network on extrinsic hindrance. The analysis also deciphered the existence of communities (cluster of TF, miRNA, and genes) working together to help plants in acclimatizing to multiple stresses. It highlighted that genes, TFs, and miRNAs shared by multiple stress conditions that work as hubs or bottlenecks for signal propagation, for example, during the interaction between stress-responsive genes (TFs/miRNAs/other genes) and genes involved in floral development pathways under multiple environmental stresses. This study further highlights how the fine-tuning feedback mechanism works for balancing stress tolerance and how timely flowering enable crops to survive in adverse conditions. This study developed the abiotic stress-responsive regulatory network, APRegNet database (http://lms.snu.edu.in/APRegNet), which may help researchers studying the roles of miRNAs and TFs. Furthermore, it advances current understanding of multiple abiotic stress tolerance mechanisms.
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Affiliation(s)
- Rinku Sharma
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
| | | | | | - Ashutosh Singh
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
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Zhang W, Sun Y, Liu J, Xu C, Zou X, Chen X, Liu Y, Wu P, Yang X, Zhou S. DNA barcoding of Oryza: conventional, specific, and super barcodes. PLANT MOLECULAR BIOLOGY 2021; 105:215-228. [PMID: 32880855 PMCID: PMC7858216 DOI: 10.1007/s11103-020-01054-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.
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Affiliation(s)
- Wen Zhang
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuzhe Sun
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia Liu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China
| | - Chao Xu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xinhui Zou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xun Chen
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Landscape Architecture, Northeast Forestry University, Haerbin, 150040, China
| | - Yanlei Liu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Wu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueying Yang
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, China, Beijing, 100038, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Hori K, Saisho D, Nagata K, Nonoue Y, Uehara-Yamaguchi Y, Kanatani A, Shu K, Hirayama T, Yonemaru JI, Fukuoka S, Mochida K. Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars. Int J Mol Sci 2021; 22:1024. [PMID: 33498523 PMCID: PMC7864171 DOI: 10.3390/ijms22031024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/27/2022] Open
Abstract
Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars "Koshihikari" × "Khao Nam Jen", each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years' field tests was large in "Khao Nam Jen" (36.7 days) but small in "Koshihikari" (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a "Khao Nam Jen" segment on chromosome 11 showed 28.0 days' difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from "Khao Nam Jen" in the region around Hd16 on chromosome 3 showed 23.4 days" difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days' difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with "Koshihikari". Our results unravel the molecular control of flowering time under ambient temperature fluctuations.
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Affiliation(s)
- Kiyosumi Hori
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Daisuke Saisho
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
| | - Kazufumi Nagata
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | | | - Asaka Kanatani
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; (Y.U.-Y.); (A.K.)
| | - Koka Shu
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Keiichi Mochida
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; (Y.U.-Y.); (A.K.)
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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50
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He W, Chen C, Xiang K, Wang J, Zheng P, Tembrock LR, Jin D, Wu Z. The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:781793. [PMID: 34868182 PMCID: PMC8637288 DOI: 10.3389/fpls.2021.781793] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 05/19/2023]
Abstract
The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.
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Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caijin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Kunli Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Luke R. Tembrock,
| | - Deming Jin
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Deming Jin,
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Zhiqiang Wu,
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