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Akanmu AO, Asemoloye MD, Marchisio MA, Babalola OO. Adoption of CRISPR-Cas for crop production: present status and future prospects. PeerJ 2024; 12:e17402. [PMID: 38860212 PMCID: PMC11164064 DOI: 10.7717/peerj.17402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Background Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time. Methods This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security. Results The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops. Conclusion Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.
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Affiliation(s)
- Akinlolu Olalekan Akanmu
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | - Michael Dare Asemoloye
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
| | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, University of North-West, Mmabatho, South Africa
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Sherif A, Zhang B, Wu B, Hu Y, Li S, Zhou X, Elbadri AM, Elshenawy M, El-Badawy MEM, Hassan IO, Sedhom SA, Abo-Yousef M, Ayaad M, Xing Y. A Pseudo-near isogenic F 2 population strategy for rapid QTL cloning. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:61. [PMID: 37496827 PMCID: PMC10366042 DOI: 10.1007/s11032-023-01408-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Near isogenic F2 (NIF2) population frequently developed by conventional backcross has dramatically contributed to QTL identification in plants. Developing such a NIF2 population is time-consuming. Thus, it is urgent to rapidly produce a NIF2 population for QTL cloning. Here, we proposed a rapid QTL cloning strategy by generating a Pseudo-near isogenic F2 population (Pseudo-NIF2), which segregates at the target QTL but is fixed at other QTLs for the target trait. Nineteen QTLs for GL, GW, and TGW were detected in the F2 population from the cross between Zhenshan 97 and Egy316. To verify the efficiency of Pseudo-NIF2 in QTL quick cloning, the novel moderate QTL qGL10.1 which explained 9.1% and 5.6% of grain length variation in F2 and F2:3 populations was taken as an example. An F2 plant (F2-120), which segregated at qGL10.1 but fixed at other 8 QTLs for grain length, was screened to generate a Pseudo-NIF2 population by selfing cross. In the Pseudo-NIF2 population, the segregation ratio of plants with long grains to short grains fits 3:1, indicating that one gene controlled the variation of grain length. Based on the Pseudo-NIF2 and its progeny, qGL10.1 was fine mapped to a 19.3-kb region, where a gene OsMADS56 was verified as the candidate by functional polymorphism between parental alleles. Pseudo-NIF2 strategy is a rapid way for QTL cloning, which saves 3 to 4 cropping seasons compared to the conventional way. Applying the method for cloning QTL with moderate or major effects is promising. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01408-x.
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Affiliation(s)
- Ahmed Sherif
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Sakha, 33717 Egypt
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Ali Mahmoud Elbadri
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Mostafa Elshenawy
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Sakha, 33717 Egypt
| | - Mahmoud El. M. El-Badawy
- Agronomy Department, Faculty of Agriculture, Benha University, Qalyubia Governorate, Benha, 13736 Egypt
| | - Ibrahim O. Hassan
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, 13759 Egypt
| | - Sedhom A. Sedhom
- Agronomy Department, Faculty of Agriculture, Benha University, Qalyubia Governorate, Benha, 13736 Egypt
| | - Mahmoud Abo-Yousef
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Sakha, 33717 Egypt
| | - Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, 13759 Egypt
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
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Chattopadhyay T, Sangam S, Akhtar S. Rapid genotyping in tomato by VPCR using agarose gel-resolvable InDel markers. 3 Biotech 2023; 13:85. [PMID: 36816752 PMCID: PMC9929007 DOI: 10.1007/s13205-023-03499-x] [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: 06/06/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Insertion/deletion (InDel) markers are second most abundant polymerase chain reaction (PCR)-based molecular markers having enormous applications in genotyping and molecular breeding in different crops. Although standard polymerase chain reaction (PCR) for DNA amplification generally takes ~ 1.5 to 2 h, small amplicons can be effectively generated using dynamic heating and cooling through PCR with "V"-shaped thermal profile (VPCR) in ~ 15 to 20 min. Here, we evaluated the applicability of a partly modified VPCR method for amplifying InDels of tomato genome. Out of the 31 InDel markers tested in 15 diverse tomato genotypes, 29 markers resulted in sharp amplicons, where 26 markers were found to be polymorphic. Using this method, the individual DNA amplification reactions could be completed within ~ 30 min. The method was effective for primers varying in melting temperature (T m) and GC contents. Furthermore, the need for empirically determining suitable annealing temperature could be bypassed using this generalised thermal profile. Through our results, we advocate the use of this method of DNA amplification in other plants to achieve rapid genotyping using standard molecular biology equipments and procedures. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03499-x.
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Affiliation(s)
- Tirthartha Chattopadhyay
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Surabhi Sangam
- Department of Horticulture (Vegetable and Floriculture), Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Shirin Akhtar
- Department of Horticulture (Vegetable and Floriculture), Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
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4
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B J, Hosahatti R, Koti PS, Devappa VH, Ngangkham U, Devanna P, Yadav MK, Mishra KK, Aditya JP, Boraiah PK, Gaber A, Hossain A. Phenotypic and Genotypic screening of fifty-two rice (Oryza sativa L.) genotypes for desirable cultivars against blast disease. PLoS One 2023; 18:e0280762. [PMID: 36897889 PMCID: PMC10004593 DOI: 10.1371/journal.pone.0280762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/08/2023] [Indexed: 03/11/2023] Open
Abstract
Magnaporthe oryzae, the rice blast fungus, is one of the most dangerous rice pathogens, causing considerable crop losses around the world. In order to explore the rice blast-resistant sources, initially performed a large-scale screening of 277 rice accessions. In parallel with field evaluations, fifty-two rice accessions were genotyped for 25 major blast resistance genes utilizing functional/gene-based markers based on their reactivity against rice blast disease. According to the phenotypic examination, 29 (58%) and 22 (42%) entries were found to be highly resistant, 18 (36%) and 29 (57%) showed moderate resistance, and 05 (6%) and 01 (1%), respectively, were highly susceptible to leaf and neck blast. The genetic frequency of 25 major blast resistance genes ranged from 32 to 60%, with two genotypes having a maximum of 16 R-genes each. The 52 rice accessions were divided into two groups based on cluster and population structure analysis. The highly resistant and moderately resistant accessions are divided into different groups using the principal coordinate analysis. According to the analysis of molecular variance, the maximum diversity was found within the population, while the minimum diversity was found between the populations. Two markers (RM5647 and K39512), which correspond to the blast-resistant genes Pi36 and Pik, respectively, showed a significant association to the neck blast disease, whereas three markers (Pi2-i, Pita3, and k2167), which correspond to the blast-resistant genes Pi2, Pita/Pita2, and Pikm, respectively, showed a significant association to the leaf blast disease. The associated R-genes might be utilized in rice breeding programmes through marker-assisted breeding, and the identified resistant rice accessions could be used as prospective donors for the production of new resistant varieties in India and around the world.
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Affiliation(s)
- Jeevan B
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | | | - Prasanna S Koti
- The University of Trans-Disciplinary Health Sciences and Technology, Jarakabande Kaval, Bengaluru, Karnataka, India
| | | | - Umakanta Ngangkham
- ICAR- Research Complex for North- Eastern Hill Region, Manipur centre, Imphal, Manipur, India
| | - Pramesh Devanna
- Rice Pathology Laboratory, AICRIP, Gangavathi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Manoj Kumar Yadav
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India
| | - Krishna Kant Mishra
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Jay Prakash Aditya
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Palanna Kaki Boraiah
- Project Coordinating Unit, ICAR-AICRP on Small Millets, UAS, GKVK, Bengaluru, Karnataka, India
| | - Ahmed Gaber
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh
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5
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Long W, Li Y, Yuan Z, Luo L, Luo L, Xu W, Cai Y, Xie H. Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. PLoS One 2022; 17:e0274418. [PMID: 36215240 PMCID: PMC9550083 DOI: 10.1371/journal.pone.0274418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.
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Affiliation(s)
- Weixiong Long
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yonghui Li
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Zhengqing Yuan
- State key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
| | - Lihua Luo
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Laiyang Luo
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Weibiao Xu
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China,* E-mail:
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6
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Wang X, Zhou T, Li G, Yao W, Hu W, Wei X, Che J, Yang H, Shao L, Hua J, Li X, Xiao J, Xing Y, Ouyang Y, Zhang Q. A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:68-83. [PMID: 35912411 DOI: 10.1111/tpj.15928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F2 s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.
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Affiliation(s)
- Xianmeng Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tianhao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen Yao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Hu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wei
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Che
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haichuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Shao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinping Hua
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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7
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Kawasaki E, Wenjing D, Sawada A, Nakajima M, Momose K, Yoshino T, Amano T, Endoh D, Nakajima N, Teraoka H. Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan. Animals (Basel) 2022; 12:ani12172293. [PMID: 36078013 PMCID: PMC9455020 DOI: 10.3390/ani12172293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.
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Affiliation(s)
- Erika Kawasaki
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Dong Wenjing
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Akira Sawada
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Momoko Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | | | | | - Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
- NPO Red-Crowned Crane Conservancy, Kushiro 085-0036, Japan
- Correspondence:
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8
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Long W, Luo L, Luo L, Xu W, Li Y, Cai Y, Xie H. Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2. FRONTIERS IN PLANT SCIENCE 2022; 13:857435. [PMID: 35548287 PMCID: PMC9083905 DOI: 10.3389/fpls.2022.857435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/01/2022] [Indexed: 06/15/2023]
Abstract
The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion-deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.
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9
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Grain Size Associated Genes and the Molecular Regulatory Mechanism in Rice. Int J Mol Sci 2022; 23:ijms23063169. [PMID: 35328589 PMCID: PMC8953112 DOI: 10.3390/ijms23063169] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 01/17/2023] Open
Abstract
Grain size is a quantitative trait that is controlled by multiple genes. It is not only a yield trait, but also an important appearance quality of rice. In addition, grain size is easy to be selected in evolution, which is also a significant trait for studying rice evolution. In recent years, many quantitative trait loci (QTL)/genes for rice grain size were isolated by map-based cloning or genome-wide association studies, which revealed the genetic and molecular mechanism of grain size regulation in part. Here, we summarized the QTL/genes cloned for grain size and the regulation mechanism with a view to provide the theoretical basis for improving rice yield and breeding superior varieties.
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10
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Ji H, Shin Y, Lee C, Oh H, Yoon IS, Baek J, Cha YS, Lee GS, Kim SL, Kim KH. Genomic Variation in Korean japonica Rice Varieties. Genes (Basel) 2021; 12:genes12111749. [PMID: 34828355 PMCID: PMC8623644 DOI: 10.3390/genes12111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022] Open
Abstract
Next-generation sequencing technologies have enabled the discovery of numerous sequence variations among closely related crop varieties. We analyzed genome resequencing data from 24 Korean temperate japonica rice varieties and discovered 954,233 sequence variations, including 791,121 single nucleotide polymorphisms (SNPs) and 163,112 insertions/deletions (InDels). On average, there was one variant per 391 base-pairs (bp), a variant density of 2.6 per 1 kbp. Of the InDels, 10,860 were longer than 20 bp, which enabled conversion to markers resolvable on an agarose gel. The effect of each variant on gene function was predicted using the SnpEff program. The variants were categorized into four groups according to their impact: high, moderate, low, and modifier. These groups contained 3524 (0.4%), 27,656 (2.9%), 24,875 (2.6%), and 898,178 (94.1%) variants, respectively. To test the accuracy of these data, eight InDels from a pre-harvest sprouting resistance QTL (qPHS11) target region, four highly polymorphic InDels, and four functional sequence variations in known agronomically important genes were selected and successfully developed into markers. These results will be useful to develop markers for marker-assisted selection, to select candidate genes in map-based cloning, and to produce efficient high-throughput genome-wide genotyping systems for Korean temperate japonica rice varieties.
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11
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Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species. Sci Rep 2021; 11:8962. [PMID: 33903715 PMCID: PMC8076200 DOI: 10.1038/s41598-021-88533-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/09/2021] [Indexed: 02/02/2023] Open
Abstract
Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a "genetic reservoir" for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.
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Adedze YMN, Lu X, Xia Y, Sun Q, Nchongboh CG, Alam MA, Liu M, Yang X, Zhang W, Deng Z, Li W, Si L. Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber. Sci Rep 2021; 11:3872. [PMID: 33594240 PMCID: PMC7886880 DOI: 10.1038/s41598-021-83313-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Insertion and Deletion (InDel) are common features in genomes and are associated with genetic variation. The whole-genome re-sequencing data from two parents (X1 and X2) of the elite cucumber (Cucumis sativus) hybrid variety Lvmei No.1 was used for genome-wide InDel polymorphisms analysis. Obtained sequence reads were mapped to the genome reference sequence of Chinese fresh market type inbred line ‘9930’ and gaps conforming to InDel were pinpointed. Further, the level of cross-parents polymorphism among five pairs of cucumber breeding parents and their corresponding hybrid varieties were used for evaluating hybrid seeds purity test efficiency of InDel markers. A panel of 48 cucumber breeding lines was utilized for PCR amplification versatility and phylogenetic analysis of these markers. In total, 10,470 candidate InDel markers were identified for X1 and X2. Among these, 385 markers with more than 30 nucleotide difference were arbitrary chosen. These markers were selected for experimental resolvability through electrophoresis on an Agarose gel. Two hundred and eleven (211) accounting for 54.81% of markers could be validated as single and clear polymorphic pattern while 174 (45.19%) showed unclear or monomorphic genetic bands between X1 and X2. Cross-parents polymorphism evaluation recorded 68 (32.23%) of these markers, which were designated as cross-parents transferable (CPT) InDel markers. Interestingly, the marker InDel114 presented experimental transferability between cucumber and melon. A panel of 48 cucumber breeding lines including parents of Lvmei No. 1 subjected to PCR amplification versatility using CPT InDel markers successfully clustered them into fruit and common cucumber varieties based on phylogenetic analysis. It is worth noting that 16 of these markers were predominately associated to enzymatic activities in cucumber. These agarose-based InDel markers could constitute a valuable resource for hybrid seeds purity testing, germplasm classification and marker-assisted breeding in cucumber.
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Affiliation(s)
- Yawo Mawunyo Nevame Adedze
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China.
| | - Xia Lu
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Yingchun Xia
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Qiuyue Sun
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Chofong G Nchongboh
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Brunswick, Germany
| | - Md Amirul Alam
- Faculty of Sustainable Agriculture, Horticulture and Landscaping Program, University Malaysia Sabah, Sandakan Campus, 90509, Sandakan, Sabah, Malaysia
| | - Menghua Liu
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Xue Yang
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Wenting Zhang
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Zhijun Deng
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Wenhu Li
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
| | - Longting Si
- Molecular Biology Laboratory of Jiangsu Green Port Modern Agriculture Development Company, Suqian, 223800, Jiangsu, China
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Olanrewaju OS, Oyatomi O, Babalola OO, Abberton M. Breeding Potentials of Bambara Groundnut for Food and Nutrition Security in the Face of Climate Change. FRONTIERS IN PLANT SCIENCE 2021; 12:798993. [PMID: 35069656 PMCID: PMC8768941 DOI: 10.3389/fpls.2021.798993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/09/2021] [Indexed: 05/22/2023]
Abstract
Constant production of quality food should be a norm in any community, but climate change, increasing population, and unavailability of land for farming affect food production. As a result, food scarcity is affecting some communities, especially in the developing world. Finding a stable solution to this problem is a major cause of concern for researchers. Synergistic application of molecular marker techniques with next generation sequencing (NGS) technologies can unlock the potentials hidden in most crop genomes for improving yield and food availability. Most crops such as Bambara groundnut (BGN), Winged bean, and African yam bean are underutilized. These underutilized crops can compete with the major crops such as cowpea, soybean, maize, and rice, in areas of nutrition, ability to withstand drought stress, economic importance, and food production. One of these underutilized crops, BGN [Vigna subterranea (L.), Verdc.], is an indigenous African legume and can survive in tropical climates and marginal soils. In this review, we focus on the roles of BGN and the opportunities it possesses in tackling food insecurity and its benefits to local farmers. We will discuss BGN's potential impact on global food production and how the advances in NGS technologies can enhance its production.
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Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Genetic Resources Center (GRC), International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olaniyi Oyatomi
- Genetic Resources Center (GRC), International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Michael Abberton
- Genetic Resources Center (GRC), International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- *Correspondence: Michael Abberton,
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Yang L, Xing F, He Q, Tahir ul Qamar M, Chen LL, Xing Y. Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. Int J Mol Sci 2020; 21:ijms21249618. [PMID: 33348666 PMCID: PMC7765902 DOI: 10.3390/ijms21249618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon in which a subset of genes express dependent on the origin of their parents. In plants, it is unclear whether imprinted genes are conserved between subspecies in rice. Here we identified imprinted genes from embryo and endosperm 5-7 days after pollination from three pairs of reciprocal hybrids, including inter-subspecies, japonica intra-subspecies, and indica intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in japonica intra-subspecies hybrids, and 286 in indica intra-subspecies hybrids. In general, the number of maternally expressed genes (MEGs) is more than paternally expressed genes (PEGs). Moreover, imprinted genes tend to be in mini clusters. The number of shared genes by R9N (reciprocal crosses between 9311 and Nipponbare) and R9Z (reciprocal crosses between 9311 and Zhenshan 97), R9N and RZN (reciprocal crosses between Zhonghua11 and Nipponbare), R9Z and RZN was 72, 46, and 16. These genes frequently involved in energy metabolism and seed development. Five imprinted genes (Os01g0151700, Os07g0103100, Os10g0340600, Os11g0679700, and Os12g0632800) are commonly detected in all three pairs of reciprocal hybrids and were validated by RT-PCR sequencing. Gene editing of two imprinted genes revealed that both genes conferred grain filling. Moreover, 15 and 27 imprinted genes with diverse functions in rice were shared with Arabidopsis and maize, respectively. This study provided valuable resources for identification of imprinting genes in rice or even in cereals.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
| | - Feng Xing
- College of Life Science, Xinyang Normal University, Xinyang 464000, China;
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
| | - Muhammad Tahir ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China;
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
- Correspondence: (L.-L.C.); (Y.X.)
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (L.Y.); (Q.H.)
- Correspondence: (L.-L.C.); (Y.X.)
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Genome-Wide Discovery of InDel Markers in Sesame ( Sesamum indicum L.) Using ddRADSeq. PLANTS 2020; 9:plants9101262. [PMID: 32987937 PMCID: PMC7599716 DOI: 10.3390/plants9101262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 01/15/2023]
Abstract
The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1-2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3'- and 5'- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.
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Zhang L, Ma B, Bian Z, Li X, Zhang C, Liu J, Li Q, Liu Q, He Z. Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice. RICE (NEW YORK, N.Y.) 2020; 13:63. [PMID: 32902771 PMCID: PMC7481322 DOI: 10.1186/s12284-020-00427-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/02/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers. RESULT In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio. CONCLUSIONS The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.
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Affiliation(s)
- Lin Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Bin Ma
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210 China
| | - Zhong Bian
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
| | - Xiaoyuan Li
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210 China
| | - Changquan Zhang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Zuhua He
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
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