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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Lyons JB, Bredeson JV, Mansfeld BN, Bauchet GJ, Berry J, Boyher A, Mueller LA, Rokhsar DS, Bart RS. Current status and impending progress for cassava structural genomics. PLANT MOLECULAR BIOLOGY 2022; 109:177-191. [PMID: 33604743 PMCID: PMC9162999 DOI: 10.1007/s11103-020-01104-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/08/2020] [Indexed: 05/26/2023]
Abstract
We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.
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Affiliation(s)
- Jessica B. Lyons
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
| | - Jessen V. Bredeson
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Ben N. Mansfeld
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Jeffrey Berry
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | - Adam Boyher
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Daniel S. Rokhsar
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Chan-Zuckerberg BioHub, 499 Illinois, San Francisco, CA 94158 USA
| | - Rebecca S. Bart
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
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Ehounou AE, Cormier F, Maledon E, Nudol E, Vignes H, Gravillon MC, N'guetta ASP, Mournet P, Chaïr H, Kouakou AM, Arnau G. Identification and validation of QTLs for tuber quality related traits in greater yam (Dioscorea alata L.). Sci Rep 2022; 12:8423. [PMID: 35589821 PMCID: PMC9120205 DOI: 10.1038/s41598-022-12135-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
Two Dioscorea alata populations were generated by hand pollination between contrasted diploid genitors. Population A (74F × Kabusa) was composed of 121 progenies while population B (74F × 14M) involved 193 progenies. These two populations were assessed over two consecutive years regarding important tuber quality traits. Analysis of variance showed that the genotype had the greatest influence on the phenotypic scores. Also for some traits, effect of the year_replicate was strong. The heritabilities of most traits were high. Based on these data and a reference high-density genetic map of greater yam, a total of 34 quantitative trait loci (QTLs) were detected on 8 of the 20 yam chromosomes. They corresponded to five of each of the following traits: tuber size, shape regularity, tubercular roots, skin texture, tuber flesh oxidation, six for oxidation ratio and three for flesh colour. The fraction of total phenotypic variance attributable to a single QTL ranged from 11.1 to 43.5%. We detected significant correlations between traits and QTL colocalizations that were consistent with these correlations. A majority of QTLs (62%) were found on linkage group LG16, indicating that this chromosome could play a major role in genetic control of the investigated traits. In addition, an inversion involving this chromosome was detected in the Kabusa male. Nine QTLs were validated on a diversity panel, including three for tuber size, three for shape regularity, two for skin texture and one for tubercular roots. The approximate physical localization of validated QTLs allowed the identification of various candidates genes. The validated QTLs should be useful for breeding programs using marker-assisted selection to improve yam tuber quality.
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Affiliation(s)
- Adou Emmanuel Ehounou
- CNRA, Station de Recherche sur les Cultures Vivrières (SRCV), 01 BP 633, Bouaké, Côte d'Ivoire
| | - Fabien Cormier
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | - Erick Maledon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | - Elie Nudol
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | - Hélène Vignes
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Marie Claire Gravillon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | | | - Pierre Mournet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Hâna Chaïr
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Amani Michel Kouakou
- CNRA, Station de Recherche sur les Cultures Vivrières (SRCV), 01 BP 633, Bouaké, Côte d'Ivoire
| | - Gemma Arnau
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France. .,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France.
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4
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Hu W, Ji C, Liang Z, Ye J, Ou W, Ding Z, Zhou G, Tie W, Yan Y, Yang J, Ma L, Yang X, Wei Y, Jin Z, Xie J, Peng M, Wang W, Guo A, Xu B, Guo J, Chen S, Wang M, Zhou Y, Li X, Li R, Xiao X, Wan Z, An F, Zhang J, Leng Q, Li Y, Shi H, Ming R, Li K. Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity. Genome Biol 2021; 22:316. [PMID: 34784936 PMCID: PMC8594203 DOI: 10.1186/s13059-021-02524-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/24/2021] [Indexed: 01/30/2023] Open
Abstract
Background Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. Results We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. Conclusions This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02524-7.
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Affiliation(s)
- Wei Hu
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China. .,Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
| | - Changmian Ji
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.,Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zehong Ding
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.,Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | - Weiwei Tie
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.,Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yan Yan
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.,Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jinghao Yang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Liming Ma
- Biomarker Technologies Corporation, Beijing, China
| | - Xiaoying Yang
- College of Food Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Zhiqiang Jin
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jianghui Xie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ming Peng
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Wenquan Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Anping Guo
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.,Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Biyu Xu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jianchun Guo
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | | | - Yang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, Beijing, China
| | - Ruoxi Li
- Fu Foundation School of Engineering and Applied Science, Columbia University, New York, NY, 10027, USA
| | - Xinhui Xiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zhongqing Wan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Feifei An
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jie Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Qingyun Leng
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan, China.
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
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5
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Malik AI, Kongsil P, Nguyễn VA, Ou W, Sholihin, Srean P, Sheela MN, Becerra López-Lavalle LA, Utsumi Y, Lu C, Kittipadakul P, Nguyễn HH, Ceballos H, Nguyễn TH, Selvaraj Gomez M, Aiemnaka P, Labarta R, Chen S, Amawan S, Sok S, Youabee L, Seki M, Tokunaga H, Wang W, Li K, Nguyễn HA, Nguyễn VĐ, Hàm LH, Ishitani M. Cassava breeding and agronomy in Asia: 50 years of history and future directions. BREEDING SCIENCE 2020; 70:145-166. [PMID: 32523397 PMCID: PMC7272245 DOI: 10.1270/jsbbs.18180] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/29/2019] [Indexed: 09/29/2023]
Abstract
In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.
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Affiliation(s)
- Al Imran Malik
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Pasajee Kongsil
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Vũ Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Wenjun Ou
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Sholihin
- Indonesian Legume and Tuber Crops Research Institute, Kendalpayak Km 8, PO BOX 66, Malang 65101, Indonesia
| | - Pao Srean
- Faculty of Agriculture & Food Processing, University of Battambang, Battambang, Cambodia
| | - MN Sheela
- Central Tuber Crops Research Institute Sreekariyam, Thiruvananthapuram-605 017, Kerala, India
| | | | - Yoshinori Utsumi
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Cheng Lu
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Piya Kittipadakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Hữu Hỷ Nguyễn
- Hung Loc Agricultural Research Center, Institute for Agriculture in Southern Vietnam, 121 Nguyen Binh Khiem, District 1, HCM City, Vietnam
| | - Hernan Ceballos
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Trọng Hiển Nguyễn
- Root and Tuber Crop Research and Development Center, Food and Field Crop Research Institute, Vinh Quynh, Thanh Tri, Hanoi, Vietnam
| | - Michael Selvaraj Gomez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Pornsak Aiemnaka
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Ricardo Labarta
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Songbi Chen
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Suwaluk Amawan
- Rayong Field Crops Research Center, Sukumvit Rd, Huaypong, Meang, Rayong 21150, Thailand
| | - Sophearith Sok
- International Center for Tropical Agriculture (CIAT-Asia), Phnom Penh, Cambodia
| | - Laothao Youabee
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Motoaki Seki
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Tokunaga
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Wenquan Wang
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Kaimian Li
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Hai Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Văn Đồng Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Lê Huy Hàm
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
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Tsvetkov I, Atanassov A, Vlahova M, Carlier L, Christov N, Lefort F, Rusanov K, Badjakov I, Dincheva I, Tchamitchian M, Rakleova G, Georgieva L, Tamm L, Iantcheva A, Herforth-Rahmé J, Paplomatas E, Atanassov I. Plant organic farming research – current status and opportunities for future development. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1427509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Ivan Tsvetkov
- AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Atanas Atanassov
- Joint Genomic Center, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Mariana Vlahova
- Joint Genomic Center, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Lucien Carlier
- Plant Sciences Department, Institute for Agricultural and Fisheries Research, Merelbeke, Belgium
| | | | - Francois Lefort
- University of Applied Sciences and Arts Western Switzerland, Delemont, Switzerland
| | | | | | | | - Mark Tchamitchian
- INRA French National Institute for Agricultural Research, Avignon, France
| | - Goritsa Rakleova
- Joint Genomic Center, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | | | - Lucius Tamm
- FiBL Forschungsinstitut für biologischen Landbau, Frick, Switzerland
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7
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Xia Z, Zhang S, Wen M, Lu C, Sun Y, Zou M, Wang W. Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:3. [PMID: 29321812 PMCID: PMC5759280 DOI: 10.1186/s13068-017-1004-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/22/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. RESULTS An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF-1, qNF-2a, qNF-2b, qNF-2c, qNF-3, qNF-4, qNF-6, qNF-7a, qNF-7b and qNF-8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF-1, qTWF-2 and qTWF-3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. CONCLUSION This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha.
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Affiliation(s)
- Zhiqiang Xia
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Shengkui Zhang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Mingfu Wen
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Cheng Lu
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Yufang Sun
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
| | - Meiling Zou
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
- Huazhong Agricultural University, Wuhan, China
| | - Wenquan Wang
- The Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China
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8
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Zhang S, Chen X, Lu C, Ye J, Zou M, Lu K, Feng S, Pei J, Liu C, Zhou X, Ma P, Li Z, Liu C, Liao Q, Xia Z, Wang W. Genome-Wide Association Studies of 11 Agronomic Traits in Cassava ( Manihot esculenta Crantz). FRONTIERS IN PLANT SCIENCE 2018; 9:503. [PMID: 29725343 PMCID: PMC5917017 DOI: 10.3389/fpls.2018.00503] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.
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Affiliation(s)
- Shengkui Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Cheng Lu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Meiling Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kundian Lu
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Subin Feng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinli Pei
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chen Liu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ping’an Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhaogui Li
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Cuijuan Liu
- Hepu Institute of Agricultural Science, Beihai, China
| | - Qi Liao
- Hepu Institute of Agricultural Science, Beihai, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
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Yao Y, Geng MT, Wu XH, Sun C, Wang YL, Chen X, Shang L, Lu XH, Li Z, Li RM, Fu SP, Duan RJ, Liu J, Hu XW, Guo JC. Identification, Expression, and Functional Analysis of the Fructokinase Gene Family in Cassava. Int J Mol Sci 2017; 18:E2398. [PMID: 29137155 PMCID: PMC5713366 DOI: 10.3390/ijms18112398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/03/2022] Open
Abstract
Fructokinase (FRK) proteins play important roles in catalyzing fructose phosphorylation and participate in the carbohydrate metabolism of storage organs in plants. To investigate the roles of FRKs in cassava tuber root development, seven FRK genes (MeFRK1-7) were identified, and MeFRK1-6 were isolated. Phylogenetic analysis revealed that the MeFRK family genes can be divided into α (MeFRK1, 2, 6, 7) and β (MeFRK3, 4, 5) groups. All the MeFRK proteins have typical conserved regions and substrate binding residues similar to those of the FRKs. The overall predicted three-dimensional structures of MeFRK1-6 were similar, folding into a catalytic domain and a β-sheet ''lid" region, forming a substrate binding cleft, which contains many residues involved in the binding to fructose. The gene and the predicted three-dimensional structures of MeFRK3 and MeFRK4 were the most similar. MeFRK1-6 displayed different expression patterns across different tissues, including leaves, stems, tuber roots, flowers, and fruits. In tuber roots, the expressions of MeFRK3 and MeFRK4 were much higher compared to those of the other genes. Notably, the expression of MeFRK3 and MeFRK4 as well as the enzymatic activity of FRK were higher at the initial and early expanding tuber stages and were lower at the later expanding and mature tuber stages. The FRK activity of MeFRK3 and MeFRK4 was identified by the functional complementation of triple mutant yeast cells that were unable to phosphorylate either glucose or fructose. The gene expression and enzymatic activity of MeFRK3 and MeFRK4 suggest that they might be the main enzymes in fructose phosphorylation for regulating the formation of tuber roots and starch accumulation at the tuber root initial and expanding stages.
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Affiliation(s)
- Yuan Yao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Meng-Ting Geng
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Xiao-Hui Wu
- Prisys Biotechnologies Company Limited, Shanghai 201203, China.
| | - Chong Sun
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing 163319, China.
| | - Yun-Lin Wang
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Xia Chen
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Lu Shang
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Xiao-Hua Lu
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Zhan Li
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Rui-Mei Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shao-Ping Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Rui-Jun Duan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Jiao Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Xin-Wen Hu
- College of Agriculture, Hainan University, Haikou 570228, China.
| | - Jian-Chun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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