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Liu F, Baye W, Zhao K, Tang S, Xie Q, Xie P. Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects. J Genet Genomics 2024:S1673-8527(24)00194-2. [PMID: 39053846 DOI: 10.1016/j.jgg.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Sorghum, renowned for its substantial biomass production and remarkable tolerance to various stresses, possesses extensive gene resources and phenotypic variations. A comprehensive understanding of the genetic basis underlying complex agronomic traits is essential for unlocking the potential of sorghum in addressing food and feed security and utilizing marginal lands. In this context, we provide an overview of the major trends in genomic resource studies focusing on key agronomic traits over the past decade, accompanied by a summary of functional genomic platforms. We also delve into the molecular functions and regulatory networks of impactful genes for important agricultural traits. Lastly, we discuss and synthesize the current challenges and prospects for advancing molecular design breeding by gene-editing and polymerization of the excellent alleles, with the aim of accelerating the development of desired sorghum varieties.
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Affiliation(s)
- Fangyuan Liu
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wodajo Baye
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Natural and Computational Science, Woldia University, Woldia, Po.box-400, Ethiopia.
| | - Kangxu Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Xie
- School of Agriculture and Biotechnology, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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2
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Alam O, Purugganan MD. Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements. THE PLANT CELL 2024; 36:1227-1241. [PMID: 38243576 PMCID: PMC11062453 DOI: 10.1093/plcell/koae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.
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Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, 10028, USA
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3
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Zheng H, Dang Y, Sui N. Sorghum: A Multipurpose Crop. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17570-17583. [PMID: 37933850 DOI: 10.1021/acs.jafc.3c04942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Sorghum (Sorghum bicolor L.) is one of the top five cereal crops in the world in terms of production and planting area and is widely grown in areas with severe abiotic stresses such as drought and saline-alkali land due to its excellent stress resistance. Moreover, sorghum is a rare multipurpose crop that can be classified into grain sorghum, energy sorghum, and silage sorghum according to its domestication direction and utilization traits, endowing it with broad breeding and economic value. In this review, we mainly discuss the latest research progress and regulatory genes of agronomic traits of sorghum as a grain, energy, and silage crop, as well as the future improvement direction of multipurpose sorghum. We also emphasize the feasibility of cultivating multipurpose sorghum through genetic engineering methods by exploring potential targets using wild sorghum germplasm and genetic resources, as well as genomic resources.
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Affiliation(s)
- Hongxiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Yingying Dang
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
- Dongying Institute, Shandong Normal University, Dongying, 257000, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, 250014, China
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4
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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5
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Takanashi H. Genetic control of morphological traits useful for improving sorghum. BREEDING SCIENCE 2023; 73:57-69. [PMID: 37168813 PMCID: PMC10165342 DOI: 10.1270/jsbbs.22069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 05/13/2023]
Abstract
Global climate change and global warming, coupled with the growing population, have raised concerns about sustainable food supply and bioenergy demand. Sorghum [Sorghum bicolor (L.) Moench] ranks fifth among cereals produced worldwide; it is a C4 crop with a higher stress tolerance than other major cereals and has a wide range of uses, such as grains, forage, and biomass. Therefore, sorghum has attracted attention as a promising crop for achieving sustainable development goals (SDGs). In addition, sorghum is a suitable genetic model for C4 grasses because of its high morphological diversity and relatively small genome size compared to other C4 grasses. Although sorghum breeding and genetic studies have lagged compared to other crops such as rice and maize, recent advances in research have identified several genes and many quantitative trait loci (QTLs) that control important agronomic traits in sorghum. This review outlines traits and genetic information with a focus on morphogenetic aspects that may be useful in sorghum breeding for grain and biomass utilization.
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Affiliation(s)
- Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding author (e-mail: )
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Feng L, Su Q, Yue H, Wang L, Gao J, Xing L, Xu M, Zhou C, Yang Y, Zhou B. TIP41L, a putative candidate gene conferring both seed size and boll weight, was fine-mapped in an introgression line of Gossypium hirsutum-Gossypium arboreum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 317:111197. [PMID: 35193746 DOI: 10.1016/j.plantsci.2022.111197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/12/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
QTLs for yield-related traits in tetraploid cotton have been widely mapped, but QTLs introduced from diploid species into tetraploid cotton background remain uninvolved. Here, a stable introgression line with the traits of small boll and seed on Chr. A12, IL197 derived from Gossypium hirsutum (2n = AADD = 52) × Gossypium arboreum (2n = AA = 26), was employed to construct the F2 and F3 secondary populations for fine-mapping QTLs of yield-related traits. QTL analysis showed eight QTLs were detected for three traits, boll weight (BW), seed index (SI, one-hundred-seed weight in g), and lint percentage, with 3.94-28.13 % of the phenotypic variance explained. Of them, a stable major QTL, q(BW + SI)-A12-1 controlling both BW and SI and covering the shortest region in Chr. A12, was further narrowed into a 60.09 kb-interval through substitution mapping. Finally, five candidate genes were detected in the interval. The qRT-PCR analysis revealed only TIP41-like family protein (TIP41L) kept up-regulated expression and significantly lower in TM-1 than that in IL197 from -1 DPA to 15 DPA during cotton boll rapid developmental stage. Therefore, TIP41L gene is speculated as the most likely candidate gene. Comparative analysis with the other four allotetraploid species showed TIP41L gene was probably diverged after the formation of allotetraploid cotton, which may be selected and swept during domestication of modern upland cotton because small boll and seed are detrimental to fibre yield of cotton. This research would lay a solid foundation for further elucidating the molecular mechanism of cotton boll and seed development.
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Affiliation(s)
- Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, People's Republic of China
| | - Qiao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Haoran Yue
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liang Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liangshuai Xing
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ying Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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7
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Wu X, Liu Y, Luo H, Shang L, Leng C, Liu Z, Li Z, Lu X, Cai H, Hao H, Jing HC. Genomic footprints of sorghum domestication and breeding selection for multiple end uses. MOLECULAR PLANT 2022; 15:537-551. [PMID: 34999019 DOI: 10.1016/j.molp.2022.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Domestication and diversification have had profound effects on crop genomes. Originating in Africa and subsequently spreading to different continents, sorghum (Sorghum bicolor) has experienced multiple onsets of domestication and intensive breeding selection for various end uses. However, how these processes have shaped sorghum genomes is not fully understood. In the present study, population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild sorghum and four end-use subpopulations with diverse agronomic traits. Frequent genetic exchanges were found among various subpopulations, and strong selective sweeps affected 14.68% (∼107.5 Mb) of the sorghum genome, including 3649, 4287, and 3888 genes during sorghum domestication, improvement of grain sorghum, and improvement of sweet sorghum, respectively. Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed, and Sh1- and SbTB1-type genes were representative of two prominent models, one of soft selection or multiple origins and one of hard selection or an early single domestication event. We also demonstrated that the Dry gene, which regulates stem juiciness, was unconsciously selected during the improvement of grain sorghum. Taken together, these findings provide new genomic insights into sorghum domestication and breeding selection, and will facilitate further dissection of the domestication and molecular breeding of sorghum.
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Affiliation(s)
- Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaochun Lu
- Institute of Sorghum Research, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Hongwei Cai
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Xie P, Tang S, Chen C, Zhang H, Yu F, Li C, Wei H, Sui Y, Wu C, Diao X, Wu Y, Xie Q. Natural variation in Glume Coverage 1 causes naked grains in sorghum. Nat Commun 2022; 13:1068. [PMID: 35217660 PMCID: PMC8881591 DOI: 10.1038/s41467-022-28680-3] [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: 09/15/2021] [Accepted: 02/07/2022] [Indexed: 12/30/2022] Open
Abstract
One of the most critical steps in cereal threshing is the ease with which seeds are detached from sticky glumes. Naked grains with low glume coverage have dramatically increased threshing efficiency and seed quality. Here, we demonstrate that GC1 (Glume Coverage 1), encoding an atypical G protein γ subunit, negatively regulates sorghum glume coverage. Naturally truncated variations of GC1 C-terminus accumulate at higher protein levels and affect the stability of a patatin-related phospholipase SbpPLAII-1. A strong positive selection signature around the GC1 genic region is found in the naked sorghum cultivars. Our findings reveal a crucial event during sorghum domestication through a subtle regulation of glume development by GC1 C-terminus variation, and establish a strategy for future breeding of naked grains. Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.
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Affiliation(s)
- Peng Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China. .,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China.
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Chengxuan Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China.,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Huili Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Feifei Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Chao Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Huimin Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China.,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, P. R. China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China.
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 100101, Beijing, P. R. China. .,University of Chinese Academy of Sciences, 100049, Beijing, P. R. China.
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9
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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10
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Tao Y, Trusov Y, Zhao X, Wang X, Cruickshank AW, Hunt C, van Oosterom EJ, Hathorn A, Liu G, Godwin ID, Botella JR, Mace ES, Jordan DR. Manipulating assimilate availability provides insight into the genes controlling grain size in sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:231-243. [PMID: 34309934 DOI: 10.1111/tpj.15437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Variation in grain size, a major determinant of grain yield and quality in cereal crops, is determined by both the plant's genetic potential and the available assimilate to fill the grain in the absence of stress. This study investigated grain size variation in response to variation in assimilate supply in sorghum using a diversity panel (n = 837) and a backcross-nested association mapping population (n = 1421) across four experiments. To explore the effects of genetic potential and assimilate availability on grain size, the top half of selected panicles was removed at anthesis. Results showed substantial variation in five grain size parameters with high heritability. Artificial reduction in grain number resulted in a general increase in grain weight, with the extent of the increase varying across genotypes. Genome-wide association studies identified 44 grain size quantitative trait locus (QTL) that were likely to act on assimilate availability and 50 QTL that were likely to act on genetic potential. This finding was further supported by functional enrichment analysis and co-location analysis with known grain number QTL and candidate genes. RNA interference and overexpression experiments were conducted to validate the function of one of the identified gene, SbDEP1, showing that SbDEP1 positively regulates grain number and negatively regulates grain size by controlling primary branching in sorghum. Haplotype analysis of SbDEP1 suggested a possible role in racial differentiation. The enhanced understanding of grain size variation in relation to assimilate availability presented in this study will benefit sorghum improvement and have implications for other cereal crops.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Qld, 4370, Australia
| | - Yuri Trusov
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Qld, 4370, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Qld, 4370, Australia
| | - Alan W Cruickshank
- Department of Agriculture and Fisheries (DAF), Agri-Science Queensland, Hermitage Research Facility, Warwick, Qld, 4370, Australia
| | - Colleen Hunt
- Department of Agriculture and Fisheries (DAF), Agri-Science Queensland, Hermitage Research Facility, Warwick, Qld, 4370, Australia
| | - Erik J van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Qld, 4370, Australia
| | - Guoquan Liu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ian D Godwin
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Jose R Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Emma S Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Qld, 4370, Australia
- Department of Agriculture and Fisheries (DAF), Agri-Science Queensland, Hermitage Research Facility, Warwick, Qld, 4370, Australia
| | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, The University of Queensland, Warwick, Qld, 4370, Australia
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11
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Zhou C, Wang S, Zhou H, Yuan Z, Zhou T, Zhang Y, Xiang S, Yang F, Shen X, Zhang D. Transcriptome sequencing analysis of sorghum callus with various regeneration capacities. PLANTA 2021; 254:33. [PMID: 34287698 DOI: 10.1007/s00425-021-03683-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
The possible molecular mechanisms regulating sorghum callus regeneration were revealed by RNA-sequencing. Plant callus regeneration has been widely applied in agricultural improvement. Recently, callus regeneration has been successfully applied in the genetic transformation of sorghum by using immature sorghum embryos as explants. However, the mechanism underlying callus regeneration in sorghum is still largely unknown. Here, we describe three types of callus (Callus I-III) with different redifferentiation abilities undergoing distinct induction from immature embryos of the Hiro-1 variety. Compared with nonembryonic Callus III, Callus I produced only some identifiable roots, and embryonic Callus II was sufficient to regenerate whole plants. Genome-wide transcriptome profiles were generated to reveal the underlying mechanisms. The numbers of differentially expressed genes for the three types of callus varied from 5906 to 8029. In accordance with the diverse regeneration abilities observed for different types of callus and leaf tissues, the principal component analysis revealed that the gene expression patterns of Callus I and Callus II were different from those of Callus III and leaves regenerated from Callus II. Notably, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, pharmacological treatment, and substance content determinations revealed that plant ribosomes, lignin metabolic processes, and metabolism of starch and sucrose were significantly enriched, suggesting that these factors are associated with callus regeneration. These results helped elucidate the molecular regulation of three types of callus with different regeneration abilities in sorghum.
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Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Sijia Wang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Zhu Yuan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Tao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, 442000, China
| | - Sen Xiang
- School of Information Science and Engineering, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Xiangling Shen
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China.
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12
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum. Sci Rep 2021; 11:9398. [PMID: 33931706 PMCID: PMC8087780 DOI: 10.1038/s41598-021-88917-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associated with sexual reproduction in grasses, no QTLs have been reported in sorghum. Additionally, there are only a few reports on sorghum QTLs related to grain size, such as grain length, width, and thickness. In this study, we performed QTL analyses of nine spikelet-related traits (length of sessile spikelet, pedicellate spikelet, pedicel, anther, style, and stigma; width of sessile spikelet and stigma; and stigma pigmentation) and six grain-related traits (length, width, thickness, length/width ratio, length/thickness ratio, and width/thickness ratio) using sorghum recombinant inbred lines. We identified 36 and 7 QTLs for spikelet-related traits and grain-related traits, respectively, and found that most sorghum spikelet organ length- and width-related traits were partially controlled by the dwarf genes Dw1 and Dw3. Conversely, we found that these Dw genes were not strongly involved in the regulation of grain size. The QTLs identified in this study aid in understanding the genetic basis of spikelet- and grain-related traits in sorghum.
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14
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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15
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Zou G, Zhai G, Yan S, Li S, Zhou L, Ding Y, Liu H, Zhang Z, Zou J, Zhang L, Chen J, Xin Z, Tao Y. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5389-5401. [PMID: 32497208 DOI: 10.1093/jxb/eraa277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.
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Affiliation(s)
- Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Yan
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lengbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Heqin Liu
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhipeng Zhang
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jianqiu Zou
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junping Chen
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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16
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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17
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Tao Y, Zhao X, Wang X, Hathorn A, Hunt C, Cruickshank AW, van Oosterom EJ, Godwin ID, Mace ES, Jordan DR. Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1093-1105. [PMID: 31659829 PMCID: PMC7061873 DOI: 10.1111/pbi.13284] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/30/2019] [Accepted: 10/24/2019] [Indexed: 05/20/2023]
Abstract
Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype's genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome-wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC-NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype's capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Alan W. Cruickshank
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Erik J. van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Ian D. Godwin
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Emma S. Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
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18
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Ahmed MM, Huang C, Shen C, Khan AQ, Lin Z. Map-based cloning of qBWT-c12 discovered brassinosteroid-mediated control of organ size in cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110315. [PMID: 31928681 DOI: 10.1016/j.plantsci.2019.110315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Assuring fiber yield stability is the primary objective for cotton breeders since the world population is on the rise, and the demand for cotton fiber is increasing every year. Thus, enhancing average cotton boll weight (BWT) could improve seed cotton production, and ultimately to increase cotton fiber yield. This study accomplished the map-based cloning of a novel boll weight regulating locus, qBWT-c12, in cotton. Bulk segregation analysis detected linked markers, aided in the detection of a stable BWT regulating locus, qBWT-c12, on Chr12 in a novel boll size mutant, BS41. Progeny evaluation confined the qBWT-c12 to a 0.89 cM interval between the AD-A12_07 and AD-FM_44 markers in recombinant derived F3 and F4 populations. Homology mapping detected a 40 bp insertion-deletion (InDel) site in the AD-FM_44 clone sequence situated +341 downstream of GhBRH1_A12, which showed complete linkage to the BWT phenotype. The suppressed expression of GhBRH1_A12 suggested its putative involvement during early boll development events in BS41. Although brassinosteroid (BR) biosynthesis and signaling pathway genes were up regulated in different tissues, but the organ growth was suppressed leading to dwarf plants, smaller leaves, and de-morphed smaller bolls in BS41. Thus, a disruption in the BR signal cascade is anticipated and could be related to lower GhBRH1_A12 expression in BS41.This study firstly reported the genetic dissection of boll size regulation of G. barbadense in G. hirsutum background using map-based cloning of a BWT regulating locus, qBWT-c12. Moreover, it also emphasized the putative role GhBRH1_A12 in regulating BR homeostasis and its potential to modulate plant growth and boll development in cotton.
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Affiliation(s)
- Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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19
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Yang H, Wang W, He Q, Xiang S, Tian D, Zhao T, Gai J. Identifying a wild allele conferring small seed size, high protein content and low oil content using chromosome segment substitution lines in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2793-2807. [PMID: 31280342 DOI: 10.1007/s00122-019-03388-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/24/2019] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE A wild soybean allele conferring 100-seed weight, protein content and oil content simultaneously was fine-mapped to a 329-kb region on Chromosome 15, in which Glyma.15g049200 was predicted a candidate gene. Annual wild soybean characterized with small 100-seed weight (100SW), high protein content (PRC), low oil content (OIC) may contain favourable alleles for broadening the genetic base of cultivated soybeans. To evaluate these alleles, a population composed of 195 chromosome segment substitution lines (SojaCSSLP4), with wild N24852 as donor and cultivated NN1138-2 as recurrent parent, was tested. In SojaCSSLP4, 10, 9 and 8 wild segments/QTL were detected for 100SW, PRC and OIC, respectively. Using a backcross-derived secondary population, one segment for the three traits (q100SW15, qPro15 and qOil15) and one for 100SW (q100SW18.2) were fine-mapped into a 329-kb region on chromosome 15 and a 286-kb region on chromosome 18, respectively. Integrated with the transcription data in SoyBase, 42 genes were predicted in the 329-kb region where Glyma.15g049200 showed significant expression differences at all seed development stages. Furthermore, the Glyma.15g049200 segments of the two parents were sequenced and compared, which showed two base insertions in CDS (coding sequence) in the wild N24852 comparing to the NN1138-2. Since only Glyma.15g049200 performed differential CDS between the two parents but related to the three traits, Glyma.15g049200 was predicted a pleiotropic candidate gene for 100SW, PRC and OIC. The functional annotation of Glyma.15g049200 indicated a bidirectional sucrose transporter belonging to MtN3/saliva family which might be the reason that this gene provides a same biochemical basis for 100SW, PRC and OIC, therefore, is responsible for the three traits. This result may facilitate isolation of the specific gene and provide prerequisite for understanding the other two pleiotropic QTL.
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Affiliation(s)
- Hongyan Yang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Coastal Areas Institute of Agricultural Sciences, Yancheng, 224002, Jiangsu, China
| | - Wubin Wang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qingyuan He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shihua Xiang
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dong Tian
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Tuanjie Zhao
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Junyi Gai
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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20
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Genomic signatures of seed mass adaptation to global precipitation gradients in sorghum. Heredity (Edinb) 2019; 124:108-121. [PMID: 31316156 PMCID: PMC6906510 DOI: 10.1038/s41437-019-0249-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
Seed mass is a key component of adaptation in plants and a determinant of yield in crops. The climatic drivers and genomic basis of seed mass variation remain poorly understood. In the cereal crop Sorghum bicolor, globally-distributed landraces harbor abundant variation in seed mass, which is associated with precipitation in their agroclimatic zones of origin. This study aimed to test the hypothesis that diversifying selection across precipitation gradients, acting on ancestral cereal grain size regulators, underlies seed mass variation in global sorghum germplasm. We tested this hypothesis in a set of 1901 georeferenced and genotyped sorghum landraces, 100-seed mass from common gardens, and bioclimatic precipitation variables. As predicted, 100-seed mass in global germplasm varies significantly among botanical races and is correlated to proxies of the precipitation gradients. With general and mixed linear model genome-wide associations, we identified 29 and 56 of 100 a priori candidate seed size genes with polymorphisms in the top 1% of seed mass association, respectively. Eleven of these genes harbor polymorphisms associated with the precipitation gradient, including orthologs of genes that regulate seed size in other cereals. With FarmCPU, 13 significant SNPs were identified, including one at an a priori candidate gene. Finally, we identified eleven colocalized outlier SNPs associated with seed mass and precipitation that also carry signatures of selection based on FST scans and PCAdapt, which represents a significant enrichment. Our findings suggest that seed mass in sorghum was shaped by diversifying selection on drought stress, and can inform genomics-enabled breeding for climate-resilient cereals.
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21
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Unraveling the genetic complexity underlying sorghum response to water availability. PLoS One 2019; 14:e0215515. [PMID: 30998785 PMCID: PMC6472798 DOI: 10.1371/journal.pone.0215515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding the adaptation mechanisms of sorghum to drought and the underlying genetic architecture may help to improve its production in a wide range of environments. By crossing a high yielding parent (HYP) and a drought tolerant parent (DTP), we obtained 140 recombinant inbred lines (RILs), which were genotyped with 120 DArT and SSR markers covering 14 linkage groups (LGs). A subset of 100 RILs was evaluated three times in control and drought treatments to genetically dissect their response to water availability. Plants with early heading date (HD) in the drought treatment maintained yield (YLD) level by reducing seed number SN and increasing hundred seed weight (HSW). In contrast, early HD in the control treatment increased SN, HSW and YLD. In total, 133 significant QTL associated with the measured traits were detected in ten hotspot regions. Antagonistic, pleiotropic effects of a QTL cluster mapped on LG-6 may explain the observed trade-offs between SN and HSW: Alleles from DTP reduced SN and the alleles from HYP increased HSW under drought stress, but not in the control treatment. Our results illustrate the importance of considering genetic and environmental factors in QTL mapping to better understand plant responses to drought and to improve breeding programs.
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22
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Boyles RE, Brenton ZW, Kresovich S. Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:19-39. [PMID: 30260043 DOI: 10.1111/tpj.14113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/10/2023]
Abstract
With the recent development of genomic resources and high-throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C4 grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype-phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement.
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Affiliation(s)
- Richard E Boyles
- Pee Dee Research and Education Center, Clemson University, 2200 Pocket Rd, Florence, SC, 29506, USA
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
| | - Zachary W Brenton
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
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23
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Jiang J, Xing F, Zeng X, Zou Q. RicyerDB: A Database For Collecting Rice Yield-related Genes with Biological Analysis. Int J Biol Sci 2018; 14:965-970. [PMID: 29989091 PMCID: PMC6036756 DOI: 10.7150/ijbs.23328] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 12/25/2017] [Indexed: 11/16/2022] Open
Abstract
The Rice Yield-related Database (RicyerDB) was created to complement with related research of influence rice (Oryza sativa L.) yield in multiple traits by manually curating the related databases and literature, and genomics and proteomics information that could be useful for comprehensive understanding of the rice biology. RicyerDB provides a more valuable resource in which to efficiently investigate, browse and analyze yield-related genes. The whole data set can be easily queried and downloaded through the webpage. In addition, RicyerDB also constructed a protein-protein interaction network with biological analysis. The combined rice database opens a new path to facilitate researchers achieving information on rice gene in terms of their effects on traits important for rice breeding. The web server is freely available at: http://server.malab.cn/Ricyer/index.html.
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Affiliation(s)
- Jing Jiang
- School of Aerospace Engineering, Xiamen University, Xiamen, 361001, China
| | - Fei Xing
- School of Aerospace Engineering, Xiamen University, Xiamen, 361001, China
| | - Xiangxiang Zeng
- School of Information Science and Engineering, Xiamen University, Xiamen 361001, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, 300354, China
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24
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SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population. Mol Genet Genomics 2018; 293:793-805. [PMID: 29392407 DOI: 10.1007/s00438-018-1419-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/13/2018] [Indexed: 10/18/2022]
Abstract
The quality of fiber is significant in the upland cotton industry. As complex quantitative traits, fiber quality traits are worth studying at a genetic level. To investigate the genetic architecture of fiber quality traits, we conducted an association analysis using a multi-parent advanced generation inter-cross (MAGIC) population developed from eight parents and comprised of 960 lines. The reliable phenotypic data for six major fiber traits of the MAGIC population were collected from five environments in three locations. Phenotypic analysis showed that the MAGIC lines have a wider variation amplitude and coefficient than the founders. A total of 284 polymorphic SSR markers among eight parents screened from a high-density genetic map were used to genotype the MAGIC population. The MAGIC population showed abundant genetic variation and fast linkage disequilibrium (LD) decay (0.76 cM, r2 > 0.1), which revealed the advantages of high efficiency and power in QTL exploration. Association mapping via a mixed linear model identified 52 significant loci associated with six fiber quality traits; 14 of them were mapped in reported QTL regions with fiber-related or other agronomic traits. Nine markers demonstrated the pleiotropism that controls more than two fiber traits. Furthermore, two SSR markers, BNL1231 and BNL3452, were authenticated as hotspots that were mapped with multi-traits. In addition, we provided candidate regions and screened six candidate genes for identified loci according to the LD decay distance. Our results provide valuable QTL for further genetic mapping and will facilitate marker-based breeding for fiber quality in cotton.
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25
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Woldesemayat AA, Van Heusden P, Ndimba BK, Christoffels A. An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). BMC Genet 2017; 18:119. [PMID: 29273003 PMCID: PMC5741957 DOI: 10.1186/s12863-017-0584-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait. In this study, we used sorghum, one of the model crops that is well adapted to arid regions, to mine genes and define determinants for drought tolerance using drought expression libraries and RNA-seq data. RESULTS We provide an integrated and comparative in silico candidate gene identification, characterization and annotation approach, with an emphasis on genes playing a prominent role in conferring drought tolerance in sorghum. A total of 470 non-redundant functionally annotated drought responsive genes (DRGs) were identified using experimental data from drought responses by employing pairwise sequence similarity searches, pathway and interpro-domain analysis, expression profiling and orthology relation. Comparison of the genomic locations between these genes and sorghum quantitative trait loci (QTLs) showed that 40% of these genes were co-localized with QTLs known for drought tolerance. The genome reannotation conducted using the Program to Assemble Spliced Alignment (PASA), resulted in 9.6% of existing single gene models being updated. In addition, 210 putative novel genes were identified using AUGUSTUS and PASA based analysis on expression dataset. Among these, 50% were single exonic, 69.5% represented drought responsive and 5.7% were complete gene structure models. Analysis of biochemical metabolism revealed 14 metabolic pathways that are related to drought tolerance and also had a strong biological network, among categories of genes involved. Identification of these pathways, signifies the interplay of biochemical reactions that make up the metabolic network, constituting fundamental interface for sorghum defence mechanism against drought stress. CONCLUSIONS This study suggests untapped natural variability in sorghum that could be used for developing drought tolerance. The data presented here, may be regarded as an initial reference point in functional and comparative genomics in the Gramineae family.
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Affiliation(s)
- Adugna Abdi Woldesemayat
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Belleville, 7535, South Africa.
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, UNISA Science Campus, Corner of Christiaan De Wet Road and Pioneer Avenue, Johannesburg, Florida, 1710, South Africa.
| | - Peter Van Heusden
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Belleville, 7535, South Africa
| | - Bongani K Ndimba
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Belleville, Cape Town, 7535, South Africa
- Agricultural Research Council, Infruitech-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Belleville, 7535, South Africa
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26
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Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop MN, Tan L, Zhang J, Wu J, Cai H, Sun C, Wang X, Wing RA, Zhu Z. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. NATURE PLANTS 2017; 3:17064. [PMID: 28481332 DOI: 10.1038/nplants.2017.64] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/04/2017] [Indexed: 05/04/2023]
Abstract
Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated rice (Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii. Here we report the cloning and characterization of a quantitative trait locus, GL4, controlling the grain length on chromosome 4 in African rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian rice. Our data show that a single-nucleotide polymorphism (SNP) mutation in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering during African rice domestication. These results provide new insights into diverse domestication practices in African rice, and also pave the way for enhancing crop yield to meeting the challenge of cereal demand in West Africa.
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Affiliation(s)
- Wenguang Wu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xiaoyun Liu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | | | - Lubin Tan
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jianzhong Wu
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8602, Japan
| | - Hongwei Cai
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanqing Sun
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xiangkun Wang
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- International Rice Research Institute, T.T. Chang Genetic Resources Centre, Los Baños, Laguna, Philippines
| | - Zuofeng Zhu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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