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Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, Wang Z, Li F. Recent progression and future perspectives in cotton genomic breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:548-569. [PMID: 36226594 DOI: 10.1111/jipb.13388] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/11/2022] [Indexed: 05/26/2023]
Abstract
Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
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Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yihao Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qingdi Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Wang F, Tan WF, Song W, Yang ST, Qiao S. Transcriptome analysis of sweet potato responses to potassium deficiency. BMC Genomics 2022; 23:655. [PMID: 36109727 PMCID: PMC9479357 DOI: 10.1186/s12864-022-08870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Background As one of three essential nutrients, potassium is regarded as a main limiting factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of seven major food crops grown worldwide, and is both a nutrient-rich food and a bioenergy crop. It is a typical ‘K-favoring’ crop, and the level of potassium ion (K+) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K+ conditions. Here, we analyzed the transcriptomic profiles of sweet potato roots in response to K+ deficiency to determine the effect of low-K+ stress on this economically important crop. Results The roots of sweet potato seedlings with or without K+ treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K+ groups. Among the DEGs, 336 were upregulated and 223 were downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. Further analysis revealed previously unknow genes involved in low-K+ stress, which could be investigated further to improve low K+ tolerance in plants. Confirmation of RNA-sequencing results using qRT-PCR displayed a high level of consistency between the two experiments. Analysis showed that many auxin-, ethylene- and jasmonic acid-related genes respond to K+ deficiency, suggesting that these hormones have important roles in K+ nutrient signaling in sweet potato. Conclusions According to the transcriptome data of sweet potato, various DEGs showed transcriptional changes in response to low-K+ stress. However, the expression level of some kinases, transporters, transcription factors (TFs), hormone-related genes, and plant defense-related genes changed significantly, suggesting that they have important roles during K+ deficiency. Thus, this study identifies potential genes for genetic improvement of responses to low-K+ stress and provides valuable insight into the molecular mechanisms regulating low K+ tolerance in sweet potato. Further research is required to clarify the function of these DEGs under low-K+ stress. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08870-5.
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Yang X, Zhang J, Wu A, Wei H, Fu X, Tian M, Ma L, Lu J, Wang H, Yu S. Genome-Wide Identification and Expression Pattern Analysis of the HAK/KUP/KT Gene Family of Cotton in Fiber Development and Under Stresses. Front Genet 2020; 11:566469. [PMID: 33329704 PMCID: PMC7710864 DOI: 10.3389/fgene.2020.566469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
The potassium transporter family HAK/KUP/KT is a large group of proteins that are important in plant potassium transport and plays a crucial role in plant growth and development, especially in economic crops. Although HAK/KUP/KT genes have been identified in many species, research on these genes in cotton is still quite rare. In this study, in total, 21, 24, 45, and 44 HAK/KUP/KT genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. Phylogenetic analysis showed that these genes were divided into four clusters. The G. hirsutum gene promoters contained diverse cis-regulatory elements, such as drought-responsive elements, low temperature-responsive elements, and other elements. The RNA-seq data and qRT-PCR results showed that HAK/KUP/KT genes had different expression patterns in fiber development. The qRT-PCR results of drought and NaCl treatment indicated that HAK/KUP/KT genes might play important roles in abiotic stress responses. These results will provide molecular insights into potassium transporter research in cotton.
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Affiliation(s)
- Xu Yang
- School of Agronomy Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Miaomiao Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Jianhua Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
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Potassium application to the cover crop prior to cotton planting as a fertilization strategy in sandy soils. Sci Rep 2020; 10:20404. [PMID: 33230214 PMCID: PMC7684316 DOI: 10.1038/s41598-020-77354-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/03/2020] [Indexed: 11/08/2022] Open
Abstract
Urochloa grasses are used as cover crops in tropical cropping systems under no-till to improve nutrient cycling. We hypothesized that potassium (K) applied to ruzigrass (Urochloa ruziziensis) grown before cotton in a sandy soil could be timely cycled and ensure nutrition, yield and quality of cotton cultivars with no need to split K application. Field experiments were performed with different K managements, applied to ruzigrass, to cotton grown after grass and without grass, or split as it is done conventionally. No yield differences were observed on K fertilized treatments. At 0 K, cotton yields were low, but they increased by 16% when ruzigrass was grown before, and short fiber content was lower when there was more K available. Ruzigrass grown before cotton increased micronaire as much as the application of 116 kg ha-1 of K without the grass. Fiber maturity was higher when K was applied to the grass or split in the grass and sidedressed in cotton. Growing ruzigrass before cotton allows for early K fertilization, i.e., application of all the fertilizer to de grass, since the nutrient is recycled, and cotton K nutrition is not harmed. Eventually K rates could be reduced as a result of higher efficiency of the systems.
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Wang Z, Yang Z, Li F. Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1706-1722. [PMID: 31111642 PMCID: PMC6686129 DOI: 10.1111/pbi.13167] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 05/11/2023]
Abstract
Trichomes are specialized epidermal cells and a vital plant organ that protect plants from various harms and provide valuable resources for plant development and use. Some key genes related to trichomes have been identified in the model plant Arabidopsis thaliana through glabrous mutants and gene cloning, and the hub MYB-bHLH-WD40, consisting of several factors including GLABRA1 (GL1), GL3, TRANSPARENT TESTA GLABRA1 (TTG1), and ENHANCER OF GLABRA3 (EGL3), has been established. Subsequently, some upstream transcription factors, phytohormones and epigenetic modification factors have also been studied in depth. In cotton, a very important fibre and oil crop globally, in addition to the key MYB-like factors, more important regulators and potential molecular mechanisms (e.g. epigenetic modifiers, distinct metabolic pathways) are being exploited during different fibre developmental stages. This occurs due to increased cotton research, resulting in the discovery of more complex regulation mechanisms from the allotetraploid genome of cotton. In addition, some conservative as well as specific mediators are involved in trichome development in other species. This study summarizes molecular mechanisms in trichome development and provides a detailed comparison of the similarities and differences between Arabidopsis and cotton, analyses the possible reasons for the discrepancy in identification of regulators, and raises future questions and foci for understanding trichome development in more detail.
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Affiliation(s)
- Zhi Wang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zuoren Yang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Fuguang Li
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
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Bashandy SR, Abd‐Alla MH, Bagy MMK. Biological Nitrogen Fixation and Biofertilizers as Ideal Potential Solutions for Sustainable Agriculture. INTEGRATING GREEN CHEMISTRY AND SUSTAINABLE ENGINEERING 2019:343-396. [DOI: 10.1002/9781119509868.ch12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Guo K, Tu L, He Y, Deng J, Wang M, Huang H, Li Z, Zhang X. Interaction between calcium and potassium modulates elongation rate in cotton fiber cells. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5161-5175. [PMID: 29045717 PMCID: PMC5853336 DOI: 10.1093/jxb/erx346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/14/2017] [Indexed: 05/20/2023]
Abstract
Calcium (Ca2+) is necessary for fiber cell development in cotton (Gossypium hirsutum), both as a cell wall structural component and for environmental signaling responses. It is also known that potassium (K+) plays a critical role in cotton fiber cell elongation. However, it is unclear whether Ca2+ integrates its activities with K+ to regulate fiber elongation. Here, we report the novel discovery that Ca2+ deficiency, when integrated with K+ signaling, promotes fiber elongation. Using inductively coupled plasma-mass spectrometry (ICP-MS), we determined dynamic profiles of the ionome in ovules and fibers at different developmental stages, and found that a high accumulation of macro-elements, but not Ca2+, was associated with longer fibers. Using an in vitro ovule culture system, we found that under Ca2+-deficient conditions, sufficient K+ (52 mM) rapidly induced ovule and fiber browning, while reduced K+ (2 or 27 mM) not only suppressed tissue browning but also altered fiber elongation. Reduced K+ also enhanced reactive oxygen species scavenging ability and maintained abscisic acid and jasmonic acid levels, which in turn compensated for Ca2+ deficiency. Ca2+ deficiency combined with reduced K+ (0 mM Ca2+ and 27 mM K+) produced longer fibers in cultured ovules, due to cell wall loosening by phytosulfokine (PSK), expansin (EXP), and xyloglucan endotransglycosylase/hydrolase (XTH), and an increase of the K+ content of fiber cells. Using transgenic cotton, we showed that the CBL-INTERACTING PROTEIN KINASE 6 (GhCIPK6) gene mediates the uptake of K+ under Ca2+-deficient conditions. This study establishes a new link between Ca2+, K+, and fiber elongation.
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Affiliation(s)
- Kai Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- Correspondence:
| | - Yonghui He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinwu Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hui Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhonghua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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Luan M, Tang RJ, Tang Y, Tian W, Hou C, Zhao F, Lan W, Luan S. Transport and homeostasis of potassium and phosphate: limiting factors for sustainable crop production. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3091-3105. [PMID: 27965362 DOI: 10.1093/jxb/erw444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Potassium (K) and phosphate (Pi) are both macronutrients essential for plant growth and crop production, but the unrenewable resources of phosphorus rock and potash have become limiting factors for food security. One critical measure to help solve this problem is to improve nutrient use efficiency (NUE) in plants by understanding and engineering genetic networks for ion uptake, translocation, and storage. Plants have evolved multiple systems to adapt to various nutrient conditions for growth and production. Within the NUE networks, transport proteins and their regulators are the primary players for maintaining nutrient homeostasis and could be utilized to engineer high NUE traits in crop plants. A large number of publications have detailed K+ and Pi transport proteins in plants over the past three decades. Meanwhile, the discovery and validation of their regulatory mechanisms are fast-track topics for research. Here, we provide an overview of K+ and Pi transport proteins and their regulatory mechanisms, which participate in the uptake, translocation, storage, and recycling of these nutrients in plants.
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Affiliation(s)
- Mingda Luan
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yumei Tang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Wang Tian
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Congong Hou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Fugeng Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Wenzhi Lan
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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