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Rehman A, Tian C, Li X, Wang X, Li H, He S, Jiao Z, Qayyum A, Du X, Peng Z. GhiPLATZ17 and GhiPLATZ22, zinc-dependent DNA-binding transcription factors, promote salt tolerance in upland cotton. PLANT CELL REPORTS 2024; 43:140. [PMID: 38740586 DOI: 10.1007/s00299-024-03178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE The utilization of transcriptome analysis, functional validation, VIGS, and DAB techniques have provided evidence that GhiPLATZ17 and GhiPLATZ22 play a pivotal role in improving the salt tolerance of upland cotton. PLATZ (Plant AT-rich sequences and zinc-binding proteins) are known to be key regulators in plant growth, development, and response to salt stress. In this study, we comprehensively analyzed the PLATZ family in ten cotton species in response to salinity stress. Gossypium herbaceum boasts 25 distinct PLATZ genes, paralleled by 24 in G. raimondii, 25 in G. arboreum, 46 in G. hirsutum, 48 in G. barbadense, 43 in G. tomentosum, 67 in G. mustelinum, 60 in G. darwinii, 46 in G. ekmanianum, and a total of 53 PLATZ genes attributed to G. stephensii. The PLATZ gene family shed light on the hybridization and allopolyploidy events that occurred during the evolutionary history of allotetraploid cotton. Ka/Ks analysis suggested that the PLATZ gene family underwent intense purifying selection during cotton evolution. Analysis of synteny and gene collinearity revealed a complex pattern of segmental and dispersed duplication events to expand PLATZ genes in cotton. Cis-acting elements and gene expressions revealed that GhiPLATZ exhibited salt stress resistance. Transcriptome analysis, functional validation, virus-induced gene silencing (VIGS), and diaminobenzidine staining (DAB) demonstrated that GhiPLATZ17 and GhiPLATZ22 enhance salt tolerance in upland cotton. The study can potentially advance our understanding of identifying salt-resistant genes in cotton.
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Affiliation(s)
- Abdul Rehman
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Chunyan Tian
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiawen Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoyang Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Hongge Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Shoupu He
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China
| | - Zhen Jiao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 66000, Pakistan
| | - Xiongming Du
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
| | - Zhen Peng
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572025, China.
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Zhang T, Xie Z, Zhou J, Feng H, Zhang T. Temperature impacts on cotton yield superposed by effects on plant growth and verticillium wilt infection in China. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:199-209. [PMID: 38010415 DOI: 10.1007/s00484-023-02583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
China produces and consumes the largest amount of cotton, playing a critical role in the world's fiber and textile industries. Theoretically, an increase in temperature poses a complex set of impacts on both cotton and pathogen diseases. However, empirical evidence regarding the overall effect on regional cotton yield in China is currently lacking. In this study, we employ county-level cotton statistics and degree-day indices (n = 30,502) to demonstrate a temperature effect on cotton yield, influenced by both direct temperature effects and indirect effects on verticillium wilt infection in China. Our findings indicate that temperatures between the base growing temperature (15 °C) and the optimal infection threshold for cotton wilt disease (25 °C) reduce cotton yield. However, beyond this threshold, when disease infection is significantly limited, higher temperatures become beneficial. Temperatures exceeding 32 °C causes heat stress, which dominates and drives a decline in yield. Furthermore, we provide a risk assessment of warming on cotton in future climate scenarios. Our model projections reveal an overall decrease in cotton yield ranging from 6.2 to 30.6%, accompanied by amplified heat stress (resulting in a yield decrease of 11.6 to 48.7%) but a reduced threat of verticillium wilt (yield increase of 8.2 to 23.6%) in future. Particularly, the Northwest Region, currently responsible for 80% of cotton production, is expected to be particularly vulnerable. This study emphasizes the importance of investing in long-term technological advancements such as cotton heat-tolerance breeding and redistributing cotton growing areas.
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Affiliation(s)
- Tianyi Zhang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China.
- Collaborative Innovation Center On Forecast and Evaluation of Meteorological Disasters, Nanjing University of Information Science & Technology, Nanjing, China.
| | - Zongming Xie
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Key Laboratory of Cotton Biology and Genetic Breeding in the Northwest Inland Cotton Production Region, Ministry of Agriculture and Rural Affairs, Shihezi, China
| | - Jinglong Zhou
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Hongjie Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Tao Zhang
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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Yu H, Guo Q, Ji W, Wang H, Tao J, Xu P, Chen X, Ali W, Wu X, Shen X, Xie Y, Xu Z. Transcriptome Expression Profiling Reveals the Molecular Response to Salt Stress in Gossypium anomalum Seedlings. PLANTS (BASEL, SWITZERLAND) 2024; 13:312. [PMID: 38276767 PMCID: PMC10819910 DOI: 10.3390/plants13020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
Some wild cotton species are remarkably tolerant to salt stress, and hence represent valuable resources for improving salt tolerance of the domesticated allotetraploid species Gossypium hirsutum L. Here, we first detected salt-induced stress changes in physiological and biochemical indexes of G. anomalum, a wild African diploid cotton species. Under 350 mmol/L NaCl treatment, the photosynthetic parameters declined significantly, whereas hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents increased. Catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activity and proline (PRO) content also significantly increased, reaching peak values at different stages of salt stress. We used RNA-Seq to characterize 15,476 differentially expressed genes in G. anomalum roots after 6, 12, 24, 72, and 144 h of salt stress. Gene Ontology enrichment analysis revealed these genes to be related to sequence-specific DNA and iron ion binding and oxidoreductase, peroxidase, antioxidant, and transferase activity; meanwhile, the top enriched pathways from the Kyoto Encyclopedia of Genes and Genomes database were plant hormone signal transduction, phenylpropanoid biosynthesis, fatty acid degradation, carotenoid biosynthesis, zeatin biosynthesis, starch and sucrose metabolism, and MAPK signaling. A total of 1231 transcription factors were found to be expressed in response to salt stress, representing ERF, MYB, WRKY, NAC, C2H2, bZIP, and HD-ZIP families. Nine candidate genes were validated by quantitative real-time PCR and their expression patterns were found to be consistent with the RNA-Seq data. These data promise to significantly advance our understanding of the molecular response to salt stress in Gossypium spp., with potential value for breeding applications.
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Affiliation(s)
- Huan Yu
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wei Ji
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Heyang Wang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Jingqi Tao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xianglong Chen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wuzhimu Ali
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xuan Wu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Yinfeng Xie
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
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Joshi B, Singh S, Tiwari GJ, Kumar H, Boopathi NM, Jaiswal S, Adhikari D, Kumar D, Sawant SV, Iquebal MA, Jena SN. Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1252746. [PMID: 37941674 PMCID: PMC10630025 DOI: 10.3389/fpls.2023.1252746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 11/10/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.
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Affiliation(s)
- Babita Joshi
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Singh
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gopal Ji Tiwari
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
| | - Harish Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Narayanan Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dibyendu Adhikari
- Plant Ecology and Climate Change Science, CSIR-National Botanical Research Institute, Lucknow, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samir V. Sawant
- Molecular Biology & Biotechnology, CSIR-National Botanical Research Institute, Lucknow, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Satya Narayan Jena
- Plant Genetic Resources and Improvement, CSIR-National Botanical Research Institute, Lucknow, India
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5
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Ren W, Chen L. Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings. Genes (Basel) 2023; 14:1825. [PMID: 37761965 PMCID: PMC10531431 DOI: 10.3390/genes14091825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland cotton Gossypium hirsutum L. was utilized to determine its salt tolerance. Foliar treatment with the β-alanine solution at different concentrations was applied to the seedlings stressed with 0.8% NaCl solution. On the 10th day of treatment, samples were collected for transcriptome and metabolome analyses. β-alanine solution at a concentration of 25 mM was found to be the best treatment with the lowest mortality rate and highest plant height and above-ground biomass under salt stress. Both differentially expressed genes and accumulated metabolites analyses showed improved tolerance of treated seedlings. The photosynthetic efficiency improved in seedlings due to higher expression of photosynthesis-antenna proteins and activation of hormones signal transduction after treatment with β-alanine. Highly expressed transcription factors observed were MYB, HD-ZIP, ARF, MYC, EREB, DELLA, ABF, H2A, H4, WRKY, and HK involved in the positive regulation of salinity tolerance in β-alanine-treated seedlings. Furthermore, compared to the control, the high accumulation of polyamines, coumarins, organic acids, and phenolic compounds in the β-alanine-treated seedlings helped regulate cellular antioxidant (glutathione and L-Cysteine) production. Hence, to improve salt tolerance and productivity in cotton, foliar application of β-alanine at the seedling stage can be a valuable management practice.
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Affiliation(s)
- Wei Ren
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China;
- Fukang Station of Desert Ecology, Chinese Academy of Sciences, Fukang 831505, China
| | - Li Chen
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China;
- Fukang Station of Desert Ecology, Chinese Academy of Sciences, Fukang 831505, China
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Ye Y, Wang P, Zhang M, Abbas M, Zhang J, Liang C, Wang Y, Wei Y, Meng Z, Zhang R. UAV-based time-series phenotyping reveals the genetic basis of plant height in upland cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:937-951. [PMID: 37154288 DOI: 10.1111/tpj.16272] [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: 01/18/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
Plant height (PH) is an important agronomic trait affecting crop architecture, biomass, resistance to lodging and mechanical harvesting. Elucidating the genetic governance of plant height is crucial because of the global demand for high crop yields. However, during the rapid growth period of plants the PH changes a lot on a daily basis, which makes it difficult to accurately phenotype the trait by hand on a large scale. In this study, an unmanned aerial vehicle (UAV)-based remote-sensing phenotyping platform was applied to obtain time-series PHs of 320 upland cotton accessions in three different field trials. The results showed that the PHs obtained from UAV images were significantly correlated with ground-based manual measurements, for three trials (R2 = 0.96, 0.95 and 0.96). Two genetic loci on chromosomes A01 and A11 associated with PH were identified by genome-wide association studies (GWAS). GhUBP15 and GhCUL1 were identified to influence PH in further analysis. We obtained a time series of PH values for three field conditions based on remote sensing with UAV. The key genes identified in this study are of great value for the breeding of ideal plant architecture in cotton.
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Affiliation(s)
- Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Man Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaxin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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7
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Xu N, Chen B, Cheng Y, Su Y, Song M, Guo R, Wang M, Deng K, Lan T, Bao S, Wang G, Guo Z, Yu L. Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean. Genes (Basel) 2023; 14:1294. [PMID: 37372474 DOI: 10.3390/genes14061294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132-346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.
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Affiliation(s)
- Ning Xu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Bingru Chen
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yuxin Cheng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yufei Su
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Mengyuan Song
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Rongqiu Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Minghai Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Kunpeng Deng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Tianjiao Lan
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Shuying Bao
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Guifang Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Zhongxiao Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Lihe Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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8
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Anwar Z, Ijaz A, Ditta A, Wang B, Liu F, Khan SMUD, Haidar S, Hassan HM, Khan MKR. Genomic Dynamics and Functional Insights under Salt Stress in Gossypium hirsutum L. Genes (Basel) 2023; 14:1103. [PMID: 37239463 PMCID: PMC10218025 DOI: 10.3390/genes14051103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead to delayed flowering, a reduced number of fruiting positions, shedding of fruits, decreased boll weight, and yellowing of fiber, all of which have an adverse effect on the yield and quality of the seed cotton. However, sensitivity toward salt stress is dependent on the salt type, cotton growth phase, and genotype. As the threat of salt stress continues to grow, it is crucial to gain a comprehensive understanding of the mechanisms underlying salt tolerance in plants and to identify potential avenues for enhancing the salt tolerance of cotton. The emergence of marker-assisted selection, in conjunction with next-generation sequencing technologies, has streamlined cotton breeding efforts. This review begins by providing an overview of the causes of salt stress in cotton, as well as the underlying theory of salt tolerance. Subsequently, it summarizes the breeding methods that utilize marker-assisted selection, genomic selection, and techniques for identifying elite salt-tolerant markers in wild species or mutated materials. Finally, novel cotton breeding possibilities based on the approaches stated above are presented and debated.
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Affiliation(s)
- Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
| | - Allah Ditta
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong 226000, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang 455000, China;
| | - Sana Muhy-Ud-Din Khan
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
| | - Sajjad Haidar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Hafiz Mumtaz Hassan
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 45650, Pakistan; (Z.A.); (A.I.); (A.D.); (S.M.-U.-D.K.); (S.H.); (H.M.H.)
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
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9
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Gao Q, Wang H, Yin X, Wang F, Hu S, Liu W, Chen L, Dai X, Liang M. Identification of Salt Tolerance Related Candidate Genes in 'Sea Rice 86' at the Seedling and Reproductive Stages Using QTL-Seq and BSA-Seq. Genes (Basel) 2023; 14:458. [PMID: 36833384 PMCID: PMC9956910 DOI: 10.3390/genes14020458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Salt stress seriously affects plant growth and development and reduces the yield of rice. Therefore, the development of salt-tolerant high-yielding rice cultivars through quantitative trait locus (QTL) identification and bulked segregant analysis (BSA) is the main focus of molecular breeding projects. In this study, sea rice (SR86) showed greater salt tolerance than conventional rice. Under salt stress, the cell membrane and chlorophyll were more stable and the antioxidant enzyme activity was higher in SR86 than in conventional rice. Thirty extremely salt-tolerant plants and thirty extremely salt-sensitive plants were selected from the F2 progenies of SR86 × Nipponbare (Nip) and SR86 × 9311 crosses during the whole vegetative and reproductive growth period and mixed bulks were generated. Eleven salt tolerance related candidate genes were located using QTL-seq together with BSA. Real time quantitative PCR (RT-qPCR) analysis showed that LOC_Os04g03320.1 and BGIOSGA019540 were expressed at higher levels in the SR86 plants than in Nip and 9311 plants, suggesting that these genes are critical for the salt tolerance of SR86. The QTLs identified using this method could be effectively utilized in future salt tolerance breeding programs, providing important theoretical significance and application value for rice salt tolerance breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Manzhong Liang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Hunan Normal University, Changsha 410081, China
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10
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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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11
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Ren X, Fan J, Li X, Shan Y, Wang L, Ma L, Li Y, Li X. Application of RNA sequencing to understand the response of rice seedlings to salt-alkali stress. BMC Genomics 2023; 24:21. [PMID: 36641451 PMCID: PMC9840837 DOI: 10.1186/s12864-023-09121-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Salt-alkali stress represents one of the most stressful events with deleterious consequences for plant growth and crop productivity. Despite studies focusing on the effects of salt-alkali stress on morphology and physiology, its molecular mechanisms remain unclear. Here, we employed RNA-sequencing (RNA-seq) to understand how Na2CO3 stress inhibits rice seedling growth. RESULTS Na2CO3 stress significantly inhibited the growth of rice seedlings. Through RNA-seq, many differentially expressed genes (DEGs) were shown to be potentially involved in the rice seedling response to salt-alkali stress. After 1-day and 5-day treatments, RNA-seq identified 1780 and 2315 DEGs in the Na2CO3-treated versus -untreated rice seedling shoots, respectively. According to the gene ontology enrichment and the Kyoto Encylopedia of Genes and Genomes annotation of DEGs, the growth-inhibition processes associated with salt-alkali stress involve a myriad of molecular events, including biosynthesis and metabolism, enzyme activity, and binding, etc. CONCLUSION: Collectively, the transcriptome analyses in the present work revealed several potential key regulators of plant response to salt-alkali stress, and might pave a way to improve salt-alkali stress tolerance in rice.
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Affiliation(s)
- Xiaoning Ren
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Jiahui Fan
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Xin Li
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Yu Shan
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Lanlan Wang
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Lianju Ma
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Yueying Li
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
| | - Xuemei Li
- grid.263484.f0000 0004 1759 8467College of Life Science, Shenyang Normal University, 110034 Shenyang, China
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12
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Transcriptomic Analysis Provides Insight into the ROS Scavenging System and Regulatory Mechanisms in Atriplex canescens Response to Salinity. Int J Mol Sci 2022; 24:ijms24010242. [PMID: 36613685 PMCID: PMC9820716 DOI: 10.3390/ijms24010242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Atriplex canescens is a representative halophyte with excellent tolerance to salt. Previous studies have revealed certain physiological mechanisms and detected functional genes associated with salt tolerance. However, knowledge on the ROS scavenging system and regulatory mechanisms in this species when adapting to salinity is limited. Therefore, this study further analyzed the transcriptional changes in genes related to the ROS scavenging system and important regulatory mechanisms in A. canescens under saline conditions using our previous RNA sequencing data. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in signal transduction- and reactive oxygen species-related biological processes, including "response to oxidative stress", "oxidoreductase activity", "protein kinase activity", "transcription factor activity", and "plant hormone signal transduction". Further analyses suggested that the transcription abundance of many genes involved in SOD, the AsA-GSH cycle, the GPX pathway, PrxR/Trx, and the flavonoid biosynthesis pathway were obviously enhanced. These pathways are favorable for scavenging excessive ROS induced by salt and maintaining the integrity of the cell membrane. Meanwhile, many vital transcription factor genes (WRKY, MYB, ZF, HSF, DREB, and NAC) exhibited increased transcripts, which is conducive to dealing with saline conditions by regulating downstream salt-responsive genes. Furthermore, a larger number of genes encoding protein kinases (RLK, CDPK, MAPK, and CTR1) were significantly induced by saline conditions, which is beneficial to the reception/transduction of salt-related signals. This study describes the abundant genetic resources for enhancing the salt tolerance in salt-sensitive plants, especially in forages and crops.
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Yasir M, Kanwal HH, Hussain Q, Riaz MW, Sajjad M, Rong J, Jiang Y. Status and prospects of genome-wide association studies in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1019347. [PMID: 36330239 PMCID: PMC9623101 DOI: 10.3389/fpls.2022.1019347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.
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Affiliation(s)
- Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Hafiza Hamrah Kanwal
- School of Computer Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
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14
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Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum. Int J Biol Macromol 2022; 224:1101-1117. [DOI: 10.1016/j.ijbiomac.2022.10.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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15
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Saud S, Wang L. Mechanism of cotton resistance to abiotic stress, and recent research advances in the osmoregulation related genes. FRONTIERS IN PLANT SCIENCE 2022; 13:972635. [PMID: 36061778 PMCID: PMC9428623 DOI: 10.3389/fpls.2022.972635] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/25/2022] [Indexed: 05/27/2023]
Abstract
Abiotic stress is an important factor affecting the normal growth and development of plants and crop yield. To reduce the impact of abiotic adversity on cotton growth and development, the material basis of cotton resistance and its physiological functions are analyzed at the molecular level. At the same time, the use of genetic engineering methods to recombine resistance genes has become a hot spot in cotton resistance research. This paper provides an overviews of the resistance mechanism of cotton against the threat of non-biological adversity, as well as the research progress of osmoregulation-related genes, protein-acting genes, and transcription regulatory factor genes in recent years, and outlines the explored gene resources in cotton resistance genetic engineering, with the aim to provide ideas and reference bases for future research on cotton resistance.
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16
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Rai KK. Integrating speed breeding with artificial intelligence for developing climate-smart crops. Mol Biol Rep 2022; 49:11385-11402. [PMID: 35941420 PMCID: PMC9360691 DOI: 10.1007/s11033-022-07769-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION In climate change, breeding crop plants with improved productivity, sustainability, and adaptability has become a daunting challenge to ensure global food security for the ever-growing global population. Correspondingly, climate-smart crops are also the need to regulate biomass production, which is imperative for the maintenance of ecosystem services worldwide. Since conventional breeding technologies for crop improvement are limited, time-consuming, and involve laborious selection processes to foster new and improved crop varieties. An urgent need is to accelerate the plant breeding cycle using artificial intelligence (AI) to depict plant responses to environmental perturbations in real-time. MATERIALS AND METHODS The review is a collection of authorized information from various sources such as journals, books, book chapters, technical bulletins, conference papers, and verified online contents. CONCLUSIONS Speed breeding has emerged as an essential strategy for accelerating the breeding cycles of crop plants by growing them under artificial light and temperature conditions. Furthermore, speed breeding can also integrate marker-assisted selection and cutting-edged gene-editing tools for early selection and manipulation of essential crops with superior agronomic traits. Scientists have recently applied next-generation AI to delve deeper into the complex biological and molecular mechanisms that govern plant functions under environmental cues. In addition, AIs can integrate, assimilate, and analyze complex OMICS data sets, an essential prerequisite for successful speed breeding protocol implementation to breed crop plants with superior yield and adaptability.
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Affiliation(s)
- Krishna Kumar Rai
- Centre of Advanced Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University (BHU), 221005, Varanasi, Uttar Pradesh, India.
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Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-wide Association Study of Thai Rice Populations. Int J Mol Sci 2022; 23:ijms23031842. [PMID: 35163767 PMCID: PMC8836775 DOI: 10.3390/ijms23031842] [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: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 02/01/2023] Open
Abstract
Salt stress is a major limiting factor in crop production and yield in many regions of the world. The objective of this study was to identify the genes responsible for salt tolerance in Thai rice populations. We performed a genome-wide association study with growth traits, relative water content, and cell membrane stability at the seedling stage, and predicted 25 putative genes. Eleven of them were located within previously reported salt-tolerant QTLs (ST-QTLs). OsCRN, located outside the ST-QTLs, was selected for gene characterization using the Arabidopsis mutant line with T-DNA insertion in the orthologous gene. Mutations in the AtCRN gene led to the enhancement of salt tolerance by increasing the ability to maintain photosynthetic pigment content and relative water content, while the complemented lines with ectopic expression of OsCRN showed more susceptibility to salt stress detected by photosynthesis performance. Moreover, the salt-tolerant rice varieties showed lower expression of this gene than the susceptible rice varieties under salt stress conditions. The study concludes that by acting as a negative regulator, OsCRN plays an important role in salt tolerance in rice.
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18
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Shaheen M, Abdul Rauf H, Taj MA, Yousaf Ali M, Bashir MA, Atta S, Farooq H, Alajmi RA, Hashem M, Alamri S. Path analysis based on genetic association of yield components and insects pest in upland cotton varieties. PLoS One 2021; 16:e0260971. [PMID: 34969047 PMCID: PMC8717984 DOI: 10.1371/journal.pone.0260971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/19/2021] [Indexed: 12/02/2022] Open
Abstract
Gossypium hirsutum L. is also called upland cotton or Mexican cotton. It is the most widely cultivated species of cotton in the whole world. Globally, about 90% of all cotton production comes from the cultivars derived from this species. Some genetic parameters like monopodial branches per plant, sympodial branches per plant, sympodial branch length, bolls per plant, boll weight, sympo-boll distance, Ginning Out Turn%, staple length (rg = 0.9199**), and fiber strength along with seed cotton yield were evaluated for their potential utilization via selection in seed cotton yield improvement. Significant positive genetic correlations were estimated for monopodial branches per plant (rg = 0.9722**), sympodial branches per plant (rg = 0.7098**), sympodial branch length (rg = 0.617**), bolls per plant (rg = 0.8271**), boll weight (rg = 0.8065**), sympo-boll distance (rg = 0.6507**), Ginning Out Turn (GOT)% (rg = 0.7541**), staple length (rg = 0.9199**), and fiber strength (rg = 0.7534**) with seed cotton yield. A path analysis of all the yield traits under study revealed strong positive direct effects of monopodial branch length (1.1556), sympo-boll distance (0.8173) and staple length (0.7633), while plant height exerted a highly strong direct negative effect (-1.2096) on yield. It is concluded that a direct selection based on monopodial branch length and sympo-boll distance, and staple length is effective, whereas, monopodial branch length, and sympodial branch length are good selection indicators via bolls per plant for yield improvement in cotton.
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Affiliation(s)
| | | | - Muhammad Ahmed Taj
- Rural Health center 222EB, Health department Govt. of Punjab, District Vehari, Pakistan
| | - Muhammad Yousaf Ali
- Research & Education Development Department, Rural Education and Economic Development Society (REEDS) Pakistan, Rahim Yar Khan, Punjab, Pakistan
- * E-mail:
| | - Muhammad Amjad Bashir
- Department of plant protection faculty of agricultural sciences, Ghazi University, Dera Ghazi Khan, Punjab, Pakistan
| | - Sagheer Atta
- Department of plant protection faculty of agricultural sciences, Ghazi University, Dera Ghazi Khan, Punjab, Pakistan
| | - Hasnain Farooq
- Department of Environmental Sciences, University of California, Riverside, CA, United States of America
- Department of Forestry, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Reem A. Alajmi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabi
| | - Mohamed Hashem
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Faculty of Science, Botany and Microbiology Department, Assiut University, Assiut, Egypt
| | - Saad Alamri
- Faculty of Science, Botany and Microbiology Department, Assiut University, Assiut, Egypt
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19
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Zheng J, Zhang Z, Gong Z, Liang Y, Sang Z, Xu Y, Li X, Wang J. Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010097. [PMID: 35009100 PMCID: PMC8747425 DOI: 10.3390/plants11010097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/01/2021] [Accepted: 12/11/2021] [Indexed: 06/01/2023]
Abstract
Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline-alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.
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Affiliation(s)
- Juyun Zheng
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Zeliang Zhang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Zhaolong Gong
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Yajun Liang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Zhiwei Sang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology (China), Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang 455000, China;
| | - Xueyuan Li
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Junduo Wang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
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20
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Zhou T, Yue CP, Liu Y, Zhang TY, Huang JY, Hua YP. Multiomics reveal pivotal roles of sodium translocation and compartmentation in regulating salinity resistance in allotetraploid rapeseed. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5687-5708. [PMID: 33989425 DOI: 10.1093/jxb/erab215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
The large size and complexity of the allotetraploid rapeseed (Brassica napus) genome present huge challenges for understanding salinity resistance in this important crop. In this study, we identified two rapeseed genotypes with significantly different degrees of salinity resistance and examined the underlying mechanisms using an integrated analysis of phenomics, ionomics, genomics, and transcriptomics. Under salinity, a higher accumulation of osmoregulation substances and better root-system architecture was observed in the resistant genotype, H159, than in the sensitive one, L339. A lower shoot Na+ concentration and a higher root vacuolar Na+ concentration indicated lower root-to-shoot translocation and higher compartmentation in H159 than in L339. Whole-genome re-sequencing (WGRS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport. Combining ionomics with transcriptomics identified plasma membrane-localized BnaC2.HKT1;1 and tonoplast-localized BnaC5.NHX2 as the central factors regulating differential root xylem unloading and vacuolar sequestration of Na+ between the two genotypes. Identification of polymorphisms by WGRS and PCR revealed two polymorphic MYB-binding sites in the promoter regions that might determine the differential gene expression of BnaC2.HKT1;1 and BnaC5.NHX2. Our multiomics approach thus identified core transporters involved in Na+ translocation and compartmentation that regulate salinity resistance in rapeseed. Our results may provide elite gene resources for the improvement of salinity resistance in this crop, and our multiomics approach can be applied to other similar studies.
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Affiliation(s)
- Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jin-Yong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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