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Ijaz A, Anwar Z, Ali A, Ditta A, Shani MY, Haidar S, Wang B, Fang L, Khan SMUD, Khan MKR. Unraveling the genetic and molecular basis of heat stress in cotton. Front Genet 2024; 15:1296622. [PMID: 38919956 PMCID: PMC11196824 DOI: 10.3389/fgene.2024.1296622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/29/2024] [Indexed: 06/27/2024] Open
Abstract
Human activities and climate change have resulted in frequent and intense weather fluctuations, leading to diverse abiotic stresses on crops which hampers greatly their metabolic activities. Heat stress, a prevalent abiotic factor, significantly influences cotton plant biological activities resulting in reducing yield and production. We must deepen our understanding of how plants respond to heat stress across various dimensions, encompassing genes, RNAs, proteins, metabolites for effective cotton breeding. Multi-omics methods, primarily genomics, transcriptomics, proteomics, metabolomics, and phenomics, proves instrumental in studying cotton's responses to abiotic stresses. Integrating genomics, transcriptomics, proteomics, and metabolomic is imperative for our better understanding regarding genetics and molecular basis of heat tolerance in cotton. The current review explores fundamental omics techniques, covering genomics, transcriptomics, proteomics, and metabolomics, to highlight the progress made in cotton omics research.
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Affiliation(s)
- Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Allah Ditta
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Muhammad Yousaf Shani
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Sajjad Haidar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Boahua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Liu Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | | | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
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Hua J, Zhong C, Chen W, Fu J, Wang J, Wang Q, Zhu G, Li Y, Tao Y, Zhang M, Dong Y, Lu S, Liu W, Qiang J. Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides). BMC Genomics 2024; 25:64. [PMID: 38229016 DOI: 10.1186/s12864-024-09962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China's freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. RESULTS We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). CONCLUSIONS Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.
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Grants
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- No. JBGS [2021] 130 Project of Seed Industry Revitalization in Jiangsu Province, China
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- 2022-ZYXT-07 Major Technology Collaborative Promotion Plan for Largemouth bass Industry in Jiangsu Province
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- NO. 2023JBFR02 the central public-interest scientific institution basal research fund, freshwater fisheries research center, CAFS
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
- No. SNG2021009 the Suzhou Science and Technology Program
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Affiliation(s)
- Jixiang Hua
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Chunyi Zhong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenhua Chen
- Suzhou Aquatic Technology Extension Station, Suzhou, 215004, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jian Wang
- Guangxi Xinjian Investment Group Limited Company, Hechi, 530201, China
| | - Qingchun Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Geyan Zhu
- Suzhou Aquatic Technology Extension Station, Suzhou, 215004, China
| | - Yan Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yifan Tao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Maoyou Zhang
- Suzhou Aquatic Technology Extension Station, Suzhou, 215004, China
| | - Yalun Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Siqi Lu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenting Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jun Qiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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Yue GH, Tay YX, Wong J, Shen Y, Xia J. Aquaculture species diversification in China. AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture. Animal 2022; 16:100642. [PMID: 36183431 PMCID: PMC9553672 DOI: 10.1016/j.animal.2022.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022] Open
Abstract
The extent of application of genetic technologies to aquaculture production varies widely by species and geography. Achieving a more universal application of seed derived from scientifically based breeding programmes is an important goal in order to meet increasing global demands for seafood production. This article reviews the status of genetic technologies across the world’s top 10 highly produced species. Opportunities and barriers to achieving broad-scale uptake of genetic technologies in global aquaculture are discussed. A future outlook for potential disruptive genetic technologies and how they might affect global aquaculture production is given.
Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.
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Breeding Asian seabass to increase survival against big belly disease and growth. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Babu KM, Bentall D, Ashton DT, Puklowski M, Fantham W, Lin HT, Tuckey NPL, Wellenreuther M, Jesson LK. Computer vision in aquaculture: a case study of juvenile fish counting. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2101484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Krishna Moorthy Babu
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Daniel Bentall
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - David T. Ashton
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
| | - Morgan Puklowski
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
| | - Warren Fantham
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
| | - Harris T. Lin
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | | | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
- The University of Auckland, Auckland, New Zealand
| | - Linley K. Jesson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
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Xia J, Gomes GB, Yue GH. Editorial special issue: Emerging and disruptive technologies for aquaculture. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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