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Li J, Yang Y, Sun X, Liu R, Xia W, Shi P, Zhou L, Wang Y, Wu Y, Lei X, Xiao Y. Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm. FRONTIERS IN PLANT SCIENCE 2022; 13:885418. [PMID: 35720541 PMCID: PMC9201816 DOI: 10.3389/fpls.2022.885418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a tropical woody oil crop of the palm family and is known as "the oil king of the world," but its palm oil contains about 50% palmitic acid, which is considered unhealthy for humans. Intron polymorphisms (IP) are highly efficient and easily examined molecular markers located adjacent to exon regions of functional genes, thus may be associated with targeted trait variation. In order to speed up the breeding of oil palm fatty acid composition, the current study identified a total of 310 introns located within 52 candidate genes involved in fatty acid biosynthesis in the oil palm genome. Based on the intron sequences, 205 primer pairs were designed, 64 of which showed polymorphism among 70 oil palm individuals. Phenotypic variation of fatty acid content in the 70 oil palm individuals was also investigated. Association analysis revealed that 13 IP markers were significantly associated with fatty acid content variation, and these IP markers were located on chromosomes 2, 5, 6, 8, 9, and 10 of oil palm. The development of such IP markers may be useful for the genetic improvement of fatty acid composition in oil palm.
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Affiliation(s)
- Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Xiwei Sun
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Rui Liu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Wei Xia
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Peng Shi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yong Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Xintao Lei
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Kumar P, Parveen A, Sharma H, Rahim MS, Mishra A, Kumar P, Shah K, Rishi V, Roy J. Understanding the regulatory relationship of abscisic acid and bZIP transcription factors towards amylose biosynthesis in wheat. Mol Biol Rep 2021; 48:2473-2483. [PMID: 33834358 DOI: 10.1007/s11033-021-06282-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
Starch is biosynthesized during seed development and this process is regulated by many bZIP proteins in bread wheat. Abscisic acid (ABA), an important phyto-hormone involved in various physiological processes mediated by bZIPs in plants including seed development. The 'Group A' TabZIP transcription factors play important roles in the ABA signaling pathway in Arabidopsis, rice and other cereal crops but their role in regulation of amylose biosynthesis in wheat is limited. In this study 83 'Group A' TabZIPs were characterized by gene expression analysis in wheat amylose mutants. A set of 17 TabZIPs was selected on the basis of differential expression (> 2 fold) in low and high amylose mutants from RNA-seq data and validated by qRT PCR. Based on qRT PCR and correlation analysis out of the 17 TabZIPs six differentially expressed candidate TabZIPs were identified, involving in high amylose biosynthesis. The TabZIP175.2, identified as upregulated in all high amylose lines and TabZIP90.2, TabZIP129.1, TabZIP132.2, TabZIP143 and TabZIP159.2 were found downregulated in all low amylose lines, after exogenous supply of ABA. Proximal promoter analysis of starch pathway genes revealed the presence of ABA-responsive elements (ABREs) that are putative binding sites for bZIPs. Collectively, these findings indicated the involvement of putative six candidate TabZIPs as transcriptional regulators of amylose related genes via an ABA-dependent pathway in wheat. This study could help the investigators to make an informed decision to edit wheat genome for high/low amylose content using gene-editing technologies.
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Affiliation(s)
- Pankaj Kumar
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, 160014, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Mohammed Saba Rahim
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Prashant Kumar
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Koushik Shah
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.
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Genome-wide identification and characterization of novel non-coding RNA-derived SSRs in wheat. Mol Biol Rep 2020; 47:6111-6125. [PMID: 32794134 DOI: 10.1007/s11033-020-05687-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/26/2020] [Indexed: 02/02/2023]
Abstract
Expression of eukaryotic genes is largely regulated by non-coding RNAs (ncRNA). Sequence variations in the regulatory RNAs may have critical biological consequences including transcriptional and post-transcriptional gene regulation. ncRNA-derived markers thus can be proved useful in molecular breeding, QTL mapping and association studies for trait dissection. In present study, we identified a total of 661 SSRs dwelling in pre-miRNA (15), small nuclear RNA (25) and lncRNA (621). Of these, 46 were validated and 100% amplification success was observed in selected wheat genotypes. A set of 36 ncRNA-SSRs markers was utilized for genetic variability assessment in forty-eight Indian wheat genotypes (which includes bread wheat, durum wheat and relatives). Number of alleles ranged from 1 to 4 with an average of two alleles per SSR locus. Mean PIC, observed heterozygosity and Shannon information index were found to be 0.258, 0.37 and 0.476 which suggests ncRNA-SSRs show higher polymorphism compared to genic SSRs but lower polymorphism compared to genomic SSRs. Thirty-six ncRNA-SSRs showed transferability ranging from 42.1% to 100%. Average genetic dissimilarity among wheat genotypes was found to be 0.29 based on Jaccard's dissimilarity. This is the first report of ncRNA-SSRs in wheat which will be useful for molecular breeding and genetic improvement of wheat.
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