Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm
Abstract Background Genomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. Howe...
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04473-8 |
| _version_ | 1797453329145528320 |
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| author | Xiaomei Dong Haishan Luo Wenjing Bi Hanyu Chen Shuai Yu Xiaoyu Zhang Yuxin Dai Xipeng Cheng Yupeng Xing Xiaoqin Fan Yanbin Zhu Yanling Guo Dexuan Meng |
| author_facet | Xiaomei Dong Haishan Luo Wenjing Bi Hanyu Chen Shuai Yu Xiaoyu Zhang Yuxin Dai Xipeng Cheng Yupeng Xing Xiaoqin Fan Yanbin Zhu Yanling Guo Dexuan Meng |
| author_sort | Xiaomei Dong |
| collection | DOAJ |
| description | Abstract Background Genomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. However, there have been few studies on the functional analysis of allele-specific imprinted genes. Results Here, we generated three reciprocal crosses among the B73, Mo17 and CAU5 inbred lines. Based on the transcriptome-wide analysis of allele-specific expression using RNA sequencing technology, 305 allele-specific imprinting genes (ASIGs) were identified in embryos, and 655 ASIGs were identified in endosperms from three maize F1 hybrids. Of these ASIGs, most did not show consistent maternal or paternal bias between the same tissue from different hybrids or different tissues from one hybrid cross. By gene ontology (GO) analysis, five and eight categories of GO exhibited significantly higher functional enrichments for ASIGs identified in embryo and endosperm, respectively. These functional categories indicated that ASIGs are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Finally, the mutation and overexpression of one ASIG (Zm305) affected the length and width of the kernel. Conclusion In this study, our data will be helpful in gaining further knowledge of genes exhibiting allele-specific imprinting patterns in seeds. The gain- and loss-of-function phenotypes of ASIGs associated with agronomically important seed traits provide compelling evidence for ASIGs as crucial targets to optimize seed traits in crop plants. |
| first_indexed | 2024-03-09T15:21:15Z |
| format | Article |
| id | doaj.art-362b1d737be34e7abb43188aa920fe2d |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-09T15:21:15Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-362b1d737be34e7abb43188aa920fe2d2023-11-26T12:47:28ZengBMCBMC Plant Biology1471-22292023-10-0123111210.1186/s12870-023-04473-8Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endospermXiaomei Dong0Haishan Luo1Wenjing Bi2Hanyu Chen3Shuai Yu4Xiaoyu Zhang5Yuxin Dai6Xipeng Cheng7Yupeng Xing8Xiaoqin Fan9Yanbin Zhu10Yanling Guo11Dexuan Meng12College of Bioscience and Biotechnology, Shenyang Agricultural UniversityCollege of Agronomy, Shenyang Agricultural UniversityCollege of Agronomy, Shenyang Agricultural UniversityCollege of Agronomy, Shenyang Agricultural UniversityCollege of Bioscience and Biotechnology, Shenyang Agricultural UniversityCollege of Bioscience and Biotechnology, Shenyang Agricultural UniversityCollege of Bioscience and Biotechnology, Shenyang Agricultural UniversityCollege of Bioscience and Biotechnology, Shenyang Agricultural UniversityCollege of Bioscience and Biotechnology, Shenyang Agricultural UniversityManas Agricultural Experimental Station of Xinjiang Academy of Agricultural SciencesNational Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., LtdNational Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., LtdCollege of Agronomy, Shenyang Agricultural UniversityAbstract Background Genomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. However, there have been few studies on the functional analysis of allele-specific imprinted genes. Results Here, we generated three reciprocal crosses among the B73, Mo17 and CAU5 inbred lines. Based on the transcriptome-wide analysis of allele-specific expression using RNA sequencing technology, 305 allele-specific imprinting genes (ASIGs) were identified in embryos, and 655 ASIGs were identified in endosperms from three maize F1 hybrids. Of these ASIGs, most did not show consistent maternal or paternal bias between the same tissue from different hybrids or different tissues from one hybrid cross. By gene ontology (GO) analysis, five and eight categories of GO exhibited significantly higher functional enrichments for ASIGs identified in embryo and endosperm, respectively. These functional categories indicated that ASIGs are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Finally, the mutation and overexpression of one ASIG (Zm305) affected the length and width of the kernel. Conclusion In this study, our data will be helpful in gaining further knowledge of genes exhibiting allele-specific imprinting patterns in seeds. The gain- and loss-of-function phenotypes of ASIGs associated with agronomically important seed traits provide compelling evidence for ASIGs as crucial targets to optimize seed traits in crop plants.https://doi.org/10.1186/s12870-023-04473-8MaizeAllele-specific imprintingEmbryoEndospermKernel development |
| spellingShingle | Xiaomei Dong Haishan Luo Wenjing Bi Hanyu Chen Shuai Yu Xiaoyu Zhang Yuxin Dai Xipeng Cheng Yupeng Xing Xiaoqin Fan Yanbin Zhu Yanling Guo Dexuan Meng Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm BMC Plant Biology Maize Allele-specific imprinting Embryo Endosperm Kernel development |
| title | Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm |
| title_full | Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm |
| title_fullStr | Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm |
| title_full_unstemmed | Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm |
| title_short | Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm |
| title_sort | transcriptome wide identification and characterization of genes exhibit allele specific imprinting in maize embryo and endosperm |
| topic | Maize Allele-specific imprinting Embryo Endosperm Kernel development |
| url | https://doi.org/10.1186/s12870-023-04473-8 |
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