Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel

Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expres...
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Autor*in:	Xiaomei Dong [verfasserIn] Haishan Luo [verfasserIn] Jiabin Yao [verfasserIn] Qingfeng Guo [verfasserIn] Shuai Yu [verfasserIn] Xiaoyu Zhang [verfasserIn] Xipeng Cheng [verfasserIn] Dexuan Meng [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	maize heterosis kernel development allelic expression epigenetic regulation

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 24(2023), 5, p 4766
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:5, p 4766

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms24054766

Katalog-ID:	DOAJ088002586

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520			\|a Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.
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authorswithroles_txt_mv	Xiaomei Dong @@aut@@ Haishan Luo @@aut@@ Jiabin Yao @@aut@@ Qingfeng Guo @@aut@@ Shuai Yu @@aut@@ Xiaoyu Zhang @@aut@@ Xipeng Cheng @@aut@@ Dexuan Meng @@aut@@
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callnumber-first	Q - Science
author	Xiaomei Dong
spellingShingle	Xiaomei Dong misc QH301-705.5 misc QD1-999 misc maize misc heterosis misc kernel development misc allelic expression misc epigenetic regulation misc Biology (General) misc Chemistry Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel
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topic_title	QH301-705.5 QD1-999 Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel maize heterosis kernel development allelic expression epigenetic regulation
topic	misc QH301-705.5 misc QD1-999 misc maize misc heterosis misc kernel development misc allelic expression misc epigenetic regulation misc Biology (General) misc Chemistry
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title	Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel
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title_sort	characterization of genes that exhibit genotype-dependent allele-specific expression and its implications for the development of maize kernel
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title_auth	Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel
abstract	Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.
abstractGer	Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.
abstract_unstemmed	Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.
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title_short	Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel
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An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. 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Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel

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