Gene expression variation explains maize seed germination heterosis

Wan, Jiong; Wang, Qiyue; Zhao, Jiawen; Zhang, Xuehai; Guo, Zhanyong; Hu, Desheng; Meng, Shujun; Lin, Yuan; Qiu, Xiaoqian; Mu, Liqin; Ding, Dong; Tang, Jihua

doi:10.1186/s12870-022-03690-x

Cited by 9 publications

(5 citation statements)

References 87 publications

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“…6 ). Surprisingly, 80 and 229 ASEGs in this study were consistent with heterosis-related genes in buds and seeds [ 58 , 59 ], respectively. However, no significant enrichment region associated with heterosis-related genes was observed, which could be attributed to the single environmental condition.…”

Section: Discussionmentioning

confidence: 55%

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

Zhan,

Cui,

Yang

et al. 2024

BMC Genomics

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Background Heterosis has successfully enhanced maize productivity and quality. Although significant progress has been made in delineating the genetic basis of heterosis, the molecular mechanisms underlying its genetic components remain less explored. Allele-specific expression (ASE), the imbalanced expression between two parental alleles in hybrids, is increasingly being recognized as a factor contributing to heterosis. ASE is a complex process regulated by both epigenetic and genetic variations in response to developmental and environmental conditions. Results In this study, we explored the differential characteristics of ASE by analyzing the transcriptome data of two maize hybrids and their parents under four light conditions. On the basis of allele expression patterns in different hybrids under various conditions, ASE genes were divided into three categories: bias-consistent genes involved in basal metabolic processes in a functionally complementary manner, bias-reversal genes adapting to the light environment, and bias-specific genes maintaining cell homeostasis. We observed that 758 ASE genes (ASEGs) were significantly overlapped with heterosis quantitative trait loci (QTLs), and high-frequency variations in the promoter regions of heterosis-related ASEGs were identified between parents. In addition, 10 heterosis-related ASEGs participating in yield heterosis were selected during domestication. Conclusions The comprehensive analysis of ASEGs offers a distinctive perspective on how light quality influences gene expression patterns and gene-environment interactions, with implications for the identification of heterosis-related ASEGs to enhance maize yield.

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Section: Discussionmentioning

confidence: 55%

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

Zhan,

Cui,

Yang

et al. 2024

BMC Genomics

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“…Changes in gene expression have been linked to heterosis in many plant traits, such as seed germination and plant height in maize (Birdseye et al ., 2021; Wan et al ., 2022), yield in rice (Sun et al ., 2023), and nicotine biosynthesis in Nicotiana tabacum (Tian et al ., 2018). However, such changes in transcriptional programs can (and possibly will) vary in a spatiotemporal scale, resulting in tissue- or condition-specific changes in the strength of heterosis (Ko et al ., 2016; Yang et al ., 2021).…”

Section: Resultsmentioning

confidence: 99%

HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Almeida-Silva,

Prost-Boxoen,

Van de Peer

2024

Preprint

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Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex non-additive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. Here, we introduceHybridExpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors).HybridExpressprovides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility ofHybridExpressthrough comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis.HybridExpressis designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies.HybridExpressis freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

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“…Changes in gene expression have been linked to heterosis in many plant traits, such as seed germination and plant height in maize (Birdseye et al ., 2021; Wan et al ., 2022), yield in rice (Sun et al ., 2023), and nicotine biosynthesis in Nicotiana tabacum (Tian et al ., 2018). However, such changes in transcriptional programs can (and possibly will) vary in a spatiotemporal scale, resulting in tissue‐ or condition‐specific changes in the strength of heterosis (Ko et al ., 2016; Yang et al ., 2021).…”

Section: Resultsmentioning

confidence: 99%

hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Almeida‐Silva,

Prost‐Boxoen,

Van de Peer

2024

New Phytologist

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Summary Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user‐friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression‐based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

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Gene expression variation explains maize seed germination heterosis

Cited by 9 publications

References 87 publications

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize

HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

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