Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

Shen, Lin; Feng, Xing; Xu, Conghao; Zhang, Qinghua; Che, Jian; Wang, Xianmeng; Song, Jia‐Ming; Li, Xianghua; Xiao, Jinghua; Chen, Lingling; Ouyang, Yidan

doi:10.1073/pnas.1820513116

Cited by 148 publications

(187 citation statements)

References 48 publications

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“…Owing to more and more high‐profile omics data and functional genomics data (Sun et al ; Zhao et al ; Shao et al ), the heterosis related allelic variation, especially the key causative variation, could be excavated, but more challenges may fall over the decoding of regulation networks of the heterosis genes. Near‐isogenic lines for multiple important heterosis genes or the genome editing technology that mimics natural alleles need to be used to picture the developmental processes that underlie how the heterozygous states of genes play a role in gene regulation.…”

Section: Genetic Basis Of Heterosismentioning

confidence: 99%

Exploring the molecular basis of heterosis for plant breeding

Liu

Zhang

et al. 2019

JIPB

106

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Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

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Section: Genetic Basis Of Heterosismentioning

confidence: 99%

Exploring the molecular basis of heterosis for plant breeding

Liu

Zhang

et al. 2019

JIPB

106

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“…In mouse, Pinter et al (2015) showed that 95% and 82% of the identified ASE genes in F1 hybrids and in a reciprocal cross were also with tissue specificity, respectively [54]. Two alleles in rice hybrids might play different role in different environmental conditions and developmental stages, a higher proportion of ASE genes in those hybrids showed inconsistent patterns [55]. In the current study, 22, 81 and 25 ASE genes were identified in samples from skeleton muscle, adipose and both sharing tissues, respectively.…”

Section: Discussionmentioning

confidence: 99%

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Shao¹,

He²,

Pan³

et al. 2020

Preprint

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Background: The thin-tailed sheep breeds from Europe and the fat-tailed sheep breeds from China exhibit distinct phenotypic differences in fat deposition and meat production traits. However, the molecular mechanisms underlying gene expression related to these phenotypic differences are not well understood. Allele-specific expression (ASE) refers to the significant imbalance of expression levels of two parental alleles. Characterization of such events in F1 hybrid offspring generated from these two groups of sheep breeds can minimize the external factors influencing gene expression and reveal the variants with a cis -regulatory effect on gene expression. The aim of the present study was to investigate the genetic factors that influence different fat-deposition and meat production traits between thin- and fat-tailed sheep.Results: Fifteen F1 hybrids were generated from crosses between Texel and Kazakh sheep as the representative phenotypes of thin- and fat-tailed breeds, respectively. Totally, 33 whole genomes from F1 individuals and their parents were sequenced with an average depth of ~17.21× coverage per sample. ASE analysis results from 70 RNA-seq samples of adipose and skeleton muscle tissues showed 128 ASE candidate genes were related to the function of fat deposition and meat production traits. A genome-wide scan of selective sweeps was also conducted between these two groups of sheep breeds in an effort to identify genomic regions related to fat deposition and meat production, respectively. We detected signatures of selection in ASE genes associated with fat deposition (e.g., PDGFD ) and meat production traits (e.g., LRCC2 ). Further analysis suggested that PDGFD and LRCC2 genes were speculated to be causative genes for fat deposition and meat production traits in sheep, respectively. Furthermore, AMPK signaling pathway was significantly enriched in ASE genes related to fatty acid biosynthesis in both adipose and skeleton muscle tissues, while PPAR signaling pathway was significantly enriched in ASE genes related to lipid metabolism in adipose tissue. Conclusions: Our finding illustrates that the expression of identified ASE genes could potentially lead to the differences in traits of fat deposition and meat production between thin- and fat-tailed sheep. Keywords: allele-specific expression, phenotypic difference, thin- and fat-tailed sheep, whole-genome sequencing, transcriptome

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“…8a-c). 9 To phase Iso-Seq transcripts, we developed a new tool called IsoPhase. For each gene, we aligned all full-length reads to the gene region, and then called SNPs individually (currently, IsoPhase only calls substitution SNPs).…”

Section: Isoform Characterization In Maize B73 Ki11 and Reciprocal mentioning

confidence: 99%

“…Previously, ASEs were studied using short-read RNA-seq, which could quantify alleles at the SNP level but was unable to provide full-length haplotype information 8,9 . Third-generation sequencing technologies such as PacBio and Oxford Nanopore offer full-length transcript sequencing that eliminates the need for transcript reconstruction, and these methods have been widely adopted for genome annotations 10,11,12,13,14 .…”

Section: Introductionmentioning

confidence: 99%

Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize

Wang

Tseng

Baybayan

et al. 2019

Preprint

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Haplotype phasing of genetic variants in maize is important for interpretation of the genome, population genetic analysis and functional genomic analysis of allelic activity. Accordingly, accurate methods for phasing the full-length isoforms are essential for functional genomics studies. We performed an isoform-level phasing study in maize, using two inbred lines and their reciprocal crosses, based on the single-molecule full-length cDNA sequencing. To phase and analyze the full-length transcripts between hybrids and parents, we developed a tool called IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data and identified cases of allele-specific, gene-level and isoform-level expression. Our results revealed that maize parental lines and hybrid lines exhibit different splicing activities. After phasing 6,907 genes in two reciprocal hybrids using embryo, endosperm and root tissues, we annotated the SNPs and identified large-effect genes. In addition, based on single-molecule sequencing, we identified parent-of-origin isoforms in maize hybrids, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.

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Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

Cited by 148 publications

References 48 publications

Exploring the molecular basis of heterosis for plant breeding

Exploring the molecular basis of heterosis for plant breeding

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize

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