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The hybrid protein interactome contributes to rice heterosis as epistatic effects

文献类型： 外文期刊

作者： Li, Hong 1 ; Jiang, Shuqin 1 ; Li, Chen 2 ; Liu, Lei 3 ; Lin, Zechuan 4 ; He, Hang 4 ; Deng, Xing-Wang 4 ; Zhang, Ziding; 1 ;

作者机构： 1.China Agr Univ, Coll Agron & Biotechnol, Natl Maize Improvement Ctr, Beijing 100193, Peoples R China

2.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou 510640, Guangdong, Peoples R China

3.Beijing Technol & Business Univ, Sch Sci, Beijing Key Lab Plant Resources Res & Dev, Beijing 100048, Peoples R China

4.Peking Univ, Sch Adv Agr Sci, Peking Tsinghua Ctr Life Sci, State Key Lab Prot & Plant Gene Res, Beijing, Peoples R China

5.Peking Univ, Sch Life Sci, Beijing, Peoples R China

6.China Agr Univ, Coll Biol Sci, State Key Lab Agrobiotechnol, Beijing 100193, Peoples R China

7.Hainan Univ, Sch Life & Pharmaceut Sci, Minist Educ, Key Lab Trop Biol Resources, Haikou 570228, Hainan, Peoples R China

关键词： protein interactome; heterosis; epistatic effects; protein-protein interaction prediction; genomic selection analysis

期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）

ISSN： 0960-7412

年卷期：

页码：

收录情况： SCI

摘要： Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F-1 hybrids (F-1-specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F-1-specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F-1-specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F-1-specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F-1-specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F-1-specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F-1-specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.

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