Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster

Wu, Xianwen; Li, Rongni; Li, Qianqian; Bao, Haigang; Wu, Changxin

doi:10.1038/srep21124

Cited by 19 publications

(25 citation statements)

References 45 publications

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“…Therefore, the livers of females obtained at six weeks of age were used for RNA sequencing. A large number of DEGs were identified between reciprocal crosses and parental lines, indicating that heterosis is a consequence of polygenic effects; this was consistent with results given by previous studies [30,31].…”

Section: Discussionsupporting

confidence: 91%

“…A pathway of steroid biosynthesis was significantly enriched in high-parent dominant genes for the RC group. Mu et al [30] reported that steroid biosynthesis gene up-regulation increased fat deposition in ovariectomized chickens. However, in our study, no shared significant KEGG pathway was enriched in the high-parent dominant genes of reciprocal crosses.…”

Section: Discussionmentioning

confidence: 99%

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Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens

Mai

Wen

Sun

et al. 2019

Genes

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Heterosis, a phenomenon characterized by the superior performance of hybrid individuals relative to their parents, has been widely utilized in livestock and crop breeding, while the underlying genetic basis remains elusive in chickens. Here, we performed a reciprocal crossing experiment with broiler and layer chickens and conducted RNA sequencing on liver tissues for reciprocal crosses and their parental lines to identify inheritance patterns of gene expression. Our results showed that heterosis of the abdominal fat percentage was 69.28%–154.71% in reciprocal crosses. Over-dominant genes of reciprocal crosses were significantly enriched in three biological pathways, namely, butanoate metabolism, the synthesis and degradation of ketone bodies, and valine, leucine, and isoleucine degradation. Among these shared over-dominant genes, we found that a lipid-related gene, HMGCL, was enriched in these pathways. Furthermore, we validated this gene as over-dominant using qRT-PCR. Although no shared significant pathway was detected in the high-parent dominant genes of reciprocal crosses, high-parent dominant gene expression was the major gene inheritance pattern in reciprocal crosses and we could not exclude the effect of high-parent dominant genes. These findings suggest that non-additive genes play important roles in the heterosis of important traits in chickens and have important implications regarding our understanding of heterosis.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens

Mai

Wen

Sun

et al. 2019

Genes

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“…Hybrid vigor, or heterosis, refers to the superior performance of hybrid progeny relative to their inbred parents 1 – 4 . Heterosis in plants of diverse species is associated with many superior agronomic characteristics, including larger plant stature, increased biomass, growth rate, grain yield, and tolerance to abiotic stresses.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm

Jin

Sun

et al. 2017

Sci Rep

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Oil palm is the most productive oil crop in the world and composes 36% of the world production. However, the molecular mechanisms of hybrids vigor (or heterosis) between Dura, Pisifera and their hybrid progeny Tenera has not yet been well understood. Here we compared the temporal and spatial compositions of lipids and transcriptomes for two oil yielding organs mesocarp and endosperm from Dura, Pisifera and Tenera. Multiple lipid biosynthesis pathways are highly enriched in all non-additive expression pattern in endosperm, while cytokinine biosynthesis and cell cycle pathways are highly enriched both in endosperm and mesocarp. Compared with parental palms, the high oil content in Tenera was associated with much higher transcript levels of EgWRI1, homolog of Arabidopsis thaliana WRINKLED1. Among 338 identified genes in lipid synthesis, 207 (61%) has been identified to contain the WRI1 specific binding AW motif. We further functionally identified EgWRI1-1, one of three EgWRI1 orthologs, by genetic complementation of the Arabidopsis wri1 mutant. Ectopic expression of EgWRI1-1 in plant produced dramatically increased seed mass and oil content, with oil profile changed. Our findings provide an explanation for EgWRI1 as an important gene contributing hybrid vigor in lipid biosynthesis in oil palm.

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“…Next-generation sequencing (NGS) especially high-throughput RNA sequencing (RNA-seq) technology is advantageously used for discovering heterotic genes over other expression profiling technologies in plants and animals 13,[24][25][26] . In plants, using RNA-Seq technology, expression patterns of DEGs between hybrids and their parents can be analyzed that might contribute to understanding the genetic basis of heterosis 13,27,28 .…”

mentioning

confidence: 99%

Transcriptome Analysis by RNA–Seq Reveals Genes Related to Plant Height in Two Sets of Parent-hybrid Combinations in Easter lily (Lilium longiflorum)

Howlader

Robin

Natarajan

et al. 2020

Sci Rep

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In this study, two different hybrids of Easter lily (Lilium longiflorum), obtained from two cross combinations, along with their four parents were sequenced by high-throughput RNA-sequencing (RNA-Seq) to find out differentially expressed gene in parent-hybrid combinations. The leaf mRNA profiles of two hybrids and their four parents were RNA-sequenced with a view to identify the potential candidate genes related to plant height heterosis. In both cross combinations, based to morphological traits mid-parent heterosis (MPH) was higher than high-parent heterosis (HPH) for plant height, leaf length, and number of flowers whereas HPH was higher than MPH for flowering time. A total of 4,327 differentially expressed genes (DEGs) were identified through RNA-Seq between the hybrids and their parents based on fold changes (fc) ≥ 2 for up-and ≤-2 for down-regulation. Venn diagram analysis revealed that there were 703 common DEGs in two hybrid combinations, those were either up-or down-regulated. Most of the commonly expressed DEGs exhibited higher non-additive effects especially overdominance (75.9%) rather than additive (19.4%) and dominance (4.76%) effects. Among the 384 functionally annotated DEGs identified through Blast2GO tool, 12 DEGs were up-regulated and 16 of them were down-regulated in a similar fashion in both hybrids as revealed by heat map analysis. These 28 universally expressed DEGs were found to encode different types of proteins and enzymes those might regulate heterosis by modulating growth, development and stress-related functions in lily. In addition, gene ontology (GO) analysis of 260 annotated DEGs revealed that biological process might play dominant role in heterotic expression. In this first report of transcriptome sequencing in Easter lily, the notable universally up-regulated DEGs annotated ABC transporter A family member-like, B3 domain-containing, disease resistance RPP13/1, auxin-responsive SAUR68-like, and vicilin-like antimicrobial peptides 2-2 proteins those were perhaps associated with plant height heterosis. The genes expressed universally due to their overdominace function perhaps influenced MPH for greater plant height-largely by modulating biological processes involved therein. The genes identified in this study might be exploited in heterosis breeding for plant height of L. longiflorum. Heterosis refers to the higher performance in any trait (s) of interest of F 1 hybrid as compared to homozygous parental lines. Charles Darwin 1 described this phenomenon for the first time ever and later Shull 2 and East 3 independently confirmed this phenomenon. Improvements in many traits of different crop and livestock species have

show abstract

Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster

Cited by 19 publications

References 45 publications

Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens

Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens

Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm

Transcriptome Analysis by RNA–Seq Reveals Genes Related to Plant Height in Two Sets of Parent-hybrid Combinations in Easter lily (Lilium longiflorum)

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