Transcriptome Analysis of Interspecific Hybrid between<i>Brassica napus</i>and<i>B. rapa</i>Reveals Heterosis for Oil Rape Improvement

Zhang, Jinfang; Li, Chang-Jiu; Li, Haojie; XiaoBin, Pu; Jiang, Jun; Chai, Linna; Zheng, Beibei; Cui, Cheng; Yang, Zujun; Zhu, Yongqing; Jiang, Long

doi:10.1155/2015/230985

Cited by 21 publications

(14 citation statements)

References 35 publications

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“…Zhang et al . observed that coexistence of multiple gene actions cause oil rape improvement in Brassica 39 . Similarly, in our study, we also identified one important transcription factor WRI1 and lipid related genes showing additive mode in hybrid Tenera , which implies heterosis regulation every node of the gene regulation network in a hybrid.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Transcriptome analysis as a powerful tool facilitates the identification of DEGs with their expression level and regulatory mechanisms. Previous investigations identified various heterotic DEGs related to a variety of traits between hybrids and parents in plants and animals 13,31,52,53 . Heterotic genes are robust due to multiple allelic combinations between genomes of two parents in both cross and reciprocal cross combinations suggesting that major genes genetically govern this phenomenon 31,54 .…”

Section: Discussionmentioning

confidence: 99%

“…In this study, the majority of the commonly expressed DEGs revealed non-additive effect especially overdominance (transgressive up-and down-regulation) mode of gene expression patterns in both cross combinations (Table 2). Thus, overdominance mode of gene expression patterns might contribute more than the additive as well as dominance effects to intraspecific heterosis between hybrids and parents in L. longiflorum 52 . (2020) 10:9082 | https://doi.org/10.1038/s41598-020-65909-x www.nature.com/scientificreports www.nature.com/scientificreports/ Functional analysis placed the 260 DEGs into 45 subcategories (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Calculation of mid-parent heterosis (MPH) and high-parent heterosis (HPH) were performed using the following formulas, MPH = (F1 -MP)/MP in % and HPH = (F1 -HP)/HP in %, where F 1 denotes the average performance of the hybrid, MP denotes the average performance of the two parents, and HP denotes the average performance of the better-parent between two parents. The mode of gene expression patterns including additivity and non-additivity were performed based on Rapp et al 97 , Zhang et al 52 , and Wu et al 31 . The relative expression level of DEGs were categorized into additive and non-additive (dominant and overdominant) classes based on Wu et al 31 .…”

Section: Methodsmentioning

confidence: 99%

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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

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“…Alternatively, the change of gene expression provides another source of phenotypic novelty [8]. There is growing evidence that merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression patterns in hybrids, a phenomenon called "transcriptome shock" [9][10][11][12]. As manifestations, many genes would be non-additively expressed in hybrids (diverge from the mid-parental value), which contribute to their transgressive phenotypes at some extent [13,14].…”

Section: Introductionmentioning

confidence: 99%

Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

Zhang

Tang

et al. 2019

Preprint

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Background: The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis. Results : Three species of Camellia with a range of genetic divergence and their F 1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allelic expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent . In addition, the proportion of genes with significant evidence of cis -regulatory divergence increased , whereas with trans -regulatory divergence decreased with parental genetic divergence. Conclusions : The discordance within hybrid would intensify as the parents become more divergent, manifesting as more DEGs would be non-additively expressed. Trans -regulatory divergence contributed more to the additively inherited genes than cis , however, its contribution to expression difference would be weakened as cis mutations accumulated over time; and this might be an important reason for that the more divergent the parents are, the greater proportion of DEGs would be non-additively expressed in hybrid.

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Transcriptome Analysis of Interspecific Hybrid betweenBrassica napusandB. rapaReveals Heterosis for Oil Rape Improvement

Cited by 21 publications

References 35 publications

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

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)

Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia

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