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

Jin, Jingjing; Sun, Yanwei; Qu, Jing; syah, Rahmad; Lim, Chin-Huat; Alfiko, Yuzer; Rahman, Nur Estya; Suwanto, Antonius; Yue, Gen Hua; Wong, Limsoon; Chua, Nam‐Hai; Ye, Jian

doi:10.1038/s41598-017-00438-8

Cited by 31 publications

(30 citation statements)

References 50 publications

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“…In this case, the lysine to asparagine substitution encoded by sh AVROS is predicted to disrupt DNA binding, as this highly conserved lysine residue is involved in DNA binding of MADS-box proteins in other plants (Huang et al, 1996;Immink et al, 2010). Although the data reported here do not directly prove a heterotic mechanism, we and others have postulated that heterozygosity for SHELL variants, in combination with a wildtype Sh DeliDura allele, represents a case of single-gene heterosis for oil yield (Singh et al, 2013a, Jin et al, 2017Li et al, 2017;Fievet et al, 2018). Models proposed to account for heterosis include dominance, overdominance, pseudodominance, epistasis and dosage models involving copy number variation or polyploidy, allelic variation, gene expression differences and/or dominant negative macromolecular interactions.…”

Section: Researchmentioning

confidence: 62%

Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles

et al. 2020

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Summary Oil palm breeding involves crossing dura and pisifera palms to produce tenera progeny with greatly improved oil yield. Oil yield is controlled by variant alleles of a type II MADS‐box gene, SHELL, that impact the presence and thickness of the endocarp, or shell, surrounding the fruit kernel. We identified six novel SHELL alleles in noncommercial African germplasm populations from the Malaysian Palm Oil Board. These populations provide extensive diversity to harness genetic, mechanistic and phenotypic variation associated with oil yield in a globally critical crop. We investigated phenotypes in heteroallelic combinations, as well as SHELL heterodimerization and subcellular localization by yeast two‐hybrid, bimolecular fluorescence complementation and gene expression analyses. Four novel SHELL alleles were associated with fruit form phenotype. Candidate heterodimerization partners were identified, and interactions with EgSEP3 and subcellular localization were SHELL allele‐specific. Our findings reveal allele‐specific mechanisms by which variant SHELL alleles impact yield, as well as speculative insights into the potential role of SHELL in single‐gene oil yield heterosis. Future field trials for combinability and introgression may further optimize yield and improve sustainability.

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Section: Researchmentioning

confidence: 62%

Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles

et al. 2020

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“…Heatmaps analysis of DEGs was generated with R (3.4.1 version) (Lucent Technologies, Murray Hill, NJ, USA) pheatmap package [ 52 ]. Box plots were displayed according to the methods of Jin [ 53 ].…”

Section: Methodsmentioning

confidence: 99%

Biochemical, Physiological and Transcriptomic Comparison between Burley and Flue-Cured Tobacco Seedlings in Relation to Carbohydrates and Nitrate Content

Yang

Chang

et al. 2017

Molecules

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Burley tobacco is a genotype of chloroplast-deficient mutant with accumulates high levels of tobacco-specific nitrosamines (TSNAs) which would induce malignant tumors in animals. Nitrate is a principle precursor of tobacco-specific nitrosamines. Nitrate content in burley tobacco was significantly higher than that in flue-cured tobacco. The present study investigated differences between the two tobacco types to explore the mechanisms of nitrate accumulation in burley tobacco. transcripts (3079) related to the nitrogen and carbon metabolism were observed. Expression of genes involved in carbon fixation, glucose and starch biosynthesis, nitrate translocation and assimilation were significantly low in burley tobacco than flue-cured tobacco. Being relative to flue-cured tobacco, burley tobacco was significantly lower at total nitrogen and carbohydrate content, nitrate reductase and glutamine synthetase activities, chlorophyll content and photosynthetic rate (Pn), but higher nitrate content. Burley tobacco required six-fold more nitrogen fertilizers than flue-cured tobacco, but both tobaccos had a similar leaf biomass. Reduced chlorophyll content and photosynthetic rate (Pn) might result in low carbohydrate formation, and low capacity of nitrogen assimilation and translocation might lead to nitrate accumulation in burley tobacco.

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“…Overexpression of JcWRI1 increased Jatropha seed OC and seed mass [51]. Heterologus overexpression of homologs of ArabidopsisAtWRI1, such as B. napus, Zea mays and Elaeis guineenis, led to seed OC increase in Arabidopsis [52,53,54]. FUS3 is an well-known TF on enhencing TAG biosynthesis.…”

Section: Grf5 Wri1mentioning

confidence: 99%

Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds

Niu

Wu²,

et al. 2020

Preprint

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Background: Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear.Results: We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa.Conclusions: This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.

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

Cited by 31 publications

References 50 publications

Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles

Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles

Biochemical, Physiological and Transcriptomic Comparison between Burley and Flue-Cured Tobacco Seedlings in Relation to Carbohydrates and Nitrate Content

Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds

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