Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq

Zhang, Chunbao; Lin, Chung-Hung; Fu, Fuyou; Zhong, Xiaofang; Peng, Bao; Yan, Hao; Zhang, Jingyong; Zhang, Weilong; Wang, Pengnian; Ding, Xiaoyang; Zhang, Wei; Zhao, Limei

doi:10.1371/journal.pone.0181061

Cited by 29 publications

(19 citation statements)

References 47 publications

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“…The total RNA was extracted using TRIzol (Thermo Scientific TM). cDNA was synthesized using PrimeScript RT Reagent Kit (TaKaRa, Dalian, China) . A 5 μL PCR mixture consisted of 2.5 μL of SYBR mixture (TaKaRa), 0.2 μL of cDNA, 0.2 μL of each PCR primer, and 2.1 μL of ddH 2 O.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of growth heterosis in pearl oyster Pinctada fucata martensii

Yang

Luo

et al. 2018

FEBS Open Bio

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Heterosis improves growth and survival of shellfish species. Although breeders have widely exploited heterosis, its underlying molecular mechanisms remain unclear. In this study, a 2 × 2 complete diallel cross was facilitated between two full‐sib families to produce two inbred families (A and D) and their reciprocal hybrid families (B and C) of pearl oyster Pinctada fucata martensii . Growth traits of the four families were compared at the adult stages. Transcriptome analysis was conducted on the four families using an Illumina sequencing platform. The results revealed that the growth traits of the four families significantly varied ( P < 0.05). The mid‐parent heterosis values of shell length, shell height, shell width, shell weight, and total weight were 12.9%, 14.9%, 18.2%, 17.2%, and 33.2%, respectively. The B‐ and C‐inbred (A and D) triads had 79 and 68 differentially expressed genes (DEGs), respectively, which were dominantly nonadditive, including overdominance, underdominance, and low‐parent dominance. Gene ontology term analysis showed that the DEGs in the B‐ and C‐inbred triads were enriched for metabolic process, cellular process cell part, binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the DEGs in the B‐ and C‐inbred triads were involved in focal adhesion, the P13K‐Akt signaling pathway, the mRNA surveillance pathway, and the focal adhesion pathway. The reliability of the sequencing data was confirmed by real‐time polymerase chain reaction analysis of six growth‐related genes. The findings of this study provide new insights into heterosis for growth traits and the design of genetic breeding programs for this species.

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Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of growth heterosis in pearl oyster Pinctada fucata martensii

Yang

Luo

et al. 2018

FEBS Open Bio

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“…Plant secondary metabolites are crucial for the plant in adapting to an adverse environment for defense [31]. A large number of DEGs were assigned to the pathway related to various secondary metabolite syntheses, indicating their role in making the hybrids better-suited to the environment [11,32]. Similarly, early light-induced protein (ELIP) and chloroplast precursor genes were also highly up-regulated in both the hybrids at the GF stage.…”

Section: Stress Tolerance Potential Of the Hybridsmentioning

confidence: 99%

Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

Katara

Verma

Parida

et al. 2020

IJMS

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RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

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“…Acquiring such information through transcriptome-wide methods has recently gained traction in understanding gene expression basis of heterosis. Using microarray or RNA-Seq, heterosis has been analyzed in species such as rice [9], maize [10], soybeans [11], and silkworm [12]. However, to the best of our knowledge, there is no published report on gene expression analysis of heterosis in chickens or in any other livestock species.…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq Analyses Identify Additivity as the Predominant Gene Expression Pattern in F1 Chicken Embryonic Brain and Liver

Zhu

Lamont

Abasht

2019

Genes

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The superior performance of hybrids to parents, termed heterosis, has been widely utilized in animal and plant breeding programs, but the molecular mechanism underlying heterosis remains an enigma. RNA-Seq provides a novel way to investigate heterosis at the transcriptome-wide level, because gene expression functions as an intermediate phenotype that contributes to observable traits. Here we compared embryonic gene expression between chicken hybrids and their inbred parental lines to identify inheritance patterns of gene expression. Inbred Fayoumi and Leghorn were crossed reciprocally to obtain F1 fertile eggs. RNA-Seq was carried out using 24 brain and liver samples taken from day 12 embryos, and the differentially expressed (DE) genes were identified by pairwise comparison among the hybrids, parental lines, and mid-parent expression values. Our results indicated the expression levels of the majority of the genes in the F1 cross are not significantly different from the mid-parental values, suggesting additivity as the predominant gene expression pattern in the F1. The second and third prevalent gene expression patterns are dominance and over-dominance. Additionally, we found only 7–20% of the DE genes exhibit allele-specific expression in the F1, suggesting that trans regulation is the main driver for differential gene expression and thus contributes to heterosis effect in the F1 crosses.

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Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq

Cited by 29 publications

References 47 publications

Transcriptome analysis of growth heterosis in pearl oyster Pinctada fucata martensii

Transcriptome analysis of growth heterosis in pearl oyster Pinctada fucata martensii

Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

RNA-Seq Analyses Identify Additivity as the Predominant Gene Expression Pattern in F1 Chicken Embryonic Brain and Liver

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