Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Ren, Li; Li, Wuhui; Tao, Min; Qin, Qinbo; Luo, Jing; Chai, Jing; Tang, Chenchen; Xiao, Jun; Tang, Xiaojun; Lin, Guoliang; Zhang, Chun; Duan, Wei; Hong, Yunhan; Liu, Shaojun

doi:10.1038/srep27040

Cited by 27 publications

(34 citation statements)

References 47 publications

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“…The re-expression of mstn reflected the new regulatory mechanism influencing growth that may contribute to an increased growth rate in G 4 individuals. This mstn expression pattern was similar to that observed in F 1 24 . However, additional studies are required to verify that a rediploidization accelerates the emergence of new phenotypes via changes to the HEB and homoeolog silencing.…”

Section: Discussionsupporting

confidence: 87%

“…We next investigated the expression level changes resulting from the rediploidization events and compared it with the hybridization and tetraploidization events (They had been described in latest reports 24 ). Differences in total gene expression levels were identified by comparing each hybrid offspring with the original maternal C .…”

Section: Resultsmentioning

confidence: 99%

“…These changes were closely related to gene expression, especially homoeolog expression levels. Additionally, the maternal R-HEB phenomenon was detected in three hybrids (Table 3 ) 24 . Maternal expression bias is frequently observed in hybrid fish, including the M .…”

Section: Discussionmentioning

confidence: 98%

“…auratus red var. 24 . The C-HEB of igf1 likely promotes the dominance of the paternal growth characteristic in G 4 , possibly inducing a rapid growth rate.…”

Section: Discussionmentioning

confidence: 99%

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Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. × Cyprinus carpio

Ren

Cui

Wang

et al. 2017

Sci Rep

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Rediploidization is considered to be a part of the evolutionary history of allotetraploids, and resulted in the emergence of novel epigenetic regulatory activities. To study the changing patterns of gene expression following the reduction of a genome by 50%, we used RNA-seq and quantitative real-time PCR (qPCR) to investigate total gene expression and homoeolog expression in three hybrids of a C. auratus red var. (2n = 100, ♀) (R) and C. carpio (2n = 100, ♂) (C) (i.e., F1, F18, and G4) and their original parents. A comparison of homoeolog expression between G4 and F18 identified 7 genes (0.22%) that exhibited novel R/C homoeolog expression patterns in G4, while 4 genes (0.12%) were affected by R/C homoeolog silencing. We determined the direction and extent of the homoeolog expression bias (HEB). The C-HEB genes (i.e., nrp1a and igf1) and R-HEB genes (i.e., fgf23 and esm1) provided insights into the effects of the dominance of one parental homoeolog expression on growth regulation. This dominance may contribute to the rapid growth of G4 fish. Our findings may be relevant for clarifying the relationship between growth heterosis and differences in homoeolog expression patterns.

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Section: Discussionsupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 98%

“…auratus red var. 24 . The C-HEB of igf1 likely promotes the dominance of the paternal growth characteristic in G 4 , possibly inducing a rapid growth rate.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. × Cyprinus carpio

Ren

Cui

Wang

et al. 2017

Sci Rep

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“…and C. carpio L. provided an effective animal model to investigate mechanisms of polyploidy in animal (Liu et al, 2001. In comparison of diploid and tetraploid individuals, appropriate cell line were urgently needed to discover the different traits related to growth, fertility and disease resistance and various changes in molecular mechanisms for studying the potential mechanisms of these differences (Liu et al, 2001Long et al, 2009;Ren et al, 2016). Here, we assessed the diploid and tetraploid cultured cell in gene expression level, and discussed them whether could be used to study polyploidy as comparison to in vitro.…”

Section: Discussionmentioning

confidence: 99%

Expression Profile Analysis of the Cell Cycle in Diploid and Tetraploid Carassius auratus red var.

et al. 2020

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Polyploidization often leads to "transcriptome shock," and is considered an important factor in evolution of species. Analysis of the cell cycle, which is associated with survival in polyploidy, has proved useful in investigating polyploidization. Here, we used mRNA sequencing to investigate global expression in vitro (in cultured cells) and in vivo (in fin and liver tissues) in both the diploid and tetraploid Carassius auratus red var.. Differential expression (DE) of genes in diploid (7482, 36.0%) and tetraploid (3787, 18.2%) states suggested that in vitro and in vivo conditions dramatically change mRNA expression levels. However, of the 20,771 total shared expressed genes, 18,050 (87.0%), including 17,905 (86.2%) non-differentially expressed genes (DEGs) and 145 (0.7%) DEGs between diploids and tetraploids, showed the same expression trends in both cultured cells and liver tissues. Of the DEGs, four of seven genes in the cell cycle pathway had the same expression trends (upregulated in diploids and tetraploids) in both cultured cells and liver tissues. Quantitative PCR analysis confirmed the same expression trends in the nine DEGs associated with regulation of the cell cycle. This research on common characteristics between diploids and tetraploids provides insights into the potential molecular regulatory mechanisms of polyploidization. The steady changes that occur between diploids and tetraploids in vitro and in vivo show the potential value of studying polyploidy processes using cultured cell lines, especially with respect to cell cycle regulation.

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Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization

Shahzad

Zhang

et al. 2022

Funct Integr Genomics

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Hybridization is useful to enhance yield potential of agronomic crops in the world. Cotton has genome doubling due to alloteraploidy process and hybridization process in coordinate with duplicated genome can produce more yield and adaptability. Therefore, expression of homoeolog gene pairs between hybrids and inbred parents are vital to characterize genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identi ed 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents.Besides, very few homoeolog genes (An average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids.These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton. BackgroundHybridization or polyploidy is a vital process, produces exceptional phenotypes through the interaction of two distinct genomes, and has a substantial in uence on the plant genome (1, 2). The novel phenotypes in plants can be consequent of many modi cations not only at genomic and epigenetic levels but also in gene expression patterns (3, 4). Several examples in cotton (5) Brassica napus (6), and Spartina (7) stated that hybridization (genome merger) modi ed more transcriptome than polyploidy. About 15% of owering plants are polyploidy (8) and divided into categories of autopolyploid and allopolyploid. Autopolyploid is evolved from a genome merger of the same or similar species but allopolyploids contain a genomic combination of two different species (3). Allopolyploids have enhanced growth and wider adaptations relative to autopolyploid. Many important crops are allopolyploids together with upland cotton (Gossypium hirsutum). In allopolyploids, hybridization or polyploidy is allied with various kinds of exchanges and interactions between homoeolog genes (duplicate genes) (9-11). Further modi cations are consisting of epigenetic (3, 12), gene activation (4, 13), and sequence removal (14,15). The result of different genomic interactions by hybridization or polyploidy produced several expression patterns of duplicate or genes with similar functions. For instance, these may be gene silencing, gene activation, novel expression, and altered parental contribution (2, 16). However, the direction and magnitude of duplicate gene expression are varied with crop, tissue, and organ (17)(18)(19)(20).Previous studies have identi ed four different expression forms of duplicated genes in plants e.g., one duplicate gene copy ...

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Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae

Cited by 27 publications

References 47 publications

Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. × Cyprinus carpio

Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. × Cyprinus carpio

Expression Profile Analysis of the Cell Cycle in Diploid and Tetraploid Carassius auratus red var.

Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization

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