Rapid gene expression change in a novel synthesized allopolyploid population of cultivated peanut×Arachis doigoi cross by cDNA-SCoT and HFO-TAG technique

Abstract

Allopolyploidy has played an important role in plant evolution and heterosis. Recent studies indicate that the process of wide hybridization and (or) polyploidization may induce rapid and extensive genetic and epigenetic changes in some plant species. To better understand the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, this study was conducted to monitor the gene expression variation by cDNA-start codon-targeted (SCoT) polymorphism and cDNA-high-frequency oligonucleotide-targeting active gene (cDNA-HFO-TAG) techniques, from the hybrids (F 1) and newly synthesized allopolyploid generations (S 0 to S 3) between tetraploid cultivated peanut Zhongkaihua No.4 with diploid wild one Arachis doigoi. Rapid and considerable gene expression variations began as early as in the F 1 hybrid or immediately after chromosome doubling. Three types of gene expression changes were observed, including complete silence (gene from progenitors was not expressed in all progenies), incomplete silence (gene expressed only in some progenies) and new genes activation. Those silent genes mainly involved in RNA transcription, metabolism, disease resistance, signal transduction and unknown functions. The activated genes with known function were almost retroelements by cDNA-SCoT technique and all metabolisms by cDNA-HFO-TAG. These findings indicated that interspecific hybridization and ploidy change affected gene expression via genetic and epigenetic alterations immediately upon allopolyploid formation, and some obtained transcripts derived fragments (TDFs) probably could be used in the research of molecular mechanism of Arachis allopolyploidization which contribute to the genetic diploidization of newly formed allopolyploids. Our research is valuable for understanding of peanut evolution and improving the utilization of putative and beneficial genes from the wild peanut.

Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

“…The results showed that non-additive expression significantly differed among the eight synthetic allotetraploids of B. napus . This also proves that the newly synthesized allopolyploid is unstable, and the expression of genes in the selfed-offspring drastically changes [ 44 , 45 ]. Furthermore, the results of GO enrichment analysis were consistent with the hypothesis that “non-additive gene expression and multi-molecular mechanism promote heterosis”, which also indicates that non-additive expression genes play a key role in the field performance of offspring [ 26 ].…”

Characterization of Interspecific Hybrids between Flowering Chinese Cabbage and Chinese Kale

“…Previous studies have shown that synthetic B. napus has abundant variation, such as in flowering time, flower size, plant fresh weight, leaf shape and size, the surface wax layer, and other traits [13,18]. However, there have been few studies on the mechanism of variation in traits in the field between different genetic combinations and different generations [14]. In our investigation of the field characteristics of synthetic B. napus, traits were separated in different combinations and generations.…”

“…Allopolyploid-induced variant DNA sequences are mainly concentrated in transposon sequences, random sequences, or repetitive sequences [31][32][33]. Through bioinformatics analysis, it was found that the microsatellite sequence density of the coding region in natural B. napus was higher than that of its diploid parent species, indicating that the SSRs in the gene coding region changed significantly during the polyploidization of B. napus [14,[34][35][36]. In our study, novel and missing SSR sequences were detected in the hybrids.…”

“…The hybridization of flowering Chinese cabbage and Chinese kale to form B. napus is a process of allopolyploidization. Synthetic allopolyploids show some abnormal and unstable mutations in cytology and phenotype, such as flowering time, plant height, and stalk diameter [13,14]. Such variation enriches the genetic background while also causing some drawbacks: in particular, stabilizing target traits takes a long time.…”

Natural Biostimulant Attenuates Salinity Stress Effects in Chili Pepper by Remodeling Antioxidant, Ion, and Phytohormone Balances, and Augments Gene Expression

“…He et al [107] reported that transcript silencing, which could be reversible, resulted in a loss of gene or expression repressing, which was reported irreversible. As we found, one or more treatments resulted in losing transcripts (7 ScDNA out of 41 by 17%) (Figures 1 and 2).…”