Genome-Wide Identification and Evolutionary Analysis of Argonaute Genes in Hexaploid Bread Wheat

Argonaute (AGO) proteins play a pivotal role in plant growth and development as the core components of RNA-induced silencing complex (RISC). However, no systematic characterization of AGO genes in wheat has been reported to date. In this study, a total number of 69 TaAGO genes in the hexaploid bread wheat (Triticum aestivum cv. Chinese Spring) genome, divided into 10 subfamilies, were identified. Compared to all wheat genes, TaAGOs showed a significantly lower evolutionary rate, which is consistent with their high conservation in eukaryotes. However, the homoeolog retention was remarkably higher than the average, implying the nonredundant biological importance of TaAGO genes in bread wheat. Further homoeologous gene expression bias analyses revealed that TaAGOs may have undergone neofunctionalization after polyploidization and duplication through the divergent expression of homoeologous gene copies, to provide new opportunities for the generation of adaptive traits. Moreover, quantitative real-time polymerase chain reaction (qRT-PCR) analyses indicated that TaAGO gene expression was involved in response to heat, drought, and salt stresses. Our results would provide a theoretical basis for future studies on the biological functions of TaAGO genes in wheat and other gramineous species.

Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat

Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala x Culter alburnus

Abstract Background Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animal. Results Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB and TC homoeolog expression from the two reciprocal cross hybrids, we identified 49–347 differentially expressed BSB-homoeologous genes and 54–354 TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF 3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF 3 homoeologous gene pairs. These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a with belonged to the bone morphogenetic protein family was selected as an AS model to investigate expression diversity and their potential effects to body shape traits. Conclusions The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects are the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala x Culter alburnus

Background Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animal. Results Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB and TC homoeolog expression from the two reciprocal cross hybrids, we identified 49–347 differentially expressed BSB-homoeologous genes and 54–354 TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TB F3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BT F3 homoeologous gene pairs. These results further improve AS prediction at the homoeolog level. To analyze body shape traits, bmpr2a of the bone morphogenetic protein family was selected as an AS model to investigate expression diversity. Conclusions The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects are the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

The MRN complex of wheat

The MRN complex is formed by the interaction of the products of the Mre11, Rad50 and Nbs1 genes. This complex plays a central role on repair of double-strand breaks (DSBs) and acts in a great number of cellular processes. In this study we have performed the analysis of the MRN complex in diploid and polyploid species of wheat. The molecular characterization was carried out in the diploid T. monococcum (genome A) and Ae. tauschii (genome D) and in the tetraploid T. turgidum (genomes A and B). The results obtained showed that in all cases the genes presented the main characteristics previously described in other species. A modified FISH protocol was used to locate the Rad50, Mre11 and the Nbs1 genes on the homoeologous chromosomes 5, 2 and 1, respectively. Analysis of expression showed that the hexaploid T. aestivum was the species with the higher level of expression whereas the rest of the species analysed showed no relation with its ploidy. Also, quantification of the expression of each homoeologous gene in the polyploid species evidenced in some cases a process of silencing after polyploidization. The study of the interaction between the proteins demonstrated that the interaction of proteins was not restricted to each genome, detecting interaction between proteins belonging to different genomes.