scholarly journals Small RNA expression pattern in multiply inbred lines and their hybrids of maize embryo

2019 ◽  
Author(s):  
Yong-Xin Liu
Keyword(s):  
Expression Pattern ◽  
Small Rna ◽  
Protein Translation ◽  
Inbred Lines ◽  
Hybrid Vigor ◽  
Differentially Expressed ◽  
F1 Hybrids ◽  
F1 Hybrid ◽  
Dna Transposon ◽  
Flanking Regions

AbstractHeterosis, also known as hybrid vigor or transgression, is the phenomenon wherein an F1 hybrid produced from crossing two cultivars of the same or different species shows superior phenotypes. Heterosis in maize has been found and applied in breeding for more than one hundred years. However, its underlying molecular mechanisms are still poorly understood. To investigate whether small RNAs (sRNAs) participate in the regulation of heterosis, we profiled the sRNA expression patterns in the germ seeds of five inbred lines and theirs three F1 hybrids using high-throughput sequencing technology. The sequencing result show maize sRNAs are enriched in 22-nt length. Nearly 90% of 22-nt small RNA dominated clusters (SRCs) are in repeat regions, which mainly originated from Gypsy and Copia in retrotransposon. About 25% differentially expressed SRCs exist between parents, and hybrid gain almost all differentially expressed 22-nt SRCs. Twenty-four-nt sRNA also enriched in maize, which showed great sequence diversity and overall low expression across the genome. More than half of 24-nt SRCs originate from repeat, and 80% of them come from DNA transposon. Nearly 30% of 24-nt SRCs located in genes or their flanking regions, especially in flanking regions of “lipid metabolic process” and “macromolecule modification” related genes. Several thousands 24-nt SRCs are paternal or maternal specific expressed, and hybrids gain only half of differentially expressed 24-nt SRCs. Hundreds of 24-nt SRCs show high parent or above high parent expression pattern in different hybrids, and them mainly from Tourist, haT, and CACTA in DNA transposon and enrich nearby “tRNA aminoacylation for protein translation” related genes. Also, some 21-nt SRCs show conserved expression pattern in low parent. They were enriched in anti-sense region of some genes, which functions are about oxidative phosphorylation and translation. miRNAs have a global downregulated tendency in hybrids. zma-miR408-5p, zma-miR1432-5p and zma-miR528-5p are significant downregulated in each hybrid, and this phenomenon may cause their target genes more stable and contribute to hybrid vigor. Taken together, our results illustrated that sRNAs may contribute to heterosis at the very early stage of seed germination through repressing of retrotransposon activity, regulation gene activity at gene and genic flanking regions, and promotion some gene expressions by downregulated miRNAs.

scholarly journals Hybrid mimics and hybrid vigor in Arabidopsis

2015 ◽  
Vol 112 (35) ◽  
pp. E4959-E4967 ◽  
Author(s):  
Li Wang ◽  
Ian K. Greaves ◽  
Michael Groszmann ◽  
Li Min Wu ◽  
Elizabeth S. Dennis ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Recurrent Selection ◽  
Hybrid Vigor ◽  
F1 Hybrids ◽  
Parent Plant ◽  
F1 Hybrid ◽  
Altered Expression ◽  
Cell Numbers ◽  
Seed Industry ◽  
Vegetative Biomass

F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.

Genetic Techniques in Flatfish Culture

1976 ◽  
Vol 33 (4) ◽  
pp. 1088-1093 ◽  
Author(s):  
C. E. Purdom
Keyword(s):  
Fish Farming ◽  
Inbred Lines ◽  
Hybrid Vigor ◽  
Fish Culture ◽  
Common Phenomenon ◽  
F1 Hybrid ◽  
Hybrid Production ◽  
Environmental Component ◽  
Genetic Techniques ◽  
Selection For

Selection for improved growth rate does not appear to be feasible in flatfish because the environmental component of variation is very large. Selection for other characters has not been studied. The development of inbred lines, and their use in F1 hybrid production, seems warranted in fish farming if only as a means of avoiding inbreeding depression of fitness. Gynogenesis may be a practical means for accelerating the rate of inbreeding in fish. Induced triploidy is a potentially useful technique in fish culture in that it prevents sexual maturation and limits the depression of growth associated with this. Hybridization is a common phenomenon among fish and can lead to a form of hybrid vigor. Its application in fish culture may be limited by marketing problems where fish are sold under a specific name.

Male sterility in field beans (Vicia faba L.). II. Yield trials of F1 hybrid winter beans produced with the aid of male sterility

1964 ◽  
Vol 63 (2) ◽  
pp. 235-243 ◽  
Author(s):  
D. A. Bond ◽  
J. L. Fyfe ◽  
Gillian Toynbee-Clarke
Keyword(s):  
Male Sterility ◽  
Inbred Lines ◽  
F1 Hybrids ◽  
Male Sterile ◽  
Male Sterile Line ◽  
F1 Hybrid ◽  
Vicia Faba L ◽  
The Mean ◽  
Yield Trials ◽  
Field Beans

1. F1 hybrids between inbred lines of winter beans were obtained by roguing male-fertile plants from segregating progenies of a genetic male-sterile line which had been interplanted with a pollinator.2. In a series of trials the mean yields of many hybrids were significantly higher than those of open-pollinated varieties. Over the 4 years, 1959–62, with trials at three centres in each year, the mean advantages of all hybrids over the two control varieties was 6·4 cwt./acre over Gartons S.Q., 4·7 cwt./acre over Throws M.S.

Rice F1 hybrids: the breeding goal or a costly solution?

2003 ◽  
Vol 54 (10) ◽  
pp. 1005 ◽  
Author(s):  
D. A. Ntanos ◽  
D. G. Roupakias
Keyword(s):  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Yield Potential ◽  
F1 Hybrids ◽  
Quality Traits ◽  
F1 Hybrid ◽  
Yielding Ability ◽  
Grain Length ◽  
Honeycomb Selection

Whether to develop inbred cultivars or F1 hybrids is a dilemma faced by many rice (Oryza sativa L.) breeders. This could be partially answered if one could select superior recombinant inbred lines with an equal yielding ability and good quality traits from commercial F1 hybrids. Thus, it was attempted in this study to select superior inbred lines from 2 commercial F1 hybrids after application of honeycomb selection and panicle-to-row selection. The 2 F2 populations were advanced to F6 generation by both methods and, finally, 5 F5:6 lines with high yield potential and good grain quality were selected from each population and selection method and were tested in a randomised complete block design for 2 years in Kalochori, Thessaloniki, Greece. In each case the respective F1 hybrid and the check cultivar Strymonas were used as checks. Fourteen of the 20 lines selected by honeycomb selection and panicle-to-row selection from both populations exhibited a yielding ability that was not significantly different from the yield of the F1 hybrids in both years. Three of them, however, in 1 of the 2 years, had a significantly higher grain yield than the corresponding F1 hybrid. In addition, 6 of the above lines exhibited significantly higher values for more than 1 of the 4 quality traits (total milling yield, grain vitreosity, grain length, and grain length/width ratio) and they were not inferior for the remaining ones. It was concluded that application of combined selection for yield and quality could lead to the isolation of recombinant inbred lines with equal yielding ability and quality equal to or higher than the F1 hybrids. This, together with the higher cost associated with hybrid technology, indicates that the long-term goal of a rice-breeding program should be the production of superior inbred lines, unless hybrid production cost is low and quality is not critical for the particular market.

Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

2019 ◽  
Vol 14 (7) ◽  
pp. 591-601 ◽  
Author(s):  
Aravind K. Konda ◽  
Parasappa R. Sabale ◽  
Khela R. Soren ◽  
Shanmugavadivel P. Subramaniam ◽  
Pallavi Singh ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Wrky Transcription Factor ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Callose Deposition ◽  
Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

scholarly journals Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 408 ◽  
Author(s):  
Jing-Yao Yu ◽  
Zhan-Guo Zhang ◽  
Shi-Yu Huang ◽  
Xue Han ◽  
Xin-Yu Wang ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Seed Development ◽  
Small Rna ◽  
Target Genes ◽  
Soybean Seed ◽  
Regulatory Genes ◽  
Small Rna Sequencing ◽  
Grain Development ◽  
Regulatory Relationship ◽  
Novel Mirna

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

scholarly journals Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weitao Chen ◽  
Ming Zou ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Xinhui Li ◽  
...  
Keyword(s):  
De Novo ◽  
Parental Species ◽  
F1 Hybrids ◽  
Pelteobagrus Fulvidraco ◽  
F1 Hybrid ◽  
Short Reads ◽  
Final Assembly ◽  
Genome Complexity ◽  
Hybrid Genome ◽  
Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

scholarly journals Fitness of F1 hybrids between 10 maternal wild soybean populations and transgenic soybean

2021 ◽  
Author(s):  
Jin Yue Liu ◽  
Ze Wen Sheng ◽  
Yu Qi Hu ◽  
Qi Liu ◽  
Sheng Qiang ◽  
...  
Keyword(s):  
Seed Weight ◽  
Wild Soybean ◽  
F1 Hybrids ◽  
Weed Competition ◽  
Transgenic Soybean ◽  
Wild Progenitor ◽  
F1 Hybrid ◽  
Dry Biomass ◽  
100 Seed Weight ◽  
Pod Number

AbstractThe releasing of transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises concerns that transgenes might escape from the soybeans via pollen into their endemic wild relatives, the wild soybean (Glycine soja Sieb. et Zucc.). The fitness of F1 hybrids obtained from 10 wild soybean populations collected from China and transgenic glyphosate-resistant soybean was measured without weed competition, as well as one JLBC-1 F1 hybrid under weed competition. All crossed seeds emerged at a lower rate from 13.33–63.33%. Compared with those of their wild progenitors, most F1 hybrids were shorter, smaller, and with decreased aboveground dry biomass, pod number, and 100-seed weight. All F1 hybrids had lower pollen viability and filled seeds per plant. Finally, the composite fitness of nine F1 hybrids was significantly lower. One exceptional F1 hybrid was IMBT F1, in which the composite fitness was 1.28, which was similar to that of its wild progenitor due to the similarities in pod number, increased aboveground dry biomass, and 100-seed weight. Under weed competition, plant height, aboveground dry biomass, pod number per plant, filled seed number per plant, and 100-seed weight of JLBC-1 F1 were lower than those of the wild progenitor JLBC-1. JLBC-1 F1 hybrids produced 60 filled seeds per plant. Therefore, F1 hybrids could emerge and produce offspring. Thus, effective measures should be taken to prevent gene flow from transgenic soybean to wild soybean to avoid the production F1 hybrids when releasing transgenic soybean in fields in the future.

scholarly journals Unravelling the hybrid vigor in domestic equids: the effect of hybridization on bone shape variation and covariation

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Pauline Hanot ◽  
Anthony Herrel ◽  
Claude Guintard ◽  
Raphaël Cornette
Keyword(s):  
First Generation ◽  
Shape Change ◽  
Morphological Integration ◽  
Hybrid Vigor ◽  
F1 Hybrids ◽  
Shape Variation ◽  
Locomotor System ◽  
Domestic Horses ◽  
Functional Mechanisms ◽  
Underlying Processes

Abstract Background Hybridization has been widely practiced in plant and animal breeding as a means to enhance the quality and fitness of the organisms. In domestic equids, this hybrid vigor takes the form of improved physical and physiological characteristics, notably for strength or endurance. Because the offspring of horse and donkey is generally sterile, this widely recognized vigor is expressed in the first generation (F1). However, in the absence of recombination between the two parental genomes, F1 hybrids can be expected to be phenotypically intermediate between their parents which could potentially restrict the possibilities of an increase in overall fitness. In this study, we examine the morphology of the main limb bones of domestic horses, donkeys and their hybrids to investigate the phenotypic impact of hybridization on the locomotor system. We explore bone shape variation and covariation to gain insights into the morphological and functional expressions of the hybrid vigor commonly described in domestic equids. Results Our data reveal the occurrence of transgressive effects on several bones in the F1 generation. The patterns of morphological integration further demonstrate that the developmental processes producing covariation are not disrupted by hybridization, contrary to functional ones. Conclusions These results suggest that an increase in overall fitness could be related to more flexibility in shape change in hybrids, except for the main forelimb long bones of which the morphology is strongly driven by muscle interactions. More broadly, this study illustrates the interest of investigating not only bone shape variation but also underlying processes, in order to contribute to better understanding how developmental and functional mechanisms are affected by hybridization.

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