The individual and interactive role of arbuscular mycorrhizal fungi and Trichoderma viride on growth, protein content, amino acids fractionation, and phosphatases enzyme activities of onion plants amended with fish waste

The Green Revolution faced a great cost to meet ever-increasing demands for food, where indiscriminate use of agrochemicals resulted in non-friendly habitats. Therefore, the development of a sustainable approach to better crop production of onion seeds (Allium cepa L.) is very crucial. It is time to use organic waste as a replacement for agrochemicals by using arbuscular mycorrhizal fungi (AMF) and Trichoderma. Fish waste as representative of food waste acts as a leading cause of contamination of the environment. The interaction of AMF and Trichoderma viride on biomass, total soluble protein, mycorrhizal colonization, amino acids, phosphatases and phosphorus and nitrogen contents of onion plants grown in fish waste amended soil was studied. Fish waste has caused a slight increase in onions biomass, total free amino acids, and soluble protein content while with AMF and T. viride dual inoculation more increments were recorded; such increases were related to an increase in mycorrhizal colonization. T. viride application significantly increased the mycorrhizal colonization levels, but these were significantly reduced with waste addition. Analysis of amino acids in plants showed that their concentrations had changed as a result of waste addition combined with AMF and/or T. viride. The effectiveness of fish waste combined with low cost and health/environmental safety leads to a prediction that the introduction of fish waste coupled with fungi will become a more popular feature of agriculture in the future.

Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor results in a white bulb color of onions (Allium cepa L.)

A DNA transposon was found in the gene encoding a bHLH transcription factor. Genotypes of the marker tagging this DNA transposon perfectly co-segregated with color phenotypes in large F_2:3 populations A combined approach of bulked segregant analysis and RNA-Seq was used to isolate causal gene for C locus controlling white bulb color in onions (Allium cepa L.). A total of 114 contigs containing homozygous single nucleotide polymorphisms (SNPs) between white and yellow bulked RNAs were identified. Four of them showed high homologies with loci clustered in the middle of chromosome 5. SNPs in 34 contigs were confirmed by sequencing of PCR products. One of these contigs showed perfect linkage to the C locus in F_2:3 populations consisting of 2491 individuals. However, genotypes of molecular marker tagging this contig were inconsistent with color phenotypes of diverse breeding lines. A total of 146 contigs showed differential expression between yellow and white bulks. Among them, transcription levels of B2 gene encoding a bHLH transcription factor were significantly reduced in white RNA bulk and F_2:3 individuals, although there was no SNP in the coding region. Phylogenetic analysis showed that onion B2 was orthologous to bHLH-coding genes regulating anthocyanin biosynthesis pathway in other plant species. Promoter regions of B2 gene were obtained by genome walking and a 577-bp non-autonomous DNA transposon designated as AcWHITE was found in the white allele. Molecular marker tagging AcWHITE showed perfect linkage with the C locus. Marker genotypes of the white allele were detected in some white accessions. However, none of tested red or yellow onions contained AcWHITE insertion, implying that B2 gene was likely to be a casual gene for the C locus.

Transcriptome de novo assembly and analysis of differentially expressed genes related to cytoplasmic male sterility in onion

Onion (Allium cepa L.) is one of the major vegetables in China and accounts for a large proportion of China's vegetable exports. Onion cytoplasmic male sterility, which is often used in onion breeding, is caused by the interaction between the nuclear genes and the cytoplasm. However, the underlying molecular mechanism of onion cytoplasmic male sterility remains unclear. In this study, we analysed the anther microstructure of the onion cytoplasmic male sterile line SA2 and the onion maintainer line SB2. We found that the pollen abortion in SA2 occurred at the tetrad stage during the microspore development, which was very different from that in SB2. We used the Illumina HiSeq platform to sequence RNA from anthers at the tetrad stage collected from the SA2 and SB2 lines. The RNA sequencing and transcriptome assembly produced 146,413 All-Unigenes. Based on an analysis of the differentially expressed genes, we identified two cytoplasmic control genes, atp9 and cox1, and three nuclear-related genes, SERK1, AG and AMS. These transcriptomic results were also verified by fluorescence quantitative PCR. Our study provides important information about genes related to onion cytoplasmic male sterility, and it will help improve the understanding of the molecular mechanism of onion cytoplasmic male sterility.

Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split

Cytoplasmic male-sterility (CMS) conferred by the CMS-S cytoplasm has been most commonly used for onion (Allium cepa L.) F₁ hybrid seed production. We first report the complete mitochondrial genome sequence containing CMS-S cytoplasm in this study. Initially, seven contigs were de novo assembled from 150-bp paired-end raw reads produced from the total genomic DNA using the Illumina NextSeq500 platform. These contigs were connected into a single circular genome consisting of 316,363 bp (GenBank accession: KU318712) by PCR amplification. Although all 24 core protein-coding genes were present, no ribosomal protein-coding genes, except rps12, were identified in the onion mitochondrial genome. Unusual trans-splicing of the cox2 gene was verified, and the cox1 gene was identified as part of the chimeric orf725 gene, which is a candidate gene responsible for inducing CMS. In addition to orf725, two small chimeric genes were identified, but no transcripts were detected for these two open reading frames. Thirteen chloroplast-derived sequences, with sizes of 126-13,986 bp, were identified in the intergenic regions. Almost 10 % of the onion mitochondrial genome was composed of repeat sequences. The vast majority of repeats were short repeats of <100 base pairs. Interestingly, the gene encoding ccmF_N was split into two genes. The ccmF _N gene split is first identified outside the Brassicaceae family. The breakpoint in the onion ccmF _N gene was different from that of other Brassicaceae species. This split of the ccmF _N gene was also present in 30 other Allium species. The complete onion mitochondrial genome sequence reported in this study would be fundamental information for elucidation of onion CMS evolution.