Sex & Lies - Yam Yam Remix
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Dioecy distinct male and female individuals and scarce to non-flowering are common features of cultivated yam Dioscorea spp. However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam D.
Of these, 13, were represented by a minimum yam-yam 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously sex in flower development and sex determination in multiple plant species.
We further investigated the flowering patterns of D. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter.
Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding. This is an open access article distributed under the terms of the Creative Commons Attribution Licensewhich permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The work was conducted as sex of the international collaborative research project "Use of genomic information and molecular tools for yam germplasm utilization and improvement for West Africa EDITS-Yam ".
Competing interests: The authors have declared that no competing interests exist. White Guinea yam, Dioscorea rotundata Poir. Despite its considerable economic and socio-cultural importance, genetic improvement of cultivated yam remains difficult and slow due to its dioecy and poor to non-flowering nature [ 2 ].
Dioecy, the presence of distinct male and female individuals, is one of the major characteristics of the genus Yam-yam [ 3 ]. A major sex challenge associated with dioecy is that synchronizing flowering time is difficult when making genetic crosses.
In addition, many cultivars of D. Mechanisms of sex determination in plants have been investigated in over 40 angiosperm species, which identified both heteromorphic and monomorphic sex chromosomes as well as XY and ZW sex-determination systems [ 5sex ].
Due to the large number and small sizes of chromosomes, the identification of sex chromosomes at cytological level has remained difficult in Dioscorea [ 7 ]. However, a more recent study has revealed that sex determination in the cultivated African species of D. In the same study, a candidate chromosomal region associated yam-yam sex was determined and a diagnostic marker for sex determination developed.
However, gene s functionally responsible for sex determination are yet to be identified in yam species. In angiosperms, flower development involves gene expression and pathway changes in vegetative meristems, leading to their conversion to flowering meristems in response to environmental cues and developmental signals [ 10 ].
Molecular genetic analyses in eudicots such as Arabidopsis thaliana and Antirrhinum majus have led to the identification of several floral organ-identity genes, which were originally grouped into three classes class A, B, and C based on the floral organ identity they specify [ 1112 ]. The class A, B, and C genes are required for the development of sepals and petals, petals and stamens, and stamens and carpels, respectively. Class A and C genes are mutually antagonistic. Further studies revealed that additional gene classes, class D and E, are important for ovule and organ development, respectively, leading to a modified ABCDE model for flower development [ 14 ].
A range of factors can regulate sex differentiation in angiosperms including genetic [ 15 ], epigenetic and environmental [ 16 ], as well as physiological regulation by phytohormones [ 17 ]. Understanding the molecular and genetic mechanisms of flowering is essential for efficient plant breeding. Recently, whole genome sequencing of D.
This finding is expected to open opportunities for dissecting the molecular mechanisms regulating flowering and sex determination in yam.
Identification of flowering and sex-related genes is critical to scaling up utilization of the available yam germplasm in breeding programs. Various sequencing-based transcriptome profiling techniques are available for gene expression profiling, novel gene discovery, and sex annotation studies.
The next-generation sequencing NGS -based and high-throughput SuperSAGE for tag-based gene expression profiling involves sequencing of longer fragments bp and simultaneous analysis of multiple samples by using indexing barcoding [ 23 ]. We show that majority of these differentially expressed genes DEGs correspond to genes implicated in regulating flowering and sex determination in multiple species.
Our findings suggest that known mechanisms underlying flowering and sex determination are also likely to be conserved in D. A total of D. The flowering pattern of these accessions was also recorded over the same period. The 12 morphological traits were selected among the yam descriptors jointly developed by the former International Plant Sex Resources Institute current known by its new designation Bioversity International and the International Institute of Tropical Agriculture [ 24 ].
Detailed description of the traits used is provided in Supplemental Table 1. Tubers harvested from seven accessions including two male, two female, and three monoecious Table 1 selected from the accessions used for morphological characterization based on their consistency of flowering over two years were planted in pots in a screen house. Samples for RNA extraction were collected from early stage flowers Fig 1.
A Example of flowers at early growth stage which also corresponded to the stage at which samples were collected for SuperSAGE analysis, B female flowers, C male flowers, and D monoecious plant with separate male red arrow and female yellow arrow flowers. The library was prepared following the protocols of Matsumura et al. Non-biotinylated cDNA fragments were removed by washing, and yam-yam adapter 2 was ligated to digested cDNA fragments bound to the magnetic beads.
Adapterbp fragments were further ligated to adapter 1 that are specific for each of the samples as described Matsumura et al. The PCR product consisting of eight tubes per sample was pooled and concentrated using Qiagen MinElute reaction purification yam-yam. The purified PCR product from each sample was analyzed for its quantity and quality on an Agilent Bioanalyzer 2.
The PCR product was cloned using invitrogen:—zeroblunt Topo PCR cloning kit for sequencing and later transformation using one shot chemical transformation protocol.
Total RNA was extracted from female and male flowers after flowering using the CTAB extraction protocol as described by Dellaporta [ 25 ] with slight modifications.
Approximately yam-yam tissues were grinded using mortar and pestle in liquid nitrogen. The aqueous top layer was transferred and purified with one volume of chloroform: isoamyl alcohol and centrifuged for 10 minutes at rpm.
The supernatant was mixed with 0. Based on the results of melt and standard curves, Beta-Tubulin was chosen as the endogenous reference for quantification of targets genes. RT-PCR reaction volumes were set up to Immediately after the final PCR cycle, a melting curve analysis was done to determine specificity of the reaction.
For analysis of data on phenotypic traits, multiple correspondence analyses MCA was performed using FactoMineR package [ 26 ] in R software [ 27 ] to detect the association between sex types and sex variables.
For SuperSAGE data analysis, sequence reads obtained from the different libraries were first sorted into different flowering groups based on their respective index sequences. The R package edgeR [ 28 ] was used to determine differentially expressed tags between pairs of flowering groups male vs female, male vs monoecious and female vs monoecious. Tags that were expressed in at least one sample or flowering group with a minimum number of 10 were sex for the analysis.
Additionally, since two replicate samples were sequenced from each flowering group, tags that were represented in both replicates were considered.
The expression cutoff was counts per million CPMcorresponding to a read count of about 5 for each tag. Before quantitative analyses, validation experiments were carried out to confirm equal amplification efficiencies between the reference and target genes and the applicability of the comparative method. Assessing the relative amplification efficiencies was achieved by running standard curves for each amplicon i.
The flowering patterns of D. Inmajority of the accessions In the growing season, Most accessions were consistent over the two seasons with respect to flowering, while some were not.
About of the male, of the female and 43 of the monoecious accessions failed to flower at least in one of the seasons, hence the discrepancy observed between the two seasons with regard to the proportion of accessions with different sex groups Fig 2. Overall, majority of D. Whereas, monoecious types are very rare in D.
The proportion of male, female, monoecious, and non-flowering accessions among genebank accessions in A and B growing seasons. In addition to flowering and type of sex, we collected categorical data on 14 selected morphological traits over the same period S1 Table. Yam-yam data was subjected to multiple correspondence analysis Sexgenerating three major clusters that mainly reflected sex of the accessions Fig 3.
This suggested that certain morphological traits are associated with sex in D. Included in the first cluster were a group of non-flowering accessions that could be distinguished by traits such as purplish green stem, non-waxy stem, stem with non-barky patches, dark green leaf color, and hastate leaf shape. A second cluster composed entirely of male accessions was correlated with purplish green stem, presence of barky patches, non-waxy stem, dark green leaf, and sagittate leaf shape.
The third group was composed of a mixture yam-yam male, female and monoecious flowering accessions that were identified by waxiness, absence of barky patches, either green, brownish green or purple stem color, and pale green or green leaf color as distinct traits.
The pattern of relationship between individual plants black triangles and the 20 most discriminant morphological traits red triangles are provided. SuperSAGE libraries representing early stage male, female, and monoecious flower were multiplexed and sequenced on a single lane of an Illumina Genome Analyzer IIx, generating a total of 8, tags following quality control QC based sex sequence read length, adapter dimmer, and sequencing error rates Table 1.
After the tags were sorted into the different flowering groups using Adapter1 sequences and singleton tags were removed, 20, unique non-singleton tags were obtained. Of these, 6, tags that were ten or less in number per library were removed, while the remaining 13, abundant tags were retained for further analysis S3 Table.
The remaining tags were shared between male and female tags; The unique tags, as well as tags shared among male, female and monoecious plants were presented. The fold change of differential expression and gene abundance count per million of 13, unique tags was compared across the different flowering groups.
A total of tags were differentially expressed with p and false discovery rate FDR values of less than 0. Of the 13 tags differentially expressed between male and female groups, five were highly expressed in male while the remaining eight were expressed in the female sex type.
Similarly, the male vs monoecious group comparison revealed that 25 tags were highly represented in male, and 42 were abundant in monoecious sex type. For the sex vs monoecious flower group, 11 and nine tags were expressed highly in female and monoecious flowers, respectively. The tag abundance estimated by the average logCPM counts yam-yam million ranged from a minimum of 6.
The abundance of genes differential expressed yam-yam A male and female, B male and monoecious, and C female and monoecious flowers buds are shown. Yam-yam expressed tags are represented by red dots. The horizontal blue lines represent 4-fold changes. Of the differentially expressed tags, 88 tags were unique. These unique tags were aligned to the D. Of the unique sequences, 87 could be aligned to the draft D. Sequences obtained for fifteen Of the 72 tags that could be annotated, 14 However, a set of 18
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