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Comparative analysis of citrus polyembryonic and monoembryonic ovule transcriptomes identifies candidate transcripts related to nucellar embryony initiation

ABSTRACT: Next-generation sequencing was employed to compare transcriptomic profiling of ovules at and prior to the appearance of nucellar embryony initial cells. To exclude the unwanted genetic background noise and variations among years, two biological replicates for each sample were set by sampling in two consecutive years from two pairs of polyembryonic and monoembryonic cultivars, i.e. one pair of mandarin and the other of grapefruit/pummelo. In that manner, 71 embryo-type enriched transcripts were determined by overlaying differentially expressed transcripts, derived from pairwise comparisons between polyembryonic and monoembryonic cultivars in each basic taxa, which revealed commonly genes that indeed regulated nucellar embryogenesis. Transcriptome profiling indicated that cell wall remodelling transcripts, such as pectinesterase, endochitinase, glucan endo-1,3-β-glucosidase precursor, UDP-glucosyltransferase and laccase were significantly enriched in the polyembryonic cultivars. The expression of transcription factors containing AP2/ERF and WRKY domains were also up-regulated in polyembryonic cultivars compared with monoembryonic cultivars. In addition, the embryo-type enriched transcripts were associated with hormone regulation and signal transduction, as well as carbohydrate metabolism.

OTHER RELATED OMICS DATASETS IN: PRJNA300206PRJNA299149

ORGANISM(S): Citrus x clementina Citrus x paradisi Citrus reticulata Citrus maxima

PROVIDER: GSE74384 | GEO | 2016/12/01

SECONDARY ACCESSION(S): PRJNA300206

REPOSITORIES: GEO

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Project description:Somatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic ‘Hamlin’ sweet orange by antisense-overexpression. The candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain proteins. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryony type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)-like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred. Loss of CitRKD1 function by antisense-overexpression abolished somatic embryogenesis in transgenic sweet orange and the transgenic T1 plants were confirmed to derive from zygotic embryos produced by self-pollination by DNA diagnosis. Genotyping PCR analysis of 95 citrus traditional and breeding varieties revealed that the CitRKD1 allele with the MITE insertion (polyembryonic allele) was dominant and major citrus varieties with the polyembryonic allele produced polyembryonic seeds.

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Comparative analysis of citrus polyembryonic and monoembryonic ovule transcriptomes identifies candidate transcripts related to nucellar embryony initiation

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