Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome

Zeng, Yajuan; Conner, Joann A.; Ozias‐Akins, Peggy

doi:10.1186/1471-2164-12-206

Cited by 21 publications

(22 citation statements)

References 49 publications

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“…In the case of Tripsacum , the current evidence suggests the presence of barriers in the transfer of apomixis to maize (Leblanc et al 2009). The greatest progress has been made with the introgression of apomixis into pearl millet from Pennisetum , where a single alien chromosome persists in the most advanced apomictic lines (Singh et al 2010; Zeng et al 2011). In the sexual model plant Arabidopsis , for each element of apomixis identified by mutation so far, the penetrance was shown to be generally low and the related candidate genes were never found to be associated with any feature of apomixis in natural apomicts.…”

Section: Discussionmentioning

confidence: 99%

Apomixis in plant reproduction: a novel perspective on an old dilemma

2013

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Seed is one of the key factors of crop productivity. Therefore, a comprehension of the mechanisms underlying seed formation in cultivated plants is crucial for the quantitative and qualitative progress of agricultural production. In angiosperms, two pathways of reproduction through seed exist: sexual or amphimictic, and asexual or apomictic; the former is largely exploited by seed companies for breeding new varieties, whereas the latter is receiving continuously increasing attention from both scientific and industrial sectors in basic research projects. If apomixis is engineered into sexual crops in a controlled manner, its impact on agriculture will be broad and profound. In fact, apomixis will allow clonal seed production and thus enable efficient and consistent yields of high-quality seeds, fruits, and vegetables at lower costs. The development of apomixis technology is expected to have a revolutionary impact on agricultural and food production by reducing cost and breeding time, and avoiding the complications that are typical of sexual reproduction (e.g., incompatibility barriers) and vegetative propagation (e.g., viral transfer). However, the development of apomixis technology in agriculture requires a deeper knowledge of the mechanisms that regulate reproductive development in plants. This knowledge is a necessary prerequisite to understanding the genetic control of the apomictic process and its deviations from the sexual process. Our molecular understanding of apomixis will be greatly advanced when genes that are specifically or differentially expressed during embryo and embryo sac formation are discovered. In our review, we report the main findings on this subject by examining two approaches: i) analysis of the apomictic process in natural apomictic species to search for genes controlling apomixis and ii) analysis of gene mutations resembling apomixis or its components in species that normally reproduce sexually. In fact, our opinion is that a novel perspective on this old dilemma pertaining to the molecular control of apomixis can emerge from a cross-check among candidate genes in natural apomicts and a high-throughput analysis of sexual mutants.

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Section: Discussionmentioning

confidence: 99%

Apomixis in plant reproduction: a novel perspective on an old dilemma

2013

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“…These read lengths enable effective assembly of sequence data even in the absence of a reference genome sequence and have spurred a recent flurry of transcriptome projects in non-model organisms (e.g. Vera et al 2008;Meyer et al 2009;Schwartz et al 2010), including numerous angiosperms (Novaes et al 2008;Alagna et al 2009;Barakat et al 2009;Bellin et al 2009;Soltis et al 2009;Wang et al 2009;Buggs et al 2010;Peng et al 2010;Sun et al 2010;Zeng et al 2010Zeng et al , 2011Angeloni et al 2011;Bai et al 2011;Blanca et al 2011;Dutta et al 2011;Franssen et al 2011;Fu et al 2011;Kaur et al 2011;Logacheva et al 2011;Lu et al 2011;McDowell et al 2011;Portnoy et al 2011;Swarbreck et al 2011;Yang et al 2011). In this study, we report the results of using 454 sequencing to analyse a normalized cDNA library derived from a pooled sample of multiple tissue types and populations of S. vulgaris, including functional annotation of expressed gene content, marker discovery and an analysis of nucleotide diversity.…”

Section: Introductionmentioning

confidence: 99%

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

Sloan

Keller

Berardi

et al. 2011

Molecular Ecology Resources

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Members of the angiosperm genus Silene are widely used in studies of ecology and evolution, but available genomic and population genetic resources within Silene remain limited. Deep transcriptome (i.e. expressed sequence tag or EST) sequencing has proven to be a rapid and cost-effective means to characterize gene content and identify polymorphic markers in non-model organisms. In this study, we report the results of 454 GS-FLX Titanium sequencing of a polyA-selected and normalized cDNA library from Silene vulgaris. The library was generated from a single pool of transcripts, combining RNA from leaf, root and floral tissue from three genetically divergent European subpopulations of S. vulgaris. A single full-plate 454 run produced 959,520 reads totalling 363.6 Mb of sequence data with an average read length of 379.0 bp after quality trimming and removal of custom library adaptors. We assembled 832,251 (86.7%) of these reads into 40,964 contigs, which have a total length of 25.4 Mb and can be organized into 18,178 graph-based clusters or 'isogroups'. Assembled sequences were annotated based on homology to genes in multiple public databases. Analysis of sequence variants identified 13,432 putative single-nucleotide polymorphisms (SNPs) and 1320 simple sequence repeats (SSRs) that are candidates for microsatellite analysis. Estimates of nucleotide diversity from 1577 contigs were used to generate genome-wide distributions that revealed several outliers with high diversity. All of these resources are publicly available through NCBI and/or our website (http://silenegenomics.biology.virginia.edu) and should provide valuable genomic and population genetic tools for the Silene research community.

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“…Recent transcriptome analyses of the ASGR-carrier chromosome of Pennisetum show that one transcript, which is tightly linked to the heterochromatic ASGR and has similarity to the Transposase_24 domain, is expressed in vegetative and reproductive tissues. A MADS domain-containing gene and a Lon protease present on the ASGR-carrier chromosome were also expressed only in reproductive tissues, but their cosegregation with the ASGR was not confirmed (Zeng et al, 2011). Our cytogenetic analysis of H. caespitosum C36 chromosomes indicated that the chromosomal region containing the LOA locus and associated repetitive sequences is not enriched in heterochromatic marks relative to other chromosomes, suggesting that it may also be transcriptionally active.…”

Section: Convergent Evolution Of Chromosomes Containing Apospory Locimentioning

confidence: 99%

Chromosomes Carrying Meiotic Avoidance Loci in Three Apomictic Eudicot Hieracium Subgenus Pilosella Species Share Structural Features with Two Monocot Apomicts

et al. 2011

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The LOSS OF APOMEIOSIS (LOA) locus is one of two dominant loci known to control apomixis in the eudicot Hieracium praealtum. LOA stimulates the differentiation of somatic aposporous initial cells after the initiation of meiosis in ovules. Aposporous initial cells undergo nuclear proliferation close to sexual megaspores, forming unreduced aposporous embryo sacs, and the sexual program ceases. LOA-linked genetic markers were used to isolate 1.2 Mb of LOA-associated DNAs from H. praealtum. Physical mapping defined the genomic region essential for LOA function between two markers, flanking 400 kb of identified sequence and central unknown sequences. Cytogenetic and sequence analyses revealed that the LOA locus is located on a single chromosome near the tip of the long arm and surrounded by extensive, abundant complex repeat and transposon sequences. Chromosomal features and LOA-linked markers are conserved in aposporous Hieracium caespitosum and Hieracium piloselloides but absent in sexual Hieracium pilosella. Their absence in apomictic Hieracium aurantiacum suggests that meiotic avoidance may have evolved independently in aposporous subgenus Pilosella species. The structure of the hemizygous chromosomal region containing the LOA locus in the three Hieracium subgenus Pilosella species resembles that of the hemizygous apospory-specific genomic regions in monocot Pennisetum squamulatum and Cenchrus ciliaris. Analyses of partial DNA sequences at these loci show no obvious conservation, indicating that they are unlikely to share a common ancestral origin. This suggests convergent evolution of repeat-rich hemizygous chromosomal regions containing apospory loci in these monocot and eudicot species, which may be required for the function and maintenance of the trait.Asexual seed formation, or apomixis, occurs in both monocot and eudicot plants and has evolved in more than 40 plant genera. Approximately 75% of apomicts exist in three families, the Poaceae, Asteraceae, and Rosaceae. Apomixis bypasses meiosis during female gametophyte formation. This contrasts with sexual female gametophyte development, which requires the meiosis of a megaspore mother cell (MMC) in the ovule (megasporogenesis) followed by nuclear proliferation of typically one of the meiotic

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Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome

Cited by 21 publications

References 49 publications

Apomixis in plant reproduction: a novel perspective on an old dilemma

Apomixis in plant reproduction: a novel perspective on an old dilemma

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

Chromosomes Carrying Meiotic Avoidance Loci in Three Apomictic Eudicot Hieracium Subgenus Pilosella Species Share Structural Features with Two Monocot Apomicts

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