Meili Xiao

Horizontal gene transfer in plants

Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries. HGT often occurs in microbic and eukaryotic genomes. However, the pathways by which HGTs occur in multicellular eukaryotes, especially in plants, are not well understood. We systematically summarized more than ten possible pathways for HGT. The intimate contact which frequently occurs in parasitism, symbiosis, pathogen, epiphyte, entophyte, and grafting interactions could promote HGTs between two species. Besides these direct transfer methods, genes can be exchanged with a vector as a bridge: possible vectors include pollen, fungi, bacteria, viruses, viroids, plasmids, transposons, and insects. HGT, especially when involving horizontal transfer of transposable elements, is recognized as a significant force propelling genomic variation and biological innovation, playing an important functional and evolutionary role in both eukaryotic and prokaryotic genomes. We proposed possible mechanisms by which HGTs can occur, which is useful in understanding the genetic information exchange among distant species or distant cellular components.

Utilization of crop heterosis: a review

Heterosis (or hybrid vigor) is a natural phenomenon whereby hybrid offspring of genetically diverse individuals display improved physical and functional characteristics relative to their parents. Heterosis has been increasingly applied in crop production for nearly a century, with the aim of developing more vigorous, higher yielding and better performing cultivars. In this review we present and compare three categories of crop heterosis utilization: intraspecific heterosis, intersubspecific heterosis and wide-hybridization heterosis, with particular focus on polyploid species. Different pollination-control systems used to breed for heterosis are also comparatively analyzed. Finally, we highlight problems involved in heterosis research and crop improvement. We aim to provide insight into best practices for amplifying heterosis potential.

Characterization and functional annotation of nested transposable elements in eukaryotic genomes.

The movement of transposable elements (TE) in eukaryotic genomes can often result in the occurrence of nested TEs (the insertion of TEs into pre-existing TEs). We performed a general TE assessment using available databases to detect nested TEs and analyze their characteristics and putative functions in eukaryote genomes. A total of 802 TEs were found to be inserted into 690 host TEs from a total number of 11,329 TEs. We reveal that repetitive sequences are associated with an increased occurrence of nested TEs and sequence biased of TE insertion. A high proportion of the genes which were associated with nested TEs are predicted to localize to organelles and participate in nucleic acid and protein binding. Many of these function in metabolic processes, and encode important enzymes for transposition and integration. Therefore, nested TEs in eukaryotic genomes may negatively influence genome expansion, and enrich the diversity of gene expression or regulation.

What is crop heterosis: new insights into an old topic

Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the ‘omics’ of heterosis and the role of non-coding regions, particularly in relation to energy–use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive ‘omics’ networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.

New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.

Revisiting an important component of plant genomes: microsatellites

Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.

Research progress and strategies for multifunctional rapeseed： A case study of China

Abstract Rapeseed ( Brassica napus ), is an important source of edible oil, animal fodder, vegetables, condiments and biodiesel, and plays a significant role in securing edible oil production worldwide. However, in countries with comparatively low levels of agricultural mechanization, such as China, increasing costs of labor and agricultural inputs are decreasing rapeseed profitability, and hence the area of rapeseed under cultivation. If the value of rapeseed crops is not further increased, the rapeseed growing area will continue to decrease, potentially jeopardizing oil production. Therefore, full exploitation of the existing and potential value of rapeseed is desirable. Different rapeseed products are already utilized in different ways, with more applications currently underutilized. As well as oil extraction from the seeds, the shoot and leaves can be used as vegetables, the roots to absorb soil cadmium for pollution remediation, the flowers for sightseeing and as a source of nectar, the pollen for extracting flavonoids and useful amino acids, the seeds/seed meal for extracting isthiocyanates and other important sulforaphane compounds, the straw and seed meal for fodder, and immature whole plants for green manure. This review summarizes recent research on ways to explore the potential holistic value of rapeseed, by taking the example of multifunctionality of rapeseed in China.

New insights into helitron transposable elements in the mesopolyploid species Brassica rapa

Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs.

Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species

Transposable elements (TEs) have attracted increasing attention because of their tremendous contributions to genome reorganization and gene variation through dramatic proliferation and excision via transposition. However, less known are the transcriptional activation of various TEs and the characteristics of TE insertion into genomes at the genome-wide level. In the present study, we focused on TE genes for transposition and gene disruption by insertion of TEs in expression sequences of Brassica, to investigate the transcriptional activation of TEs, the biased insertion of TEs into genes, and their salient characteristics. Long terminal repeat (LTR-retrotransposon) accounted for the majority of these active TE genes (70.8%), suggesting that transposition activation varied with TE type. 6.1% genes were interrupted by LTR-retrotransposons, which indicated their preference for insertion into genes. TEs were preferentially inserted into cellular component-specific genes acted as “binding” elements and involved in metabolic processes. TEs have a biased insertion into some host genes that were involved with important molecular functions and TE genes exhibited spatiotemporal expression. These results suggested that various types of transposons differentially contributed to gene variation and affected gene function.

Repetitive sequence characterization and development of SSR and CMS-gene-specific markers in the Brassica mitochondrial genomes

In the Brassica genus, relatively little is known about repetitive sequences in the mitochondrial genomes, and few mitochondrial molecular markers are available. In this study, repetitive sequences in the mitochondrial genomes of six Brassica species (Brassica rapa subsp. campestris, B. oleracea, B. nigra, B. napus (pol and nap), B. juncea and B. carinata) were analyzed. The distribution and characteristics of simple sequence repeats (SSRs), transposons, tandem repeat sequences, and inverted repeat sequences were assessed. A total of 148 SSRs were detected, with a density ranging from one SSR per 15.4 kbp to one SSR per 11.1 kbp per Brassica species. The most commonly identified SSRs were mononucleotide repeats. Many transposons, tandem repeats, and inverted repeats were also detected, with the most repeats in B. oleracea of all the species. Forty-eight bands amplified from 31 polymorphic SSR primers designed from the six Brassica mitochondrial genome sequences were screened across 92 Brassica accessions. Of these 48, 13 clear and reproducible bands (from 12 rimer pairs) could be used to distinguish between mitochondria from different species. Twelve polymorphic CMS (cytoplasmic male sterility)-gene-specific primers were developed from CMS-associated genes in the B. napus mitochondrial genome, and five primers could be used to distinguish mitochondria from different species, providing alternative markers for the identification of different Brassica mitochondrial types. Our results suggest that these SSR markers and CMS-gene-specific markers can be widely applied to characterize Brassica mitochondrial genomes. Further investigation of CMS-gene-associated markers may facilitate identification and utilization of CMS cytoplasm for future breeding approaches.