In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4-5 years) made in plant genetics using SSR markers.
MicroRNAs (miRNAs) are important for plant development and stress responses. However, factors regulating miRNA metabolism are not completely understood. SICKLE (SIC), a proline-rich protein critical for development and abiotic stress tolerance of Arabidopsis, was identified in this study. Loss-of-function sic-1 mutant plants exhibited a serrated, sickle-like leaf margin, reduced height, delayed flowering, and abnormal inflorescence phyllotaxy, which are common characteristics of mutants involved in miRNA biogenesis. The sic-1 mutant plants accumulated lower levels of a subset of miRNAs and transacting siRNAs but higher levels of corresponding primary miRNAs than the WT. The SIC protein colocalizes with the miRNA biogenesis component HYL1 in distinct subnuclear bodies. sic-1 mutant plants also accumulated higher levels of introns from hundreds of loci. In addition, sic-1 mutant plants are hypersensitive to chilling and salt stresses. These results suggest that SIC is a unique factor required for the biogenesis of some miRNAs and degradation of some spliced introns and important for plant development and abiotic stress responses.cold stress | hydroxyproline-rich glycoprotein | intron decay | mRNA stability M icroRNAs (miRNAs) are a class of endogenous small RNAs that function in gene regulation by guiding mRNA cleavage and translational repression and are critical for plant development and stress responses (1-9). The core components involved in miRNA biogenesis have been identified in plants. RNA polymerase II transcribes MIR genes; a 5′ 7-methyl guanosine cap and a 3′ poly(A) tail are added to produce primary miRNA (primiRNA) transcripts, which form imperfect stem-loop secondary structures by Watson-Crick base pairing between self-complementary foldback regions. In the Arabidopsis nucleus, the stemloop structure of the pri-miRNA is processed by the RNase III enzyme DICER-LIKE1 (DCL1) to produce a pre-miRNA, which is further processed to generate a 21-nt-long miRNA/miRNA* duplex. For accurate dicing, DCL1 requires the help of HYPO-NASTIC LEAVES1 (HYL1, a dsRNA-binding protein) and SERRATE (SE, a C2H2zinc-finger protein) (10). The HUA EN-HANCER 1 (HEN1) methyltransferase catalyzes 2'-O-methylation of the ribose sugar in the 3′ termini of miRNA/miRNA* duplexes (11). HASTY (HST), a homolog of mammalian EXPORTIN 5, helps export methylated miRNA/miRNA* duplexes from the nucleus to the cytosol (12). The mature miRNA is incorporated into ARGONAUTE1 (AGO1), forming an RNA-induced silencing complex, which scans for miRNA-complementary mRNAs and directs the cleavage or translational repression of the target mRNAs (1). miR173 and miRNA390 direct the biogenesis of transacting siRNAs (ta-siRNAs). Noncoding transcripts from TRANS-ACT-ING siRNA genes (TAS) are cleaved by the miRNA-containing AGO1/AGO7 complex (13, 14). The cleaved transcripts are converted into dsRNA by RDR6, and these dsRNAs are processed by DCL4 to yield ∼21-nt ta-siRNAs. Like miRNAs, tasiRNAs negatively regulate gene expression posttranscriptionally (15-18).N...
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