Intraspecific phenotypic diversity is controlled by natural genetic and epigenetic variation. Kawakatsu et al. recently sequenced the DNA methylomes of a global collection of over 1000 Arabidopsis accessions, and have thereby provided a comprehensive resource for studying natural genetic and epigenetic variation as well as the association of such variation with phenotypic diversity.

Arabidopsis encodes four DICER-like (DCL) proteins. DCL1 produces miRNAs, DCL2 produces some virus-derived siRNAs, and DCL3 produces endogenous RDR2-dependent siRNAs, but the role of DCL4 is unknown. We show that DCL4 is the primary processor of endogenous RDR6-dependent trans-acting siRNAs (tasiRNAs). Molecular and phenotypic analyses of all dcl double mutants also revealed partially compensat...

The Generalized Bernoulli Modeling approach is used to analyze the pattern change in intron sequences of a model plant species Arabidopsis thaliana. The influence of the intron length and the number of GC on the intron sequence pattern changes is examined. Two other gene properties, the gene expression level and the protein function encoded are also assessed. Among the random sampled intron seq...

In higher plants, peroxisomes have been believed to play a pivotal role in three metabolic pathways, which are lipid breakdown, photorespiration and H2O2-detoxificaton. Recently, significant progress in the study of plant peroxisomes was established by forward-/reverse-genetics and post-genomic approaches using Arabidopsis thaliana, the first higher plant to have its entire genome sequenced. Th...

The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequenc...

Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the eluci...

transition from vegetative to reproductive growth is an important stage in plant’s life. flowering pathways including photoperiod, vernalization, gibberellins, and autonomous pathway are regulated by different genes. identification of flowering genes is essential for the development of bolting-resistant sugar beet cultivars. in this study, a set of 118 arabidopsis thaliana genes involved in flo...

The completion of the Arabidopsis genome sequence is the culmination of a remarkable decade of world-wide growth and collaboration in developing Arabidopsis as a model genetic and genomic system. Since the 1930s, plant geneticists have been drawn to the study of Arabidopsis because of its small size, its predilection to self-pollinate, its quick generation time, and its copious production of ti...

In this chapter, we will describe a method set up to synthesize two profluorescent strigolactone (SL) mimic probes (GC240 and GC242) the optimized protocols developed study enzymatic properties of various receptors. The Arabidopsis AtD14 SL receptor is used here as model for purpose.