SmARF8, a transcription factor involved in parthenocarpy in eggplant.

Parthenocarpic fruit is a very attractive trait for consumers and especially in eggplants where seeds can lead to browning of the flesh and bitterness. However, the molecular mechanisms underlying parthenocarpy in eggplant still remain unknown. Some auxin response factors have been previously shown in model species, such as Arabidopsis and tomato, to play an important role in such a process. Here, we have identified a natural parthenocarpic mutant and showed that ARF8 from eggplant (SmARF8), is down-regulated in buds compared to wild-type plants. Further characterization of SmARF8 showed that it is a nuclear protein and an active transcriptional regulator. We determined that amino acids 629-773 of SmARF8 act as the transcriptional activation domain, the C terminus of SmARF8 is the protein-binding domain, and that SmARF8 might form homodimers. Expression analysis in eggplant showed that SmARF8 is expressed ubiquitously in all tissues and organs and is responsive to auxin. Eggplant transgenic lines harboring RNA interference of SmARF8 exhibited parthenocarpy in unfertilized flowers, suggesting that SmARF8 negatively regulates fruit initiation. Interestingly, SmARF8-overexpressing Arabidopsis lines also induced parthenocarpy. These results indicate that SmARF8 could affect the dimerization of auxin/indole acetic acid repressors with SmARF8 via domains III and IV and thus induce fruit development. Furthermore, the introduction of SmARF8 full-length cDNA could partially complement the parthenocarpic phenotypes in Arabidopsis arf8-1 and arf8-4 mutants. Collectively, our results demonstrate that SmARF8 may act as a key negative regulator involved in parthenocarpic fruit development of eggplant. These findings give more insights into the conserved mechanisms leading to parthenocarpy in which auxin signaling plays a pivotal role, and provide potential target for eggplant breeding.

Repetitive sequence analysis and karyotyping reveals centromere-associated DNA sequences in radish (Raphanus sativus L.).

BACKGROUND: Radish (Raphanus sativus L., 2n = 2x = 18) is a major root vegetable crop especially in eastern Asia. Radish root contains various nutritions which play an important role in strengthening immunity. Repetitive elements are primary components of the genomic sequence and the most important factors in genome size variations in higher eukaryotes. To date, studies about repetitive elements of radish are still limited. To better understand genome structure of radish, we undertook a study to evaluate the proportion of repetitive elements and their distribution in radish. RESULTS: We conducted genome-wide characterization of repetitive elements in radish with low coverage genome sequencing followed by similarity-based cluster analysis. Results showed that about 31% of the genome was composed of repetitive sequences. Satellite repeats were the most dominating elements of the genome. The distribution pattern of three satellite repeat sequences (CL1, CL25, and CL43) on radish chromosomes was characterized using fluorescence in situ hybridization (FISH). CL1 was predominantly located at the centromeric region of all chromosomes, CL25 located at the subtelomeric region, and CL43 was a telomeric satellite. FISH signals of two satellite repeats, CL1 and CL25, together with 5S rDNA and 45S rDNA, provide useful cytogenetic markers to identify each individual somatic metaphase chromosome. The centromere-specific histone H3 (CENH3) has been used as a marker to identify centromere DNA sequences. One putative CENH3 (RsCENH3) was characterized and cloned from radish. Its deduced amino acid sequence shares high similarities to those of the CENH3s in Brassica species. An antibody against B. rapa CENH3, specifically stained radish centromeres. Immunostaining and chromatin immunoprecipitation (ChIP) tests with anti-BrCENH3 antibody demonstrated that both the centromere-specific retrotransposon (CR-Radish) and satellite repeat (CL1) are directly associated with RsCENH3 in radish. CONCLUSIONS: Proportions of repetitive elements in radish were estimated and satellite repeats were the most dominating elements. Fine karyotyping analysis was established which allow us to easily identify each individual somatic metaphase chromosome. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of satellite and centromere-specific retrotransposon at centromeres. Our study provides a valuable basis for future genomic studies in radish.

Genome-wide identification and characterization of Dof transcription factors in eggplant (Solanum melongena L.).

Eggplant (Solanum melongena L.) is an important vegetable cultivated in Asia, Africa and southern Europe and, following tomato and pepper, ranks as the third most important solanaceous vegetable crop. The Dof (DNA-binding with one finger) family is a group of plant-specific transcription factors that play important roles in plant growth, development, and response to biotic and abiotic stresses. The genes in the Dof family have been identified and analysed in many plant species, but the information remains lacking for eggplant. In the present study, we identified 29 SmeDof members from the eggplant genome database, which were classifed into nine subgroups. The phylogeny, gene structure, conserved motifs and homologous genes of SmeDof genes were comprehensively investigated. Subsequently, we analysed the expression patterns of SmeDof genes in six different eggplant subspecies. The results provide novel insights into the family of SmeDof genes and will promote the understanding of the structure and function of Dof genes in eggplant, and the role of Dof expression during stress.

Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus).

Floral induction that initiates bolting and flowering is crucial for reproductive fitness in radishes. CONSTANS-like (CO-like, COL) genes play an important role in the circadian clock, which ensures regular development through complicated time-keeping mechanisms. However, the specific biological and functional roles of each COL transcription factor gene in the radish remain unknown. In this study, we performed a genome-wide identification of COL genes in the radish genome of three cultivars including 'Aokubi', 'kazusa' and 'WK10039', and we analyzed their exon-intron structure, gene phylogeny and synteny, and expression levels in different tissues. The bioinformatics analysis identified 20 COL transcription factors in the radish genome, which were divided into three subgroups (Group I to Group III). RsaCOL-09 and RsaCOL-12 might be tandem duplicated genes, whereas the others may have resulted from segmental duplication. The Ka/Ks ratio indicated that all the COL genes in radish, Arabidopsis, Brassica rapa, Brassica oleracea, Capsella rubella and rice were under purifying selection. We identified 6 orthologous and 19 co-orthologous COL gene pairs between the radish and Arabidopsis, and we constructed an interaction network among these gene pairs. The expression values for each COL gene during vegetable and flower development showed that the majority of Group I members had similar expression patterns. In general, the expression of radish COL genes in Groups I and III decreased during development, whereas the expression of radish COL genes in Group II first increased and then decreased. Substantial numbers of radish COL genes were differentially expressed after vernalization treatment. The expression levels of RsaCOL-02 and RsaCOL-04 were significantly increased during vernalization treatment, while the expression of RsaCOL-10 was significantly decreased. These outcomes provide insights for improving the genetic control of bolting and flowering in radish and other root vegetable crops, and they facilitate genetic improvements to radish yields and quality.