ORCID Profile
0000-0001-7355-4408
Current Organisation
Nanjing Agricultural University
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Publisher: Wiley
Date: 04-07-2019
DOI: 10.1111/PBI.13195
Publisher: Wiley
Date: 02-02-2023
DOI: 10.1111/PBI.14011
Abstract: High‐quality radish ( Raphanus sativus ) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly h ered functional genomics research and genome‐assisted breeding. Here, using a NAU‐LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi‐C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein‐coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole‐genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus . By comparing against the existing Xin‐li‐mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647‐bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3 , resulting into its low promoter activity and late‐bolting phenotype of NAU‐LB cultivar. Importantly, introgression of this 647‐bp insertion allele, RsVRN1 In‐536 , into early‐bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late‐bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome‐guided breeding and improvement in radish.
Publisher: Wiley
Date: 15-05-2020
DOI: 10.1111/JPI.12659
Publisher: Springer Science and Business Media LLC
Date: 08-08-2020
DOI: 10.1186/S12870-020-02585-Z
Abstract: Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size. A total of 2606 differentially expressed genes (DEGs) were shared between ‘NAU-DY’ (large acicular) and ‘NAU-YB’ (medium obovate), which were significantly enriched in ‘phenylpropanoid biosynthesis’, ‘glucosinolate biosynthesis’, and ‘starch and sucrose metabolism’ pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between ‘NAU-DY’ and ‘NAU-YH’ (small circular), whereas 12 miRNAs exhibited specific differential expression in ‘NAU-DY’. Association analysis indicated that miR393a- bHLH77 , miR167c- ARF8 , and miR5658- APL might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including SUS1 , EXPB3 , and CDC5 were characterized and profiled by RT-qPCR analysis. This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.
No related grants have been discovered for Liwang Liu.