Chromosome-level genome assembly of yellow lupin (Lupinus luteus) provides novel insights into genome evolution, crop adaptation and seed protein in the three most cultivated lupins DOI Creative Commons
Eduardo Martínez,

Haroldo Salvo-Garrido,

Daniela Levicoy

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: March 27, 2024

Abstract Lupinus luteus is a grain legume crop of agricultural importance due to its high seed protein content. In this study, the first chromosome-scale genome assembly L. (962.97 Mb) presented, integrating data from Illumina, PacBio, and Hi-C platforms. The exhibits exceptional completeness (98.9% BUSCO score) repetition rate (76.15%). Genomic annotation identifies 36,884 protein-coding genes, including 2,492 transcription factors 23 microRNA families. Synteny analysis with lupin species reveals important chromosomal rearrangements, indicating complex interactions between conserved regions structural variations. Our analyses suggest that chromosome 8 may have originated translocation event involving two chromosomes during speciation . Orthologous group characterization related indicates an enrichment in gene families associated biotic abiotic stress responses, secondary metabolism, nutrient reservoir activity. Moreover, 911 resistance (R) genes are identified, highlighting their pathogen defence. Exploration alkaloid biosynthesis regulation 16 quinolizidine alkaloids (QAs) expression revealing tissue-specific patterns for key enzymes QA biosynthesis. Furthermore, metabolite transporters explored, angustifolius PUP1 ortholog, providing insights into mechanisms. This comprehensive provides valuable resources further understanding genetic basis traits , facilitating advancements adaptation, improvement, sustainability.

Language: Английский

Radish (Raphanus sativus L.) Germplasm Resources DOI

Xixiang Li,

Xiaoman Li, Jalil Ahmad

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
RsLBD3 regulates the secondary growth of taproot by integrating auxin and cytokinin signaling in radish (Raphanus sativus L.) DOI

Junhui Dong,

Yan Wang, Liang Xu

et al.

Journal of Integrative Plant Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 7, 2025

Radish (Raphanus sativus L.) is a globally important root vegetable crop known for its diverse varieties and unique taproot characteristics. The LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene family, specific to plants, plays pivotal role in the development of lateral plant organs. Nonetheless, precise biological functions molecular regulatory mechanisms genes radish remain largely unexplored. In this study, RsLBD3 was identified as potential candidate affecting size through genome-wide association study. Further investigation revealed two insertions C-terminal region RsLBD3, with insertion363 notably enhancing transcriptional activation capability RsLBD3. It observed that taproots RsLBD3Ins-363 haplotype displayed significantly greater length weight compared those RsLBD3Del-363 haplotype. RNA situ hybridization reverse transcription quantitative polymerase chain reaction analysis exhibits high expression level vascular cambium induced by cytokinin treatment. Silencing resulted inhibition activity taproot, thereby impeding thickening. Exogenous treatment could partially rescue small-taproot phenotypes caused silencing. Moreover, RsARF5 (AUXIN RESPONSE FACTOR 5), RsRR7b (RESPONSE REGULATOR 7), RsCYCD3-1 (CYCLIN D3;1) were target Notably, found directly regulate RsWOX4 (WUSCHEL-RELATED HOMEOBOX 4). Additionally, biochemical demonstrated RsTCP14 interacts contributing binding genes. Collectively, these findings contribute better understanding underlying morphogenesis, provide novel allelic variations genetic enhancement shape traits radish.

Language: Английский

Citations

0
Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis DOI Creative Commons
Eduardo Martínez,

Haroldo Salvo-Garrido,

Daniela Levicoy

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: May 14, 2025

Language: Английский

Citations

0
A near‐complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods DOI Creative Commons
Yi Yang, Zhikun Wu, Zengxiang Wu

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(12), P. 2473 - 2489

Published: Aug. 9, 2023

Summary Asparagus bean ( Vigna unguiculata ssp. sesquipedialis ), a subspecies of V. , is vital legume crop widely cultivated in Asia for its tender pods consumed as vegetables. However, the existing asparagus assemblies still contain numerous gaps and unanchored sequences, which presents challenges to functional genomics research. Here, we present an improved reference genome sequence elite variety, Fengchan 6, achieved through integration nanopore ultra‐long reads, PacBio high‐fidelity Hi‐C technology. The assembly 521.3 Mb length demonstrates several enhancements, including higher N50 (46.4 Mb), anchor ratio 99.8%, presence only one gap. Furthermore, successfully assembled 14 telomeres all 11 centromeres, four telomere‐to‐telomere chromosomes. Remarkably, centromeric regions cover total 38.1 Mb, providing valuable insights into complex architecture centromeres. Among 30 594 predicted protein‐coding genes, identified 2356 genes that are tandemly duplicated segmental duplication regions. These findings have implications defence responses may contribute evolutionary processes. By utilizing genome, were able effectively identify gene VuMYB114 regulates accumulation anthocyanins, thereby controlling purple coloration pods. This discovery holds significant understanding underlying mechanisms color determination breeding process. Overall, highly serves crucial resource lays solid foundation genomic studies genetic improvement efforts.

Language: Английский

Citations

9
RsPDR8, a member of ABCG subfamily, plays a positive role in regulating cadmium efflux and tolerance in radish (Raphanus sativus L.) DOI
Xinyu Zhang,

Yingfei Ma,

Deqiang Lai

et al.

Plant Physiology and Biochemistry, Journal Year: 2023, Volume and Issue: 205, P. 108149 - 108149

Published: Oct. 29, 2023

Language: Английский

Citations

9
RsVQ4-RsWRKY26 module positively regulates thermotolerance by activating RsHSP70-20 transcription in radish (Raphanus sativus L.) DOI
Qing He, Min He, Xiaoli Zhang

et al.

Environmental and Experimental Botany, Journal Year: 2023, Volume and Issue: 214, P. 105467 - 105467

Published: Aug. 8, 2023

Language: Английский

Citations

8
Genome-wide analysis of radish AHL gene family and functional verification of RsAHL14 in tomato DOI Creative Commons
Weifang Chen,

Leifu Chen,

Lei Cui

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: May 30, 2024

The AT-hook motif nuclear localized ( AHL ) gene family is a highly conserved transcription factors involved in plant growth, development, and stress responses. However, AHLs have not been systematically analyzed radish Raphanus sativus ). Therefore, we performed genome-wide identification expression pattern, structure, function verifications of . We identified 52 RsAHL1–RsAHL52 ), which were unevenly distributed across nine chromosomes. Phylogenetic analysis showed that the RsAHLs divided into two clades (A B) subdivided three types (I, II, III). Collinearity revealed produced 49 repeat events. Tissue profiles differential different tissues, with higher observed flower organs, particularly petals anthers. qRT-PCR results indicated responded to abscisic acid, methyl jasmonate, abiotic (low high temperatures drought). Additionally, RsAHL14 induced dwarf phenotype tomato plants, -overexpression plants presented significantly decreased levels gibberellin (GA) synthetic genes ent-Copalyl diphosphatase , GA3ox-3/-4/-5 GA20ox-1/-2/-3 but increased degradation GA2ox-1/-3 Thus, might affect growth by regulating GA content. Collectively, our study comprehensively provided reference for further research on these genes.

Language: Английский

Citations

3
Genome-wide characterization of the CPA gene family in potato and a preliminary functional analysis of its role in NaCl tolerance DOI Creative Commons
Jintao Liu,

Dianjue Li,

Jing Wang

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 5, 2024

Abstract Background The cation/proton antiporter (CPA) superfamily plays a crucial role in regulating ion homeostasis and pH plant cells, contributing to stress resistance. However, potato ( Solanum tuberosum L.), systematic identification analysis of CPA genes are lacking. Results A total 33 StCPA members were identified classified into StNHX n = 7), StKEA 6), StCHX 20) subfamilies. owned the highest number conserved motifs, followed by StNHX. subfamilies more exons than StCHX. NaCl induced differentially expression 19 roots or leaves, among which StCHX14 StCHX16 specifically while StCHX2 StCHX19 expressed roots. 11 strongly responded further verified qPCR. Six family members, StNHX1 , StNHX2 StNHX3 StNHX5 StNHX6 proved transport Na + through yeast complementation experiments. Conclusions This study provides comprehensive insights StCPAs their response stress, facilitating functional characterization.

Language: Английский

Citations

2
Establishing VIGS and CRISPR/Cas9 techniques to verify RsPDS function in radish DOI Creative Commons
Jiali Ying, Yan Wang,

Liang Xu

et al.

Journal of Integrative Agriculture, Journal Year: 2024, Volume and Issue: 23(5), P. 1557 - 1567

Published: March 22, 2024

Virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are effective technologies for rapid accurate function verification in modern plant biotechnology. However, the investigation of editing radish remains limited. In this study, a bleaching phenotype was generated through knockdown RsPDS using tobacco rattle virus (TRV)- turnip yellow mosaic (TYMV)-mediated vectors. The TYMV-mediated efficiency higher than TRV-based VIGS system radish. expression level significantly inhibited 'NAU-067' leaves. rootless seedlings were infected with Agrobacterium rhizogenes 2300GN-Ubi-RsPDS-Cas9 vector two target sequences. Nine adventitious roots blue GUS staining, four these edited at sequence 1 as indicated by Sanger sequencing. Furthermore, albino lines A. tumefaciens-mediated transformation cotyledons. Five base substitutions three deletions occurred 2 Line 1, insertions 2. This study shows that CRISPR/Cas9 techniques can be employed to precisely verify biological functions genes radish, which will facilitate genetic improvement vital horticultural traits breeding programs.

Language: Английский

Citations

2
Whole Genome Sequencing and Analysis of Tumour-Forming Radish (<em>Raphanus sativus</em> L.) Line DOI Open Access
Xenia A. Kuznetsova, И. Е. Додуева, Alexey М. Afonin

et al.

Published: May 8, 2024

Spontaneous tumours in higher plants can develop depending on plant genotype without any pathogen invasion. tumour formation the taproots is consistently observed certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this work, we have sequenced genomes two closely related that differ their ability to spontaneously form tumours. We identified numerous single nucleotide variants (amino acid substitutions, insertions or deletions) are likely be associated with spontaneous formation. Furthermore, performed identification CLE and WOX genes genomic sequences and, as a result, unique which probably encode proteins multiple domains. The results obtained provide basis for investigating mechanisms also future genetic studies radish.

Language: Английский

Citations

2