Insights into early generation synthetic amphidiploid Brassica juncea: a strategy to harness maximum parental genomic diversity for improving Indian mustard DOI Creative Commons
Pooja Garg, Shikha Tripathi, Anamika Kashyap

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 13, 2025

In India, amphidiploid Brassica juncea (AABB, 2n=36) is a significant oilseed crop, but its small gene pool limits ability to develop traits of higher breeding and economic value. Through interspecific hybridization from various lines the progenitor species, resynthesized B. (RBJ) can provide breeders with additional resources for creating genetically diverse stress-tolerant high-yielding cultivars. Three rapa accessions eight nigra were crossed in this study 33 synthetic lines. A total 28 crosses attempted, including three-way crosses, only cross combinations cytoplasm led successful embryonic development. Molecular diversity analysis these S 2 generation revealed genetic levels heterozygosity allelic richness, along variations yield-related traits. These results suggest that synthesized could effectively enrich base generate variability agronomically important shorter time duration. The characterized needs be utilized hybridization, already evolved genotypes, early generations before it lost due chromosomal rearrangements, recombination natural selection.

Language: Английский

Stigma receptors control intraspecies and interspecies barriers in Brassicaceae DOI Creative Commons
Jiabao Huang, Lin Yang, Yang Liu

et al.

Nature, Journal Year: 2023, Volume and Issue: 614(7947), P. 303 - 308

Published: Jan. 25, 2023

Abstract Flowering plants have evolved numerous intraspecific and interspecific prezygotic reproductive barriers to prevent production of unfavourable offspring 1 . Within a species, self-incompatibility (SI) is widely utilized mechanism that rejects self-pollen 2,3 avoid inbreeding depression. Interspecific restrain breeding between species often follow the SI × self-compatible (SC) rule, is, pollen unilaterally incompatible (UI) on pistils but compatible (UC) SC 1,4–6 The molecular mechanisms underlying SI, UI, UC their interconnections in Brassicaceae remain unclear. Here we demonstrate determinant S -locus cysteine-rich protein/ protein 11 (SCR/SP11) or signal from UI binds female receptor kinase (SRK) , recruits FERONIA (FER) 7–9 activates FER-mediated reactive oxygen stigmas 10,11 reject pollen. For responses, diverged coat B-class 12–14 differentially trigger nitric oxide, nitrosate FER suppress facilitate growth an intraspecies-preferential manner, maintaining integrity. Our results show SRK integrate offer paths achieve distant crops.

Language: Английский

Citations

87
A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres DOI Creative Commons
Lei Zhang,

Jianli Liang,

Haixu Chen

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(5), P. 1022 - 1032

Published: Jan. 23, 2023

Summary Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. reference genome, still contains hundreds of gaps. Here, we presented a near‐complete genome assembly v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong‐read sequencing Hi‐C technologies. The new 12 contigs, contig N50 38.26 Mb. Eight ten chromosomes were entirely reconstructed in single from telomere to telomere. We found that centromeres mainly invaded by ALE CRM long terminal repeats (LTRs). Moreover, there is high divergence centromere length sequence among genomes. further are enriched for Copia at 0.14 MYA on average, while pericentromeres Gypsy LTRs 0.51 average. These results indicated different invasion mechanisms between structures. In addition, novel repetitive PCR630 identified . Overall, assembly, offers valuable tools genomic genetic studies species provides insights into evolution centromeres.

Language: Английский

Citations

54
Bioinformatics and Functional Genomics DOI
Sarahani Harun, Rabiatul‐Adawiah Zainal‐Abidin

Springer eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 243 - 271

Published: Jan. 1, 2024

Language: Английский

Citations

12
Cold stress in Brassica vegetables: Morpho-physiological and molecular responses underlying adaptive mechanism DOI
Muhammad Adnan Raza, Hamza Sohail, Muhammad Ahmad Hassan

et al.

Scientia Horticulturae, Journal Year: 2024, Volume and Issue: 329, P. 113002 - 113002

Published: Feb. 16, 2024

Language: Английский

Citations

10
The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection DOI Creative Commons
Daniel J. Rigden, Xosé M. Fernández

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(D1), P. D1 - D10

Published: Dec. 27, 2021

Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide most recently elsewhere. Seven focus specifically COVID-19 SARS-CoV-2, SCoV2-MD, first of Issue's Breakthrough Articles. Major nucleic acid include MODOMICS, JASPAR miRTarBase. AlphaFold Protein Structure Database, described second Article, is stand-out protein section, where Human Proteoform Atlas GproteinDb are other notable arrivals. Updates DisProt, FuzDB ELM comprehensively cover disordered proteins. Under metabolism signalling section Reactome, ConsensusPathDB, HMDB CAZy major returning resources. In microbial viral genomes taxonomy systematics well covered by LPSN, TYGS GTDB. Genomics Ensembl, Ensembl Genomes UCSC Genome Browser. pharmacology resource names IUPHAR/BPS guide Therapeutic Target Database. New plant PlantGSAD for gene lists qPTMplants post-translational modifications. entire freely available online website (https://academic.oup.com/nar). Our latest update to NAR Molecular Biology Collection brings total number entries 1645. Following last year's cleanup, we have updated 317 entries, listing 89 trimming 80 discontinued URLs. current release at http://www.oxfordjournals.org/nar/database/c/.

Language: Английский

Citations

55
Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits DOI Creative Commons
Jorge Poveda, Sandra Díaz-González, María Díaz-Urbano

et al.

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 5, 2022

Brassicaceae family includes an important group of plants great scientific interest, e.g., the model plant Arabidopsis thaliana , and economic such as crops genus Brassica ( oleracea, napus rapa etc.). This is characterized by synthesis accumulation in their tissues secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved defense against pathogens pests. are among 30% species that cannot establish optimal associations with mycorrhizal hosts (together other families Proteaceae, Chenopodiaceae, Caryophyllaceae), GSLs could be this evolutionary process non-interaction. However, can beneficial interactions endophytic fungi, which requires a reduction defensive responses host and/or evasion, tolerance, or suppression defenses fungus. Although much remains to known about mechanisms Brassicaceae-endophyte fungal interaction, several cases have been described, fungi need interfere GSL hydrolysis plant, even directly degrade before they hydrolyzed antifungal isothiocyanates. Once fungus symbiosis formed, obtain benefits from agricultural point view, growth promotion increase yield quality, increased tolerance abiotic stresses, direct indirect control pests diseases. review compiles studies on interaction between plants, discussing success symbiosis, together obtained these plants. Due unique characteristics, seen fruitful source novel endophytes applications crops, well generate new models study allow us better understand amazing

Language: Английский

Citations

30
Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing DOI Creative Commons
Zhicheng Zhang, Jing Guo, Xu Cai

et al.

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: March 17, 2022

The species Brassica rapa includes several important vegetable crops. draft reference genome of B. ssp. pekinensis was completed in 2011, and it has since been updated twice. pangenome with structural variations 18 accessions published 2021. Although extensive genomic analysis conducted on rapa, a comprehensive annotation including gene structure, alternative splicing (AS) events, non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve models produced annotated version 3.5. In total, obtained 753,041 full-length non-chimeric (FLNC) reads collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% v3.1. Based isoform data, identified 830 novel protein-coding that were missed previous annotations, defined untranslated regions (UTRs) 20,340 corrected 886 wrongly spliced genes. We also 28,564 AS events 1,480 long RNAs (lncRNAs). relatively complete high-quality transcriptome for can facilitate further functional research.

Language: Английский

Citations

29
Natural variation in Arabidopsis responses to Plasmodiophora brassicae reveals an essential role for Resistance to Plasmodiophora brasssicae 1 (RPB1) DOI Creative Commons
Juan Camilo Ochoa, Soham Mukhopadhyay, Tomasz Bieluszewski

et al.

The Plant Journal, Journal Year: 2023, Volume and Issue: 116(5), P. 1421 - 1440

Published: Aug. 30, 2023

Despite the identification of clubroot resistance genes in various Brassica crops our understanding genetic basis immunity to Plasmodiophora brassicae infection model plant Arabidopsis thaliana remains limited. To address this issue, we performed a screen 142 natural accessions and identified 11 clubroot-resistant lines. Genome-wide association analysis several loci significantly linked with resistance. Three from two these were targeted for deletion by CRISPR/Cas9 mutation resistant Est-1 Uod-1. Deletion Resistance 1 (RPB1) rendered both lines susceptible P. pathotype P1+. Further rpb1 knock-out Uod-1 showed that RPB1 protein is required activation downstream defence responses, such as expression phytoalexin biosynthesis gene CYP71A13. has recently been shown encode cation channel localised endoplasmic reticulum. The accession Col-0 lacks functional gene; when transformed driven its native promoter it capable activating transcription response infection, but not sufficient confer Transient Nicotiana tabacum induced programmed cell death leaves. We conclude critical component Arabidopsis, acting pathogen recognition elaboration effective

Language: Английский

Citations

20
The story of a decade: Genomics, functional genomics, and molecular breeding in Brassica napus DOI Creative Commons

Jianwei Gu,

Zhilin Guan,

Yushun Jiao

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(4), P. 100884 - 100884

Published: March 16, 2024

Rapeseed (Brassica napus L.) is one of the major global sources edible vegetable oil and also used as a feed pioneer crop for sightseeing industrial purposes. Improvements in genome sequencing molecular marker technology have fueled boom functional genomic studies agronomic characters such yield, quality, flowering time, stress resistance. Moreover, introgression pyramiding key genes greatly accelerated genetic improvement important traits. Here we summarize recent progress rapeseed genomics genetics, discuss effective breeding strategies by exploring these findings rapeseed. These insights will extend our understanding mechanisms regulatory networks underlying traits facilitate process, ultimately contributing to more sustainable agriculture throughout world.

Language: Английский

Citations

6
Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species DOI Creative Commons
Daozong Chen, Haidong Chen,

Guoqiang Dai

et al.

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: June 14, 2022

Brassica species include important oil crops and vegetables in the world. The R2R3-MYB gene participates a variety of plant functions, including activation or inhibition anthocyanin biosynthesis. Although previous studies have reported its phylogenetic relationships, structures, expression patterns Arabidopsis, number sequence variation this family involvement natural quantitative biosynthesis regulation are still largely unknown. In study, by using whole genome sequences comprehensive genome-wide comparative analysis among six cultivated species, 2120 genes were identified total These phylogenetically clustered into 12 groups. between A C subgenomes showed better collinearity than B B. From comparing transcriptional changes five with purple green leaves for detection associated biosynthesis, 7 co-differentially expressed. promoter structure these that some variations non-coding region, but they highly conserved at protein level spatial structure. Co-expression anthocyanin-related R2R3-MYBs indicated MYB90 was strongly co-expressed TT8, structural F3H, LDOX, ANS UF3GT same time. results further clarified roles leaf coloration Brasica which provided new insights functions species.

Language: Английский

Citations

24