BnaOmics: A comprehensive platform combining pan-genome and multi-omics data from Brassica napus

Genome-Wide Analysis of the PERK Gene Family in Brassica napus L. and Their Potential Roles in Clubroot Disease

The proline-rich extensin-like receptor kinase (PERK) gene family is crucial to various molecular and cellular processes in plants. We identified 50 PERK genes in Brassica napus to explore their evolutionary dynamics, structural diversity, and functional roles. These genes were grouped into four classes and unevenly distributed across 18 chromosomes. Phylogenetic studies and Ka/Ks ratios revealed purifying selection during the evolution process. They exhibited significant diversification in gene length, molecular weight, and isoelectric points, suggesting specialized function. Gene structure and motif analyses revealed variations among the BnPERK family members, with conserved tyrosine kinase domains suggesting functional importance. Cis-element analysis predicted the involvement in hormone signaling and stress responses. Expression profiling showed diverse patterns across tissues and hormone treatments, highlighting potential roles in growth regulation and hormone signaling. Protein-protein interaction networks suggested BnPERK proteins interact with a wide array of proteins, implicating them in multiple biological processes. The transcriptional downregulation of four BnPERK genes upon Plasmodiophora brassicae infection implied a role in clubroot disease response. Furthermore, the Arabidopsis perk9 mutant displayed relieved disease severity and enhanced basal immune response, suggesting the negative role of PERK9 in plant immunity. The study highlighted the potential role of BnPERKs in crop improvement strategies against clubroot disease.

Integrated Transcriptome and Metabolome Analysis Reveals the Resistance Mechanisms of Brassica napus Against Xanthomonas campestris

Rapeseed (Brassica napus L.) is an important crop for healthy edible oil and stockfeed worldwide. However, its growth and yield are severely hampered by black rot, a destructive disease caused by Xanthomonas campestris pv. campestris (Xcc). Despite the identification of several quantitative trait loci (QTLs) associated with resistance to black rot in Brassica crops, the underlying molecular mechanisms remain largely unexplored. In this study, we investigated Xcc-induced transcriptomic and metabolic changes in the leaves of two rapeseed varieties: Westar (susceptible) and ZS5 (resistant). Our findings indicated that Xcc infection elicited more pronounced overall transcriptomic and metabolic changes in Westar compared to ZS5. Transcriptomic analyses revealed that the phenylpropanoid biosynthesis, cutin, suberine and wax biosynthesis, tryptophan metabolism, and phenylalanine metabolism were enriched in both varieties. Notably, photosynthesis was down-regulated in Westar after infection, whereas this down-regulation occurred at a later stage in ZS5. Integrated analyses of transcriptome and metabolome revealed that the tryptophan metabolism pathway was enriched in both varieties. Indolic glucosinolates and indole-3-acetic acid (IAA) are two metabolites derived from tryptophan. The expression of genes involved in the indolic glucosinolate pathway and the levels of indolic glucosinolates were significantly elevated in both varieties post-infection. Additionally, exogenous application of IAA promoted the development of black rot, whereas the use of an IAA synthesis inhibitor attenuated black rot development in both resistant and susceptible rapeseed varieties. These findings provide valuable molecular insights into the interactions between rapeseed and Xcc, facilitating the advancement of black rot resistance breeding in Brassica crops.

New perspectives of post-GWAS analyses: From markers to causal genes for more precise crop breeding

Crop breeding advancement is hindered by the imperfection of methods to reveal genes underlying key traits. Genome-wide Association Study (GWAS) is one such method, identifying genomic regions linked to phenotypes. Post-GWAS analyses predict candidate genes and assist in causative mutation (CM) recognition. Here, we assess post-GWAS approaches, address limitations in omics data integration and stress the importance of evaluating associated variants within a broader context of publicly available datasets. Recent advances in bioinformatics tools and genomic strategies for CM identification and allelic variation exploration are reviewed. We discuss the role of markers and marker panel development for more precise breeding. Finally, we highlight the perspectives and challenges of GWAS-based CM prediction for complex quantitative traits.

Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions

Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV-gene expression-trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.

The era of panomics-driven gene discovery in plants

Panomics is an approach to integrate multiple 'omics' datasets, generated using different individuals or natural variations. Considering their diverse phenotypic spectrum, the phenome is inherently associated with panomics-based science, which is further combined with genomics, transcriptomics, metabolomics, and other omics techniques, either independently or collectively. Panomics has been accelerated through recent technological advancements in the field of genomics that enable the detection of population-wide structural variations (SVs) and hence offer unprecedented insights into the genetic variations contributing to important agronomic traits. The present review provides the recent trends of panomics-driven gene discovery toward various traits related to plant development, stress tolerance, accumulation of specialized metabolites, and domestication/dedomestication. In addition, the success stories are highlighted in the broader context of enhancing crop productivity.

Polyploids of Brassicaceae: Genomic Insights and Assembly Strategies

The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods.

PPGV: a comprehensive database of peach population genome variation

Peach tree is one of the most important fruit trees in the world, and it has been cultivated for more than 7,500 years. In recent years, the genome and population resequencing of peach trees have been published continuously, which has effectively promoted the research of peach tree genetics and breeding. In order to promote the further mining and utilization of these data, we integrated and constructed a comprehensive peach genome and variation database (PPGV, http://peachtree.work/home ). The PPGV contains 10 sets of published peach tree genome data, as well as genomic variation information for 1,378 peach tree samples (the resequencing data of 1,378 samples were aligned with the high-quality genomes of Lovell, CN14 and Chinesecling, respectively, for mutation detection). A variety of useful and flexible tools, such as BLAST, Gene ID Convert, KEGG/GO Enrichment, Primer Design and Gene function, were also specially designed for searching data and assisting in breeding.

Technology-enabled great leap in deciphering plant genomes

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.

Novel quantitative trait loci from an interspecific Brassica rapa derivative improve pod shatter resistance in Brassica napus

Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (Brassica napus L.) crops. An interspecific breeding line BC95042 derived from a B. rapa/B. napus cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone B. napus variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F2 and F2:3 derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (AG, ABI3, ARF3, BP1, CEL6, FIL, FUL, GA2OX2, IND, LATE, LEUNIG, MAGL15, RPL, QRT2, RGA, SPT and TCP10) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the FUL (FRUITFULL) homologues BnaA03g39820D and BnaA09g05500D. Focusing on the FUL, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced B. napus accessions of interest. BnaA09g05500D is subjected to purifying selection as it had a low Ka/Ks ratio compared to other FUL homologues in B. napus. This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in Brassica species.