This book provides insights into the latest achievements in genomics research on Brassica rapa. It describes the findings on this Brassica species, the first of the U’s triangle that has been sequenced and a close relative to the model plant Arabidopsis, which provide a basis for investigations of major Brassica crop species. Further, the book focuses on the development of tools to facilitate the transfer of our rich knowledge on Arabidopsis to a cultivated Brassica crop. Key topics covered include genomic resources, assembly tools, annotation of the genome, transposable elements, comparative genomics, evolution of Brassica genomes, and advances in the application of genomics in the breeding of Brassica rapa crops.

This book provides insights into the latest achievements in genomics research on Brassica rapa. It describes the findings on this Brassica species, the first of the U's triangle that has been sequenced and a close relative to the model plant Arabidopsis, which provide a basis for investigations of major Brassica crop species. Further, the book focuses on the development of tools to facilitate the transfer of our rich knowledge on Arabidopsis to a cultivated Brassica crop. Key topics covered include genomic resources, assembly tools, annotation of the genome, transposable elements, comparative genomics, evolution of Brassica genomes, and advances in the application of genomics in the breeding of Brassica rapa crops.

Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history. Brassica rapa is particularly valuable for studying genome evolution because it also experienced whole genome triplication shortly after it diverged from the common ancestor it shares with Arabidopsis thaliana about 17-20 million years ago. While many B. rapa genes appear resistant to paralog retention, close to 50% of B. rapa genes have retained multiple, paralogous loci for millions of years and appear to be multi-copy tolerant. Based on previous studies, gene function may contribute to the selective pressure driving certain genes back to singleton status. It is suspected that other factors, such as gene expression patterns, also play a role in determining the fate of genes following whole genome triplication. Published RNA-seq data was used to determine if gene expression patterns influence the retention of extra gene copies. It is hypothesized that retention of genes in duplicate and triplicate is more likely if those genes are expressed in a tissue-specific manner, as opposed to being expressed globally across all tissues. This study shows that genes expressed specifically in flowers and roots in B. rapa are more resistant to fractionation than globally expressed genes following whole genome triplication. In particular, there appears to have been selection on genes expressed specifically in flower tissues to retain higher copy numbers and for all three copies to exhibit the same flower-specific expression pattern. Future research to determine if these observations in Brassica rapa are consistent with other angiosperms that have undergone recent whole genome duplication would confirm that retention of flower-specific-expressed genes is a general feature in plant genome evolution and not specific to B. rapa.

Due to their diversity, vegetable Brassicas are of great economic import and offer unique opportunities to enrich our knowledge about plant growth, development, and rapid phenotypic evolution. By applying emerging genomic technologies, we may greatly increase our understanding of the Brassica biology and breeding efficiency. This volume contains 11

The book describes the history of Brassica oilseed crops, introduces the Brassica genome, its evolution, diversity, classical genetic studies, and breeding. It also delves into molecular genetic linkage and physical maps, progress with genome sequencing initiatives, mutagenesis approaches for trait improvement, proteomics, metabolomics, and bioinfo

This book describes how the genome sequence contributes to our understanding of allopolyploidisation and the genome evolution, genetic diversity, complex trait regulation and knowledge-based breeding of this important crop. Numerous examples demonstrate how widespread homoeologous genome rearrangements and exchanges have moulded structural genome diversity following a severe polyploidy bottleneck. The allopolyploid crop species Brassica napus has the most highly duplicated plant genome to be assembled to date, with the largest number of annotated genes. Examples are provided for use of the genome sequence to identify and capture diversity for important agronomic traits, including seed quality and disease resistance. The increased potential for detailed gene discovery using high-density genetic mapping, quantitative genetics and transcriptomic analyses is described in the context of genome availability and illustrated with recent examples. Intimate knowledge of the highly-duplicated gene space, on the one hand, and the repeat landscape on the other, particularly in comparison to the two diploid progenitor genomes, provide a fundamental basis for new insights into the regulatory mechanisms that are coupled with selection for polyploid success and crop evolution.