New pre-breeding tools for canola - facilitating canola improvement by accessing diploid variation
Term: 4 years, beginning 2024
Status: Ongoing
Researcher(s): Steve Robinson, AAFC
SaskCanola Investment: $88,000
Total Project Cost: $176,000
Funding Partners: WGRF
Objective
1. We will deploy the bridging material (CARP#2021.31) to generate synthetic B. napus lines already adapted to Canadian environments. At its conclusion, project #2021.31 will have successfully generated bridging lines for B. oleracea and B. rapa. This material provides the genotypes to manage the array of alleles required to domesticate the Brassica wild-relatives proposed in this project.
2. Additionally, this project proposes to improve hybridization success between B. napus and B. oleracea, by inactivating genes that contribute to post-fertilization barriers creating another method to increase diversity. The ability of the gene edited alleles will be evaluated for improvements towards the reproductive success of synthetic B. napus from B. oleracea and B. rapa and any improvements will be combined into the bridging lines.
Project Description
Access to genetic diversity is key to the success of crop breeding programs and, in this regard, the canola gene pool is particularly limited. This is due to the natural history of amphidiploid Brassica napus (AACC) being formed from an interspecific hybridization event between its diploid progenitor species B. rapa (A genome) and B. oleracea (C genome). This hybridization event(s) occurred recently (ca. 2000 years ago) meaning that there has been limited time for mutations and introgressions to occur and natural selection to increase the frequency of alleles required for further crop improvement. Canola breeders use a range of strategies to overcome this deficiency including mutagenesis, wide genetic crosses and crosses involving wild relatives. Crop wild relatives possess greater levels of diversity and the diploid progenitor species which are evolutionarily much older than B. napus, have had more time to accumulate higher frequencies of valuable alleles. These crop relatives act as a rich reservoir of alleles that offer solutions to breeding objectives if they can be effectively deployed. Unfortunately, significant barriers are present to impede the transfer of useful alleles from crop relatives into B. napus.
Major differences separate crop species from their wild relatives. These are traits that are often found in many crop species, including polyploids, flowering time, plant size and shape, shatter resistance and self-compatibility. The factors underlying these differences can be reduced to favourable alleles at only a few loci. They constitute what is called the “domestication syndrome” as these alleles are not competitive under natural conditions and are often referred to as crop domestication traits. These few traits have played an enormous part in the development of agriculture and human civilization. The domestication process is often described as a genetic bottleneck since it is associated with a reduction in genetic diversity, a phenomenon that is further exacerbated in modern crops by selection for additional desirable agronomic traits. Unfortunately, these selections can leave modern crops susceptible to disease, insect herbivory and abiotic stresses with no alleles immediately available to resist the stresses.
Self-fertilization is often observed in polyploid species as it improves the chances of finding a mate following the genetic isolation caused by the genome duplication event. Additional benefits of polyploidy include the presence of multiple gene copies protecting the polyploid from inbreeding depression that might otherwise become evident following repeated self-fertilization. Domestication traits in B. napus include seed size, self-compatibility, adaptations to photoperiod vernalization, chromosome pairing control, growth vigour, reduced primary dormancy and shatter resistance. These traits are essential for growth of B. napus in Canada and are equally critical to efficiently evaluate new germplasm. Therefore, elimination of any vernalization requirement and selection for early flowering time while retaining robust growth vigour is highly desirable. This combination of characters forms a baseline requirement that all new B. napus material needs to possess in order to be of interest to Canadian farmers.
However, newly formed polyploids become instantly isolated from their parents in terms of reproduction. This is a major impediment given that whenever useful resistance genes are identified in crop wild relatives, they are frustratingly difficult to deploy effectively. This phenomenon is a direct result of post-fertilization barriers that have evolved to promote the success of intraspecific hybridizations that possess balanced chromosome numbers and limit the success of interspecific crosses that possess an unbalanced chromosome number. These barriers play a major role in the diversification of species, evolution of genes, and the domestication of crops, but in so doing limit gene flow from progenitor diploid species into the newly formed polyploidy species. Although the direct introduction of desirable alleles into B. napus from its relatives is possible, it is complicated by the union of imbalanced gametes resulting in triploid plants and sterility. Some success has been achieved by generating synthetic B. napus lines by directly crossing B. rapa with B. oleracea and doubling the chromosome number to promote disomic inheritance and genome stability. However, the breeding potential of the resulting synthetic lines are difficult to evaluate as they are often sterile, exhibit self-incompatibility, flower late and require vernalization. In other words, they possess the exact opposite characteristics of a domesticated B. napus adapted to the Canadian environment. For this reason, their generation and use in breeding programs is not favored.
Recent genome analyses in Brassica species has elucidated the DNA sequence of B. rapa, B. oleracea and B. napus. These advances have led to the generation of key genomics infrastructure that allow high-throughput genotyping strategies to support marker-assisted selection including the Brassica 60K SNP Array. These genomics resources are now routinely used to characterize defined genetic populations. Detailed results from the molecular characterization of B. napus Nested Association Mapping (NAM) populations highlights that the B. napus C-genome in particular, as lacking genetic diversity with large chromosomal regions in linkage disequilibrium making this sub-genome an obvious target for improvement. Genetic mapping of key domestication traits in B. napus has identified the location of loci controlling vernalization, flowering time, seedling vigour, self-incompatibility and control over chromosome pairing providing a foundation to understand and manipulate these traits. Recent work at SRDC has integrated this information onto a common marker framework aiding marker-assisted selection (MAS). Additionally, genomic resources can be used to transfer knowledge from model organisms such as Arabidopsis thaliana where genetic dissection of traits is more rapid, and it is now a simple process to identify Brassica homologues to Arabidopsis alleles using alignment algorithms.