Control of chromosomal meiotic pairing in the allopolyploid species, oilseed rape.

Brassica napus is an important species in world and UK agriculture. Oilseed rape (Canola) has become a major temperate oilseed crop over the past 40 years, and swede (rutabaga) has been established as a root vegetable and fodder crop for several centuries. We wish to develop a way of allowing breeders to more easily introduce useful genes. B. napus has 19 chromosomes, containing essentially the same 10 chromosomes as B. rapa ('A' genome; includes turnips, Chinese cabbage, pak choi) and the 9 chromosomes of B. oleracea ('C' genome; includes cabbage, cauliflower, broccoli, Brussels sprouts). The ploidy of a species refers to the typical number of copies of a given set of chromosomes in non-reproductive cells of an organism. Most organisms are normally diploid, meaning they have two sets of chromosomes - one set inherited from each parent. B. napus is an 'allopolyploid', since it contains chromosomes inherited from more than one species. Many other important crop species are allopolyploids, including wheat, cotton and potato. Genetic diversity in allopolyploids is often lower than in closely related diploid species and plant breeders frequently wish to introduce useful genes for traits such as disease resistance from diploids into the allopolyploid.
Unlike B. rapa and B. oleracea, which diverged from each other about 5 million years ago, B. napus is not found in natural populations in the wild. It appears to have arisen, probably in or near human cultivation, on more than one occasion within the past 1-2000 years from a hybridisation between domesticated B. rapa and B. oleracea. Most forms of B. napus generally have stable pairing between corresponding parental copies of each of the 19 chromosomes. Such behaviour means they are called amphidiploids (a form of allopolyploid that has stable pairing between homologous chromosomes and so behaves genetically like a diploid).
However, although recombination generally occurs between homologous chromosomes (i.e. specific A genome chromosomes or specific C genome chromosomes) within B. napus, a low incidence of recombination can occur between A and C genome homoeologues within oilseed rape cultivars. Homoeologues are similar but not identical chromosomes in each of the A and C genomes that correspond to common ancestral chromosomes and so still retain a generally conserved gene order since they diverged about 5 million years ago.
Due to the relatively low genetic diversity within B. napus, plant breeders sometimes wish to introduce novel genes (e.g. conferring disease resistance) from one of the diploid progenitor species (e.g. B. rapa) into B. napus, or by resynthesising B. napus. It is possible to produce "resynthesized" B. napus by crossing the two diploid species, performing an operation called embryo rescue (early in seed development), and doubling the chromosome number with a treatment of a chemical colchicine. In resynthesized B. napus recombination between homoeologues occurs more frequently, leading to chromosomal rearrangements and genetically unbalanced gametes. The difference between established B. napus and resynthesized B. napus can be used to explore the genetical basis of pairing control.
We have used a population derived from natural and resynthesized B. napus to locate a region of one chromosome (A9) that appears to contain a gene (or genes) that control the level of pairing between homoeologues. In this project we aim to characterise the effect that this locus has on the detailed process that occurs when chromosomes pair and recombine, and to pinpoint the likely candidate genes causing the differences in pairing. We will exploit the recently established genome sequence of B. rapa, and also try to identify subsets of the genepool of B. rapa that may have contributed stable pairing genes during the early hybridisation of B. napus. The information we generate will be of direct interest to plant breeders wishing to bring genes into modern varieties of oilseed rape.

A key factor in the stabilisation of allopolyploids is the control of chromosome pairing during meiosis so that homologues pair but homoeologues do not. Recombination between homoeologues can result in chromosomal structural changes affecting fertility. Breeders' attempts to introduce useful alleles from related diploids into the allopolyploid oilseed rape (AACC) using resynthesized hybrids often result in genetically unbalanced plants due to increased recombination between A and C homoeologues. Using cytogenetics and genetic mapping of a doubled haploid population from a stable/resynthesized cross, we have identified a QTL on A9 with a large effect on the control of homoeologous pairing (BHP1). To translate this exciting result into applications, we wish to characterise the gene(s).
We will characterise meiotic progression in lines that we have already identified as having either normal or high levels of homoeologous pairing, providing insights into mechanisms contributing to this control. We will use the new Affymetrix GeneChip Brassica Array to detect differences in gene expression within anthers of representative lines to provide information about candidate genes and additional locus resolution in the form of expression QTLs. We will also increase locus resolution using additional lines from the population and a series of SNP markers on A9 which we will develop guided by the newly available annotated genome sequence.It is likely that the non-permissive allele was inherited from the AA parent. Using information from the eQTL and locus resolution, SNP markers will be developed around the BHP1 locus to carry out association analysis in oilseed rape and closely related diploids. We will screen allelic variation across the selected germplasm to resolve the locus further and identify likely diploid progenitors.
This project will make a major contribution to breeding of stable resynthesized lines and may enable genetic diversity of elite cultivars to be increased.

Plant crops have played a major role in meeting Mankind's food demands for the last ten millennia. Today, plants are at the heart of a European food industry with an annual turnover of more than a trillion Euros. Intensive breeding has boosted plants' yield, quality and resistance to stress, but current predictions suggest that over the next 50 years, population growth and climate change mean we will need to produce more food than has been previously developed in the past 10,000 years. To achieve this, we will need to adopt ever-more novel approaches to crop plant breeding, including developing crops matched to individual world populations.
The end-use impact plan for this project focuses on interactions with the Oilseed Rape (OSR) pre-breeding pipeline and the plant breeding industry. Plant breeders have selected crops that now have a limited gene pool and one route to transfer useful traits from the diploid progenitors to the B. napus allopolyploid is via a resynthesized B. napus. Crossing the resynthesized B. napus with an established cultivar followed by back-crossing and selection for the trait introduces it into the established B. napus background. However, the instability of the resynthesized line leads to problems with genetic stability and yield of the progeny. Development of stable resynthesized B. napus would improve the efficiency of these breeding programmes.
We will present results on progress in resolving the BHP1 locus at the annual stakeholder meetings of the Defra-funded Oilseed Rape Genetic Improvement Network (OREGIN; www.oregin.info), and at the UK Brassica research community annual meetings (http://www.brassica.info/ukbrc/). Both of these meetings provide a platform for interactions with UK brassica breeders and the scientific community. One of the priorities within OREGIN that has been established with active input from the breeders, is the assessment of genetic diversity within the B. napus and wider gene pool in order to identify traits and alleles that can be introgressed into pre-breeding material. There will be opportunities to liaise with plant breeders who have already been introgressing disease resistance loci from e.g. B. rapa into B. napus, in order to discover alternative breeding schemes that involve prior crossing with B. rapa material containing non-permissive homoeologous pairing alleles. Given the potential wider impact, we will also engage with the British Society of Plant Breeders (BSPB), and provide an article to be disseminated to their members.
Once we have made sufficient progress in resolving the pairing loci, there are opportunities for wider dissemination through articles in e.g. BBSRC Business magazine. We will also produce newsletter at 36 months to circulate our results to interested parties including plant breeders.
We anticipate there could be considerable public interest in understanding the historical and geographic context of the currently unresolved origins of Oilseed Rape. We will therefore plan a press-release for dissemination to the wider press, dependent upon the release of the associated refereed publication.