Brassica napus mapping populations and linkage maps

We have developed four Doubled Haploid (DH) B. napus populations which we have genotyped and used as mapping populations in our research into plant architecture, seed oil content and fatty acid profiles.  These four populations are available for future collaborative work. Five new unmapped DH populations have also been developed as part of OREGIN.

TNDH population

The TNDH mapping population was developed by Prof. Jinling Meng, at the Huazhong Agricultural University, Wuhan, China in collaboration with Prof. Ian Bancroft at JIC as part of the EU-funded IMSORB project.

This population is derived from an F1 cross between Tapidor, a European Winter B. napus variety, and Ningyou7, a Chinese semi-Winter B. napus line. These parents were selected on the basis of their genetic dissimilarity, being the most divergent lines identified using RFLP markers (Meng et al., 1996) and for their contrasting trait characteristics and cultivation ranges.

• Tapidor is a European Winter-type cultivar (i.e. it has a strong vernalization requirement) with low seed erucic acid and glucosinolate content.
• Ningyou7 is a Chinese semi-Winter-type cultivar (i.e. it has little vernalization requirement) with high seed erucic acid and glucosinolate content. The breeding of Ningyou7 included crosses with B. rapa, and the cultivar is less Winter hardy than Tapidor.
• TNDH has been shown to segregate for a wide range of traits:

• Seed fatty acid content
• Flowering time
• Stem canker susceptibility
• Plant architecture
• Leaf chlorophyll content

Of the 202 lines, 188 informative lines were selected for genetic linkage map development as part of the IMSORB project. Details are given in Qui et al. 2006 with supporting erucic acid and oil content data.  Further work aligned the map to a B. rapa mapping population that used additional microsatellite markers (Suwabe et al. (2008)).

The TNDH population and map have been adopted as reference resources by the DEFRA-funded OREGIN project. The population has also been used for architectural and harvest index studies as part of the Novel Resources for Oilseed Rape Breeding Improving Harvest Index (NOVORB-HI) project and architecture and nitrogen use efficiency studies in collaboration with Newcastle University.

Working in collaboration with Prof. Jinling Meng of Huazhong Agricultural University, China we have developed and provide public access to the definitive map.  A genotyping file with all markers used and a high stringency map, suitable for QTL analyses, is available in text and graphic formats. 

Recently the population was transcriptome SNP mapped enabling the construction of twin high density SNP linkage maps consisting of 23,037 markers which aligned the B. napus genome with that of Arabidopsis thaliana and to the genome sequence assemblies of the napus progenitor species: B. rapa and B. oleracea (Bancroft et al., 2011).

For use of the TNDH population please contact Prof. Meng Jinling National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; jmeng@mail.hzau.edu.cn;

Relevant Publications

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing.
Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, Liu S and M Trick. (2011).
Nature Biotechnology 29 (8) 762-6

A genome genetic linkage map between Brassica napus and B. rapa.
Suwabe K, Morgan C and I. Bancroft, 2008: Integration of Brassica
Genome 51, 169—176

A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content.
Qiu D, Morgan C, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E, Weihmann T, Everett C, Vanstraelen S, Beckett P, Fraser F, Trick M, Barnes S and I Bancroft. (2006)
Theoretical and Applied Genetics114 67-80

Genetic diversity of Brassica napus accessions mainly from China detected with RFLP markers.
Meng J, Sharpe A, Bowman C, Tian Z, Qian X and D Lydiate. (1996)
Chin J Genet 23(3):221–232

 

QDH

This population is derived from a cross between a resynthesised B. napus line, developed by hybridisation of the spring turnip rape B. rapa oleifera ‘29’ var. Maleksberger and the Mediterranean cliff-dwelling wild species B. oleracea ‘Atlantica’, with the European B. napus cultivar, Tapidor. The objective was to capture a wide range of genetic diversity outside that of the conventional B. napus genepool.

A population of 92 DH lines were developed from the F1 material. Within the population segregation for a number of traits has been observed:

• Oil profile,
• Light leaf spot resistance,
• Plant architecture and
• Leaf shape.

The genotyping and map files used to generate the genetic map are available for use.

The latest map of this population and QTL identified for oleic, linoleic, linolenic, erucic acid and oil content are described by Smooker et al. (2010).

The QDH population is available through Prof. Ian Bancroft.

Relevant Publications

The identification and mapping of candidate genes and QTL involved in the fatty acid desaturation pathway in Brassica napus
Smooker A M, Wells R, Morgan C, Beaudoin F, Cho K, Fraser F and I Bancroft. (2010)
Theoretical and Applied Genetics 122 (6) 1075-1090

CRDH population

The CRDH population was developed at CPB Twyford (now KWS) as part of the NOVORB-HI DEFRA LINK Project in collaboration with Biogemma, Elsoms, CPB Twyfords, Nickersons, Monsanto, Saaten Union, HGCA and Prof. Ian Bancroft at JIC.

CRDH is derived from the F1 of a cross between Capitol, a Cargill/Monsanto variety, and Rocket, a CPB Twyfords variety. Both parents were chosen for variation in plant architecture and exhibit mid maturation times:

• Capitol is a tall, moderately stiff variety, with large internodes and pod spacing, medium sized pods, exhibiting some lodging but has a high yield potential and vegetative vigour whilst
• Rocket is short with compact internodes and pod spacing with a low yield potential.

From the original 244 plants developed, 94 were selected by the breeders for development of the mapping population. A publication containing this work is currently being prepared. For the purpose of SNP identification the parental transcriptomes have been sequenced. This data is being used within the IBTI project.

Observed varying nitrogen responses between the parental lines has lead to it also being studied as part of a DEFRA LINK project: SAPPIO 00323 [LK 0979] where the objective is Breeding Oilseed Rape with a low requirement for nitrogen fertiliser. Further mapping work is ongoing as part of this project.

Access to the population is via consortium agreement.

VGDH population

The VGDH population was also developed at CPB Twyford as part of the NOVORB-HI DEFRA LINK Project in collaboration with Biogemma, Elsoms, CPB Twyfords, Nickersons, Monsanto, Saaten Union, HGCA and Prof. Ian Bancroft at JIC.

It is derived from an F1 cross between the varieties Verona (Danisco Seeds), and Grizzly (RAGT-R2N variety). The parents were chosen for variation in plant architecture.

• Grizzly is a low biomass variety, with delayed stem elongation in the Spring, is very late to flower and mature but has good yield potential. It is fairly short with a prostrate growth habit, compact internodes and pod spacing.
• Verona is also both late flowering and maturing but is moderate height with stiff stems and good lodging resistance.

Of the original 251 lines developed, 94 were selected by the breeders for development of the mapping population. A publication describing this work is currently being prepared. For the purposes of SNP identification the parental transcriptomes have been sequenced. This data is being used within the IBTI project and for further mapping work.

Access to the population is via consortium agreement.

OREGIN populations

As part of the OREGIN project, 5 DH populations were developed to study selected traits identified as important for the improvement of B. napus but which are not being addressed by the private plant breeding community.

The 5 paternal lines were selected on the basis of:

• Genetic diversity,
• Good plant establishment and early vigour,
• N, P and K nutrient use efficiencies,
• Reduced premature seed loss and
• Plant pest resistance.

All were crossed onto a modern winter oilseed rape line; Temple, a line with good agronomy traits. This was used as the common maternal line in all crosses in order to standardise the cytoplasmic genomes across the populations.

The line characteristics are described in the table below. DH populations were developed and bulked by Elsoms Seeds with seed being available to the Brassica research community from Summer 2012.

TN145DH and TN172DH are from the TNDH mapping population (Tapidor × Ningyou 7).  Tapidor has high % N, P, K and low seedling vigour.

POSH169DH is from a mapping population for pod shattering resistance (Apex × (N-O-109 × synthetic napus)) and has poor agronomy traits.