Evolution of genomes: Structure-function relationships in the polyploid crop species Brassica napus
Final Report Abstract
The genomes of plants have evolved through cycles of polyploidy (during which whole genome duplication occurs) and diploidisation (during which those duplicated genomes stabilise). This cycle represents a fundamental mechanism by which the genetic control of biological processes evolves and is a key driver of diversity and performance in many crop species. As a model for polyploid crop species we are studying Brassica napus, which includes northern Europe’s principal oil crop, oilseed rape. A wide range of accessions are available, of both B. napus formed in nature (an allotetraploid formed by spontaneous hybridization of B. rapa and B. oleracea species; the main source of genetic diversity for rapeseed breeding) and resynthesised B. napus (formed by induced hybridization of the same species in the laboratory), which has been observed to undergo rapid genome change. We hypothesise that the genome evolution observed in resynthesised B. napus represents an accelerated form of the genome evolution that is ongoing in cultivated B. napus derived in nature. We are testing this hypothesis by characterising molecular evolution on a genome-wide scale in a large panel of natural and resynthesised B. napus, including derived populations, relating the observed variation in genome structure to trait variation of relevance for rapeseed as a crop. During this project we have (1) Established a B. napus pan-transciptome, comprising ordered gene models representing the nascent B. napus genome. (2) Shown that homoeologous genome changes are present widely in B. napus formed in nature. (3) Quantified the frequency of copy number variation and homoeologous exchanges present in resynthesised B. napus, comparing it with the frequency observed in B. napus formed in nature. (4) Developed an understanding of how genome structural and functional evolution affects plant development and crop trait variation.
Publications
- Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research. Data in Brief 4:357-362, 2015
Zhesi He, Feng Cheng, Yi Li, Xiaowu Wang, Isobel A. P. Parkin, Boulos Chalhoub, Shengyi Liu and Ian Bancroft
(See online at https://doi.org/10.1016/j.dib.2015.06.016) - Deletion of a staygreen gene associates with adaptive selection in Brassica napus. Molecular Plant 9: 1559-1569
Qian L, Voss-Fels K, Cui Y, Jan HU, Samans B, Obermeier C, Qian W, Snowdon RJ
(See online at https://doi.org/10.1016/j.molp.2016.10.017) - Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization. Plant Biotechnology Journal 15:594-604, 2016
Z. He, L. Wang, A.L. Harper, L. Havlickova, A.K. Pradhan, I.A.P. Parkin, I. Bancroft
(See online at https://doi.org/10.1111/pbi.12657) - GSRC - an R package for genome structure rearrangement calling. Bioinformatics, 33: 545-546
Grandke F, Snowdon RJ, Samans B
(See online at https://doi.org/10.1093/bioinformatics/btw648) - (2017) Surviving a genome collision: Genomic signatures of allopolyploidization in the recent crop species Brassica napus. The Plant Genome
Samans B, Chalhoub B, Snowdon RJ
(See online at https://doi.org/10.3835/plantgenome2017.02.0013) - 2017. Impact of outcrossing on the Structural evolutionary dynamic, meiotic behavior and fertility of resynthesized allotetraploid Brassica napus L. Genes, Genomes, Genetics 7: 705-717
Rousseau-Gueutin M., Morice J., Coriton O., Huteau V., Trotoux G., Negre S., Falentin C., Deniot G., Gilet M., Eber F., Pele A., Vautrin S., Laperche A., Fourment J., Lode M., Berges H., Chevre A.M.
(See online at https://doi.org/10.1534/g3.116.036517) - Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus. Plant Biotechnology Journal
Obermeier C, Parkin IAP, Chévre AM, Snowdon RJ
(See online at https://doi.org/10.1111/pbi.12732) - Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds. The Plant Journal 93:181-192, 2018
Lenka Havlickova, Zhesi He, Lihong Wang, Swen Langer, Andrea L. Harper, Harjeevan Kaur, Martin R. Broadley, Vasilis Gegas and Ian Bancroft
(See online at https://doi.org/10.1111/tpj.13767)
