Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality
RESEARCH ARTICLE

Agricultural selection and presence–absence variation in spring-type canola germplasm

Annaliese S. Mason A B , Pratibha Chauhan C , Shashi Banga C , Surinder S. Banga C , Phil Salisbury D E , Martin J. Barbetti F and Jacqueline Batley B G H
+ Author Affiliations
- Author Affiliations

A Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.

B School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, Qld 4072, Australia.

C Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141 001, India.

D Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic. 3010, Australia.

E Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Vic. 3083, Australia.

F School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia.

G School of Biological Sciences and the UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia.

H Corresponding author. Email: jacqueline.batley@uwa.edu.au

Crop and Pasture Science - https://doi.org/10.1071/CP17161
Submitted: 20 April 2017  Accepted: 4 July 2017   Published online: 14 August 2017

Abstract

Brassica napus (rapeseed, canola) is an important oilseed crop worldwide as well as a recent agricultural hybrid species, resulting from crosses between progenitor B. rapa (turnip) and B. oleracea (cabbage) species in the last few thousand years. No wild form of B. napus is known to exist, making B. napus an interesting model for studies of genetic and genomic evolution in a polyploid under agricultural selective pressure. We generated genotype (Illumina Infinium 60K Brassica array) and phenotype data for elite spring-type B. napus lines from Australia, China and India (only one line). Phenotypically, plant growth, silique development and flowering traits were more likely to differentiate Chinese germplasm, whereas resistance to blackleg disease, secondary branching and seed traits were more likely to differentiate Australian germplasm. Genetic differentiation between the Australian and Chinese populations was low (FST = 0.035). Genetic relationship was not a predictor of similarity in yield traits between lines. Presence–absence variants were detected across the population: variants shared by at least three lines were present in every chromosome in the B. napus genome, and large missing chromosome segments (>1 Mbp) putatively due to A–C genome translocations were observed on chromosomes A7, A10, C1, C2, C6, C8 and C9. Our results highlight that widespread presence–absence variation is usual in B. napus, and may suggest that phenotypic and genetic diversity are not closely linked within spring-type B. napus from Australia and China, although the low sample numbers in our study prevent strong conclusions. We propose that inbreeding and low levels of genetic diversity, coupled with exchanges between the A and C genomes, were major driving forces behind genome evolution in this recent agricultural crop species.

Additional keywords: Brassica napus, genetic diversity, phenotype, SNP genotyping.


References

Allender CJ, King GJ (2010) Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers. BMC Plant Biology 10, 54
Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers.CrossRef |

Arús P, Tanksley SD, Orton TJ, Jones RA (1982) Electrophoretic variation as a tool for determining seed purity and for breeding hybrid varieties of Brassica oleracea. Euphytica 31, 417–428.
Electrophoretic variation as a tool for determining seed purity and for breeding hybrid varieties of Brassica oleracea.CrossRef |

Bayer PE, Ruperao P, Mason AS, Stiller J, Chan C-KK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D (2015) High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 128, 1039–1047.
High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus.CrossRef |

Bus A, Korber N, Snowdon RJ, Stich B (2011) Patterns of molecular variation in a species-wide germplasm set of Brassica napus. Theoretical and Applied Genetics 123, 1413–1423.
Patterns of molecular variation in a species-wide germplasm set of Brassica napus.CrossRef |

Chalhoub B, Denoeud F, Liu SY, Parkin IAP, Tang HB, Wang XY, Chiquet J, Belcram H, Tong CB, Samans B, Correa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao MX, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan GY, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan CC, Tollenaere R, Lu YH, Battail C, Shen JX, Sidebottom CHD, Wang XF, Canaguier A, Chauveau A, Berard A, Deniot G, Guan M, Liu ZS, Sun FM, Lim YP, Lyons E, Town CD, Bancroft I, Wang XW, Meng JL, Ma JX, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou YM, Hua W, Sharpe AG, Paterson AH, Guan CY, Wincker P (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345, 950–953.
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.CrossRef | 1:CAS:528:DC%2BC2cXhtlOmsr%2FK&md5=1a8efabc0ad3089b351cba8f65b3c609CAS |

Chan E (2008) Handy R functions for genetics research. Github repository. Available at: https://github.com/ekfchan/evachan.org-Rscripts

Chen S, Nelson MN, Ghamkhar K, Fu T, Cowling WA (2008) Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napus L.) in China and Australia. Genome 51, 1–10.
Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napus L.) in China and Australia.CrossRef |

Cifuentes M, Grandont L, Moore G, Chèvre AM, Jenczewski E (2010) Genetic regulation of meiosis in polyploid species: new insights into an old question. New Phytologist 186, 29–36.
Genetic regulation of meiosis in polyploid species: new insights into an old question.CrossRef | 1:CAS:528:DC%2BC3cXkvVOksbY%3D&md5=705388df609a5eb4ddb110cf13761e85CAS |

Clarke WE, Higgins EE, Plieske J, Wieseke R, Sidebottom C, Khedikar Y, Batley J, Edwards D, Meng J, Li R, Lawley CT, Pauquet J, Laga B, Cheung W, Iniguez-Luy F, Dyrszka E, Rae S, Stich B, Snowdon RJ, Sharpe AG, Ganal MW, Parkin IAP (2016) A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. Theoretical and Applied Genetics 129, 1887–1899.
A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.CrossRef | 1:CAS:528:DC%2BC28XhtFaitrvO&md5=7564c8a21d6651cb499a35838d1c5125CAS |

Cowling WA (2007) Genetic diversity in Australian canola and implications for crop breeding for changing future environments. Field Crops Research 104, 103–111.
Genetic diversity in Australian canola and implications for crop breeding for changing future environments.CrossRef |

Cresswell JE (1994) A method for quantifying the gene flow that results from a single bumblebee visit using transgenic oilseed rape, Brassica napus L. cv. Westar. Transgenic Research 3, 134–137.
A method for quantifying the gene flow that results from a single bumblebee visit using transgenic oilseed rape, Brassica napus L. cv. Westar.CrossRef | 1:CAS:528:DyaK2MXptVKg&md5=465649feff460ad9b4483b7284416599CAS |

Doyle J (1990) Isolation of plant DNA from fresh tissue. Focus 12, 13–15.

Friesen LF, Nelson AG, Van Acker RC (2003) Evidence of contamination of pedigreed canola (Brassica napus) seedlots in western Canada with genetically engineered herbicide resistance traits. Agronomy Journal 95, 1342–1347.
Evidence of contamination of pedigreed canola (Brassica napus) seedlots in western Canada with genetically engineered herbicide resistance traits.CrossRef |

Gajardo HA, Wittkop B, Soto-Cerda B, Higgins EE, Parkin IAP, Snowdon RJ, Federico ML, Iniguez-Luy FL (2015) Association mapping of seed quality traits in Brassica napus L. using GWAS and candidate QTL approaches. Molecular Breeding 35, 143
Association mapping of seed quality traits in Brassica napus L. using GWAS and candidate QTL approaches.CrossRef |

He Z, Cheng F, Lia Y, Wang X, Parkin IAP, Chalhoub B, Liu S, Bancroft I (2015) Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research. Data in Brief 4, 357–362.
Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research.CrossRef |

Kaur S, Cogan NOI, Ye G, Baillie RC, Hand ML, Ling AE, Mcgearey AK, Kaur J, Hopkins CJ, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith KF, Forster JW, Spangenberg GC (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. Theoretical and Applied Genetics 120, 71–83.
Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars.CrossRef | 1:CAS:528:DC%2BD1MXhsVKhurzJ&md5=89823eb6b80174a5b0acb7d5f925e8afCAS |

Körber N, Bus A, Li JQ, Parkin IAP, Wittkop B, Snowdon RJ, Stich B (2016) Agronomic and seed quality traits dissected by genome-wide association mapping in Brassica napus. Frontiers in Plant Science 7, 386
Agronomic and seed quality traits dissected by genome-wide association mapping in Brassica napus.CrossRef |

Kozak M, Bocianowski J, Liersch A, Tartanus M, Bartkowiak-Broda I, Piotto FA, Azevedo RA (2011) Genetic divergence is not the same as phenotypic divergence. Molecular Breeding 28, 277–280.
Genetic divergence is not the same as phenotypic divergence.CrossRef |

Lê S, Josse J, Husson F (2008) FactoMineR: An R package for multivariate analysis. Journal of Statistical Software 25, 1–18.
FactoMineR: An R package for multivariate analysis.CrossRef |

Li H, Sivasithamparam K, Barbetti MJ (2003) Breakdown of a Brassica rapa subsp. sylvestris single dominant blackleg resistance gene in B. napus rapeseed by Leptosphaeria maculans field isolates in Australia. Plant Disease 87, 752
Breakdown of a Brassica rapa subsp. sylvestris single dominant blackleg resistance gene in B. napus rapeseed by Leptosphaeria maculans field isolates in Australia.CrossRef |

Li CX, Li H, Sivasithamparam K, Fu TD, Li YC, Liu SY, Barbetti MJ (2006) Expression of field resistance under Western Australian conditions to Sclerotinia sclerotiorum in Chinese and Australian Brassica napus and Brassica juncea germplasm and its relation with stem diameter. Australian Journal of Agricultural Research 57, 1131–1135.
Expression of field resistance under Western Australian conditions to Sclerotinia sclerotiorum in Chinese and Australian Brassica napus and Brassica juncea germplasm and its relation with stem diameter.CrossRef |

Li CX, Wratten N, Salisbury PA, Burton WA, Potter TD, Walton G, Li H, Sivasithamparam K, Banga SS, Banga S, Singh D, Liu SY, Fu TD, Barbetti MJ (2008) Response of Brassica napus and B. juncea germplasm from Australia, China and India to Australian populations of Leptosphaeria maculans. Australasian Plant Pathology 37, 162–170.
Response of Brassica napus and B. juncea germplasm from Australia, China and India to Australian populations of Leptosphaeria maculans.CrossRef |

Li CX, Liu SY, Sivasithamparam K, Barbetti MJ (2009) New sources of resistance to Sclerotinia stem rot caused by Sclerotinia sclerotiorum in Chinese and Australian Brassica napus and B. juncea germplasm screened under Western Australian conditions. Australasian Plant Pathology 38, 149–152.
New sources of resistance to Sclerotinia stem rot caused by Sclerotinia sclerotiorum in Chinese and Australian Brassica napus and B. juncea germplasm screened under Western Australian conditions.CrossRef |

Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28, 2397–2399.
GAPIT: genome association and prediction integrated tool.CrossRef | 1:CAS:528:DC%2BC38XhtlantbrP&md5=5b3622938bb6af0bc56c841f2147f179CAS |

Liu LZ, Stein A, Wittkop B, Sarvari P, Li JN, Yan XY, Dreyer F, Frauen M, Friedt W, Snowdon RJ (2012) A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds. Theoretical and Applied Genetics 124, 1573–1586.
A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds.CrossRef | 1:CAS:528:DC%2BC38XmtlGiurw%3D&md5=98bf71a02a7c68fbe22fd2f8bddd9120CAS |

Liu S, Fan CC, Li JN, Cai GQ, Yang QY, Wu J, Yi XQ, Zhang CY, Zhou YM (2016) A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. Theoretical and Applied Genetics 129, 1203–1215.
A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus.CrossRef | 1:CAS:528:DC%2BC28XjtVOgurk%3D&md5=cf33a0fae5f850d55cf3e501df9e7688CAS |

Mason AS, Snowdon RJ (2016) Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species. Plant Biology
Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species.CrossRef | In press

Mason AS, Takahira J, Atri C, Samans B, Hayward A, Cowling WA, Batley J, Nelson MN (2015) Microspore culture reveals complex meiotic behaviour in a trigenomic Brassica hybrid. BMC Plant Biology 15, 173
Microspore culture reveals complex meiotic behaviour in a trigenomic Brassica hybrid.CrossRef |

Mason AS, Higgins EE, Snowdon RJ, Batley J, Stein A, Werner C, Parkin IAP (2017) A user guide to the Brassica 60K Illumina Infinium (TM) SNP genotyping array. Theoretical and Applied Genetics 130, 621–633.
A user guide to the Brassica 60K Illumina Infinium (TM) SNP genotyping array.CrossRef | 1:CAS:528:DC%2BC2sXjtVeksL0%3D&md5=e6bcd39c416f4c6f47097fd84c89703aCAS |

Morinaga T (1934) Interspecific hybridisation in Brassica VI. The cytology of F1 hybrids of B. juncea and B. nigra. Cytologia 6, 62–67.
Interspecific hybridisation in Brassica VI. The cytology of F1 hybrids of B. juncea and B. nigra.CrossRef |

Osborn TC, Butrulle DV, Sharpe AG, Pickering KJ, Parkin IA, Parker JS, Lydiate DJ (2003) Detection and effects of a homeologous reciprocal transposition in Brassica napus. Genetics 165, 1569–1577.

Palmer JD, Shields CR, Cohen DB, Orton TJ (1983) Chloroplast DNA evolution and the origin of amphidiploid Brassica species. Theoretical and Applied Genetics 65, 181–189.
Chloroplast DNA evolution and the origin of amphidiploid Brassica species.CrossRef | 1:CAS:528:DyaL3sXksFSntro%3D&md5=f983debba4bb9a85ac3256a1c993eb89CAS |

Pascher K, Macalka S, Rau D, Gollmann G, Reiner H, Glossl J, Grabherr G (2010) Molecular differentiation of commercial varieties and feral populations of oilseed rape (Brassica napus L.). BMC Evolutionary Biology 10, 63
Molecular differentiation of commercial varieties and feral populations of oilseed rape (Brassica napus L.).CrossRef |

R Development Core Team (2015) ‘R: A language and environment for statistical computing.’ 2.10.1 edn. (R Foundation for Statistical Computing: Vienna, Austria)

Salisbury PA, Ballinger DJ, Wratten N, Plummer KM, Howlett BJ (1995) Blackleg disease on oilseed Brassica in Australia - a review. Australian Journal of Experimental Agriculture 35, 665–672.
Blackleg disease on oilseed Brassica in Australia - a review.CrossRef |

Schiessl S, Samans B, Huttel B, Reinhard R, Snowdon RJ (2014) Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus. Frontiers in Plant Science 5, 404
Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus.CrossRef |

Schmutzer T, Samans B, Dyrska E, Lespinasse D, Micic Z, Abel S, Duchscherer P, Breuer F, Abbadi A, Leckband G, Snowdon RJ, Scholz U (2015) Species-wide genome sequence and nucleotide polymorphism datasets from the model allopolyploid plant Brassica napus. Scientific Data 2, 150072
Species-wide genome sequence and nucleotide polymorphism datasets from the model allopolyploid plant Brassica napus.CrossRef | 1:CAS:528:DC%2BC2MXitVWrtb3J&md5=53eb8b77286ea849836dfe16465e65cfCAS |

Szadkowski E, Eber F, Huteau V, Lodé M, Huneau C, Belcram H, Coriton O, Manzanares-Dauleux MJ, Delourme R, King GJ, Chalhoub B, Jenczewski E, Chèvre AM (2010) The first meiosis of resynthesized Brassica napus, a genome blender. New Phytologist 186, 102–112.
The first meiosis of resynthesized Brassica napus, a genome blender.CrossRef | 1:CAS:528:DC%2BC3cXkvVOktrY%3D&md5=033a38cf7afb04fc726946b1287ca523CAS |

U (1935) Genome-analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Japanese Journal of Botany 7, 389–452.

VanRaden P (2008) Efficient methods to compute genomic predictions. Journal of Dairy Science 91, 4414–4423.
Efficient methods to compute genomic predictions.CrossRef | 1:CAS:528:DC%2BD1cXhtlajtLzO&md5=cce9411dc87b84ba4cb258bf8fdad1a8CAS |

Wang N, Li F, Chen BY, Xu K, Yan GX, Qiao JW, Li J, Gao GZ, Bancroft I, Meng JL, King GJ, Wu XM (2014) Genome-wide investigation of genetic changes during modern breeding of Brassica napus. Theoretical and Applied Genetics 127, 1817–1829.
Genome-wide investigation of genetic changes during modern breeding of Brassica napus.CrossRef |

Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370.

West JS, Kharbanda PD, Barbetti MJ, Fitt BDL (2001) Epidemiology and management of Leptosphaeria maculans (phoma stem canker) on oilseed rape in Australia, Canada and Europe. Plant Pathology 50, 10–27.
Epidemiology and management of Leptosphaeria maculans (phoma stem canker) on oilseed rape in Australia, Canada and Europe.CrossRef |

Xiao YJ, Cai DF, Yang W, Ye W, Younas M, Wu JS, Liu KD (2012) Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites. Theoretical and Applied Genetics 125, 437–447.
Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites.CrossRef | 1:CAS:528:DC%2BC38XhtVGhurzM&md5=e6c5c409949f67552917a6bf67296359CAS |

Xiong Z, Gaeta RT, Pires JC (2011) Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proceedings of the National Academy of Sciences, USA 108, 7908–7913.

Xu LP, Hu KN, Zhang ZQ, Guan CY, Chen S, Hua W, Li JN, Wen J, Yi B, Shen JX, Ma CZ, Tu JX, Fu TD (2016) Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Research 23, 43–52.

Zhou Q-H, Fu D-H, Mason AS, Zeng Y-J, Zhao C-X, Huang Y-J (2014) In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus. Molecular Breeding 33, 881–894.
In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus.CrossRef |

Zou J, Jiang CC, Cao ZY, Li RY, Long Y, Chen S, Meng JL (2010) Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mapping. Genome 53, 908–916.
Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mapping.CrossRef | 1:CAS:528:DC%2BC3cXhsVansLnL&md5=bdde35b46967387533a36b3154a797f9CAS |

Zou J, Fu DH, Gong HH, Qian W, Xia W, Pires JC, Li RY, Long Y, Mason AS, Yang TJ, Lim YP, Park BS, Meng JL (2011) De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. The Plant Journal 68, 212–224.
De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa.CrossRef | 1:CAS:528:DC%2BC3MXhsVCksrrP&md5=9f27f0ce4d6b8681670c26b3283a652dCAS |



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