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Genome-wide investigation of genetic changes during modern breeding of Brassica napus

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Considerable genome variation had been incorporated within rapeseed breeding programs over past decades.

Abstract

In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6–10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.

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Acknowledgments

This work was supported by the Chinese National Basic Research and Development Program (2011CB109302), National Science & Technology Pillar Program during the Twelfth Five-year Plan Period (2013BAD01B03 and 2011BAD35B09) and Crop Germplasm Protection Project (NB2011-2130135). GK is supported in part by the Chutian Scholar program of Hubei province.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors declare that the study comply with the current laws of the country in which they were performed.

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Authors and Affiliations

  1. Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China

    Nian Wang, Feng Li, Biyun Chen, Kun Xu, Guixin Yan, Jiangwei Qiao, Jun Li, Guizhen Gao & Xiaoming Wu

  2. Department of Biology, University of York, Heslington, York, YO10 5DD, UK

    Ian Bancroft

  3. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Jingling Meng

  4. Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia

    Graham J. King

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  1. Nian Wang
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  2. Feng Li
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  3. Biyun Chen
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  4. Kun Xu
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  12. Xiaoming Wu
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Corresponding author

Correspondence to Xiaoming Wu.

Additional information

Communicated by Michael Gore.

N. Wang and F. Li have contributed equally.

Electronic supplementary material

Below is the link to the electronic supplementary material.

LD decay of rapeseed chromosomes A1 to A9 (TIFF 2292 kb)

LD decay of rapeseed chromosomes A10, C1 to C8 (TIFF 2482 kb)

LD decay of rapeseed chromosome C9 (TIFF 257 kb)

122_2014_2343_MOESM4_ESM.tif

Genomic distribution of putative artificial selection among sub-populations classified by five breeding regions. Signatures of putative artificial selection were measured by FST based on calculation of genetic differentiation among sub-populations five from five breeding regions. From the top to bottom, these five panels are corresponding to sub-populations of Australia, China, Europe, North America and Northeast Asia, respectively. FST was smoothed with a 0.5 Mb window and a 50 kb siding bin (see M&M). The red dash lines indicate value of 1st percentile of the empirical distribution of high FST-windows. Chromosomes were differed by black and gray plots sequentially (TIFF 1588 kb)

122_2014_2343_MOESM5_ESM.tif

Genomic distribution of putative artificial selection among sub-populations classified by three growth types. From the top to bottom, these three panels are corresponding to sub-populations of spring, semi-winter and winter, respectively. All other information is similar with Figure S4 (TIFF 1226 kb)

122_2014_2343_MOESM6_ESM.tif

Genomic distribution of putative artificial selection among sub-populations classified by five breeding periods in China. From the top to the bottom, these five panels are corresponding to sub-populations of 1950-1970, 1971-1980, 1981-1990, 1991-2000 and 2001-2011, respectively. All other information is similar with Figure S4. (TIFF 1723 kb)

122_2014_2343_MOESM7_ESM.tif

Genomic distribution of putative artificial selection among sub-populations classified by four breeding period in Europe. From the top to the bottom, these four panels are corresponding to sub-populations of 1950-1970, 1971-1980, 1981-1990 and 1991-2000, respectively. All other information is similar with Figure S4. (TIFF 1260 kb)

Accessions and their classification in this study (XLSX 29 kb)

LD decay for all 19 chromosomes and whole genome in rapeseed (XLSX 10 kb)

Change of nucleotide diversity between 1950-1970 and 1971-1980 in China and Europe (XLSX 9 kb)

Genomic regions with outlier FST windows based on sub-populations classified by breeding region (XLSX 14 kb)

Genomic regions with outlier FST windows based on sub-populations classified by growth type (XLSX 13 kb)

122_2014_2343_MOESM13_ESM.xlsx

Genomic regions with outlier FST windows based on sub-populations classified by different breeding periods in China and Europe (XLSX 17 kb)

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Wang, N., Li, F., Chen, B. et al. Genome-wide investigation of genetic changes during modern breeding of Brassica napus . Theor Appl Genet 127, 1817–1829 (2014). https://doi.org/10.1007/s00122-014-2343-6

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