Genetic dissection of plant architecture-related traits by GWAS with PCA in Brassica napus

ZHANG Xu, Safdar Luqman Bin, TANG Min-qiang, LIU Yue-ying, ZHANG Yuan-yuan, LIU Sheng-yi

CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2021, Vol. 43 ›› Issue (3) : 462.

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CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2021, Vol. 43 ›› Issue (3) : 462. DOI: 10.19802/j.issn.1007-9084.2020032

Genetic dissection of plant architecture-related traits by GWAS with PCA in Brassica napus

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Abstract

     For global demand of high yield breeding, complex genetic regulation on plant architecture was focused by genome-wide association study (GWAS) and principal component analysis (PCA), based on 4 typical traits related to plant architecture (PA) of 373 B. napus (L.) accessions. The 4 traits included plant height, branch height,branch number and main inflorescence length in 3 environments (Wuhan 2014-2015, Wuhan 2015-2016, and Yangzhou 2015-2016). Results showed that PCA could reasonably explain the phenotypes related to PA. PCAGWA Sand normal GWAS could verify and complement each other and provide the most information on traits that determine rapeseed architecture. Further, 19 PA related candidate genes were obtained from chromosomes A01, A10 and C06. Two genes on chromosome C06 were related to the new loci identified by PC1-GWAS. This method and results provide new ideas and strategies for the analysis of the formation mechanism of complex traits such as PA.

Key words

  / plant architecture；Brassica napus；principal component analysis；GWAS

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ZHANG Xu, Safdar Luqman Bin, TANG Min-qiang, LIU Yue-ying, ZHANG Yuan-yuan, LIU Sheng-yi. Genetic dissection of plant architecture-related traits by GWAS with PCA in Brassica napus[J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(3): 462 https://doi.org/10.19802/j.issn.1007-9084.2020032

References

［1］ Barthelemy D，Caraglio Y. Plant architecture：A dynamic， multilevel and comprehensive approach to plant
form，structure and ontogeny［J］. Ann Bot，2007，99（3）：375-407. DOI：10.1093/aob/mcl260.
［2］ Chalhoub B，Denoeud F，Liu S Y，et al. Plant genetics.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome［J］. Science， 2014， 345（6199）：950-953.DOI：10.1126/science.1253435.
［3］ Schmidt R，and Bancroft I. Genetics and genomics of the nBrassicaceae［M］. New York：Springer，2011. DOI：10.1007/978-1-4419-7118-0_21.
［4］ 陈新军，戚存扣，浦惠明，等. 甘蓝型油菜抗倒性评价及抗倒性与株型结构的关系［J］. 中国油料作物学
报，2007，29（1）：54-57，62.
［5］ 张洁夫，严建民. 油菜株型结构及其理想型研究Ⅱ.无花瓣性状对构建理想株型的作用［J］. 中国油料作
物学报，1998，20（1）：33-37.
［6］ 张洁夫，傅寿仲. 油菜株型结构及其理想型研究Ⅲ.若干高产品种的株型及冠层结构［J］. 中国油料作物学
报，1998，20（3）：36-41.
［7］ 周清元，李军庆，崔翠，等. 油菜半矮秆新品系10D130株型性状的遗传分析［J］. 作物学报，2013，39
（2）：207-215.
［8］ Cai G Q，Yang Q Y，Chen H，et al. Genetic dissectionof plant architecture and yield-related traits in Brassicanapus［J］. Sci Rep，2016，6：21625. DOI：10.1038/srep21625.
［9］ Lu K，Peng L，Zhang C，et al. Genome-wide associa⁃tion and transcriptome analyses reveal candidate genes underlying yield-determining traits in Brassica napus［J］. Front Plant Sci，2017，8：206. DOI：10.3389/
fpls.2017.00206.
［10］ Wu D Z，Liang Z，Yan T，et al. Whole-genome resequencing of a worldwide collection of rapeseed accessions reveals the genetic basis of ecotype divergence［J］.Mol Plant，2019，12（1）：30-43. DOI：10.1016/j.molp.2018.11.007.
［11］ Wei L，Jian H，Lu K，et al. Genome-wide associationanalysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus［J］. Plant Biotechnol J，2015：n/a-n/a.DOI：10.1111/pbi.12501.
［12］ Xu L P，Hu K N，Zhang Z Q，et al. Genome-wide association study reveals the genetic architecture of flowering time in rapeseed（Brassica napus L.）［J］. DNA Res，2016，23（1）：43-52. DOI：10.1093/dnares/dsv035.
［13］ He L N，Liu Y J，Xiao P，et al. Genomewide linkage scan for combined obesity phenotypes using principal component analysis［J］. Ann Human Genet，2008，72（3） ： 319-326. DOI： 10.1111/j. 1469-
1809.2007.00423.x.
［14］ Porebski S，Bailey L G，Baum B R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components［J］. Plant Mol Biol Rep，1997，15（1）：8-15. DOI：10.1007/
BF02772108.
［15］ Chalhoub B，Denoeud F，Liu S Y，et al. Plant genetics.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome［J］. Science， 2014， 345（6199）：950-953. DOI：10.1126/science.1253435.
［16］ Yang J，Lee S H，Goddard M E，et al. GCTA：a tool for genome-wide complex trait analysis［J］. Am J Hum Genet，2011，88（1）：76-82.DOI：10.1016/j.ajhg.2010.11.011.
［17］ Bates D，Mächler，M，Dai B. lme4：Linear mixed-effects models using S4 classes［M/OL］. http：//lme4. rforger-project.org/，2011.
［18］ Kang H M，Sul J H，Service S K，et al. Variance component model to account for sample structure in genomewide association studies［J］. Nat Genet，2010，42（4）：348-354. DOI：10.1038/ng.548.
［19］ Barrett J C，Fry B，Maller J，Daly M J. Haploview：analysis and visualization of LD and haplotype maps［J］. Bioinformatics，2005，21：263-265. DOI：10.1093/bioin⁃formatics/bth457.
［20］ Busov V B，Brunner A M，Strauss S H. Genes for control of plant stature and form［J］. New Phytol，2008，177（3） ： 589-607. DOI： 10. 1111/j. 1469-8137.2007.02324.x.
［21］ Doebley J F，Gaut B S，Smith B D. The molecular genetics of crop domestication［J］. Cell，2006，127（7）：1309-1321. DOI：10. 1016/j.cell.2006.12.006.
［22］ Wang Y H，Li J Y. Molecular basis of plant architecture［J］. Annu Rev Plant Biol，200859（1）：253-279.DOI：CNKI：SUN：ZJJJ.0.2013-01-025.
［23］ Jiao Y Q，Wang Y H，Xue D W，et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice［J］. Nature Genetics，2010，42（6）：541-544.DOI：10. 1038/ng.591.
［24］ Barthélémy D，Caraglio Y. Plant architecture：a dynamic， multilevel and comprehensive approach to plant form，structure and ontogeny［J］. Ann Bot，2007，99（3）：375-407. DOI：10. 1093/aob/mcl260.

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