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Construction of a worldwide core collection of rapeseed and association analysis for waterlogging tolerance

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Abstract

Rapeseed (Brassica napus) is an important oilseed crop and widely planted in the world. In our previous study, we collected 991 accessions of rapeseed from the worldwide germplasm and revealed the genetic polymorphisms within this germplasm by whole-genome resequencing. However, management of such a large amount of accessions is time-consuming, laborious and costly. Therefore, we constructed a worldwide core collection of rapeseed germplasm consisting of 300 accessions based on their genetic diversity. Compared with 991 accessions, the worldwide core collection showed similar geographic distribution, the proportion of ecotypes and nucleotide diversity. These results indicate that the genetic diversity of the worldwide core collection can represent that of 991 accessions. Moreover, 43 significantly associated SNPs for waterlogging tolerance of rapeseed at the seedling stage were identified by the genome-wide association study (GWAS) using the core collection. A major QTL was found at Chr. C07 and 11 candidate genes within this region encoding squalene monooxygenase, GDSL esterase/lipase and calcineurin B-like protein 4. The results indicate that the 300 accessions of the worldwide core collection could be more efficiently used for phenotypic and genetic studies in rapeseed.

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References

  • Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9):1655–1664. https://doi.org/10.1101/gr.094052.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ashraf M, Arfan M (2005) Gas exchange characteristics and water relations in two cultivars of Hibiscus esculentus under waterlogging. Biol Plant 49:459–462. https://doi.org/10.1007/s10535-005-0029-2

    Article  Google Scholar 

  • Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31(2):818–824. https://doi.org/10.1139/g89-144

    Article  Google Scholar 

  • Corak KE, Ellison SL, Simon PW, Spooner DM, Dawson JC (2019) Comparison of representative and custom methods of generating core subsets of a carrot germplasm collection. Crop Sci 59(3):1107–1121. https://doi.org/10.2135/cropsci2018.09.0602

    Article  Google Scholar 

  • Chalhoub B, Denoeud F, Liu SY, Parkin IAP, Tang HB, Wang XJ, 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(6199):950–953. https://doi.org/10.1126/science.1253435

    Article  CAS  PubMed  Google Scholar 

  • De Beukelaer H, Davenport GF, Fack V (2018) Core Hunter 3: flexible core subset selection. BMC Bioinformatics 19(203). https://doi.org/10.1186/s12859-018-2209-z

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

    Article  CAS  PubMed  Google Scholar 

  • Frankel OH (1984) Genetic perspectives of germplasm conservation. In: W. Arber (ed) Genetic manipulation: impact on man and society, Cambridge, England, pp 161–170

  • Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: An algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness. J Hered 92(1):93–94. https://doi.org/10.1093/jhered/92.1.93

    Article  CAS  PubMed  Google Scholar 

  • Guo ZF, Zhou SZ, Wang SH, Li WX, Du HW, Xu YB (2010) Identification of major QTL for waterlogging tolerance in maize using genome-wide association study and bulked sample analysis. J Appl Genetics 62:405–418. https://doi.org/10.1007/s13353-021-00629-0

    Article  CAS  Google Scholar 

  • Holbrook CC, Timper P, Xue HQ (2000) Evaluation of the core collection approach for identifying resistance to Meloidogyne arenaria in peanut. Crop Sci 40(4):1172–1175. https://doi.org/10.2135/cropsci2000.4041172x

    Article  Google Scholar 

  • Hu J, Zhu J, Xu HM (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101(1–2):264–268. https://doi.org/10.1007/s001220051478

    Article  CAS  Google Scholar 

  • Kanamaru K, Tanaka K (2004) Roles of chloroplast RNA polymerase sigma factors in chloroplast development and stress response in higher plants. Biosci Biotechnol Biochem 68(11):2215–2223. https://doi.org/10.1271/bbb.68.2215

    Article  CAS  PubMed  Google Scholar 

  • Kim KW, Chung HK, Cho GT, Ma KH, Chandrabalan D, Gwag JG, Kim TS, Cho EG, Park YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23(16):2155–2162. https://doi.org/10.1093/bioinformatics/btm313

    Article  CAS  PubMed  Google Scholar 

  • Kuroh T, Nagai K, Gamuyao R, Wang DR, Furuta T, Nakamori M, Kitaoka T, Adachi K, Minami A, Mori Y, Mashiguchi K, Seto Y, Yamaguchi S, Kojima M, Sakakibara H, Wu JZ, Ebana K, Mitsuda N, Ohme-Takagi M, Yanagisawa S, Yamasaka M, Yokoyama R, Nishitani K, Mochizuki T, Tamiya G, McCouch SR, Ashikari M (2018) Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding. Science 361(6398):181–185. https://doi.org/10.1126/science.aat1577

    Article  CAS  Google Scholar 

  • Lai CP, Huang LM, Chen LO, Chan MT, Shaw JF (2017) Genome-wide analysis of GDSL-type esterases/lipases in Arabidopsis. Plant Mol Biol 95(1–2):181–197. https://doi.org/10.1007/s11103-017-0648-y

    Article  CAS  PubMed  Google Scholar 

  • Li ZC, Zhang HL, Cao YS, Qiu ZE, Wei XH, Tang SY, Yu P, Wang XK (2003) Studies on the sampling strategy for primary core collection of Chinese ingenious rice. Acta Agron Sinica 29(1):20–24. https://doi.org/10.3321/j.issn:0496-3490.2003.01.004

    Article  CAS  Google Scholar 

  • Li W, Jiang W, Zhao HX, Vyvadilova M, Stamm M, Hu SW (2012) Genetic diversity of rapeseed accessions from different geographic locations revealed by expressed sequence tag-simple sequence repeat and random amplified polymorphic DNA markers. Crop Sci 52(1):201–210. https://doi.org/10.2135/cropsci2011.06.0301

    Article  CAS  Google Scholar 

  • Liu XB, Li J, Yang ZL (2018) Genetic diversity and structure of core collection of winter mushroom (Flammulina velutipes) developed by genomic SSR markers. Hereditas 155(1):3. https://doi.org/10.1186/s41065-017-0038-0

    Article  PubMed  Google Scholar 

  • Liu YQ, Wang HR, Jiang ZM, Wang W, Xu RN, Wang QH, Zhang ZH, Li AF, Liang Y, Ou SJ, Liu XJ, Cao SY, Tong HN, Wang YH, Zhou F, Liao H, Hu B, Chu CC (2021) Genomic basis of geographical adaptation to soil nitrogen in rice. Nature 590(7847). https://doi.org/10.1038/s41586-020-03091-w

  • Lv JB, Li CR, Zhou CP, Chen JB, Li FG, Weng QJ, Li M, Wang YQ, Chen SK, Chen JC, Gan SM (2020) Genetic diversity analysis of a breeding population of Eucalyptus cloeziana F. Muell. (Myrtaceae) and extraction of a core germplasm collection using microsatellite markers. Ind Crop Prod 145(112157). https://doi.org/10.1016/j.indcrop.2020.112157

  • Ma ZY, He SP, Wang XF, Sun JL, Zhang Y, Zhang GY, Wu LQ, Li ZK, Liu ZH, Sun GF, Yan YY, Jia YH, Yang J, Pan ZE, Gu QS, Li XY, Sun ZW, Dai PH, Liu ZW, Gong WF, Wu JH, Wang M, Liu HW, Feng KY, Ke HF, Wang JD, Lan HY, Wang GN, Peng J, Wang N, Wang LR, Pang BY, Peng Z, Li RQ, Tian SL, Du XM (2018) Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet 50(6):803–813. https://doi.org/10.1038/s41588-018-0119-7

    Article  CAS  PubMed  Google Scholar 

  • Mackay MC (1995) One core collection or many? In: Hodgkin T, Brown AHD, van Hintum TJL, Morales EAV (eds) Core collections of plant genetic resources. John Wiley & Sons Ltd, Chichester, pp 199–210

    Google Scholar 

  • Mahajan RK, Bisht IS, Dhillon BS (2007) Establishment of a core collection of world sesame (Sesamum indicum L.) germplasm accessions. SABRAO J Breed Genet 39(1):53–64. https://doi.org/10.1016/j.postharvbio.2006.12.006

    Article  CAS  Google Scholar 

  • Milner SG, Jost M, Taketa S, Mazon ER, Himmelbach A, Oppermann M, Weise S, Knuepffer H, Basterrechea M, Koenig P, Schueler D, Sharma R, Pasam RK, Rutten T, Guo GG, Xu DD, Zhang J, Herren G, Mueller T, Krattinger SG, Keller B, Jiang Y, Gonzalez MY, Zhao YS, Habekuss A, Faerber S, Ordon F, Lange M, Boerner A, Graner A, Reif JC, Scholz U, Mascher M, Stein N (2019) Genebank genomics highlights the diversity of a global barley collection. Nat Genet 51(2):319. https://doi.org/10.1038/s41588-018-0266-x

    Article  CAS  PubMed  Google Scholar 

  • Niu SZ, Koiwa H, Song QF, Qiao DH, Chen J, Zhao DG, Chen ZW, Wang Y, Zhang TY (2020) Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing. PEERJ 8:e8572. https://doi.org/10.7717/peerj.8572

    Article  PubMed  PubMed Central  Google Scholar 

  • Odong TL, Jansen J, Van Eeuwijk FA, Van Hintum TJL (2013) Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation. Theor Appl Genet 126(2):289–305. https://doi.org/10.1007/s00122-012-1971-y

    Article  CAS  PubMed  Google Scholar 

  • Rygulla W, Snowdon RJ, Eynck C, Koopmann B, von Tiedemann A, Luehs W, Friedt W (2007) Broadening the genetic basis of Verticillium longisporum resistance in Brassica napus by interspecific hybridization. Phytopathology 97(11):1391–1396. https://doi.org/10.1094/PHYTO-97-11-1391

    Article  CAS  PubMed  Google Scholar 

  • Ripa AS, Karikari B, Chang F, Mashiur GMAA, Hina RB, Lv A, Zhang WH, Naheeda CT, Zhao B TJ (2021) Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean. BMC Plant Biol 21:1–17. https://doi.org/10.1186/s12870-021-03268-z

    Article  CAS  Google Scholar 

  • Van Hintum ThJL, Brown AHD, Spillane C, Hodgkin T (2000) Core collections of plant genetic resources. Rome, Italy

    Google Scholar 

  • Wang JX, Chen ZL, Du JZ, Sun Y, Liang AH (2005) Novel insect resistance in Brassica napus developed by transformation of chitinase and scorpion toxin genes. Plant Cell Rep 24(9):549–555. https://doi.org/10.1007/s00299-005-0967-3

    Article  CAS  PubMed  Google Scholar 

  • Wang LX, Guan Y, Guan RX, Li YH, Ma YS, Dong ZM, Liu X, Zhang HY, Zhang YQ, Liu ZX, Chang RZ, Xu HM, Li LH, Lin FY, Luan WJ, Yan Z, Ning XC, Zhu L, Cui YH, Piao R, Liu Y, Chen PY, Qiu LJ (2006) Establishment of Chinese soybean Glycine max core collections with agronomic traits and SSR markers. Euphytica 151(2):215–223. https://doi.org/10.1007/s10681-006-9142-3

    Article  CAS  Google Scholar 

  • 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. Theor Appl Genet 127(8):1817–1829. https://doi.org/10.1007/s00122-014-2343-6

    Article  PubMed  Google Scholar 

  • Wang HR, Xu X, Vieira FG, Xiao YH, Li ZK, Wang J, Nielsen R, Chu CC (2016) The power of inbreeding: NGS-based GWAS of rice reveals convergent evolution during rice domestication. Mol Plant 9(7):975–985. https://doi.org/10.1016/j.molp.2016.04.018

    Article  CAS  PubMed  Google Scholar 

  • Wang XD, Sun LJ, Li WJ, Peng ML, Chen F, Zhang W, Sun CM, Chen S, Hua W, Zhang JF (2020) Dissecting the genetic mechanisms of waterlogging tolerance in Brassica napus through linkage mapping and a genome-wide association study. Ind Crop Prod 147:112269. https://doi.org/10.1016/j.indcrop.2020.112269

    Article  CAS  Google Scholar 

  • Wang HY, Wang Q, Pak H, Yan T, Chen MX, Chen XY, Wu DZ, Jiang LX (2021) Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus. BMC Plant Biol 21(1). https://doi.org/10.1186/s12870-020-02774-w

  • Wu DZ, Liang Z, Yan T, Xu Y, Xuan LJ, Tang J, Zhou G, Lohwasser U, Hua SJ, Wang HY, Chen XY, Wang Q, Zhu L, Maodzeka A, Hussain N, Li ZL, Li XM, Shamsi IH, Jilani G, Wu LD, Zheng HK, Zhang GP, Chalhoub B, Shen LS, Yu H, Jiang LX (2019) Whole-genome resequencing of a worldwide collection of rapeseed accessions reveals the genetic basis of ecotype divergence. Mol Plant 12(1):30–43. https://doi.org/10.1016/j.molp.2018.11.007

    Article  CAS  PubMed  Google Scholar 

  • Xu HM, Mei YJ, Hu J, Zhu J, Gong P (2006) Sampling a core collection of island cotton (Gossypium barbadense L.) based on the genotypic values of fiber traits. Genet Resour Crop Ev 53(3):515–521. https://doi.org/10.1007/s10722-004-2032-4

    Article  Google Scholar 

  • Xuan LJ, Yan T, Lu LZ, Zhao XZ, Wu DZ, Hua SJ, Jiang LX (2019) Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.). Plant Cell Environ 43(3):675–691. https://doi.org/10.1111/pce.13694

    Article  CAS  PubMed  Google Scholar 

  • Zhang XK, Fan QX, Chen J, Li JN, Wang HZ (2007) Physiological reaction differences of different waterlogging-tolerant genotype rapeseed (Brassica napus L.) to anoxia. Scientia Agricultura Sinica 3:485–491. https://oversea.cnki.net/kcms/detail/detail.aspx?dbcode=cjfd &dbname=cjfd2007&filename=ZNYK200703008

    Google Scholar 

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Acknowledgements

We are grateful to Dr. J.M. Xu (Zhejiang University, China) for the technical support. This research was supported by Jiangsu Collaborative Innovation Center for Modern Crop Production.

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Authors and Affiliations

  1. Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China

    Yiyi Guo, Liuhui Kuang, Ying Xu, Lixi Jiang & Jie Dong

  2. College of Agronomy, Hunan Agricultural University, 410128, Changsha, China

    Tao Yan & Dezhi Wu

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  1. Yiyi Guo
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  2. Liuhui Kuang
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  3. Ying Xu
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  4. Tao Yan
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  7. Dezhi Wu
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Contributions

DZ Wu and LX Jiang designed the research. YY Guo, Y Xu, Y Tao and J Dong performed the research. YY Guo and LH Kuang analyzed the data. YY Guo and DZ Wu wrote the article. The authors declare no conflict of interest.

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Correspondence to Dezhi Wu.

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Communicated by Jiayin Pang.

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Guo, Y., Kuang, L., Xu, Y. et al. Construction of a worldwide core collection of rapeseed and association analysis for waterlogging tolerance. Plant Growth Regul 98, 321–328 (2022). https://doi.org/10.1007/s10725-022-00862-5

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