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11 14, 2022;3 (6): 100352.

High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement.

Changyou Liu, Yan Wang, Jianxiang Peng, Baojie Fan, Dongxu Xu, Jing Wu, Zhimin Cao, Yunqing Gao, Xueqing Wang, Shutong Li, Qiuzhu Su, Zhixiao Zhang, Shen Wang, Xingbo Wu, Qibing Shang, Huiying Shi, Yingchao Shen, Bingbing Wang, Jing Tian
Author Information
  1. Changyou Liu: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  2. Yan Wang: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  3. Jianxiang Peng: Biobin Data Sciences, Changsha 410221, China.
  4. Baojie Fan: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  5. Dongxu Xu: Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou 075300, China.
  6. Jing Wu: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
  7. Zhimin Cao: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  8. Yunqing Gao: Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou 075300, China.
  9. Xueqing Wang: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  10. Shutong Li: Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou 075300, China.
  11. Qiuzhu Su: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  12. Zhixiao Zhang: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  13. Shen Wang: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  14. Xingbo Wu: Tropical Research and Education Center, Department of Environmental Horticulture, University of Florida, 18905 SW 280th St, Homestead, FL 33031, USA.
  15. Qibing Shang: Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou 075300, China.
  16. Huiying Shi: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  17. Yingchao Shen: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China.
  18. Bingbing Wang: Biobin Data Sciences, Changsha 410221, China. Electronic address: bwang@biobin.com.cn.
  19. Jing Tian: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050035, China. Electronic address: nkytianjing@163.com.
PMID: 35752938 DOI: 10.1016/j.xplc.2022.100352

Abstract

Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a contig N50 length of 10.34 Mb. A total of 40,125 protein-coding genes were annotated, representing ∼96.9% of the genetic region. We also sequenced 217 accessions, mainly landraces and cultivars from China, and identified 2,229,343 high-quality single-nucleotide polymorphisms (SNPs). Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines. Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road. We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences. Among the genes, 83.1% were core genes and 16.9% were variable. Presence/absence variation (PAV) events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring. Genome-wide association studies (GWASs) revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits, including a SNP in the coding region of the SWEET10 homolog (jg24043) involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits. This high-quality reference genome and pan-genome will provide insights into mung bean breeding.

Keywords

GWAS de novo assembly gene PAV long-read sequencing mung bean pan-genome

Associated Data

figshare | 10.6084/m9.figshare.19583446

References

Cell. 2021 Jun 24;184(13):3542-3558.e16 [PMID: 34051138]
Plant Biotechnol J. 2018 Jul;16(7):1265-1274 [PMID: 29205771]
Bioinformatics. 2015 Oct 1;31(19):3210-2 [PMID: 26059717]
Nat Genet. 2019 Jun;51(6):1044-1051 [PMID: 31086351]
Nature. 2021 Nov;599(7886):622-627 [PMID: 34759320]
Mol Genet Genomics. 2020 Mar;295(2):275-286 [PMID: 31705195]
BMC Bioinformatics. 2019 Feb 13;20(1):75 [PMID: 30760221]
Bioinformatics. 2013 Nov 15;29(22):2933-5 [PMID: 24008419]
BMC Genomics. 2016 Aug 31;17 Suppl 5:498 [PMID: 27585926]
Nucleic Acids Res. 2018 Nov 30;46(21):e126 [PMID: 30107434]
Bioinformatics. 2017 Sep 01;33(17):2759-2761 [PMID: 28472236]
Bioinformatics. 2006 Jul 1;22(13):1658-9 [PMID: 16731699]
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811 [PMID: 30395283]
Bioinformatics. 2012 Sep 15;28(18):i333-i339 [PMID: 22962449]
Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
Bioinformatics. 2017 Aug 01;33(15):2408-2409 [PMID: 28369371]
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:Unit 4.10 [PMID: 19274634]
Nat Genet. 2020 Jan;52(1):118-125 [PMID: 31873299]
BMC Plant Biol. 2020 Oct 14;20(Suppl 1):363 [PMID: 33050907]
Plant Biotechnol J. 2016 Apr;14(4):1099-105 [PMID: 26593040]
Nat Genet. 2017 Jul;49(7):1082-1088 [PMID: 28530677]
Brief Bioinform. 2021 Jul 20;22(4): [PMID: 33126247]
BMC Genomics. 2017 May 26;18(1):415 [PMID: 28549456]
Bioinformatics. 2003 Jan 22;19(2):301-2 [PMID: 12538260]
Bioinformatics. 2017 Jul 15;33(14):2202-2204 [PMID: 28369201]
PLoS One. 2011;6(6):e21071 [PMID: 21695166]
Bioinformatics. 2008 Mar 1;24(5):637-44 [PMID: 18218656]
Bioinformatics. 2013 Nov 1;29(21):2669-77 [PMID: 23990416]
Cell Syst. 2016 Jul;3(1):95-8 [PMID: 27467249]
Front Genet. 2020 Jun 24;11:656 [PMID: 32670356]
J Exp Bot. 2021 May 28;72(12):4401-4418 [PMID: 33825878]
Am J Hum Genet. 2018 Sep 6;103(3):338-348 [PMID: 30100085]
OMICS. 2012 May;16(5):284-7 [PMID: 22455463]
Nucleic Acids Res. 2021 Jan 8;49(D1):D192-D200 [PMID: 33211869]
Plant Genome. 2021 Nov;14(3):e20121 [PMID: 34275211]
New Phytol. 2018 Oct;220(2):360-363 [PMID: 30129229]
Nat Plants. 2020 Jan;6(1):34-45 [PMID: 31932676]
Nat Biotechnol. 2015 Apr;33(4):408-14 [PMID: 25643055]
Nat Commun. 2014 Nov 11;5:5443 [PMID: 25384727]
Plant Biotechnol J. 2021 Sep;19(9):1852-1862 [PMID: 33942475]
Plant Biotechnol J. 2020 Sep;18(9):1946-1954 [PMID: 32020732]
Natl Sci Rev. 2020 May 27;7(11):1776-1786 [PMID: 34691511]
Nat Genet. 2012 Jun 17;44(7):821-4 [PMID: 22706312]
Bioinformatics. 2018 Mar 1;34(5):867-868 [PMID: 29096012]
Nat Biotechnol. 2019 May;37(5):540-546 [PMID: 30936562]
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5 [PMID: 16172379]
Front Plant Sci. 2020 Oct 29;11:537766 [PMID: 33193476]
Genome Biol. 2017 Aug 24;18(1):161 [PMID: 28838319]
Cell Syst. 2016 Jul;3(1):99-101 [PMID: 27467250]
Bioinformatics. 2011 Aug 1;27(15):2156-8 [PMID: 21653522]
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108 [PMID: 33575650]
Fly (Austin). 2012 Apr-Jun;6(2):80-92 [PMID: 22728672]
Curr Opin Plant Biol. 2020 Apr;54:26-33 [PMID: 31981929]
Genome Biol. 2019 Nov 14;20(1):238 [PMID: 31727128]
BMC Genomics. 2015 Apr 29;16:344 [PMID: 25925106]
Sci Rep. 2017 Jul 6;7(1):4816 [PMID: 28684880]
Nat Genet. 2019 May;51(5):857-864 [PMID: 31036963]
Theor Appl Genet. 2019 Mar;132(3):797-816 [PMID: 30560464]
Bioinformatics. 2013 Apr 15;29(8):1072-5 [PMID: 23422339]
NAR Genom Bioinform. 2020 Jun;2(2):lqaa026 [PMID: 32440658]
Nat Commun. 2021 Jan 29;12(1):702 [PMID: 33514713]
Ann Bot. 2007 Nov;100(5):903-24 [PMID: 17495986]
Sci China Life Sci. 2019 Sep;62(9):1257-1260 [PMID: 31444683]
Plant J. 2019 Jun;98(5):767-782 [PMID: 31017340]
Front Plant Sci. 2018 Jan 12;8:2102 [PMID: 29375590]
Genes (Basel). 2020 Jul 07;11(7): [PMID: 32646058]
Nat Genet. 2006 Aug;38(8):904-9 [PMID: 16862161]
PLoS One. 2014 Nov 19;9(11):e112963 [PMID: 25409509]
Bioinformatics. 2006 May 15;22(10):1269-71 [PMID: 16543274]
Nat Commun. 2017 May 24;8:15323 [PMID: 28537247]
Genome Res. 2009 Sep;19(9):1655-64 [PMID: 19648217]
Cell. 2020 Jul 9;182(1):162-176.e13 [PMID: 32553274]

MeSH Term

Vigna
Genome-Wide Association Study
Plant Breeding
Fabaceae
Polymorphism, Single Nucleotide
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GWH: GWHBHSN00000000 (Vigna radiata)

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