Digging out molecular markers associated with low salinity tolerance of <italic style="font-style: italic">Nannochloropsis oceanica</italic> through bulked mutant analysis

Sijie LIANG; Zhongyi ZHANG; Hang LIU; Li GUO; Shiyang SUN; Guanpin YANG

doi:10.1007/s00343-019-9189-3

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Digging out molecular markers associated with low salinity tolerance of Nannochloropsis oceanica through bulked mutant analysis

Biology | Updated：2023-04-27

- Digging out molecular markers associated with low salinity tolerance of Nannochloropsis oceanica through bulked mutant analysis
- Journal of Oceanology and Limnology Vol. 38, Issue 6, Pages: 1867-1879(2020)
- Affiliations：
  
  1.College of Marine Life Sciences, Ocean University of China(OUC), Qingdao 266003, China
  2.Key Laboratory of Marine Genetics and Breeding of Ministry of Education, OUC, Qingdao 266003, China
  3.College of Fisheries, OUC, Qingdao 266003, China
  4.Institute of Evolution and Marine Biodiversity, OUC, Qingdao 266003, China
- Author bio：
  
  GUO Li, qdguoli@139.com
  YANG Guanpin, yguanpin@ouc.edu.cn
- Funds：
- DOI：10.1007/s00343-019-9189-3
  CLC：
- Received：22 July 2019，
  
  Accepted：09 September 2019，
  
  Online First：16 October 2019，
  
  Published：2020-11
- Accepted：
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Sijie LIANG, Zhongyi ZHANG, Hang LIU, et al. Digging out molecular markers associated with low salinity tolerance of Nannochloropsis oceanica through bulked mutant analysis[J]. Journal of Oceanology and Limnology, 2020, 38(6): 1867-1879.
DOI：

Sijie LIANG, Zhongyi ZHANG, Hang LIU, et al. Digging out molecular markers associated with low salinity tolerance of Nannochloropsis oceanica through bulked mutant analysis[J]. Journal of Oceanology and Limnology, 2020, 38(6): 1867-1879. DOI： 10.1007/s00343-019-9189-3.

摘要

Abstract

Nannochloropsis oceanica

is a marine microalgal species with both economic value and biological importance. It grows fast

contains rich oils

reproduces asexually

holds a small and haploidy genome

and is easy to be modified genetically. However

the genetic study of

N. oceanica

is scarce. Very less genetic bases of its traits have been deciphered

and no gene has been isolated from it with the function verified simultaneously via either genetic or reverse genetic approaches or both (de novo cloned). Changing medium salinity may aid to control harmful organisms met during large scale cultivation. As a stress

it may also facilitate the accumulation of desirable chemicals including fatty acids. In order to decipher the genetic basis of the low salinity tolerance of

N. oceanica

we mutated

N. oceanica

with Zeocin. In total

five mutant bulks were constructed at equal number of cells

100 mutants each

which were tolerant to a discontinuous serial of salinities from that of 100% of f/2 to that of a mixture of 4% of f/2 and 94% of BG11. The bulks were genotyped through whole genome re-sequencing and analyzed with bulked mutant analysis (BMA) newly modified from bulked segregant analysis (BSA). In total

47 SNPs and 112 InDels were found to associate with the low salinity tolerance

and around them a set of low salinity tolerance associating genes were identified. A set of annotatable genes commonly found between control and different salinities indicated that the genes functioning in gene expression

energy metabolism and cellular structure may be involved in the low salinity tolerance. These associating molecular markers and genes around them were not enough for outlining the physiological mechanism underlining the tolerance; however they should aid to improve

N. oceanica

genetically.

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Keywords

references

A Abe , S Kosugi , K Yoshida , S Natsume , H Takagi , H Kanzaki , H Matsumura , K Yoshida , C Mitsuoka , M Tamiru , H Innan , L Cano , S Kamoun , R Terauchi . Genome sequencing reveals agronomically important loci in rice using MutMap . Nature Biotechnology , 2012 . 30 ( 2 ): 174 - 178 . DOI: 10.1038/nbt.2095 http://doi.org/10.1038/nbt.2095 .

K Baek , D H Kim , J Jeong , S J Sim , A Melis , J S Kim , F Jin , S Bae . DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins . Scientific Reports , 2016 . 6 30620 DOI: 10.1038/srep30620 http://doi.org/10.1038/srep30620 .

J M Belton , R P Mccord , J H Gibcus , N Naumova , Y Zhan , J Dekker . Hi–C: a comprehensive technique to capture the conformation of genomes . Methods , 2012 . 58 ( 3 ): 268 - 276 . DOI: 10.1016/j.ymeth.2012.05.001 http://doi.org/10.1016/j.ymeth.2012.05.001 .

R Chaturvedi , Y Fujita . Isolation of enhanced eicosapentaenoic acid producing mutants of Nannochloropsis oculata ST-6 using ethyl methane sulfonate induced mutagenesis techniques and their characterization at mRNA transcript level . Phycological Research , 2010 . 54 ( 3 ): 208 - 219 . http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=b61ba9ee653ac110db628b615a6e639d http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=b61ba9ee653ac110db628b615a6e639d , .

J Dekker , K Rippe , M Dekker , N Kleckner . Capturing chromosome conformation . Science , 2002 . 295 ( 5558 ): 1 306 - 1 311 . DOI: 10.1126/science.1067799 http://doi.org/10.1126/science.1067799 .

R Fekih , H Takagi , M Tamiru , A Abe , S Natsume , H Yaegashi , S Sharma , S Sharma , H Kanzaki , H Matsumura , H Saitoh , C Mitsuoka , H Utsushi , A Uemura , E Kanzaki , S Kosugi , K Yoshida , L Cano , S Kamoun , R Terauchi . MutMap+: Genetic mapping and mutant identification without crossing in rice . PLoS One , 2013 . 8 ( 7 ): e68529 DOI: 10.1371/journal.pone.0068529 http://doi.org/10.1371/journal.pone.0068529 .

A Ferenczi , D E Pyott , A Xipnitoua , A Molnar . Efficient targeted DNA editing and replacement in Chlamydomonas reinhardtii using Cpf1 ribonucleoproteins and single-stranded DNA . Proceedings of the National Academy of Sciences of the United States of America , 2017 . 114 ( 51 ): 13 567 - 13 572 . DOI: 10.1073/pnas.1710597114 http://doi.org/10.1073/pnas.1710597114 .

Y Fu , N M Springer , D J Gerhardt , K Ying , C T Yeh , W Wu , R Swanson-Wagner , M D'Ascenzo , T Millard , L Freeberg , N Aoyama , J Kitzman , D Burgess , T Richmond , T J Albert , W B Barbazuk , J A Jeddeloh , P S Schnable . Repeat subtraction-mediated sequence capture from a complex genome . The Plant Journal , 2010 . 62 ( 5 ): 898 - 909 . DOI: 10.1111/j.1365-313X.2010.04196.x http://doi.org/10.1111/j.1365-313X.2010.04196.x .

J H Gibcus , J Dekker . The hierarchy of the 3D genome . Molecular Cell , 2013 . 49 ( 5 ): 773 - 782 . DOI: 10.1016/j.molcel.2013.02.011 http://doi.org/10.1016/j.molcel.2013.02.011 .

L Guo , S J Liang , Z Y Zhang , H Liu , S W Wang , K H Pan , J Xu , X Ren , S R Pei , G P Yang . Genome assembly of Nannochloropsis oceanica provides evidence of host nucleus overthrow by the symbiont nucleus during speciation . Communications Biology , 2019 . 2 249 DOI: 10.1038/s42003-019-0500-9 http://doi.org/10.1038/s42003-019-0500-9 .

L Guo , Y M Wang , S J Liang , G M Lin , S L Chen , G P Yang . Tissue-overlapping response of half-smooth tongue sole ( Cynoglossus semilaevis ) to thermostressing based on transcriptome profiles . Gene , 2016 . 586 ( 1 ): 97 - 104 . DOI: 10.1016/j.gene.2016.04.020 http://doi.org/10.1016/j.gene.2016.04.020 .

L Guo , G P Yang . The mechanism of the acclimation of Nannochloropsis oceanica to freshwater deduced from its transcriptome profiles . Journal of Ocean University of China , 2015 . 14 ( 5 ): 922 - 930 . DOI: 10.1007/s11802-015-2689-7 http://doi.org/10.1007/s11802-015-2689-7 .

B Head , L Griparic , M Amiri , S Gandre-Babbe , A M Van Der Bliek . Inducible proteolytic inactivation of OPA1 mediated by the OMA1 protease in mammalian cells . The Journal of Cell Biology , 2009 . 187 ( 7 ): 959 - 966 . DOI: 10.1083/jcb.200906083 http://doi.org/10.1083/jcb.200906083 .

U Iskandarov , I Khozin-Goldberg , Z Cohen . Selection of a DGLA-producing mutant of the microalga Parietochloris incisa : I. Identification of mutation site and expression of VLC-PUFA biosynthesis genes . Applied Microbiology and Biotechnology , 2011 . 90 ( 1 ): 249 - 256 . .

R J Klein , C Zeiss , E Y Chew , J Y Tsai , R S Sackler , C Haynes , A K Henning , J P SanGiovanni , S M Mane , S T Mayne , M B Bracken , F L Ferris , J Ott , C Barnstable , J Hoh . Complement factor H polymorphism in age-related macular degeneration . Science , 2005 . 308 ( 5720 ): 385 - 389 . DOI: 10.1126/science.1109557 http://doi.org/10.1126/science.1109557 .

D Y C Leung , X Wu , M K H Leung . A review on biodiesel production using catalyzed transesterification . Applied Energy , 2010 . 87 ( 4 ): 1 083 - 1 095 . DOI: 10.1016/j.apenergy.2009.10.006 http://doi.org/10.1016/j.apenergy.2009.10.006 .

H Li , R Durbin . Fast and accurate short read alignment with Burrows-Wheeler transform . Bioinformatics , 2009a . 25 ( 14 ): 1 754 - 1 760 . DOI: 10.1093/bioinformatics/btp324 http://doi.org/10.1093/bioinformatics/btp324 .

H Li , B Handsaker , A Wysoker , T Fennell , J Ruan , N Homer , G Marth , G Abecasis , R Durbin . The sequence alignment/map (SAM) format and SAMtools . Bioinformatics , 2009b . 25 ( 16 ): 1 653 - 1 654 . http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=ba1336589a48f793aa05aa1c8ac499c2 http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=ba1336589a48f793aa05aa1c8ac499c2 , .

S J Liang , L Guo , G M Lin , Z Y Zhang , H Y Ding , Y M Wang , G P Yang . Improvement of Nannochloropsis oceanica growth performance through chemical mutation and characterization of fast growth physiology by transcriptome profiling . Chinese Journal of Oceanology and Limnology , 2017 . 35 ( 4 ): 792 - 802 . DOI: 10.1007/s00343-017-6023-7 http://doi.org/10.1007/s00343-017-6023-7 .

S J Liang , Z Y Zhang , H Liu , L Guo , S Y Sun , G P Yang . Identifying the growth associating genes of Nannochloropsis oceanica by bulked mutant analysis (BMA) and RNA sequencing (BMR-seq) . Journal of Applied Phycology , 2019 . 1 - 14 . DOI: 10.1007/s10811-019-01867-w http://doi.org/10.1007/s10811-019-01867-w .

G M Lin , Y M Wang , L Guo , H Y Ding , Y M Hu , S J Liang , Z Y Zhang , G P Yang . Verification of mutagen function of Zeocin in Nannochloropsis oceanica through transcriptome analysis . Journal of Ocean University of China , 2017 . 16 ( 3 ): 501 - 508 . DOI: 10.1007/s11802-017-3231-x http://doi.org/10.1007/s11802-017-3231-x .

G M Lin , Z Y Zhang , L Guo , H Y Ding , G P Yang . Structural variation analysis of mutated Nannochloropsis oceanica caused by Zeocin through genome re-sequencing . Journal of Ocean University of China , 2018 . 17 ( 5 ): 1 225 - 1 230 . DOI: 10.1007/s11802-018-3626-3 http://doi.org/10.1007/s11802-018-3626-3 .

A McKenna , M Hanna , E Banks , A Sivachenko , K Cibulskis , A Kernytsky , K Garimella , D Altshuler , S Gabriel , M Daly , M A DePristo . The genome analysis toolkit: A map reduce framework for analyzing next-generation DNA sequencing data . Genome Research , 2010 . 20 ( 9 ): 1 297 - 1 303 . DOI: 10.1101/gr.107524.110 http://doi.org/10.1101/gr.107524.110 .

R W Michelmore , I Paran , P V Kesseli . Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations . Proceedings of the National Academy of Sciences of United States of America , 1991 . 88 ( 21 ): 9 828 - 9 832 . DOI: 10.1073/pnas.88.21.9828 http://doi.org/10.1073/pnas.88.21.9828 .

K H Pan , J J Qin , S Li , W K Dai , B H Zhu , Y C Jin , W G Yu , G P Yang , D F Li . Nuclear monoploidy and asexual propagation of Nannochloropsis oceanica (Eustigmatophyceae) as revealed by its genome sequence . Journal of Phycology , 2011 . 47 ( 6 ): 1 425 - 1 432 . DOI: 10.1111/j.1529-8817.2011.01057.x http://doi.org/10.1111/j.1529-8817.2011.01057.x .

E Poliner , J A Pulman , K Zienkiewicz , K Childs , C Benning , E M Farré . A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production . Plant Biotechnology Journal , 2018b . 16 ( 1 ): 298 - 309 . DOI: 10.1111/pbi.12772 http://doi.org/10.1111/pbi.12772 .

E Poliner , T Takeuchi , Z Y Du , C Benning , EM Farré . Nontransgenic marker-free gene disruption by an episomal CRISPR system in the oleaginous microalga, Nannochloropsis oceanica CCMP1779 . ACS Synthetic Biology , 2018a . 7 ( 4 ): 962 - 968 . DOI: 10.1021/acssynbio.7b00362 http://doi.org/10.1021/acssynbio.7b00362 .

K S Sandhu , G L Li , W K Sung , Y J Ruan . Chromatin interaction networks and higher order architectures of eukaryotic genomes . Journal of Cellular Biochemistry , 2011 . 112 ( 9 ): 2 218 - 2 221 . DOI: 10.1002/jcb.23155 http://doi.org/10.1002/jcb.23155 .

F J Steemers , W H Chang , G Lee , D L Barker , R Shen , K L Gunderson . Whole-genome genotyping with the single-base extension assay . Nature Methods , 2006 . 3 ( 1 ): 31 - 33 . DOI: 10.1038/nmeth842 http://doi.org/10.1038/nmeth842 .

H Takagi , A Abe , K Yoshida , S Kosugi , S Natsume , C Mitsuoka , A Uemura , H Utsushi , M Tamiru , S Takuno , H Innan , L M Cano , S Kamoun , R Terauchi . QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations . The Plant Journal , 2013a . 74 ( 1 ): 174 - 183 . DOI: 10.1111/tpj.12105 http://doi.org/10.1111/tpj.12105 .

H Takagi , A Uemura , H Yaegashi , M Tamiru , A Abe , C Mitsuoka , H Utsushi , S Natsume , H Kanzaki , H Matsumura , H Saitoh , K Yoshida , L M Cano , S Kamoun , R Terauchi . MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii . New Phytologist , 2013b . 200 ( 1 ): 276 - 283 . DOI: 10.1111/nph.12369 http://doi.org/10.1111/nph.12369 .

T Todorova , D Miteva , S Chankova . DNA damaging effect of zeocin and methyl methanesulfonate in Saccharomyces Cerevisiae measured by CFGE . Comptes Rendus De L'Academie Bulgare Des Sciences , 2005 . 68 ( 1 ): 71 - 78 . http://www.researchgate.net/publication/271719681_DNA_damaging_effect_of_zeocin_and_methyl_methanesulfonate_in_saccharomyces_cerevisiae_measured_by_CFGE http://www.researchgate.net/publication/271719681_DNA_damaging_effect_of_zeocin_and_methyl_methanesulfonate_in_saccharomyces_cerevisiae_measured_by_CFGE , .

P M Visscher , N R Wray , Q Zhang , P Sklar , M I McCarthy , M A Brown , J Yang . 10 years of GWAS discovery: Biology, function, and translation . The American Journal of Human Genetics , 2017 . 101 ( 1 ): 5 - 22 . DOI: 10.1016/j.ajhg.2017.06.005 http://doi.org/10.1016/j.ajhg.2017.06.005 .

C S Wang , S C Tang , Q L Zhan , Q Q Hou , Y Zhao , Q Zhao , Q Feng , C C Zhou , D F Lyu , L L Cui , Y Li , J S Miao , C R Zhu , Y Q Lu , Y C Wang , Z Q Wang , J J Zhu , Y Y Shangguan , J Y Gong , S H Yang , W Q Wang , J F Zhang , H A Xie , X H Huang , B Han . Dissecting a heterotic gene through Graded Pool-seq mapping informs a rice-improvement strategy . Nature Communications , 2019 . 10 2 982 DOI: 10.1038/s41467-019-11017-y http://doi.org/10.1038/s41467-019-11017-y .

L K Wang , Z X Feng , X Wang , X W Wang , X G Zhang . DEGseq: an R package for identifying differentially expressed genes from RNA-seq data . Bioinformatics , 2010 . 26 ( 1 ): 136 - 138 . DOI: 10.1093/bioinformatics/btp612 http://doi.org/10.1093/bioinformatics/btp612 .

Q T Wang , Y D Lu , Y Xin , L Wei , S Huang , J Xu . Genome editing of model oleaginous microalgae Nannochloropsis spp. by CRISPR/Cas9 . The Plant Journal , 2016 . 88 ( 6 ): 1 071 - 1 081 . DOI: 10.1111/tpj.13307 http://doi.org/10.1111/tpj.13307 .

L Wei , C Shen , M El Hajjami , W X You , Q T Wang , P Zhang , Y T Jia , H H Hu , Q Hu , A Poetsch , J Xu . Knockdown of carbonate anhydrase elevates Nannochloropsis productivity at high CO 2 level . Metabolic Engineering , 2019 . 54 96 - 108 . DOI: 10.1016/j.ymben.2019.03.004 http://doi.org/10.1016/j.ymben.2019.03.004 .

L Wei , Q T Wang , Y Xin , Y D Lu , J Xu . Enhancing photosynthetic biomass productivity of industrial oleaginous microalgae by overexpression of RuBisCO activase . Algal Research , 2017b . 27 366 - 375 . DOI: 10.1016/j.algal.2017.07.023 http://doi.org/10.1016/j.algal.2017.07.023 .

L Wei , Y Xin , Q T Wang , J Yang , H H Hu , J Xu . RNAi-based targeted gene knockdown in the model oleaginous microalgae Nannochloropsis oceanica . The Plant Journal , 2017a . 89 ( 6 ): 1 236 - 1 250 . DOI: 10.1111/tpj.13411 http://doi.org/10.1111/tpj.13411 .

R H Wijffels , M J Barbosa . An outlook on microalgal biofuels . Science , 2010 . 329 ( 5993 ): 796 - 799 . DOI: 10.1126/science.1189003 http://doi.org/10.1126/science.1189003 .

Y Xin , Y D Lu , Y Y Lee , L Wei , J Jia , Q T Wang , D M Wang , F L Bai , H H Hu , Q Hu , J Liu , Y T Li , J Xu . Producing designer oils in industrial microalgae by rational modulation of co-evolving type-2 diacylglycerol acyltransferases . Molecular Plant , 2017 . 10 ( 12 ): 1 523 - 1 539 . DOI: 10.1016/j.molp.2017.10.011 http://doi.org/10.1016/j.molp.2017.10.011 .

Y Xin , C Shen , Y T She , H Chen , C Wang , L Wei , K Yoon , D X Han , Q Hu , J Xu . Biosynthesis of triacylglycerol molecules with a tailored PUFA profile in industrial microalgae . Molecular Plant , 2019 . 12 ( 4 ): 474 - 488 . DOI: 10.1016/j.molp.2018.12.007 http://doi.org/10.1016/j.molp.2018.12.007 .

J L Yang , H Y Jiang , C T Yeh , J M Yu , J A Jeddeloh , D Nettleton , P S Schnable . Extreme-phenotype genome-wide association study (XP-GWAS): A method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel . The Plant Journal , 2015 . 84 ( 3 ): 587 - 596 . DOI: 10.1111/tpj.13029 http://doi.org/10.1111/tpj.13029 .

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Related Author

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Sijie LIANG

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Related Institution

College of Marine Life Sciences, Ocean University of China

Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China

Institutes of Evolution and Marine Biodiversity, Ocean University of China

College of Agriculture and Resources and Environment, Tianjin Agricultural University

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Digging out molecular markers associated with low salinity tolerance of Nannochloropsis oceanica through bulked mutant analysis

DOI：10.1007/s00343-019-9189-3

摘要

Abstract

关键词

Keywords

references