Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns in<italic style="font-style: italic">Pyropia yezoensis</italic>(Bangiales, Rhodophyta)

Lu WANG; Junhao WANG; Yunke ZHU; Zhengcai CUI; Fanna KONG; Xianghai TANG; Yunxiang MAO

doi:10.1007/s00343-020-0298-9

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Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns inPyropia yezoensis(Bangiales, Rhodophyta)

Biology | Updated：2023-05-20

- Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns inPyropia yezoensis(Bangiales, Rhodophyta)
- Journal of Oceanology and Limnology Vol. 39, Issue 4, Pages: 1447-1457(2021)
- Affiliations：
  
  1.Key Laboratory of Marine Genetics and Breeding(Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
  2.Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource(Ministry of Education), College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
- Author bio：
  
  Xianghai TANG, E-mail:txianghai@ouc.edu.cn
  Yunxiang MAO, E-mail:yxmao@hntou.edu.cn
- Funds：
- DOI：10.1007/s00343-020-0298-9
  CLC：
- Received：02 August 2020，
  
  Accepted：26 August 2020，
  
  Online First：27 August 2020，
  
  Published：2021-07
- Accepted：
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Lu WANG, Junhao WANG, Yunke ZHU, et al. Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns inPyropia yezoensis(Bangiales, Rhodophyta)[J]. Journal of Oceanology and Limnology, 2021, 39(4): 1447-1457.
DOI：

Lu WANG, Junhao WANG, Yunke ZHU, et al. Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns inPyropia yezoensis(Bangiales, Rhodophyta)[J]. Journal of Oceanology and Limnology, 2021, 39(4): 1447-1457. DOI： 10.1007/s00343-020-0298-9.

摘要

Abstract

The genus

Pyropia

contains several important cultivated species. Genetic research in nori species has mainly focused on the cell nucleus

with few studies on organelles (chloroplast and mitochondria). Due to the high copy numbers of organelles in cells

which influence the development and traits of algae

it is necessary to study their genetic mechanism. In this study

the marine red alga

Pyropia yezoensis

an important economic macroalga

was selected as the study object. To investigate organelle (chloroplast and mitochondria) inheritance in

P. yezoensis

the wild type RZ (maternal strain) was crossed with the red mutant HT (paternal strain) and 30 color-sectors from 11 F1 gametophytic blades were examined. The complete chloroplast and mitochondrial genomes of the red mutant (HT) were assembled for the first time. One reliable and stable single nucleotide polymorphism (SNP) loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA

respectively

in subsequent experiments. PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent

confirming that both chloroplast and mitochondrial genomes were inherited maternally in

P. yezoensis

. The inheritance pattern of organelles in

P. yezoensis

can be used to guide the hybridization and breeding of nori. Additionally

the organelle SNP markers developed in this study can be applied in subsequent genetic research.

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references

Avise J C, Arnold J, Ball Jr R M et al. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics , 18 : 489–522, https://doi.org/10.1146/annurev.es.18.110187.002421.

Avise J C. 1994. Molecular Markers: Natural History, and Evolution. Chapman and Hall, New York.

Bankevich A, Nurk S, Antipov D et al. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology , 19 (5): 455–477, https://doi.org/10.1089/cmb.2012.0021.

Bendich A J. 2013. DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts. Chromosome Research , 21 (3): 287–296, https://doi.org/10.1007/s10577-013-9349-9.

Birky C W. 2001. The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. Annual Review of Genetics , 35 : 125–148, https://doi.org/10.1146/annurev.genet.35.102401.090231.

Blouin N A, Brodie J A, Grossman A C et al. 2011. Porphyra : a marine crop shaped by stress. Trends in Plant Science , 16 (1): 29–37, https://doi.org/10.1016/j.tplants.2010.10.004.

Choi J W, Graf L, Peters A F et al. 2020. Organelle inheritance and genome architecture variation in isogamous brown algae. Scientific Reports , 10 (1): 1–12, https://doi.org/10.1038/s41598-020-58817-7.

Choi S J, Park E J, Endo H et al. 2008. Inheritance pattern of chloroplast and mitochondrial genomes in artificial hybrids of Porphyra yezoensis (Rhodophyta). Fisheries Science , 74 (4): 822–829, https://doi.org/10.1111/j.1444-2906.2008.01594.x.

Coyer J A, Peters A F, Hoarau G et al. 2002. Inheritance patterns of ITS1, chloroplasts and mitochondria in artificial hybrids of the seaweeds Fucus serratus and F. evanescens (Phaeophyceae). European Journal of Phycology , 37 : 173–178, https://doi.org/10.1017/S0967026202003682.

Greiner S, Sobanski J, Bock R. 2015. Why are most organelle genomes transmitted maternally? BioEssays , 37 : 80–94, https://doi.org/10.1002/bies.201400110.

Hawkes M W. 1978. Sexual reproduction in Porphyra gardneri (Smith et Hollenberg) Hawkes (Bangiales, Rhodophyta). Phycologia , 17 : 329–353.

Huang L B, Yan X H. 2019. Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades. PLoS One , 14 (3): e0209128, https://doi.org/10.1371/journal.pone.0209128.

Hwang M S, Kim S O, Ha D S et al. 2013. Complete sequence and genetic features of the mitochondrial genome of Pyropia tenera (Rhodophyta). Plant Biotechnology Reports , 7 (4): 435–443, https://doi.org/10.1007/s11816-013-0281-4.

Isoda K, Shiraishi S, Watanabe S et al. 2000. Molecular evidence of natural hybridization between Abies veitchii and A. homolepis (Pinaceae) revealed by chloroplast, mitochondrial and nuclear DNA markers. Molecular Ecology , 9 (12): 1 965–1 974, https://doi.org/10.1046/j.1365-294X.2000.01088.x.

Johannessen M M, Andersen B A, Damgaard C et al. 2005. Maternal inheritance of chloroplasts between Brassica rapa and F1-hybrids demonstrated by cpDNAmarkers specific to oilseed rape and B. rapa . Molecular Breeding , 16 : 271–278, https://doi.org/10.1007/s11032-005-0236-8.

Kato Y, Kogame K, Nagasato C et al. 2006. Inheritance of mitochondrial and chloroplast genomes in the isogamous brown alga Scytosiphon lomentaria (Phaeophyceae). Phycological Research , 54 : 65–71, https://doi.org/10.1111/j.1440-1835.2006.00409.x.

Kong F N, Sun P P, Cao M et al. 2014. Complete mitochondrial genome of Pyropia yezoensis : reasserting the revision of genus Porphyra . Mitochondrial DNA , 25 (5): 335–336, https://doi.org/10.3109/19401736.2013.803538.

Kurtz S, Phillippy A, Delcher A L et al. 2004. Versatile and open software for comparing large genomes. Genome Biology , 5 (2): R12, https://doi.org/10.1186/gb-2004-5-2-r12.

Langmead B, Trapnell C, Pop M et al. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology , 10 (3): 1–10, https://doi.org/10.1186/gb-2009-10-3-r25.

Li H, Handsaker B, Wysoker A et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics , 25 (16): 2 078–2 079, https://doi.org/10.1093/bioinformatics/btp352.

Li Q Y, Wang X L, Zhang J et al. 2016. Maternal inheritance of organellar DNA demonstrated with DNA markers in crosses of Saccharina japonica (Laminariales, Phaeophyta). Journal of Applied Phycology , 28 : 2 019–2 026, https://doi.org/10.1007/s10811-015-0687-1.

Martin, M. 2011. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet Journal , 17 : 10–12, https://doi.org/10.14806/ej.17.1.200.

Miyamura S. 2010. Cytoplasmic inheritance in green algae: patterns, mechanisms and relation to sex type. Journal of Plant Research , 123 : 171–184, https://doi.org/10.1007/s10265-010-0309-6.

Morgensen H L. 1996. The hows and whys of cytoplasmic inheritance in seed plants. American Journal of Botany , 83 (3): 383–404, https://doi.org/10.1002/j.1537-2197.1996.tb12718.x.

Moritz C, Dowling T E, Brown W M. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annual Review of Ecology & Systematics , 18 (1): 269–292, https://doi.org/10.1146/annurev.es.18.110187.001413.

Motomura T, Nagasato C, Kimura K. 2010. Cytoplasmic inheritance of organelles in brown algae. Journal of Plant Research , 123 : 185–192, https://doi.org/10.1007/s10265-010-0313-x.

Niwa K, Kobiyama A, Sakamoto T. 2010. Interspecific hybridization in the haploid blade-forming marine crop Porphyra (Bangiales, Rhodophyta): occurrence of allodiploidy in surviving F1 gametophytic blades. Journal of Phycology , 46 (4): 693–702, https://doi.org/10.1111/j.1529-8817.2010.00853.x.

Niwa K, Yamamoto T, Furuita H et al. 2011. Mutation breeding in the marine crop Porphyra yezoensis (Bangiales, Rhodophyta): cultivation experiment of the artificial red mutant isolated by heavy-ion beam mutagenesis. Aquaculture , 314 (1-4): 182–187, https://doi.org/10.1016/j.aquaculture.2011.02.007.

Niwa K. 2010. Genetic analysis of artificial green and red mutants of Porphyra yezoensis Ueda (Bangiales, Rhodophyta). Aquaculture , 308 (1-2): 6–12, https://doi.org/10.1016/j.aquaculture.2010.08.007.

Peters A F, Scornet D, Müller D G et al. 2004. Inheritance of organelles in artificial hybrids of the isogamous multicellular chromist alga Ectocarpus siliculosus (Phaeophyceae). European Journal of Phycology , 39 : 235–242, https://doi.org/10.1080/09670260410001683241.

Rebound X, Zeyl C. 1994. Organelle inheritance in plants. Heredity , 72 : 137–140, https://doi.org/10.1038/hdy.1994.19.

Sahoo D, Tang X, Yarish C. 2002. Porphyra —the economic seaweed as a new experimental system. Current Science , 83 (11): 1 313–1 316.

Sutherland J E, Lindstrom S C, Nelson W A et al. 2011. A new look at an ancient order: generic revision of the Bangiales (Rhodophyta). Journal of Phycology , 47 (5): 1 131–1 151, https://doi.org/10.1111/j.1529-8817.2011.01052.x.

Walker B J, Abeel T, Shea T et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One , 9 (11): e112963, https://doi.org/10.1371/journal.pone.0112963.

Wang L, Mao Y X, Kong F N et al. 2013. Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis . PLoS One , 8 (5): e65902, https://doi.org/10.1371/journal.pone.0065902.

Wilson K G, Vaughn K C. 1979. Organelle destruction, a new mechanism to explain maternal inheritance of plastids and mitochondria in higher-plants. Plant Physiology , 63 : 5.

Wu H L, Kim J K, Huo Y Z et al. 2017. Nutrient removal ability of seaweeds on Pyropia yezoensis aquaculture rafts in China's radial sandbanks. Aquatic Botany , 137 : 72–79, https://doi.org/10.1016/j.aquabot.2016.11.011.

Yan X H, Aruga Y. 2000. Genetic analysis of artificial pigmentation mutants in Porphyra yezoensis Ueda (Bangiales, Rhodophyta). Phycological Research . 48 (3): 177–187, https://doi.org/10.1046/j.1440-1835.2000.00203.x.

Yu X Z, Wang L, Xu K P et al. 2020. Fine mapping to identify the functional genetic locus for red coloration in Pyropia yezoensis thallus. Frontiers in Plant Science , 11 : 867, https://doi.org/10.3389/fpls.2020.00867.

Zhang Q, Liu Y, Sodmergen. 2003. Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species. Plant & Cell Physiology , 44 : 941–951, https://doi.org/10.1111/j.1574-695X.2008.00405.x.

Zhong Z R, Li N, Qian D et al. 2011. Maternal inheritance of plastids and mitochondria in Cycas L. (Cycadaceae). Molecular Genetics & Genomics , 286 : 411–416, https://doi.org/10.1007/s00438-011-0653-9.

Zuccarello G C, Burger G, West J A et al. 1999a. A mitochondrial marker for red algal intraspecific relationships. Molecular Ecology , 8 : 1 443–1 447, https://doi.org/10.1046/j.1365-294x.1999.00710.x.

Zuccarello G C, West J A, Kamiya M et al. 1999b. A rapid method to score plastid haplotypes in red seaweeds and its use in determining parental inheritance of plastids in the red alga Bostrychia (Ceramiales). Hydrobiologia , 401 : 207–214, https://doi.org/10.1023/A:1003706931897.

Zuccarello G C, West J A. 2011. Insights into evolution and speciation in the red alga Bostrychia : 15 years of research. Economic & Environmental Geology , 26 (1): 21–32, https://doi.org/10.4490/algae.2011.26.1.021.

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Related Institution

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MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, College of Fisheries and Life Science, Hainan Tropical Ocean University

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CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences

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Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns inPyropia yezoensis(Bangiales, Rhodophyta)

DOI：10.1007/s00343-020-0298-9

摘要

Abstract

关键词

Keywords

references