毛白杨S-腺苷高半胱氨酸水解酶基因PtSAHHA的克隆、表达及SNP关联分析

doi:10.11707/j.1001-7488.20131109

Abstract

Abstract:

In this study, a full-length cDNA clone encoding PtSAHHA was isolated from the cDNA library prepared from mature xylem zone of Populus tomentosa by the bioinformatics and molecular biology. The PtSAHHA cDNA had 1 935 bp length with a corresponding open reading frame (ORF) of 1 458 bp that could encode a protein of 485 amino acids. Tissue-specific expression analysis indicated that the PtSAHHA transcripts were the most abundant mRNA products in stem xylem, intermediate in stem cambium and mature leaf, and the lowest abundant in young leaf. By aligning,comparing and analyzing the genomic sequences of PtSAHHA in 45 random individuals of P.tomentosa with the software of MEGA5.0 and DnaSP5, a total of 166 single nucleotide polymorphisms (SNPs) were detected, with the SNP frequency of 1/15 bp and the diversity (π_T) of 0.010 58. There were 88 SNPs detected in the coding regions of PtSAHHA, of which 34 were synonymous nucleotide substitutions, and 53 were missense mutations and 1 was nonsense mutation. The diversity level of synonymous nucleotide substitutions (π_Synonymous=0.024 91) was tenfold of nonsynonymous nucleotide substitutions (π_{Nonsynonymous}=0.002 33), suggesting that the gene might be evolved under purifying selection at the synonoymous sites of the coding region in P. tomentosa. Linkage disequilibrium test in the PtSAHHA showed that LD declined rapidly within the regions of PtSAHHA with the length increase to 800 bp(r²< 0.1). On this basis, candidate gene-based association analysis of 42 common single-SNPs (frequency > 10%) with six wood traits in an association population of 426 unrelated individuals showed 3 SNPs that were significantly associated with 3 wood traits, respectively. This study provides an important genetic foundation for molecular marker-assisted selection breeding programs with the goals of improving the quality and quantity of wood products of P. tomentosa.

Key words: Populus tomentosa, S-adenosyl-L-homocysteine hydrolase (SAHH), single nucleotide polymorphisms, linkage disequilibrium (LD), wood property

CLC Number:

S718.46

Gong Chenrui, Wang Lu, Du Qingzhang, Zhang Deqiang. Isolation, Expression, and Association Genetics of the S-Adenosyl-L-Homocysteine Hydrolase Gene A (PtSAHHA) in Populus tomentosa[J]. Scientia Silvae Sinicae, 2013, 49(11): 67-76.

References

金晓霞,秦智伟,周秀艳,等.2012.黄瓜S-腺苷-L高半胱氨酸水解酶全长cDNA的克隆及表达分析.中国农业科学,45(7): 1338-1346.
潘炜,田佳星,杜庆章,等.2011.毛白杨蔗糖合酶基因PtSUS 1 的克隆、表达及单核苷酸多态性分析.林业科学,47(3): 52-58.
佘义斌,朱一超,张天真,等.2008.棉花腺苷高半胱氨酸水解酶cDNA的克隆、表达及染色体定位.作物学报,34(6): 958-964.
王金慧,丁燏,简纪常,等.2011.南极冰藻Chlamydomonas sp.
ICE-L S-腺苷同型半胱氨酸水解酶基因的克隆及其生物信息学分析.中国水产科学, 18(6): 1234-1242.
卫尊征,郭琦,李百炼,等.2009.小叶杨GA20氧化酶基因的克隆、表达及单核苷酸多态性分析.林业科学,45(4): 19-27.
赵谨,杨克恭,张学.2005.一种新发现的基因表达调控机制—核糖开关.中国生物化学与分子生物学报, 21(2): 151-157.
Andersen J,Schrag T,Melchinger A,et al.2005.Validation of Dwarf 8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.).Theor Appl Genet, 111(2): 206-217.
Beaulieu J,Doerksen T,Boyle B,et al.2011.Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression.Genetics, 188(1): 197-214.
Cantoni G,Scarano E.1954.The formation of S-adenosylhomocysteine in enzymeatic transmithylation reactions.Journal of Biological Chemistry,76(18): 4744.
Chalamcharla V,Curcio M J,Belfort M.2010.Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry.Genes & Dev, 24: 827-836.
Chiang V,Puumala R,Takeuchi H,et al.1988.Comparison of softwood and hardwood kraft pulping.Tappi Journal,71: 173-176.
Chu Y,Su X,Huang Q,et al.2009.Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms.Genetica, 137(2): 141-150.
Clercq E.2002.Highlights in the development of new antiviral agents.Mini Rev Med Chem, 2(2): 163-175.
Cullen B.2000.Nuclear RNA export pathways.Molecular and Cellular Biology, 20(12): 4181-4187.
Déjardin A,Laurans F,Arnaud D,et al.2010.Wood formation in Angiosperms.Am Soc Plant Biol,333(4): 325-334.
Demirbas A.2005.Bioethanol from cellulosic materials: a renewable motor fuel from biomass.Energy Sources, 27(4): 327-337.
Dillon S,Brawner J,Meder R,et al.2012.Association genetics in Corymbia citriodora subsp. variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield.New Phytol, 195(3): 596-608.
Dillon S,Nolan M,Li W,et al.2010.Allelic variation in cell wall candidate genes affecting solid wood properties in association populations and land races of Pinus radiata.Genetics, 185(4): 1477-1487.
Du Q,Pan W,Tian J,et al.2013a.The UDP-Glucuronate decarboxylase gene family in Populus: structure, expression, and association genetics.PLoS one,8(4):e60880.
Du Q,Pan W,Xu B,et al.2013b.Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa.New Phytol, 197(3): 763-776.
Du Q,Wang B,Wei Z,et al.2012.Genetic diversity and population structure of Populus tomentosa (Chinese white poplar) revealed by SSR markers.J Hered, 103(6): 853-862.
Fu Y,Li W.1993.Statistical tests of neutrality of mutatons.Genetics, 133(3): 693-709.
Gonzalez-Martinez S,Wheeler N,Ersoz E,et al.2007.Association genetics in Pinus taeda L. I. Wood property traits.Genetics, 175(1): 399-409.
Guerra F,Wegrzyn J,Sykes R,et al.2012.Association genetics of chemical wood properties in black poplar (Populus nigra).New Phytol, 197(1): 162-176.
Huang Z.1992.The study on the climatic regionalization of the distributional region of Populus tomentosa.Beijing For Univ, 14(3): 26-32.
Ingvarsson P.2005.Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae).Genetics, 169(2): 945-953.
Ingvarsson P, Street N.2011.Association genetics of complex traits in plants.New Phytol, 189(4): 909-922.
Ji Y,Li Z T,Zhu Q,et al.2005.Current status in research of S-adenosylhomocysteine hydrolase and its inhibitors.Prog Pharmac Sci, 29(11): 481-486.
Kloor D,Osswald H.2004.S-Adenosylhomocysteine hydrolase as a target for intracellular adenosine action.Trends in Pharmacol Sci, 25(6): 294-297.
Koshkin A, Singh S, Nielsen P, et al. 1998. LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine,
5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligo merisation, and unprecendented nucleic acid recognition. Tetrahedron, 54: 3607-3630.
Li C,Yu T,Jiang S,et al.2008.Down-regulation of S-adenosyl-L-homocysteine hydrolase reveals a role of cytokinin in promoting transmethylation reactions.Planta, 228(1): 125-136.
Li L,Lu S, Chiang V.2006.A genomic and molecular view of wood formation.Crit Rev Plant Sci, 25: 213-233.
Lin Z,Li W.2012.Evolution of 5'untranslated region length and gene expression reprogramming in yeasts.Mol Biol Evol, 299(1): 81-89.
Lloyd H,Schrader J.1993.Adenosine metabolism in the guinea pig heart: the role of cytosolic S-adenosyl-L-homocysteine hydrolase,
5'-nucleotidase and adenosine kinase.European Heart Journal, 14(Suppl Ⅰ): 27-33.
Miyamoto Y,Mabuchi A,Shi D,et al.2007.A functional polymorphism in the 5'UTR of GDF5 is associated with susceptibility to osteoarthritis.Nat Genet,39: 529-533.
Moor C,Meijer H,Lissendenet S.2005.Mechanisms of translational control by the 3'UTR in development and differentiation.Seminars in Cell & Developmental Biology, 16(1): 49-58.
Nordborg M,Borevitz J,Bergelson J,et al.2002.The extent of linkage disequilibrium in Arabidopsis thaliana.Nat Genet,30: 190-193.
Parker N,Yang X,Hanke J,et al.2003.Trypanosoma cruzi: molecular cloning and characterization of the S-adenosylhomocysteine hydrolase.Exp Parasitol, 105(2): 149-158.
Remington D,Thomsberry J,Matsuoka Y,et al.2001.Structure of linkage disequilibrium and phenotypic associations in the maize genome.Proc Natl Acad Sci USA,98(20): 11479-11484.
Ritland K.1996. Estimators for pairwise relatedness and individual inbreeding coefcients.Genet Res,67(2): 175-185.
Rocha P,Sheikh M,Melchiorre R,et al.2005.The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 gene codes for an S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing.The Plant Cell, 17(2): 404-417.
Sassner P,Galbe M,Zacchi G.2005.Steam pretreatment of Salix with and without SO₂ impregnation for production of bioethanol.Applied Biochem Biotech, 121/124: 1101-1118.
Slavov G,DiFazio S,Martin J,et al.2012.Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.New Phytol, 196(3): 713-725.
Sontheimer E,Gordon P,Piccirilli J.1999.Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome.Gene & Development, 13: 1729-1741.
Stich B,Melchinger A.2009.Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis.BMC Genomics, 10: 94.
Storey J,Tibshirani R.2003.Statistical signicance for genomewide studies.Proc Natl Acad Sci USA, 100(16): 9440-9445.
Suh Y,Vijg J.2005.SNP discovery in associating genetic variation with man disease phenotypes.Mutation Research,573(1/2): 41-53.
Tajima F.1989.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.Genetics, 123(3): 585-595.
Tehlivets O,Hasslacher M,Kohlwein S.2004.S-adenosyl-L-homocysteine hydrolase in yeast: key enzyme of methylation metabolism and coordinated regulation with phospholipid synthesis.FEBS Lett,577(3): 501-506.
Thumma B,Matheson B,Zhang D,et al.2009.Identification of a Cis-acting regulatory polymorphism in a eucalypt COBRA-like gene affecting cellulose content. Genetics, 183(3): 1153-1164.
Tian J,Du Q,Chang M,et al.2012.Allelic variation in PtGA 20 Ox associates with growth and wood properties in Populus spp.PLoS one,7(12): e53116.
Turner M,Yang X,Yin D,et al.2000.Structure and function of S-adenosylhomocysteine hydrolase.Cell Biochem Biophys,33(2): 101-125.
Villalobos D,Díaz-Moreno S,Said E,et al.2012.Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes.BMC Plant Biology, 12: 100.
Watterson G.1975.On the number of segregating sites in genetical models without recombination.Theor Popul Biol, 7(2): 256-276.
Yu J,Pressoir G,Briggs W,et al.2006.A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.Nature Genetics,38: 203-208.
Zhang D,Zhang Z.2005.Single nucleotide polymorphisms discovery and linkage disequilibrium.Forestry Studies in China,7(3): 1-14.

[1]	Yi Min, Lai Meng, Sun Xiaomei, Zhang Shougong, Zhao Kun. Application Prospect on Applying Nondestructive Testing Technology in Wood Property Breeding of Larix kaempferi [J]. Scientia Silvae Sinicae, 2014, 50(11): 96-103.
[2]	Zhao Xing;Guo Qi;Chen Qingqing;Li Bailian;Zhang Deqiang. Isolation, Expression and Single Nucleotide Polymorphisms Analysis of Heat Shock Transcription Factor HsfA1d in Populus [J]. Scientia Silvae Sinicae, 2011, 47(7): 82-90.
[3]	Guo Qi;Wang Baolei;Wang Bowen;Li Bailian;Zhang Deqiang. Isolation, Expression and Single Nucleotide Polymorphisms Analysis of PtDREB2A in Populus tomentosa [J]. Scientia Silvae Sinicae, 2011, 47(4): 49-56.
[4]	Pan Wei;Tian Jiaxing;Du Qingzhang;Zhang Zhiyi;Zhang Deqiang. Isolation, Expression and Single Nucleotide Polymorphisms Analysis of Sucrose Synthase Gene (PtSUS 1 ) from Populus tomentosa [J]. Scientia Silvae Sinicae, 2011, 47(3): 52-58.
[5]	Xu Baohua;Yang Xiaohui.;Li Bailian;;Zhang Zhiyi.;Zhang Deqiang.. Isolation，Expression and Single Nucleotide Polymorphisms Analysis of Cellulose Synthase gene (PtCesA4) from Populus tomentosa [J]. Scientia Silvae Sinicae, 2009, 12(5): 1-10.
[6]	Wei Zunzheng;Guo Qi;Li Bailian;;Zhang Jinfeng;Zhang Deqiang;. Isolation, Expression and Single Nucleotide Polymorphisms (SNPs) Analysis ofGA20Ox Gene in Populus simonii [J]. Scientia Silvae Sinicae, 2009, 12(4): 19-27.
[7]	Yang Xiaohui;Zhang Youhui;Zhang Zhiyi;Li Bailian;Zhang Deqiang . Isolation and Single Nucleotide Polymorphisms Analysis of Stem Cell Organizer Gene Wuschel in Populus tomentosa [J]. Scientia Silvae Sinicae, 2009, 12(1): 43-49.
[8]	Huang Qinjun Ding Mingming Zhang Xianghua Su Xiaohua. Association Analysis Between SSR Molecular Markers and Wood Properties of Populus nigra [J]. Scientia Silvae Sinicae, 2007, 43(02): 43-47.
[9]	Huang Rongfeng;Bao Fucheng;Zhang Dongmei . Model for Maturation Age of Wood Property and Extend of Juvenile Wood Zone in Poplar Trunks [J]. Scientia Silvae Sinicae, 2005, 41(3): 103-109.
[10]	Huang Qinjun;Su Xiaohua;Huang Liejian;Zhang Zhiyi. QTLs Mapping for Wood Properties of Populus deltoides×P. cathayana [J]. Scientia Silvae Sinicae, 2004, 40(2): 55-60.
[11]	Xia Yufang;Chen Honghui. STUDY ON PLANTING DENSITY AFFECTING OF THE WOOD PROPERTIES OF MASSON PINE [J]. Scientia Silvae Sinicae, 2002, 38(2): 113-118.
[12]	Bao Fuchen;Jiang Zehui;Jiang Xiaomei;Lu Xixian;Luo Xiuqin. COMPARATIVE STUDIES ON WOOD PROPERTIES OF JUVENILE VS. MATURE WOOD AND PLANTATION VS. NATUREAL FOREST OF MAIN PLANTATION TREE SPECIES IN CHENA [J]. , 1998, 34(2): 63-76.
[13]	Wang Shuli;Wu Jisheng;Zhong Congqi. STUDIES ON WOOD PROPERY AND PULP CHARACTERISTICS OF WOOD FROM LARIX OLGENSIS PULP PLANTATION [J]. , 1997, 33(3): 283-288.
[14]	Cai Zemo. WOOD PROPERTIES AND PULPING EXPERIMENT OF EUCALYPTUS ABL NO.12 [J]. , 1996, 32(4): 361-365.
[15]	Chai Xiuwu;Li Yiquan;Chen Daodong. STUDY ON THE FERTILIZATION EFFECT UPON THE WOOD PROPERTIES OF POPULUS DELTOIDES cv.“LUX”ex I-69/55 [J]. , 1993, 29(2): 145-151.

Isolation, Expression, and Association Genetics of the S-Adenosyl-L-Homocysteine Hydrolase Gene A (PtSAHHA) in Populus tomentosa

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments