Cloning and SNP Analysis of 4CL Gene in Larix kaempferi Hybrids and Their Parent Lines

ZHOU Ya-nan; LI Ai; CHEN Cheng-bin; WANG Chun-guo; SONG Wen-qin

Volume 26 Issue S1

Article Contents

Turn off MathJax

Article Navigation > Forest Research > 2013 > 26(S1): 18-24

Citation:

Cloning and SNP Analysis of 4CL Gene in Larix kaempferi Hybrids and Their Parent Lines

1.
College of Life Sciences, Nankai University, Tianjin 300071, China
2.
Department of Horticulture, Tianjin Agricultural University, Tianjin 300384, China

Received Date: 2013-08-19

Abstract

Based on transcriptome sequencing information, the 4CL gene containing 1 537 bp coding sequences was identified from 11 types of Larix kaempferi cross combinations. Sequence analysis indicated that the coding sequence contained a complete 1 368 bp-ORF fragment, and encoded 455 amino acids. Analysis of qRT-PCR showed that the expression of 4CL in Larix82×Larix13, Larix40×Larix10 and Larix82×Larix61 offsprings were higher than that in their corresponding parent lines, except Larix16×Larix61. The results suggests that the differential expression of 4CL genes in different L. kaempferi cross combinations may be involved in the lignin biosynthesis. In addition, 66 SNPs were identified in 4CL gene, among which 45 SNPs belong to transition type, accounting for 68.18% of the total variance; 20 SNPs belong to transversion type, accounting for 30.30% of the total variance and transition: transversion = 9:4. In the transition type, A/G and C/T transition accounted for 28.79% and 39.39%, respectively; in the types of transversion, A/C, A/T, G/C, and G/T account for 4.55%, 9.09%, 9.09% and 7.58%, respectively. Moreover, the phylogenetic analysis of 4 CL gene in all materials was conducted by NJ method. All results indicated that the 4CL gene showed abundant genetic diversity.
- Larix kaempferi,
- 4CL gene,
- single nucleotide polymorphisms (SNP),
- differential expression

References

[1]	李爱. 落叶松杂种优势性状形成的分子基础研究[D].天津:南开大学图书馆博士论文库, 2012
[2]	Qiu L J, Chang R Z, Wang W H, et al. Single nucleotide polymorphism (SNPs) at both loci of rhgl and Rhg4 in soybean resistant germplasm[J]. Journal of Plant Genetic Resources, 2003, 4(2): 89-93
[3]	Rafalski J A. Application of single nucleotide polymorphisms in crop genetics[J]. Current Opinion in Plant Biology, 2002, 5(2): 94-100
[4]	Wang R L, Syeca A, Hey J, et al. The limits of selection during maize domestication[J]. Nature, 1999, 398(6724): 236-239
[5]	Ayres N M, McClung A M, Larkin P D, et al. Microsatellites and a single nucleotide polymorphism in an extended pedigree of US rice germ plasm[J]. Theoretical and Applied Genetics, 1997, 94(5): 773-781
[6]	Nasu S, Suzuki J, Ohta R, et al. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza asativa, Oryza rufipogon) and establishment of SNP markers[J]. DNA Research, 2002, 9(5): 163-171
[7]	Wu L, Joshi C P, Chiang V L. A xylem-specific cellulose synthase gene from aspen (Populus tremuloides) is responsive to mechanical stress[J]. Plant J, 2000, 22: 495-502
[8]	Krutovsky K V, Neale D B. Nucleotide diversity and linkage disequilibrium in cold hardiness and wood quality related candidate genes in douglas fir[J]. Genetics, 2005, 171(4): 2029-2041
[9]	Pot D, McMillan L, Echt C, et al. Nucleotide variation in genes involved in wood formation in two pine species[J]. New Phytol, 2005, 167(1): 5101-5112
[10]	Djerbi S, Lindskog M, Arvesrad L. The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes[J]. Planta, 2005, 221: 739-746
[11]	Germano J, Klein A S. Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana and P. rubens[J]. Theoretical and Applied Genetics, 1999, 99: 37-49
[12]	Neale D B. Genomics to the tree breeding and forest health[J]. Curr Opin Genet Dev, 2007, 17(6): 539-544
[13]	Voo K S, Whetten R W, Omalley D M, et al. 4-coumarate:coenzyme a ligase from loblolly pine xylem. Isolation, characterization, and complementary DNA cloning[J]. Plant Physiol, 1995, 108(1): 85-97
[14]	Lee D, Ellard M, Wanner L A, et al. The Arabidopsis thaliana 4-coumarate:CoA ligase (4CL) gene: stress and developmentally regulated expression and nucleotide sequence of its cDNA[J]. Plant Mol Biol, 1995, 28(5): 871-884
[15]	饶国栋, 陆海. 毛白杨 4CL 基因家族的克隆与进化分析[J]. 广东农业科学, 2012, 8: 141-144
[16]	徐悦丽, 张含国, 施天元, 等. 长白落叶松群体 4CL 基因单核苷酸多态性分析[J]. 植物研究, 2013, 33(2): 208-213
[17]	冯春燕. 植物4-香豆酸: 辅酶A连接酶 (4CL)研究进展[J]. 农业基础科学, 2010(8): 39-40
[18]	Nei M, Roychoudhury A K. Sampling variance of heterozygosity and genetic distance[J]. Genetics, 1974, 76: 379-390
[19]	Kenneth J K, Thomas D S. Analysis of relative gene expression data using real-time quantitutive PCR and the 2^-ΔΔCt method[J]. Methods, 2001, 25: 402-408
[20]	陆海.形成层定位表达基金调控植物生长与性状研究[D].北京:北京林业大学,2002
[21]	王勇, 李朝恒. 小麦品种抗倒性的研究进展[J].山东农业大学学报, 1996, 27: 503-507
[22]	胡景江, 朱玮, 文建雷. 杨树细胞壁HRGP和木质素的诱导积累与其对溃疡病抗性的关系[J]. 植物病理学报, 1999, 29(2): 151-156
[23]	王佩卿, 王丽倩. 新型植物生长调节剂(ASL)在农林业上的应用[J]. 南京林业大学学报, 1999, 23(4): 1-6
[24]	许璐辰, 孙晓梅, 张守攻. 基因差异表达与杂种优势形成机制探讨[J]. 遗传, 2013, 35(6): 714-726
[25]	Stupar R M, Springer N M. Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid[J]. Genetics, 2006, 173(4): 2199-2210
[26]	Zhang H Y, He H, Chen L B, et al. A genome-wide transcription analysis reveals a close correlation of hybrids[J]. Trends Genet, 2003, 19(11): 597-600
[27]	Chodavarapu R K, Feng S, Ding B, et al. Transcriptome and methylome interactions in rice hybrids[J]. Proc Natl Acad Sci USA, 2012, 109(30): 12040-12045
[28]	Riddle N C, Birchler J A. Effects of reunited diverged regulatory hierarchies in allopolyploids and species in the F1 hybrid[J]. Genetics, 2006,173(4): 2199-2210
[29]	吴波, 刘勇. 柑橘类植物 GPAT基因片段克隆和SNP分析[J]. 江西农业大学学报, 2010, 32(1): 51-56
[30]	Altmann T, Roder M S. SNP identification in crop plants, Curr. Opin[J]. Plant Biol, 2009, 12(2): 211-217
[31]	王甲威, 林科, 姜超, 等. 16个高丛越橘品种 VcCBF基因的单核苷酸多态性(SNP)分析[J] 山东农业大学学报, 2012, 430(10): 41-44
[32]	蔡春梅, 柳伟先, 李锡河. 大豆蛋白质相关基因SNP的开发和遗传定位[J]. 延边大学农业学报, 2009, 31(2): 77-82
[33]	杜玮南,孙红霞,方福德.单核苷酸多态性的研究进展[J].国外医学: 遗传学分册, 2000, 4: 392-394

Proportional views

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Get Citation

PDF

XML

Article views(2648) PDF downloads(1423) Cited by()

Proportional views

Cloning and SNP Analysis of 4CL Gene in Larix kaempferi Hybrids and Their Parent Lines

1. College of Life Sciences, Nankai University, Tianjin 300071, China

2. Department of Horticulture, Tianjin Agricultural University, Tianjin 300384, China

Received Date: 2013-08-19

Abstract: Based on transcriptome sequencing information, the 4CL gene containing 1 537 bp coding sequences was identified from 11 types of Larix kaempferi cross combinations. Sequence analysis indicated that the coding sequence contained a complete 1 368 bp-ORF fragment, and encoded 455 amino acids. Analysis of qRT-PCR showed that the expression of 4CL in Larix82×Larix13, Larix40×Larix10 and Larix82×Larix61 offsprings were higher than that in their corresponding parent lines, except Larix16×Larix61. The results suggests that the differential expression of 4CL genes in different L. kaempferi cross combinations may be involved in the lignin biosynthesis. In addition, 66 SNPs were identified in 4CL gene, among which 45 SNPs belong to transition type, accounting for 68.18% of the total variance; 20 SNPs belong to transversion type, accounting for 30.30% of the total variance and transition: transversion = 9:4. In the transition type, A/G and C/T transition accounted for 28.79% and 39.39%, respectively; in the types of transversion, A/C, A/T, G/C, and G/T account for 4.55%, 9.09%, 9.09% and 7.58%, respectively. Moreover, the phylogenetic analysis of 4 CL gene in all materials was conducted by NJ method. All results indicated that the 4CL gene showed abundant genetic diversity.

HTML

Reference (33)

[1]	李爱. 落叶松杂种优势性状形成的分子基础研究[D].天津:南开大学图书馆博士论文库, 2012
[2]	Qiu L J, Chang R Z, Wang W H, et al. Single nucleotide polymorphism (SNPs) at both loci of rhgl and Rhg4 in soybean resistant germplasm[J]. Journal of Plant Genetic Resources, 2003, 4(2): 89-93
[3]	Rafalski J A. Application of single nucleotide polymorphisms in crop genetics[J]. Current Opinion in Plant Biology, 2002, 5(2): 94-100
[4]	Wang R L, Syeca A, Hey J, et al. The limits of selection during maize domestication[J]. Nature, 1999, 398(6724): 236-239
[5]	Ayres N M, McClung A M, Larkin P D, et al. Microsatellites and a single nucleotide polymorphism in an extended pedigree of US rice germ plasm[J]. Theoretical and Applied Genetics, 1997, 94(5): 773-781
[6]	Nasu S, Suzuki J, Ohta R, et al. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza asativa, Oryza rufipogon) and establishment of SNP markers[J]. DNA Research, 2002, 9(5): 163-171
[7]	Wu L, Joshi C P, Chiang V L. A xylem-specific cellulose synthase gene from aspen (Populus tremuloides) is responsive to mechanical stress[J]. Plant J, 2000, 22: 495-502
[8]	Krutovsky K V, Neale D B. Nucleotide diversity and linkage disequilibrium in cold hardiness and wood quality related candidate genes in douglas fir[J]. Genetics, 2005, 171(4): 2029-2041
[9]	Pot D, McMillan L, Echt C, et al. Nucleotide variation in genes involved in wood formation in two pine species[J]. New Phytol, 2005, 167(1): 5101-5112
[10]	Djerbi S, Lindskog M, Arvesrad L. The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes[J]. Planta, 2005, 221: 739-746
[11]	Germano J, Klein A S. Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana and P. rubens[J]. Theoretical and Applied Genetics, 1999, 99: 37-49
[12]	Neale D B. Genomics to the tree breeding and forest health[J]. Curr Opin Genet Dev, 2007, 17(6): 539-544
[13]	Voo K S, Whetten R W, Omalley D M, et al. 4-coumarate:coenzyme a ligase from loblolly pine xylem. Isolation, characterization, and complementary DNA cloning[J]. Plant Physiol, 1995, 108(1): 85-97
[14]	Lee D, Ellard M, Wanner L A, et al. The Arabidopsis thaliana 4-coumarate:CoA ligase (4CL) gene: stress and developmentally regulated expression and nucleotide sequence of its cDNA[J]. Plant Mol Biol, 1995, 28(5): 871-884
[15]	饶国栋, 陆海. 毛白杨 4CL 基因家族的克隆与进化分析[J]. 广东农业科学, 2012, 8: 141-144
[16]	徐悦丽, 张含国, 施天元, 等. 长白落叶松群体 4CL 基因单核苷酸多态性分析[J]. 植物研究, 2013, 33(2): 208-213
[17]	冯春燕. 植物4-香豆酸: 辅酶A连接酶 (4CL)研究进展[J]. 农业基础科学, 2010(8): 39-40
[18]	Nei M, Roychoudhury A K. Sampling variance of heterozygosity and genetic distance[J]. Genetics, 1974, 76: 379-390
[19]	Kenneth J K, Thomas D S. Analysis of relative gene expression data using real-time quantitutive PCR and the 2^-ΔΔCt method[J]. Methods, 2001, 25: 402-408
[20]	陆海.形成层定位表达基金调控植物生长与性状研究[D].北京:北京林业大学,2002
[21]	王勇, 李朝恒. 小麦品种抗倒性的研究进展[J].山东农业大学学报, 1996, 27: 503-507
[22]	胡景江, 朱玮, 文建雷. 杨树细胞壁HRGP和木质素的诱导积累与其对溃疡病抗性的关系[J]. 植物病理学报, 1999, 29(2): 151-156
[23]	王佩卿, 王丽倩. 新型植物生长调节剂(ASL)在农林业上的应用[J]. 南京林业大学学报, 1999, 23(4): 1-6
[24]	许璐辰, 孙晓梅, 张守攻. 基因差异表达与杂种优势形成机制探讨[J]. 遗传, 2013, 35(6): 714-726
[25]	Stupar R M, Springer N M. Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid[J]. Genetics, 2006, 173(4): 2199-2210
[26]	Zhang H Y, He H, Chen L B, et al. A genome-wide transcription analysis reveals a close correlation of hybrids[J]. Trends Genet, 2003, 19(11): 597-600
[27]	Chodavarapu R K, Feng S, Ding B, et al. Transcriptome and methylome interactions in rice hybrids[J]. Proc Natl Acad Sci USA, 2012, 109(30): 12040-12045
[28]	Riddle N C, Birchler J A. Effects of reunited diverged regulatory hierarchies in allopolyploids and species in the F1 hybrid[J]. Genetics, 2006,173(4): 2199-2210
[29]	吴波, 刘勇. 柑橘类植物 GPAT基因片段克隆和SNP分析[J]. 江西农业大学学报, 2010, 32(1): 51-56
[30]	Altmann T, Roder M S. SNP identification in crop plants, Curr. Opin[J]. Plant Biol, 2009, 12(2): 211-217
[31]	王甲威, 林科, 姜超, 等. 16个高丛越橘品种 VcCBF基因的单核苷酸多态性(SNP)分析[J] 山东农业大学学报, 2012, 430(10): 41-44
[32]	蔡春梅, 柳伟先, 李锡河. 大豆蛋白质相关基因SNP的开发和遗传定位[J]. 延边大学农业学报, 2009, 31(2): 77-82
[33]	杜玮南,孙红霞,方福德.单核苷酸多态性的研究进展[J].国外医学: 遗传学分册, 2000, 4: 392-394

Cloning and SNP Analysis of 4CL Gene in Larix kaempferi Hybrids and Their Parent Lines

Abstract

References

Proportional views

通讯作者: 陈斌, bchen63@163.com

Proportional views

Cloning and SNP Analysis of 4CL Gene in Larix kaempferi Hybrids and Their Parent Lines

HTML

Catalog

Export File

Citation

Format

Content