Association Analysis of Polymorphisms in  PnEXPA1 Gene with Carbon Isotope Ratios in Black Poplar (Populus nigra L.)

ZHANG Wei-xi; CHU Yan-guang; HUANG Qin-jun; ZHANG Bing-yu; DING Chang-jun; SU Xiao-hua

Volume 27 Issue 3

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Article Navigation > Forest Research > 2014 > 27(3): 349-355

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Association Analysis of Polymorphisms in PnEXPA1 Gene with Carbon Isotope Ratios in Black Poplar (Populus nigra L.)

1.
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100091, China

Received Date: 2013-11-14

Abstract

The authors report an association study of SNP polymorphisms in a α-expansin gene PnEXPA1 with stable carbon isotope ratios (δ13C) in Populus nigra. In total, 11 SNP loci were genotyped with SNaPshot technology which indicates that homozygous genotype is more commonly ocurred for each individul with higher allele frequency. Association analysis under ANOVA and GLM methods revealed that SNP8 and SNP12 were associated with δ13C values. SNP8 was a synonymous mutation located in exon 1 and could explain 6.620% of genetic variation of trait, while SNP12 positioned in intron1 and contributed to 6.613% of genetic variation of trait. These two SNPs, together with SNP 9 and SNP13, were located in a haplotype block with higher LD levels. Clones with TT homozygous at SNP8 and SNP12 were found to have higher values of δ13C. These results provide insights into the molecular basis of the effects of PnEXPA1 on genetic variation of water use efficiency (WUE), as well as genic marker assisted breeding in poplar.
- Populus nigra,
- expansin,
- single nucleotide polymorphism,
- stable carbon isotope ratio,
- association analysis

References

[1]	丁明明, 苏晓华, 黄秦军. 碳稳定同位素技术在林木遗传改良中的应用[J]. 世界林业研究, 2005, 18(5): 21-26
[2]	Thumma B R, Nolan M F, Evans R, et al. Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp[J]. Genetics, 2005, 171(3): 1257-1265
[3]	Cosgrove D J. Loosening of plant cell walls by expansins[J]. Nature, 2000, 407(6802): 321-326
[4]	Cosgrove D J. Expansive growth of plant cell walls[J]. Plant Physiol Biochem, 2000, 38(1-2): 109-142
[5]	Sampedro J, Cosgrove D J. The expansin superfamily[J]. Genome Biol, 2005, 6(12): 242
[6]	高英, 陈乃芝, 熊艳梅, 等. 扩张蛋白在旱稻的免疫组化定位及对旱稻抗旱性的表达分析[J]. 自然科学进展, 2006, 16(4): 475-479
[7]	Abuqamar S, Ajeb S, Sham A, et al. A mutation in the expansin-like A2 gene enhances resistance to necrotrophic fungi and hypersensitivity to abiotic stress in Arabidopsis thaliana[J]. Mol Plant Pathol, 2013, 14(8): 813-827
[8]	Lü P, Kang M, Jiang X, et al. RhEXPA4, a rose expansin gene, modulates leaf growth and confers drought and salt tolerance to Arabidopsis[J]. Planta, 2013, 237(6): 1547-1559
[9]	Li F, Xing S, Guo Q, et al. Drought tolerance through over-expression of the expansin gene TaEXPB23 in transgenic tobacco[J]. J Plant Physiol, 2011, 168(9): 960-966
[10]	Han Y Y, Li A X, Li F, et al. Characterization of a wheat (Triticum aestivum L.) expansin gene, TaEXPB23, involved in the abiotic stress response and phytohormone regulation[J]. Plant Physiol Biochem, 2012, 54: 49-58
[11]	Guo W, Zhao J, Li X, et al. A soybean β-expansin gene GmEXPB 2 intrinsically involved in root system architecture responses to abiotic stresses[J]. Plant J, 2011, 66(3): 541-552
[12]	Geilfus C M, Zörb C, Mühling K H. Salt stress differentially affects growth-mediating β-expansins in resistant and sensitive maize (Zea mays L.) [J]. Plant Physiol Biochem, 2010, 48(12): 993-998
[13]	Gray-Mitsumune M, Mellerowicz E J, Abe H, et al. Expansins abundant in secondary xylem belong to subgroup A of the alpha-expansin gene family[J]. Plant Physiol, 2004, 135(3): 1552-1564
[14]	高燕. 杉木木材形成过程扩展蛋白基因的克隆与表达分析[J]. 林业科学, 2011, 47(11): 44-51
[15]	欧阳昆唏, 李俊成, 黄浩, 等. 团花树α扩展蛋白基因的克隆及表达分析[J]. 林业科学, 2013, 49(9): 62-71
[16]	An C, Saha S, Jenkins J N, et al. Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton[J]. Mol Genet Genomics, 2007, 278(5): 539-553
[17]	Chu Y, Su X, Huang Q, et al. Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms[J]. Genetica, 2009, 137(2): 141-150
[18]	丁明明, 苏晓华, 黄秦军. 欧洲黑杨基因资源稳定碳同位素组成特征[J]. 林业科学研究, 2006, 19(3): 272-276
[19]	Searle S R. Linear models for unbalanced data[M]. Newyork: John Wiley & Sons, 1987
[20]	Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: Software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23(19): 2633-2635
[21]	Hill W G, Robertson A. Linkage disequilibrium in finite populations[J]. Theor Appl Genet, 1968, 38(6): 226-231
[22]	Martin B, Thorstenson Y R. Stable carbon isotope composition (delta C), water use efficiency, and biomass productivity of Lycopersicon esculentum, Lycopersicon pennellii, and the F₁ Hybrid[J]. Plant Physiol, 1988, 88(1): 213-217
[23]	Tuskan G A, Difazio S, Jansson S, et al. The genome of black cottonwood[J]. Populus trichocarpa (Torr. & Gray). Science, 2006, 313(5793): 1596-1604
[24]	Lo H S, Wang Z, Hu Y, et al. Allelic variation in gene expression is common in the human genome[J]. Genome Res, 2003, 13(8):1855-1862
[25]	Wittkopp P J, Haerum B K, Clark A G. Evolutionary changes in cis and trans gene regulation[J]. Nature, 2004, 430(6995):85-88
[26]	Ingvarsson P K, Street N R. Association genetics of complex traits in plants[J]. New Phytol, 2011, 189(4): 909-922
[27]	González-Martínez S C, Huber D, Ersoz E, et al. Association genetics in Pinus taeda L. II. Carbon isotope discrimination[J]. Heredity, 2008, 101(1): 19-26

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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

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Association Analysis of Polymorphisms in PnEXPA1 Gene with Carbon Isotope Ratios in Black Poplar (Populus nigra L.)

1. State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing 100091, China

Received Date: 2013-11-14

Abstract: The authors report an association study of SNP polymorphisms in a α-expansin gene PnEXPA1 with stable carbon isotope ratios (δ13C) in Populus nigra. In total, 11 SNP loci were genotyped with SNaPshot technology which indicates that homozygous genotype is more commonly ocurred for each individul with higher allele frequency. Association analysis under ANOVA and GLM methods revealed that SNP8 and SNP12 were associated with δ13C values. SNP8 was a synonymous mutation located in exon 1 and could explain 6.620% of genetic variation of trait, while SNP12 positioned in intron1 and contributed to 6.613% of genetic variation of trait. These two SNPs, together with SNP 9 and SNP13, were located in a haplotype block with higher LD levels. Clones with TT homozygous at SNP8 and SNP12 were found to have higher values of δ13C. These results provide insights into the molecular basis of the effects of PnEXPA1 on genetic variation of water use efficiency (WUE), as well as genic marker assisted breeding in poplar.

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Reference (27)

[1]	丁明明, 苏晓华, 黄秦军. 碳稳定同位素技术在林木遗传改良中的应用[J]. 世界林业研究, 2005, 18(5): 21-26
[2]	Thumma B R, Nolan M F, Evans R, et al. Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp[J]. Genetics, 2005, 171(3): 1257-1265
[3]	Cosgrove D J. Loosening of plant cell walls by expansins[J]. Nature, 2000, 407(6802): 321-326
[4]	Cosgrove D J. Expansive growth of plant cell walls[J]. Plant Physiol Biochem, 2000, 38(1-2): 109-142
[5]	Sampedro J, Cosgrove D J. The expansin superfamily[J]. Genome Biol, 2005, 6(12): 242
[6]	高英, 陈乃芝, 熊艳梅, 等. 扩张蛋白在旱稻的免疫组化定位及对旱稻抗旱性的表达分析[J]. 自然科学进展, 2006, 16(4): 475-479
[7]	Abuqamar S, Ajeb S, Sham A, et al. A mutation in the expansin-like A2 gene enhances resistance to necrotrophic fungi and hypersensitivity to abiotic stress in Arabidopsis thaliana[J]. Mol Plant Pathol, 2013, 14(8): 813-827
[8]	Lü P, Kang M, Jiang X, et al. RhEXPA4, a rose expansin gene, modulates leaf growth and confers drought and salt tolerance to Arabidopsis[J]. Planta, 2013, 237(6): 1547-1559
[9]	Li F, Xing S, Guo Q, et al. Drought tolerance through over-expression of the expansin gene TaEXPB23 in transgenic tobacco[J]. J Plant Physiol, 2011, 168(9): 960-966
[10]	Han Y Y, Li A X, Li F, et al. Characterization of a wheat (Triticum aestivum L.) expansin gene, TaEXPB23, involved in the abiotic stress response and phytohormone regulation[J]. Plant Physiol Biochem, 2012, 54: 49-58
[11]	Guo W, Zhao J, Li X, et al. A soybean β-expansin gene GmEXPB 2 intrinsically involved in root system architecture responses to abiotic stresses[J]. Plant J, 2011, 66(3): 541-552
[12]	Geilfus C M, Zörb C, Mühling K H. Salt stress differentially affects growth-mediating β-expansins in resistant and sensitive maize (Zea mays L.) [J]. Plant Physiol Biochem, 2010, 48(12): 993-998
[13]	Gray-Mitsumune M, Mellerowicz E J, Abe H, et al. Expansins abundant in secondary xylem belong to subgroup A of the alpha-expansin gene family[J]. Plant Physiol, 2004, 135(3): 1552-1564
[14]	高燕. 杉木木材形成过程扩展蛋白基因的克隆与表达分析[J]. 林业科学, 2011, 47(11): 44-51
[15]	欧阳昆唏, 李俊成, 黄浩, 等. 团花树α扩展蛋白基因的克隆及表达分析[J]. 林业科学, 2013, 49(9): 62-71
[16]	An C, Saha S, Jenkins J N, et al. Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton[J]. Mol Genet Genomics, 2007, 278(5): 539-553
[17]	Chu Y, Su X, Huang Q, et al. Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms[J]. Genetica, 2009, 137(2): 141-150
[18]	丁明明, 苏晓华, 黄秦军. 欧洲黑杨基因资源稳定碳同位素组成特征[J]. 林业科学研究, 2006, 19(3): 272-276
[19]	Searle S R. Linear models for unbalanced data[M]. Newyork: John Wiley & Sons, 1987
[20]	Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: Software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23(19): 2633-2635
[21]	Hill W G, Robertson A. Linkage disequilibrium in finite populations[J]. Theor Appl Genet, 1968, 38(6): 226-231
[22]	Martin B, Thorstenson Y R. Stable carbon isotope composition (delta C), water use efficiency, and biomass productivity of Lycopersicon esculentum, Lycopersicon pennellii, and the F₁ Hybrid[J]. Plant Physiol, 1988, 88(1): 213-217
[23]	Tuskan G A, Difazio S, Jansson S, et al. The genome of black cottonwood[J]. Populus trichocarpa (Torr. & Gray). Science, 2006, 313(5793): 1596-1604
[24]	Lo H S, Wang Z, Hu Y, et al. Allelic variation in gene expression is common in the human genome[J]. Genome Res, 2003, 13(8):1855-1862
[25]	Wittkopp P J, Haerum B K, Clark A G. Evolutionary changes in cis and trans gene regulation[J]. Nature, 2004, 430(6995):85-88
[26]	Ingvarsson P K, Street N R. Association genetics of complex traits in plants[J]. New Phytol, 2011, 189(4): 909-922
[27]	González-Martínez S C, Huber D, Ersoz E, et al. Association genetics in Pinus taeda L. II. Carbon isotope discrimination[J]. Heredity, 2008, 101(1): 19-26

Association Analysis of Polymorphisms in PnEXPA1 Gene with Carbon Isotope Ratios in Black Poplar (Populus nigra L.)

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通讯作者: 陈斌, bchen63@163.com

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Association Analysis of Polymorphisms in PnEXPA1 Gene with Carbon Isotope Ratios in Black Poplar (Populus nigra L.)

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