尾细桉生长和木材密度关联SNP挖掘与候选基因定位

朱显亮; 周长品; 贾翠蓉; 翁启杰; 李发根

doi:10.12302/j.issn.1000-2006.202004003

朱显亮, 周长品, 贾翠蓉, 翁启杰, 李发根

南京林业大学学报（自然科学版） ›› 2021, Vol. 45 ›› Issue (4) : 143-150.

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南京林业大学学报（自然科学版） ›› 2021, Vol. 45 ›› Issue (4) : 143-150. DOI: 10.12302/j.issn.1000-2006.202004003

研究论文

尾细桉生长和木材密度关联SNP挖掘与候选基因定位

作者信息 +

Association of SNP loci and candidate genes for growth and wood density in Eucalyptus urophylla × E. tereticornis

Author information +

文章历史 +

摘要

【目的】生长和木材基本密度是桉树的重要经济性状,挖掘其候选功能基因可为桉树遗传改良提供参考。【方法】以尾叶桉(Eucalyptus urophylla)和细叶桉(Eucalyptus tereticornis) F1全同胞子代试验林为研究对象,测定其8年生树高、胸径和木材基本密度,开展表型遗传分析。筛选极端表型个体,利用测序分型(GBS)开发SNP标记进行关联分析。挖掘与树高、胸径和木材基本密度关联的SNP位点,并进行候选基因初步定位。【结果】尾细桉F1子代树高、胸径与木材基本密度间的表型变异系数为7.51%~26.19%,生长性状与木材基本密度显著正相关。利用GBS获得了覆盖全基因组的15 185个SNP位点,关联分析共鉴定111个与生长和木材基本密度显著关联的SNP,其中2号染色体上检测到强烈的生长性状关联信号。定位40个与生长和木材基本密度相关候选基因,共富集在52个GO terms,基因功能注释分析表明其功能主要与植物抗逆性、生物与非生物胁迫、转录因子家族等相关。【结论】本研究获得了一批与尾细桉生长和材性性状关联的SNP位点和候选基因,并进行了树高、胸径及木材基本密度候选基因初步定位,挖掘的与抗逆性相关的基因可能在树木的生长和木材形成中发挥重要作用。

Abstract

【Objective】Growth and basic wood density are important economic traits of Eucalyptus; thus, searching for candidate genes will facilitate the genetic improvement in this genus.【Method】The interspecific full-sib family of E. urophylla and E. tereticornis was employed in this study. In addition, the correlation between the growth traits (height, dia-meter) and basic wood density of eight-year-old trees was investigated. The extreme phenotypes for each trait were screened for genotyping by sequencing (GBS) and developing SNP loci. Subsequently, association analyses of phenotypes and SNP loci were performed. Finally, SNP loci associated with the growth traits and basic wood density of E. urophylla × E. tereticornis were identified; candidate genes for these related traits were also identified. 【Result】① The phenotypic coefficient of variation ranged from 7.51% to 26.19% among the values of height, diameter, and basic wood density, while a significant positive correlation between the growth traits and basic wood density was found. ② A total of 15 185 whole-genome SNP loci were developed, and a total of 111 SNPs were identified as being significantly associated with growth and basic wood density; among which, strong association signals for diameter were detected on chromosome No.2. ③ In addition, 40 candidate genes related to the growth and basic wood density were identified, which were enriched in 52 GO terms. Gene annotation indicated that the candidate genes were mainly involved in plant stress resis-tance, biotic and abiotic stress, and transcription factor families.【Conclusion】In this study, a new set of SNP loci rela-ted to the growth traits and wood properties of E. urophylla × E. tereticornis were obtained, and dozens of candidate genes were identified. Our results suggest that genes related to stress resistance may play an important role in tree growth and wood formation. This information provides valuable genetic resources for research on Eucalyptus breeding.

导出引用

朱显亮, 周长品, 贾翠蓉, 等. 尾细桉生长和木材密度关联SNP挖掘与候选基因定位[J]. 南京林业大学学报（自然科学版）. 2021, 45(4): 143-150 https://doi.org/10.12302/j.issn.1000-2006.202004003

ZHU Xianliang, ZHOU Changpin, JIA Cuirong, et al. Association of SNP loci and candidate genes for growth and wood density in Eucalyptus urophylla × E. tereticornis[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2021, 45(4): 143-150 https://doi.org/10.12302/j.issn.1000-2006.202004003

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参考文献

列表( 原文顺序 | 文献年度倒序 | 文中引用次数倒序 ) 可视化分析

[1]

HILL

, JOHNSON

. Systematic studies in the eucalypts.7.A revision of the bloodwoods,genus Corymbia (Myrtaceae)[J]. Telopea, 1995, 6(2/3):185-504.DOI: 10.7751/telopea19953017.

https://doi.org/10.7751/telopea19953017

http://plantnet.rbgsyd.nsw.gov.au/emuwebnswlive/objects/common/webmedia.php?irn=75833&reftable=ebibliography

本文引用 [1]

[2]	TURNBULL J W. Eucalypt plantations[J]. New Forests, 1999, 17(1/3):37-52. DOI: 10.1023/a:1006524911242. https://doi.org/10.1023/a:1006524911242 http://link.springer.com/10.1023/A:1006524911242 本文引用 [1]

[3]	王豁然. 桉树生物学概论[M]. 北京: 科学出版社, 2010. WANG H R. Chinese appreciation of eucalyptus[M]. Beijing: Science Press, 2010. 本文引用 [1]

[4]	MYBURG A A, GRATTAPAGLIA D, TUSKAN G A, et al. The genome of Eucalyptus grandis[J]. Nature, 2014, 510(7505):356-362.DOI: 10.1038/nature13308. https://doi.org/10.1038/nature13308 https://doi.org/10.1038/nature13308 本文引用 [1]

[5]

STACKPOLE D

, VAILLANCOURT R

, AGUIGAR

, et al. Age trends in genetic parameters for growth and wood density in Eucalyptus globulus[J]. Tree Genet Genomes, 2010, 6(2):179-193.DOI: 10.1007/s11295-009-0239-4.

https://doi.org/10.1007/s11295-009-0239-4

http://link.springer.com/10.1007/s11295-009-0239-4

本文引用 [1]

[6]

李昌荣, 陈健波, 郭东强, 等. 锯材大花序桉生长和材性的综合指数选择[J]. 南京林业大学学报(自然科学版), 2019, 43(1):1-8.

LI C

, CHEN J

, GUO D

, et al. Comprehensive index selection on superior growth and wood properties of Eucalyptus cloeziana for saw timber[J]. J Nanjing For Univ (Nat Sci Ed), 2019, 43(1):1-8.DOI: 10.3969/j.issn.1000-2006.201805018.

https://doi.org/10.3969/j.issn.1000-2006.201805018

本文引用 [1]

[7]

朱显亮, 兰俊, 王建忠, 等. 中大径材尾细桉杂种无性系选择研究[J]. 南京林业大学学报(自然科学版), 2020, 44(2):43-50.

ZHU X

, LAN

, WANG J

, et al. Clonal selection of middle/large diameter timber of Eucalyptus urophylla × E.tereticornis hybrid clones[J]. J Nanjing For Univ (Nat Sci Ed), 2020, 44(2):43-50.DOI: 10.3969/j.issn.1000-2006.201904005.

https://doi.org/10.3969/j.issn.1000-2006.201904005

本文引用 [1]

[8]

YANG H

, WENG Q

, LI F

, et al. Genotypic variation and genotype-by-environment interactions in growth and wood properties in a cloned Eucalyptus urophylla × E.tereticornis family in southern China[J]. For Sci, 2018, 64(3):225-232.DOI: 10.1093/forsci/fxx011.

https://doi.org/10.1093/forsci/fxx011

本文引用 [1]

[9]	LANDER E S. The new genomics:global views of biology[J]. Science, 1996, 274(5287):536-539.DOI: 10.1126/science.274.5287.536. https://doi.org/10.1126/science.274.5287.536 https://www.sciencemag.org/lookup/doi/10.1126/science.274.5287.536 本文引用 [1]

[10]

周长品, 翁启杰, 甘四明, 等. 应用SNaPshot技术对桉树SNP的检测[J]. 南京林业大学学报(自然科学版), 2018, 42(4):83-88.

ZHOU C

, WENG Q

, GAN S

, et al. Application of SNaPshot to detect SNP markers in Eucalyptus[J]. J Nanjing For Univ (Nat Sci Ed), 2018, 42(4):83-88.DOI: 10.3969/issn.1000-2006.2017.05055.

https://doi.org/10.3969/issn.1000-2006.2017.05055

本文引用 [1]

[11]	NEALE D B, SAVOLAINEN O. Association genetics of complex traits in conifers[J]. Trends Plant Sci, 2004, 9(7):325-330.DOI: 10.1016/j.tplants.2004.05.006. https://doi.org/10.1016/j.tplants.2004.05.006 https://linkinghub.elsevier.com/retrieve/pii/S1360138504001335 本文引用 [1]

[12]

尚秀华, 张沛健, 谢耀坚, 等. 赤桉抗风和生长性状的SSR关联分析[J]. 南京林业大学学报(自然科学版), 2018, 42(4):97-105.

SHANG X

, ZHANG P

, XIE Y

, et al. SSR association analysis of Eucalyptus camaldulensis wind resistance and growth traits[J]. J Nanjing For Univ (Nat Sci Ed), 2018, 42(4):97-105.DOI: 10.3969/j.issn.1000-2006.201711019.

https://doi.org/10.3969/j.issn.1000-2006.201711019

本文引用 [2]

[13]

MÜLLER B S

, DE ALMEIDA

FILHO J E

, LIMA B

, et al. Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations[J]. New Phytol, 2019, 221(2):818-833.DOI: 10.1111/nph.15449.

https://doi.org/10.1111/nph.15449

https://onlinelibrary.wiley.com/toc/14698137/221/2

本文引用 [4]

[14]

THUMMA B

, NOLAN M

, EVANS

, 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.DOI: 10.1534/genetics.105.042028.

https://doi.org/10.1534/genetics.105.042028

https://academic.oup.com/genetics/article/171/3/1257/6060976

本文引用 [1]

[15]

CAPPA E

, EL-KASSABY

Y A

, GARCIA

M N

, et al. Impacts of population structure and analytical models in genome-wide asso-ciation studies of complex traits in forest trees:a case study in Eucalyptus globulus[J]. PLoS One, 2013, 8(11):e81267.DOI: 10.1371/journal.pone.0081267.

https://doi.org/10.1371/journal.pone.0081267

https://dx.plos.org/10.1371/journal.pone.0081267

本文引用 [2]

[16]	李昌荣. 大花序桉生长和材性遗传变异及SSR关联分析[D]. 北京:中国林业科学研究院, 2017. LI C R. Gere Variation and SSR association analyses in growth and wood properties in Eucalyptus cloeziana[D]. Beijing: Chinese Academy of Forestry, 2017. 本文引用 [2]

[17]

DILLON S

, BRAWNER J

, MEDER

, et al. Association genetics in Corymbia citriodora subsp.variegata identifies single nucleotide polymorphisms affecting wood growth and cellulosic pulp yield[J]. New Phytol, 2012, 195(3):596-608.DOI: 10.1111/j.1469-8137.2012.04200.x.

https://doi.org/10.1111/j.1469-8137.2012.04200.x

https://onlinelibrary.wiley.com/toc/14698137/195/3

本文引用 [2]

[18]

RESENDE R

, RESENDE M

, SILVA F

, et al. Regional heritability mapping and genome-wide association identify loci for complex growth,wood and disease resistance traits in Eucalyptus[J]. New Phytol, 2017, 213(3):1287-1300.DOI: 10.1111/nph.14266.

https://doi.org/10.1111/nph.14266

https://onlinelibrary.wiley.com/toc/14698137/213/3

本文引用 [4]

[19]	GRATTAPAGLIA D, PLOMION C, KIRST M, et al. Genomics of growth traits in forest trees[J]. Curr Opin Plant Biol, 2009, 12(2):148-156.DOI: 10.1016/j.pbi.2008.12.008. https://doi.org/10.1016/j.pbi.2008.12.008 https://linkinghub.elsevier.com/retrieve/pii/S1369526608002215 本文引用 [1]

[20]

彭仕尧, 徐建民, 李光友, 等. 尾细桉无性系在雷州半岛的生长与遗传分析[J]. 中南林业科技大学学报, 2013, 33(4):23-27.

PENG S

, XU J

, LI G

, et al. Growth and genetic analysis of 42 Eucalyptus urophylla × E.tereticornis clones in Leizhou Peninsula of China[J]. J Central South Univ For Technol, 2013, 33(4):23-27.DOI: 10.14067/j.cnki.1673-923x.2013.04.018.

https://doi.org/10.14067/j.cnki.1673-923x.2013.04.018

本文引用 [1]

[21]

甘四明, 李梅, 李发根, 等. 尾叶桉×细叶桉杂种无性系扦插生根和生长性状的研究[J]. 林业科学研究, 2006, 19(2):135-140.

GAN S

, LI

, LI F

, et al. Analysis on cutting and growth traits of clones of Eucalyptus urophylla × E.tereticornis[J]. For Res, 2006, 19(2):135-140.DOI: 10.3321/j.issn:1001-1498.2006.02.002.

https://doi.org/10.3321/j.issn:1001-1498.2006.02.002

本文引用 [1]

[22]

GAN S

, SHI J

, LI

, et al. Moderate-density molecular maps of Eucalyptus urophylla S.T.Blake and E.tereticornis Smith genomes based on RAPD markers[J]. Genetica, 2003, 118(1):59-67.DOI: 10.1023/a:1022966018079.

https://doi.org/10.1023/a:1022966018079

http://link.springer.com/10.1023/A:1022966018079

本文引用 [1]

[23]

POLAND J

, BROWN P

, SORRELLS M

, et al. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach[J]. PLoS One, 2012, 7(2):e32253.DOI: 10.1371/journal.pone.0032253.

https://doi.org/10.1371/journal.pone.0032253

https://dx.plos.org/10.1371/journal.pone.0032253

本文引用 [1]

[24]	CATCHEN J M, AMORES A, HOHENLOHE P, et al. Stacks:building and genotyping Loci de novo from short-read sequences[J]. G3 (Bethesda), 2011, 1(3):171-182.DOI: 10.1534/g3.111.000240. https://doi.org/10.1534/g3.111.000240 https://academic.oup.com/g3journal/article/1/3/171/5986549 本文引用 [1]

[25]	LANGMEAD B, SALZBERG S L. Fast gapped-read alignment with Bowtie 2[J]. Nat Methods, 2012, 9(4):357-359.DOI: 10.1038/nmeth.1923. https://doi.org/10.1038/nmeth.1923 https://doi.org/10.1038/nmeth.1923 本文引用 [1]

[26]

MCKENNA

, HANNA

, BANKS

, et al. The genome analysis toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Res, 2010, 20(9):1297-1303.DOI: 10.1101/gr.107524.110.

https://doi.org/10.1101/gr.107524.110

http://genome.cshlp.org/cgi/doi/10.1101/gr.107524.110

本文引用 [1]

[27]

DANECEK

, AUTON

, ABECASIS

, et al. The variant call format and VCFtools[J]. Bioinformatics, 2011, 27(15):2156-2158.DOI: 10.1093/bioinformatics/btr330.

https://doi.org/10.1093/bioinformatics/btr330

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btr330

本文引用 [1]

[28]

高美玲, 梁晓雪, 刘秀杰, 等. 基于极端个体GBS测序初步定位西瓜果形基因[J]. 分子植物育种, 2020, 18(10):3164-3171.

GAO M

, LIANG X

, LIU X

, et al. Short-term effects of different pru-ning intensities on poplar growth[J]. J Shandong For Sci Technol, 2020, 18(10):3164-3171.DOI: 10.13271/j.mpb.018.003164.

https://doi.org/10.13271/j.mpb.018.003164

本文引用 [1]

[29]

GÖTZ

, GARCÍA-GÓMEZ J

, TEROL

, et al. High-throughput functional annotation and data mining with the Blast2GO suite[J]. Nucleic Acids Res, 2008, 36(10):3420-3435.DOI: 10.1093/nar/gkn176.

https://doi.org/10.1093/nar/gkn176

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkn176

本文引用 [1]

[30]	CONTRERAS-SOTO R I, MORA F, DE OLIVEIRA M A, et al. A genome-wide association study for agronomic traits in soybean using SNP markers and SNP-based haplotype analysis[J]. PLoS One, 2017, 12(2):e0171105.DOI: 10.1371/journal.pone.0171105. https://doi.org/10.1371/journal.pone.0171105 本文引用 [1]

[31]

BRADBURY P

, ZHANG Z

, KROON D

, et al. TASSEL:software for association mapping of complex traits in diverse samples[J]. Bioinformatics, 2007, 23(19):2633-2635.DOI: 10.1093/bioinformatics/btm308.

https://doi.org/10.1093/bioinformatics/btm308

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btm308

本文引用 [1]

[32]

BEGUM

, SPINDEL J

, LALUSIN

, et al. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa)[J]. PLoS One, 2015, 10(3):e0119873.DOI: 10.1371/journal.pone.0119873.

https://doi.org/10.1371/journal.pone.0119873

https://dx.plos.org/10.1371/journal.pone.0119873

本文引用 [1]

[33]	FREEMAN J S, WHITTOCK S P, POTTS B M, et al. QTL influencing growth and wood properties in Eucalyptus globulus[J]. Tree Genet Genomes, 2009, 5(4):713-722.DOI: 10.1007/s11295-009-0222-0. https://doi.org/10.1007/s11295-009-0222-0 http://link.springer.com/10.1007/s11295-009-0222-0 本文引用 [1]

[34]

GION J

, CAROUCHÉ

, DEWEER

, et al. Comprehensive genetic dissection of wood properties in a widely-grown tropical tree:Eucalyptus[J]. BMC Genomics, 2011, 12:301.DOI: 10.1186/1471-2164-12-301.

https://doi.org/10.1186/1471-2164-12-301

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-301

本文引用 [2]

[35]

KULLAN A

, VAN DYK

M M

, HEFER

C A

, et al. Genetic dissection of growth,wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E.urophylla[J]. BMC Genet, 2012, 13:60.DOI: 10.1186/1471-2156-13-60.

https://doi.org/10.1186/1471-2156-13-60

http://bmcgenet.biomedcentral.com/articles/10.1186/1471-2156-13-60

本文引用 [1]

[36]	TAKAHASHI T, MATSUHARA S, ABE M, et al. Disruption of a DNA topoisomerase I gene affects morphogenesis in Arabidopsis[J]. Plant Cell, 2002, 14(9):2085-2093.DOI: 10.1105/tpc.001925. https://doi.org/10.1105/tpc.001925 https://academic.oup.com/plcell/article/14/9/2085-2093/6009819 本文引用 [1]

[37]

LIU

, GAO

, DINH T

, et al. DNA topoisomerase I affects polycomb group protein-mediated epigenetic regulation and plant development by altering nucleosome distribution in Arabidopsis[J]. Plant Cell, 2014, 26(7):2803-2817.DOI: 10.1105/tpc.114.124941.

https://doi.org/10.1105/tpc.114.124941

https://academic.oup.com/plcell/article/26/7/2803-2817/6100175

本文引用 [1]

[38]	ZHANG Y H, ZHENG L L, HONG J H, et al. TOPOISOMERASE1α Acts through two distinct mechanisms to regulate stele and Columella stem cell maintenance[J]. Plant Physiol, 2016, 171(1):483-493.DOI: 10.1104/pp.15.01754. https://doi.org/10.1104/pp.15.01754 本文引用 [1]

[39]

裴丽丽, 郭玉华, 徐兆师, 等. 植物逆境胁迫相关蛋白激酶的研究进展[J]. 西北植物学报, 2012, 32(5):1052-1061.

PEI L

, GUO Y

, XU Z

, et al. Research progress on stress-related protein kinases in plants[J]. Acta Bot Boreali-Occidentalia Sin, 2012, 32(5):1052-1061.DOI: 10.3969/j.issn.1000-4025.2012.05.032.

https://doi.org/10.3969/j.issn.1000-4025.2012.05.032

本文引用 [1]

[40]	LIN B L, WANG J S, LIU H C, et al. Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana[J]. Cell Stress Chape-rones, 2001, 6(3):201-208.DOI: 10.1379/1466-1268(2001)0060201:gaoths>2.0.co;2. https://doi.org/10.1379/1466-1268(2001)0060201:gaoths>2.0.co 本文引用 [1]

[41]	CHO E K, CHOI Y J. A nuclear-localized HSP70 confers thermoprotective activity and drought-stress tolerance on plants[J]. Biotechnol Lett, 2009, 31(4):597-606.DOI: 10.1007/s10529-008-9880-5. https://doi.org/10.1007/s10529-008-9880-5 http://link.springer.com/10.1007/s10529-008-9880-5 本文引用 [1]

[42]

MONTERO-BARRIENTOS

, HERMOSA

, CARDOZA R

, et al. Transgenic expression of the Trichoderma harzianum hsp70 gene increases Arabidopsis resistance to heat and other abiotic stresses[J]. J Plant Physiol, 2010, 167(8):659-665.DOI: 10.1016/j.jplph.2009.11.012.

https://doi.org/10.1016/j.jplph.2009.11.012

https://linkinghub.elsevier.com/retrieve/pii/S017616170900515X

本文引用 [1]

[43]

THUMMA B

, SOUTHERTON S

, BELL J

, et al. Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens[J]. Tree Genet Genomes, 2010, 6(2):305-317.DOI: 10.1007/s11295-009-0250-9.

https://doi.org/10.1007/s11295-009-0250-9

http://link.springer.com/10.1007/s11295-009-0250-9

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