基于全基因组重测序技术的‘红叶’杜仲SNP位点开发

doi:10.7525/j.issn.1673-5102.2019.06.018

植物研究 ›› 2019, Vol. 39 ›› Issue (6): 947-954.doi: 10.7525/j.issn.1673-5102.2019.06.018

基于全基因组重测序技术的‘红叶’杜仲SNP位点开发

杨赟^1,2, 陈梦娇³, 杜庆鑫¹, 朱景乐¹, 杜红岩¹, 杨绍彬¹

1. 国家林业和草原局泡桐研究开发中心, 经济林种质创新与利用国家林业和草原局重点实验室, 郑州 450003;
2. 南京林业大学林学院, 南京 210000;
3. 河南农业大学林学院, 郑州 450002

收稿日期:2019-01-03 出版日期:2019-11-05 发布日期:2019-11-16
通讯作者: 杨绍彬 E-mail:ysb1966327@yahoo.com.cn
作者简介:杨赟(1995-),女,博士研究生,主要从事林木遗传育种研究。
基金资助:
中国林业科学研究院中央级公益性科研院所基本业务费专项资金（CAFYBB2014QA037）

SNP Sites Developed by Whole Genome Resequencing Analysis in Eucommia ulmoides ‘Hongye’

YANG Yun^1,2, CHEN Meng-Jiao³, DU Qing-Xin¹, ZHU Jing-Le¹, DU Hong-Yan¹, YANG Shao-Bin¹

1. Paulownia Research and Development Center of State Administration of Forestry and Grassland, Key Laboratory of Non-timber Forest Germplasm Enhancement&Utilization of State Forestry and Grassland Administraion, Zhengzhou 450003;
2. Nanjing Forestry University, College of Forestry, Nanjing 210000;
3. Henan Agricultural University, College of Forestry, Zhengzhou 450002

Received:2019-01-03 Online:2019-11-05 Published:2019-11-16
Supported by:
Special Fund for Basic Business Expenses of the Central Level Public Welfare Research Institutes of the Chinese Academy of forestry(CAFYBB2014QA037)

摘要/Abstract

摘要： 为了挖掘与‘红叶’杜仲（Eucommia ulmoides ‘Hongye’）红叶性状紧密联系的SNP位点，进一步揭示红叶性状的遗传基础和分子机理。以‘红叶’杜仲和普通绿叶杜仲‘小叶’杜仲（Eucommia ulmoides ‘Xiaoye’）为研究材料，进行覆盖深度约为10x的全基因组重测序。使用SnpEff软件预测变异位点对蛋白编码的影响，结合花色苷的代谢通路和关键酶基因，筛选与‘红叶’杜仲叶色形成相关的差异位点。利用Sanger测序二代测序筛选的SNP位点，分子标记验证群体是‘红叶’杜仲和‘小叶’杜仲。结果表明，‘红叶’杜仲测序产生Clean data为14.16 Gb，‘小叶’杜仲产生Clean data为14.29 Gb。在‘红叶’杜仲中注释到严重影响蛋白质功能的有1 516个SNP，中度影响的41 328个SNP，在‘小叶’杜仲中存在严重影响蛋白质功能的SNP为1 640个，中度影响功能的SNP为47 192个。测得26 722条基因中有228条基因是与花色苷或类黄酮合成相关的酶基因。经过筛选，确定了12个特异性的SNP位点，均属于外显子区域的错义突变。利用一代测序验证，根据SNP位置设计了7对引物，SNP准确率达到100%。

关键词: ‘红叶’杜仲, 全基因组重测序, 花色苷, SNP

Abstract: We studied the SNP locus and candidate genes closely related to the red leaf traits of Eucommia ulmoides ‘Hongye’ for further revealing the genetic basis and molecular mechanism of red leaf traits. We used E.ulmoides ‘Hongye’ and the common green leaf E.ulmoides to perform whole genome sequencing with a depth of about 10x. With resequencing data and by using SnpEff software we predicted the effect of mutation sites on protein coding, selected the differential sites associated with the formation of E.ulmoides ‘Hongye’ leaf color, which were related to anthocyanin metabolic pathways and key enzyme genes. For fine mapping, 14.16 Gb clean data were generated from genome re-sequencing of E.ulmoides ‘Hongye’ and 14.29 Gb of clean data was produced by E.ulmoides ‘Xiaoye’. There are 1 516 SNPs in the E.ulmoides ‘Hongye’ which have serious effects on protein function, and 41 328 moderately affected. There are 1 640 SNPs in the E.ulmoides ‘Xiaoye’ that seriously affect protein function, and 47 192 SNPs that moderately affect function. Of the 26 722 genes, 228 were found to be involved in the synthesis of anthocyanin or flavonoids. After screening, 12 specific SNP loci were identified, all of which belonged to missense mutations in the exon region. Using a generation of sequencing verification, 7 pairs of primers were designed based on the SNP position, and the SNP accuracy rate reached 100%.

Key words: Eucommia ulmoides ‘Hongye’, whole genome resequencing, anthocyanin, SNP

中图分类号:

S687.9

杨赟, 陈梦娇, 杜庆鑫, 朱景乐, 杜红岩, 杨绍彬. 基于全基因组重测序技术的‘红叶’杜仲SNP位点开发[J]. 植物研究, 2019, 39(6): 947-954.

YANG Yun, CHEN Meng-Jiao, DU Qing-Xin, ZHU Jing-Le, DU Hong-Yan, YANG Shao-Bin. SNP Sites Developed by Whole Genome Resequencing Analysis in Eucommia ulmoides ‘Hongye’[J]. Bulletin of Botanical Research, 2019, 39(6): 947-954.

参考文献

1. 李芳东,杜红岩. 杜仲[M]. 北京:中国中医药出版社,2001. Li F D,Du H Y. Eucommia ulmoides[M]. Beijing:China Traditional Chinese Medicine Press,2001.
2. 黄浩平. 杜仲的开发与利用[J]. 水土保持通报,2001,21(3):31. Huang H P. The development and use of Eucommia[J]. Bulletin of Soil and Water Conservation,2001,21(3):31.
3. 罗海蓉,姜卫兵,魏家星,等. 杜仲的园林特性及开发利用[J]. 广东农业科学,2013,40(19):25-27. Luo H R,Jiang W B,Wei J X,et al. Landscape characteristics and developing application of Eucommia[J]. Guangdong Agricultural Sciences,2013,40(19):25-27.
4. 何文. 杜仲开发有前景[J]. 资源开发与市场,2000,16(4):221. He W. Eucommia has a promising development[J]. Resource Development & Markets,2000,16(4):221.
5. 赵欣,白伟. 杜仲叶片干旱胁迫响应相关差异蛋白的筛选与鉴定[J]. 植物研究,2018,38(3):422-432. Zhao X,Bai W. Screening and identification of the proteins related to drought response in leaves of Eucommia ulmoides[J]. Bulletin of Botanical Research,2018,38(3):422-432.
6. 杜庆鑫,刘攀峰,魏艳秀,等. 基于主成分与聚类分析的杜仲雄花品质综合评价[J]. 植物研究,2016,36(6):846-852. Du Q X,Liu P F,Wei Y X,et al. Comprehensive evaluation of Eucommia ulmoides male flowers quality by principal component and cluster analysis[J]. Bulletin of Botanical Research,2016,36(6):846-852.
7. 朱景乐,李芳东,杜红岩,等. 三个观赏型杜仲无性系叶片色素含量比较[J]. 林业科学研究,2014,27(4):562-564. Zhu J L,Li F D,Du H Y,et al. Comparison of leaf pigment content among three ornamental Eucommia ulmoides varieties[J]. Forest Research,2014,27(4):562-564.
8. 岳桂东,高强,罗龙海,等. 高通量测序技术在动植物研究领域中的应用[J]. 中国科学:生命科学,2012,42(2):107-124. Yue G D,Gao Q,Luo L H,et al. The application of high-throughput sequencing technology in plant and animal research[J]. Scientia Sinica Vitae,2012,42(2):107-124.
9. 陈勇,柳亦松,曾建国. 植物基因组测序的研究进展[J]. 生命科学研究,2014,18(1):66-74. Chen Y,Liu Y S,Zeng J G. Progresses on plant genome sequencing profile[J]. Life Science Research,2014,18(1):66-74.
10. 施季森,王占军,陈金慧. 木本植物全基因组测序研究进展[J]. 遗传,2012,34(2):145-156. Shi J S,Wang Z J,Chen J H. Progress on whole genome sequencing in woody plants[J]. Hereditas,2012,34(2):145-156.
11. 戴思兰,洪艳. 基于花青素苷合成和呈色机理的观赏植物花色改良分子育种[J]. 中国农业科学,2016,49(3):529-542. Dai S L,Hong Y. Molecular breeding for flower colors modification on ornamental plants based on the mechanism of anthocyanins biosynthesis and coloration[J]. Scientia Agricultura Sinica,2016,49(3):529-542.
12. Chen S F,Zhou Y Q,Chen Y R,et al. Fastp:an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics,2018,34(17):i884-i890.
13. Li H,Durbin R. Fast and accurate short read alignment with burrows-wheeler transform[J]. Bioinformatics,2009,25(14):1754-1760.
14. Uchimura A,Higuchi M,Minakuchi Y,et al. Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice[J]. Genome Research,2015,25(8):1125-1134.
15. Cingolani P,Platts A,Wang L L,et al. A program for annotating and predicting the effects of single nucleotide polymorphisms,SnpEff:SNPs in the genome of Drosophila melanogaster strain W1118;iso-2;iso-3[J]. Fly,2012,6(2):80-92.
16. Ni X P,Xue S,Iqbal S,et al. Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot(Prunus mume)[J]. PeerJ,2018,6(3):e4625.
17. Xu Y S,Gao Z H,Tao J M,et al. Genome-wide detection of SNP and SV variations to reveal early ripening-related genes in grape[J]. PLoS One,2016,11(2):e0147749.
18. 焦健,刘崇怀,樊秀彩,等. 中国野生种葡萄mybA转录因子SNP特征分析[J]. 植物遗传资源学报,2013,14(5):885-891. Jiao J,Liu C H,Fan X C,et al. Characterization of SNP associated with mybA transcription factor in Chinese wild grapes[J]. Journal of Plant Genetic Resources,2013,14(5):885-891.
19. Liu Y F,Wang J M,Zhang J H,et al. Characterization of SSRs and SNPs based on transcriptome of Ranunculus asiaticus L. and development of anthocyanin-related SSRs and SNPs[J]. Nanoscience and Nanotechnology Letters,2018,10(2):267-273.
20. Oh J H,Lee Y J,Byeon E J,et al. Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants[J]. 3 Biotech,2018,8(2):115.

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基于全基因组重测序技术的‘红叶’杜仲SNP位点开发

SNP Sites Developed by Whole Genome Resequencing Analysis in Eucommia ulmoides ‘Hongye’

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