中国水稻科学 ›› 2020, Vol. 34 ›› Issue (1): 8-16.DOI: 10.16819/j.1001-7216.2020.9066
李金璐, 张慧, 焦泽宇, 刘剑宇, 韩光煜, 卓晓轩, 罗琼*()
收稿日期:
2019-06-12
修回日期:
2019-06-28
出版日期:
2020-01-10
发布日期:
2020-01-10
通讯作者:
罗琼
作者简介:
作者简介:#共同第一作者
基金资助:
Jinlu LI, Hui ZHANG, Zeyu JIAO, Jianyu LIU, Guangyu HAN, Xiaoxuan ZHUO, Qiong LUO*()
Received:
2019-06-12
Revised:
2019-06-28
Online:
2020-01-10
Published:
2020-01-10
Contact:
Qiong LUO
About author:
About author:#These authors contributed equally to this work
摘要:
【目的】子预44是一具有广谱持久稻瘟病抗性的云南地方粳稻品种。为了鉴定子预44中候选稻瘟病抗性相关基因,【方法】本研究利用高通量测序技术(High-throughput sequencing)对子预44和感病水稻江南香糯进行了全基因组测序。而后使用软件GATK(3.4-46)对高质量测序结果进行SNP和InDel的检测和统计,进一步筛选出子预44和江南香糯DNA水平存在SNPs/InDels多态性抗病相关基因。【结果】通过Hiseq X10 PE150平台分别获得了4 118 170 045 bp和2 995 054 509 bp子预44和江南香糯的基因组数据,比对到参考基因组(Ensembl release 31)的比对率分别为98.56%和98.30%。在抗病水稻子预44和感病水稻江南香糯之间鉴定了922个纯合突变的差异抗病相关基因。结合基因定位结果,在子预44中鉴定了一个新的抗稻瘟病候选基因。【结论】 研究结果为子预44中抗稻瘟病新基因的克隆提供了参考,对子预44广谱持久抗瘟分子机制的研究奠定了基础。
中图分类号:
李金璐, 张慧, 焦泽宇, 刘剑宇, 韩光煜, 卓晓轩, 罗琼. 水稻子预44和江南香糯基因组比较鉴定稻瘟病抗性相关基因[J]. 中国水稻科学, 2020, 34(1): 8-16.
Jinlu LI, Hui ZHANG, Zeyu JIAO, Jianyu LIU, Guangyu HAN, Xiaoxuan ZHUO, Qiong LUO. Identification of Blast Disease Resistance-related Genes by Genomic Sequence Comparison of Rice Variety Ziyu 44 and Jiangnanxiangnuo[J]. Chinese Journal OF Rice Science, 2020, 34(1): 8-16.
样品Sample | 高质量Reads数 HQ clean reads number | 读长 Reads length/bp | 碱基数 Base number/bp | Q30(%) | |
---|---|---|---|---|---|
子预44 Ziyu 44 | 41 021 044 | 101/101 | 4 118 170 045 | 3 928 449 674(95.39%) | |
江南香糯基因Jiangnanxiangnuo | 29 931 088 | 101/101 | 2 995 054 509 | 2 840 051 178(94.82%) |
表1 子预44和江南香糯基因组序列数据
Table 1 Summary of the sequence data for Ziyu 44 and Jiangnanxiangnuo.
样品Sample | 高质量Reads数 HQ clean reads number | 读长 Reads length/bp | 碱基数 Base number/bp | Q30(%) | |
---|---|---|---|---|---|
子预44 Ziyu 44 | 41 021 044 | 101/101 | 4 118 170 045 | 3 928 449 674(95.39%) | |
江南香糯基因Jiangnanxiangnuo | 29 931 088 | 101/101 | 2 995 054 509 | 2 840 051 178(94.82%) |
突变类型 Mutant type | 终止缺失/获得 Stop loss/gain | 非同义SNP Non-synonymous SNPs | 非移码InDel Non-frame shift InDels | 移码InDel Frame shift InDels |
---|---|---|---|---|
数量 Number | 90 | 4732 | 144 | 97 |
表2 非同义突变的SNP/InDel
Table 2 Nonsynonymous mutation of SNP/InDel.
突变类型 Mutant type | 终止缺失/获得 Stop loss/gain | 非同义SNP Non-synonymous SNPs | 非移码InDel Non-frame shift InDels | 移码InDel Frame shift InDels |
---|---|---|---|---|
数量 Number | 90 | 4732 | 144 | 97 |
图3 子预44和江南香糯间抗性相关基因非同义突变Frameshift InDel-引起氨基酸编码移码突变的插入缺失突变;Nonframeshift InDel-不导致氨基酸编码移码的插入缺失突变;Nonsynonymous SNP-引起氨基酸差异的单核苷酸多态性;Stoploss/gain-SNP/InDel突变引起功能缺失或获得的氨基酸翻译终止或延伸。
Fig. 3. Nonsynonymous mutation of SNP/InDel between Ziyu 44 and Jiangnanxiangnuo. Frameshift InDel, Insertion deletion mutation of amino acid coding frameshift; Nonframeshift InDel, Insertion deletion mutation of amino acid coding nonframeshift; Nonsynonymous SNP, Single nucleotide polymorphisms causing amino acid differences; Stoploss/gain, Single nucleotide polymorphisms (SNP)/Insertion deletion mutation (InDel) causing premature termination or not end of amino acid translation.
图5 9个水稻材料中LOC_Os06g18820基因核苷酸序列和氨基酸序列比对ZY44-子预44;Digu-地谷;ZH11-中花11;JNXN-江南香糯;Nip-日本晴;LTH-丽江新团黑谷;TP309-台北309。
Fig. 5. Comparison of the nucleotide and amino acid sequences of LOC_Os06g18820 from nine rice varieties. ZY44, Ziyu 44; ZH11, Zhonghua 11; JNXN, Jiangnanxiangnuo; Nip, Nipponbare; LTH, Lijiangxintuoheigu; TP309, Taipei 309.
图6 9个水稻材料喷雾接种稻瘟病菌株LP174的症状 ZY44-子预44;Digu-地谷;ZH11-中花11;JNXN-江南香糯;Nip-日本晴;LTH-丽江新团黑谷;TP309-台北309。
Fig. 6. Symptoms of nine rice varieties inoculated with M. oryzae LP174. ZY44, Ziyu 44; ZH11, Zhonghua 11; JNXN, Jiangnanxiangnuo; Nip, Nipponbare; LTH, Lijiangxintuoheigu; TP309, Taipei 309.
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