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作物学报 ›› 2018, Vol. 44 ›› Issue (7): 977-987.doi: 10.3724/SP.J.1006.2018.00977

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

水稻抗稻瘟病基因Pi47的精细定位和候选基因分析

肖湘谊,史学涛,盛浩闻,刘金灵(),肖应辉()   

  1. 湖南农业大学农学院 / 水稻油菜抗病育种湖南省重点实验室 / 南方粮油作物协同创新中心, 湖南长沙 410128
  • 收稿日期:2017-11-21 接受日期:2018-03-26 出版日期:2018-07-10 网络出版日期:2018-04-27
  • 通讯作者: 刘金灵,肖应辉
  • 基金资助:
    本研究由国家重点研发计划项目(2016YFD0101100), 国家自然科学基金项目(31171834)和湖南省科技重大专项( 2015NK1001-1)资助

Fine Mapping and Candidate Gene Analysis of Rice Blast Resistance Gene Pi47

Xiang-Yi XIAO,Xue-Tao SHI,Hao-Wen SHENG,Jin-Ling LIU(),Ying-Hui XIAO()   

  1. Agronomy College of Hunan Agricultural University / Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance / Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
  • Received:2017-11-21 Accepted:2018-03-26 Published:2018-07-10 Published online:2018-04-27
  • Contact: Jin-Ling LIU,Ying-Hui XIAO
  • Supported by:
    This study was supported by the National Key Research and Development Program (2016YFD0101100), the National Natural Science Foundation of China (31171834), and the Science and Technology Major Project of Hunan Province (2015NK1001-2).

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摘要：

不断挖掘和克隆抗稻瘟病新基因, 是解析水稻抗病分子遗传机制和培育抗稻瘟病新品种的重要基础。Pi47是笔者从广谱、持久抗稻瘟病湖南地方品种湘资3150中鉴定的稻瘟病抗性基因, 前期研究将其初步定位于第11染色体标记RM224和RM5926间。本研究利用3个Pi47单基因系与感病亲本CO39杂交F2群体1687个感病单株对Pi47精细定位, 利用6个STS标记对3个单基因系进行背景分析, 采用生物信息学方法进行了候选基因分析。结果表明, Pi47被精细定位于CAPS标记S32与K33间0.24 cM区域的171.2 kb物理区间内, 背景分析将Pi47进一步缩小至SC12和K33间67.8 kb的区间内; 该区间含有8个结构基因, 其中2个编码NBS-LRR抗病类似蛋白, 为Pi47的候选功能基因。稻瘟菌抗谱比较分析发现, Pi47单基因系与其定位区间内4个Pik位点的等位基因Pik、Pikm、Pikh和Pikp的近等基因系抗谱不同。这些结果为进一步克隆Pi47和利用其进行分子标记辅助选择培育抗稻瘟病水稻新品种奠定了基础。

关键词: 水稻, 稻瘟病, 抗病基因, Pi47, 精细定位

Abstract:

Continuous mapping and cloning new blast resistance genes provided an important approach for revealing the molecular mechanism of resistance to rice disease and breeding new varieties resistant to rice blast. Previously, the blast resistance gene Pi47 was mapped between SSR markers RM224 and RM2956 on chromosome 11, from a broad-spectrum and durable resistance native cultivar Xiangzi 3150 in Hunan province. In this study, the fine mapping and candidate gene prediction were performed, showing that Pi47 was mapped in an interval of 0.24 cM between CAPS markers S32 and K33 with 171.2 kb on Nipponbare reference genome, and further narrowed in an interval of 67.8 kb between markers SC12 and K33, through background screening to Pi47 monogenic lines and susceptible parent CO39 with six STS markers. Eight genes were predicted in this region on the reference genome, among them two encoded NBS-LRR resistance-like proteins, which probably were Pi47 functional candidate genes. A blast resistance spectrum evaluation, using Pi47 monogenic lines and four near-isogenic lines with the Pik allelic gene Pik, Pikm, Pikh, and Pikp across Pi47 region, revealed that Pi47 shared different resistance spectra with these four alleles. These results shed light on further molecular cloning of Pi47, and the molecular marker will be useful for molecular maker assisted selection to breed new resistant cultivars.

Key words: rice, rice blast, resistance gene, Pi47, fine mapping

表1

CO39/湘资3150 RIL中Pi47单基因系的鉴定"

株系
Line		 接种菌株193-1-1的抗性表型
Phenotype inoculated with isolate 193-1-1		 Pi47连锁标记
Markers linked to Pi47		 Pi48连锁标记
Markers linked to Pi48
RM206 RM224 RM5926 RM3102 RM1337 RM7102
CX18 R + + + - - -
CX36 R + + + - - -
CX40 R + + + - - -
CX52 R + + + - - -
CX66 R + + + - - -
CX67 R + + + - - -
CX70 R + + + - - -
CX147 R + + + - - -
CX152 R + + + - - -
CX155 R + + + - - -
CX166 R + + + - - -
CX279 R + + + - - -

表2

各F2群体抗稻瘟病表型分离分析"

F2群体
F2 population		 抗病单株
Resistant individuals		 感病单株
Susceptible individuals		 作图群体株数
Individual number of mapping population		 卡方值
χ2 for 3:1 ratio
CX18/CO39 F2 1040 329 308 0.68
CX52/CO39 F2 1116 340 247 2.21
CX155/CO39 F2 1512 310 0 62.0
CX279/CO39 F2 3820 1221 1132 1.66
总数 Total / / 1687 /

表3

所用标记在3个F2群体中鉴定到的重组子数量"

群体
Population		 感病单株数目
No. of susceptible individuals		 重组子分布 Distribution of recombinants
RM224 S11, S4, S32 S10 K33 K107 K134 RM5926
CX279/CO39F2 1132 20 4 0 1 1 8 56
CX18/CO39F2 308 5 2 0 0 0 1 8
CX52/CO39F2 247 2 1 0 0 0 1 11
合计 Total 1687 27 7 0 1 1 10 75

图1

Pi47位点区域遗传图谱与物理图谱的构建A: Pi47位点区域遗传图谱。中间粗实线为第11染色体Pi47位点区域示意图, 上方为定位使用标记, 下方数字为相邻两个标记间的遗传距离; B: Pi47精细定位重组各标记重组子数。从上往下依次为对应标记在CX52/CO39 (n=247)、CX18/CO39 (n=308)、CX279/CO39 (n=1132) F2群体中鉴定的重组子数目; C: Pi47位点在日本晴参考基因组中的BAC克隆重叠群构建的物理图谱。每段黑实线代表1个BAC克隆, 每个BAC克隆名字标注在下面; 与虚线交叉点为所使用定位标记对应位置。D: Pi47最终精细定位在标记S32和S10间171.2 kb的区域。E: 分子标记鉴定单基因系Pi47位点遗传背景。"

表4

Pi47精细定位使用的标记信息"

标记
Marker		 引物顺序
Primer sequence (5°-3°)		 物理位置
Physical position		 扩增大小
Expect size		 酶
Enzyme		 标记类型
Marker type
RM224 F: TCGATCGATCTTCACGAGG
R: TGCTATAAAAGGCATTCGGG		 27673251
-27673372		 122 / SSR
S11 F: TCTTTGAACAAGAGGACCAG
R: AATTACCGAATTACTTAGCG		 27824419
-27825439		 1021 Mva I or Hinf I CAPS
S4 F: CGAATGATGACGAGGACCCG
R: ATCAGGCACGGCAGCAGAAG		 27827786
-27828843		 1058 Hinf I or Rsa I CAPS
S32 F: GCCCAGTAACCGTAGGAGTC
R: TTTGATGAGCGGCAAAGTAG		 27835604
-27836295		 692 Msp I CAPS
S10 F: AGAGCAAGAAGGGCACGGTAT
R: AGAATGGTCCTCCTGACATCG		 27992866
-27993970		 1105 Rsa I CAPS
K33 F: TTTGGTGCTCCTCTTACGGG
R: TCGGAGTTCACAGAGCCAAG		 28005690
-28006842		 1153 Hinf I CAPS
K107 F: ACATCAATGGCTACAACT
R: TGCTAACGGTGCTGGTAT		 28012753
-28012940		 184/188 / STS
K134 F: GATGGCGAGATGGTTGTC
R: GCCTTTGAGATAGGGATTGC		 28163563
-28163742		 180/168 / STS
RM5926 F: TAGGTCCATCCAAATCTCGATCC
R: TGGCAGAGGAGATTAGAGTAATACGG		 28957564
-28957858		 295 / SSR
S6 F: TCAACCGAACGCAAGAATCAC
R: GGCCCTCCAGCTCATCTACCT		 27841529
-27842431		 903 / STS
SC1 F: CCCCACAATCCCACGAGAC
R: CGGGCCGACAATCCAATAC		 27848711
-27849635		 925 / STS
SC3 F: TTTCCCACCGATGACCCAG
R: GCTCGCCATCCTTCCCTTT		 27879005
-27879906		 902 / STS
SC6 F: TATTGGTAAGTGGTAACGGGTGA
R: GCAGATTCGAGGAGGAAGG		 27891111
-27892550		 1440 / STS
SC7 F: TGGCGTGGCGGTTTGGTAG
R: GCTGGTTGGGCATGGGTTG		 27909896
-27910602		 707 / STS
SC12 F: GGGCAACAAGCGAGCCATAA
R: GTGGTGAGGCAGCGGAACAG		 27939030
-27940473		 1444 / STS

表5

Pi47位点标记SC12和K33间参考基因组区域内候选基因预测"

基因名称
Gene name		 推测功能
Putative functions
LOC_Os11g46150 Expressed protein
LOC_Os11g46180 Transposon protein
LOC_Os11g46190 Transposon protein
LOC_Os11g46200 Leucine rich repeat family protein, expressed
LOC_Os11g46210 NB-ARC domain containing protein, expressed
LOC_Os11g46220 Hypothetical protein
LOC_Os11g46230 Tetratricopeptide repeat domain containing protein
LOC_Os11g46240 Retrotransposon protein

表6

Pi47-1与Pik位点对应的已克隆基因在DNA和蛋白水平上的序列相似性"

基因 Gene Pik1-KA Pi7-1 Piks-1 Pik-2 Pikp-1 Pikm1-TS Pi1-5
Pi47-1 DNA 0.997 0.975 0.998 0.997 0.975 0.998 0.997
Pi47-1蛋白 Pi47-1 protein 0.987 0.947 0.993 0.989 0.946 0.994 0.995

表7

Pi47-2与Pik位点对应的已克隆基因在DNA和蛋白水平上的序列相似性"

基因 Gene Pik2-KA Pi7-2 Piks-2 Pik-1 Pikp-2 Pikm2-TS Pi1-6
Pi47-2 DNA 0.999 0.998 0.999 0.999 0.998 0.999 1.000
Pi47-2蛋白 Pi47-2 protein 0.999 0.996 0.999 0.999 0.996 0.999 1.000

图2

Pi47与Pik位点已克隆基因的系统进化分析"

表8

Pi47及其附近位置抗稻瘟病基因的抗谱分析"

稻瘟菌小种
Isolate		 来源
Origin		 水稻品种 Rice cultivar
CO39 CX18
(Pi47)		 IRBLk-Ka
(Pik)		 IRBLkm-Ts
(Pikm)		 IRBLkh-K3
(Pikh)		 IRBLkp-K60
(Pikp)
318-2 中国湖南 Hunan, China S R R R R R
CHL473 中国湖南 Hunan, China S R R R R R
X2007A-3 中国湖南 Hunan, China S R R R R S
CHL440 中国湖南 Hunan, China S R R R R S
CHL438 中国湖南 Hunan, China S R R R R R
X2007A-7 中国湖南 Hunan, China S R R R R R
195-2-2 中国湖南 Hunan, China S S R R R S
87-4 中国湖南 Hunan, China S R R R R R
193-1-1 中国湖南 Hunan, China S R R R R R
110-2 中国湖南 Hunan, China S R R R R R
236-1 中国湖南 Hunan, China S R R R R R
RB4 中国广东 Guangdong, China S R R R R S
RB6 中国广东 Guangdong, China S R R R R S
RB18 中国福建 Fujian, China S R S R R S
RB19 中国福建 Fujian, China S R R R R R
RB12 中国 China MR MR MR MR MR MR
KOH 日本 Japan S S S S S S
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