水稻纹枯病抗性关联分析及抗性等位变异发掘

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孙晓棠, 卢冬冬, 欧阳林娟, 胡丽芳, 边建民, 彭小松, 陈小荣, 傅军如, 贺晓鹏, 贺浩华, 朱昌兰. 水稻纹枯病抗性关联分析及抗性等位变异发掘. 作物学报, 2014, 40(5): 779-787[SUN Xiao-Tang, LU Dong-Dong, OU-YANG Lin-Juan, HU Li-Fang, BIAN Jian-Min, PENG Xiao-Song, CHEN Xiao-Rong, FU Jun-Ru, HE Xiao-Peng, HE Hao-Hua, ZHU Chang-Lan. Association Mapping and Resistant Alleles Analysis for Sheath Blight Resis-tance in Rice. 作物学报, 2014, 40(5): 779-787] 复制到剪切板

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作物学报编辑部

水稻纹枯病抗性关联分析及抗性等位变异发掘

孙晓棠, 卢冬冬, 欧阳林娟, 胡丽芳, 边建民, 彭小松, 陈小荣, 傅军如, 贺晓鹏, 贺浩华^*, 朱昌兰^*

江西农业大学农学院 / 作物生理生态与遗传育种教育部重点实验室, 江西南昌 330045

^* 通讯作者(Corresponding authors): 朱昌兰, E-mail:zhuchanglan@163.com, Tel: 0791-83828171; 贺浩华,hhhua64@163.com, Tel: 0791-83828198

收稿日期:2014-01-12

基金:本研究由江西省重大科技专项计划(20114ABF03102), 国家转基因生物新品种培育重大专项(2011ZX08001-002), 高等学校博士学科点专项科研基金项目(20113603110001)和国家科技支撑计划项目(2012BAD14B1)资助;

摘要

采用苗期微室接种鉴定法, 用144个分布于水稻全基因组的多态性标记, 利用TASSEL软件GLM (Q)、MLM (Q+K)和MLM (PCA+K) 3种模型对456份水稻材料组成的自然群体进行纹枯病抗性关联分析。结果发现, 有13个标记位点至少在2种模型中均被检测到与纹枯病抗性显著关联, 单个位点可解释表型变异的1.84%~8.42%; 其中10个标记位点位于以往报道的连锁定位的抗纹枯病QTL附近, 3个标记位点(RM1036、RM5371和RM7585)是未曾报道的新的抗病相关位点。抗性等位变异RM7585-150对纹枯病发病病级减效效应最大; 有259份材料携带抗性等位变异RM5371-129, 占供试材料总数的56.8%, 只有26份材料携带抗性等位变异RM1036-82, 占供试材料总数的5.7%。水稻纹枯病发病病级与其含有的抗性等位变异数量呈极显著的负相关。本研究结果将为水稻抗纹枯病分子标记辅助育种提供理论依据。

关键词: 水稻; 纹枯病; 关联分析; 抗性等位变异

Association Mapping and Resistant Alleles Analysis for Sheath Blight Resis-tance in Rice

SUN Xiao-Tang, LU Dong-Dong, OU-YANG Lin-Juan, HU Li-Fang, BIAN Jian-Min, PENG Xiao-Song, CHEN Xiao-Rong, FU Jun-Ru, HE Xiao-Peng, HE Hao-Hua^*, ZHU Chang-Lan^*

College of Agronomy, Jiangxi Agricultural University / Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang 330045, China

Fund:

Abstract

To identify and map sheath blight (ShB) resistance loci in rice, we carried out association analysis of 456 rice accessions using 144 genome-wide markers based on GLM (Q), MLM (Q+K), and MLM (PCA+K) models of TASSEL software. The phenotyping were assayed at the seedling stage with a micro-chamber screening method. The results showed that thirteen markers were significantly associated with ShB resistance detected by using at least two models, which explained from 1.84% to 8.42% of the phenotypic variance. In addition, ten of the identified resistant loci were either quite near or within the interval of previously identified QTLs. RM1036, RM5371, and RM7585 were novel resistant loci that had not been previously reported. The resistant allele 150 of RM7585 showed the largest negative effect to ShB rating, allele 129 of RM5371 existed in 259 (56.8%) of 456 rice accessions, and 82 of RM1036 existed in 26 (5.7%) rice accessions. The number of putative resistant alleles presented in rice was highly and significantly correlated with the decrease of ShB rating. The resistant alleles identified in this study are readily available and can be exploited for marker-assisted selection.

Keyword: Rice; Sheath blight; Association mapping; Resistant alleles

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水稻纹枯病是由立枯丝核菌( Rhizoctonia solaniKühn)侵染引起的一种世界性水稻病害, 造成水稻巨大的产量损失和品质降低^{[ 1]}。培育和种植抗病品种是防治水稻纹枯病最经济有效的方法之一。水稻对纹枯病的抗性属于典型的数量性状^{[ 2]}, 利用传统的遗传分离群体定位水稻纹枯病抗性QTL, 操作繁琐, 耗时耗力。虽然国内外利用传统的遗传分离群体已定位了30多个水稻抗纹枯病QTL^{[ 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]}, 但迄今为止, 仍然没有一个抗纹枯病基因被克隆, 除少数几个抗纹枯病QTL被精细定位外^{[ 3, 4]}, 大多数为初步定位结果^{[ 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]}。未见抗纹枯病QTL定位成果应用于分子标记辅助选择育种。

关联分析(association mapping)是利用不同基因座等位变异间的连锁不平衡(linkage disequilibrium, LD)关系, 分析标记与性状的相关性, 以达到鉴定特定目标性状基因的目的。与连锁分析相比, 关联分析可以利用具有丰富遗传多样性的自然群体为材料, 无需构建专门的作图群体, 并可实现同时检测自然群体同一座位的多个等位基因, 对QTL定位的广度和精度也相对较高^{[ 13]}。鉴于这些优势, 关联分析被广泛应用于发掘植物数量性状基因的研究^{[ 14, 15, 16]}, 成为植物遗传学研究的热点。水稻拥有非常丰富的种质资源, 是进行关联分析的理想材料^{[ 15]}, 但利用关联分析方法进行中国水稻稻种资源对纹枯病抗性基因定位的研究目前未见报道。

准确的表型鉴定是关联分析的前提。水稻纹枯病的抗性鉴定易受环境温度、湿度及水稻株高和生育期等的影响。至今虽然已研发了一些较有效的大田成株期纹枯病菌接种和抗性鉴定的方法, 但其工作量大、周期长, 难以用于大规模且农艺性状差别大的自然群体的接种鉴定^{[ 17]}。苗期微室接种鉴定法(micro-chamber method, MCM)由Jia等^{[ 18]}于2007年建立, 以水稻幼苗为接种对象, 试验周期短, 环境相对可控, 结果具有更好的重复性和可靠性。目前这一新方法已被成功地应用于水稻纹枯病抗病基因表达和QTL定位研究^{[ 6, 9]}。

本研究采用苗期微室接种鉴定法, 对456份水稻材料组成的自然群体进行纹枯病抗性关联分析, 以期定位水稻抗纹枯病相关的基因位点, 发掘各关联位点的抗性等位变异及优异的抗病种质材料, 为水稻抗纹枯病分子标记辅助育种提供理论依据。

1 材料与方法

1.1 试验材料

456份水稻材料中, 235份是来自中国23个省(自治区)的地方品种, 193份是中国常规育成品种包括现有生产上主要的恢复系材料等, 28份来自菲律宾、美国、澳大利亚、日本、印度、越南、泰国7个国家。C418和特青是抗病对照, Lemont是感病对照, 武育粳3号较感纹枯病^{[ 4, 17, 19]}。

1.2 水稻纹枯病抗性鉴定

供试水稻纹枯病菌为强致病力菌株GD118, 由江西省农业科学院植物保护研究所提供。将稻谷、稻壳按1∶2混合, 浸泡24 h后分装培养皿。灭菌后接种纹枯病菌, 28℃培养5~7 d, 待谷粒表面长满菌丝后用作接种物备用。参考Jia等^{[ 18]}的苗期微室法接种鉴定。为了消除因品种间秧苗发育进程不同而造成的抗病性差异, 根据前期不同品种发芽和秧苗发育进程试验结果, 将456份供试水稻材料分4批浸种催芽, 待种子出芽后, 从中选择芽长一致的点播到装有灭菌土的塑料盆(直径13 cm)中生长。待各品种的大部分植株处于3~4叶时, 通过间苗去除叶龄有差异的单株和弱株, 保留生长势和叶龄基本一致的3株植株。然后用镊子将带菌谷粒2粒置于紧挨植株基部两侧, 确保带菌谷粒与幼苗茎基部紧密接触, 保持土表湿润不积水。接种后马上将去除底部的2 L透明塑料瓶罩在幼苗上, 底部入土, 上口去掉瓶盖, 形成微室保湿。控制室内温度为26~30℃, 相对湿度为80%~85%。接种后5~7 d, 待感病对照Lemont的大多数植株死亡时调查各单株病级。病级=病斑高度/株高×9级^{[ 17]}。其中病斑高度为最高病斑的上界距土表的高度, 株高为秧苗最高叶尖距土表的高度。试验重复4次。用软件SPSS 19进行各品种病级差异显著性单因素方差分析和LSD法多重比较。

1.3 SSR标记全基因组扫描

提取水稻材料叶片DNA。从520对SSR标记中挑选多态性较好且均匀分布于12条染色体上的142个SSR标记和2个InDel标记, 对456份水稻材料进行PCR扩增。扩增产物经8%的聚丙烯酰胺凝胶电泳检测, 银染显色。

1.4 数据分析

用POWERMARKER3.25软件^{[ 20]}统计标记位点的等位变异及其频率和多态信息含量PIC。用NTsyspc2.2 软件完成供试材料的主成分(PCA)分析。用STRUCTURE2.2软件^{[ 21]}完成供试材料的遗传结构分析。用SPAGeDi软件^{[ 22]}计算个体间亲缘关系系数Kinship。使用TASSEL2.1软件^{[ 23]}的GLM (general linear model)和MLM (mixed linear model)模型, 分别以各材料Q值、Q+Kinship值和PCA+ Kinship值作为协变量进行关联分析。参考Breseghello等^{[ 14]}和文自翔等^{[ 24]}的方法计算标记位点等位变异的表型效应。在每一个关联位点的等位变异中, 对纹枯病发病病级减效效应最大的等位变异被认为是该位点的“抗性等位变异”^{[ 16]}。

2 结果与分析

2.1 456份水稻种质资源对纹枯病抗性分析

采用环境相对可控的苗期微室法及相对病斑高度进行抗性评价, 能有效地降低环境和形态学因素的干扰影响。结果表明接种纹枯病菌后, 感病对照品种Lemont严重发病, 平均病级8.24±0.12, 武育粳3号为6.89±0.25; 抗病对照品种C418发病轻, 平均病级3.98±0.52, 特青为5.06±0.43, 品种抗感性与前人描述基本一致^{[ 17, 25]}。456份供试水稻材料接种纹枯病后发病病级在各个等级均有分布, 抗病性变异较丰富, 且基本呈正态分布(图1), 适合做纹枯病抗性关联分析。病级最低为2.49 ± 0.45, 最高为8.86±0.29, 平均6.18±0.37。有44份(9.65%)材料的抗性显著大于抗性对照品种特青, 其中18份(3.95%)材料的抗性显著大于抗性对照品种C418 ( P<0.05)。

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	图1 456份水稻种质材料纹枯病病级分布Fig. 1 Distribution of sheath blight disease ratings among 456 rice accessions

2.2 群体遗传结构与连锁不平衡LD

用144个标记共检测到916个等位基因, 变化范围为2~18个, 平均多态信息含量PIC值为0.58。剔除遗传距离较近的标记, 用89个标记分析该自然群体的遗传结构。当 K=2时, Δ K值最大(图2-A), 推断该群体分为2个亚群, 分别包含277份和179份材料(图2-B)。144个标记位点的共线性组合和非共线性组合中都存在着极显著的LD ( P<0.01)。 D'值回归遵循方程 y = -0.0803 ln ( x) + 0.726 ( R²=0.201), 当 D'值取0.5时, LD衰减距离为16.7 cM, 适合做水稻的关联分析(图2-C)。

2.3 水稻纹枯病抗性关联分析及相关位点的主要等位变异

关联分析中, 群体分层(population stratification)被认为是引起假阳性的最主要因素^{[ 26]}, 而加入群体结构和亲缘关系控制的混合线性模型MLM (Q+K)及加入主成分分析和亲缘关系控制的混合线性模型MLM (PCA+K)均能够较好地去除由群体分层引起的假阳性^{[ 27, 28]}。因此本试验采用GLM (Q)、MLM (Q+K)和MLM (PCA+K) 3种模型对144个标记位点与水稻纹枯病病级进行关联分析。结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联( P<0.05), 分布于8条染色体上, 其中第6染色体上4个, 第11染色体上3个, 第3、第4、第5、第8、第10和第12染色体上各1个, 单个位点可解释纹枯病病级变异的1.84%~8.42% (表1)。其中11个标记位点在3种模型中均被检测到。RM6917、RM311和RM1233标记在3种模型中均达到极显著水平( P<0.01), 对表型变异解释率分别为3.89%、4.49%和3.63%; 有10个标记位点位于以往报道的连锁定位的抗纹枯病QTL附近(±5 cM)^{[ 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16]}。

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图2 456份水稻种质资源材料群体遗传结构和LD衰减分析A: Δ K值变化图; B: 456份水稻种质资源材料分为2个亚群; C: 共线性SSR标记在水稻基因组中随遗传距离衰减的散点图。Fig. 2 Analysis of population structure and LD decay in 456 rice accessionsA: Magnitude of Δ K for each K-value; B: Population structure analysis of 456 rice accessions showing two sub-groups; C: Scatter plot of D′-value of SSR pairs versus syntenic marker genetic distance (cM) in the whole population.

13个与纹枯病抗性显著关联的位点共有54个主要的等位变异(等位变异频率≥0.05), 每个关联位点均表现为既有减效等位变异又有增效等位变异(图3和表1)。减效等位变异减轻纹枯病发病病级即增加抗性, 反之, 增效等位变异增加纹枯病发病病级即降低抗性。在每一个关联位点的等位变异中, 对纹枯病发病病级减效效应最大的等位变异被认为是该位点的“抗性等位变异”^{[ 16]}。其中, 抗性等位变异RM1036-82是13个关联位点的抗性等位变异中平均病级最低的, 其次是RM6297-149; RM 7585-150对纹枯病发病病级减效效应最大, 其次是RM311-162和RM224-118; 有259份材料携带抗性等位变异RM5371-129, 占供试材料总数的56.8%; 有255份材料携带抗性等位变异RM7585-150, 占供试材料总数的55.9%; 携带抗性等位变异RM267-159或RM1036-82的材料数量较少, 只有29份和26份, 分别占供试材料总数的6.4%和5.7%。

表1 与纹枯病抗性显著相关的标记位点及各位点的主要等位变异 Table 1 Marker loci significantly associated with sheath blight resistance and their major alleles

2.4 抗性等位变异数量与抗病级别的相关性

水稻材料纹枯病病级与其含有的抗性等位变异数量呈极显著的负相关 ( r = -0.502, P<0.0001) (表2)。水稻品种霸王鞭和大叶棵同时含有9个抗性等位变异, 是含有抗性等位变异最多的材料。456份供试水稻材料中, 有27份含有5个或更多的抗性等位变异, 而且抗性显著大于抗性对照特青( P<0.05), 占材料总数的5.9%; 其中10份水稻材料抗性还显著大于抗性对照C418, 占材料总数的2.2%。这些水稻材料是优异的抗病种质材料。13个抗性等位变异在10份含5个或更多的抗性等位变异且抗性显著大于抗性对照C418的水稻材料中的分布见表3。

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	图3 13个与纹枯病抗性显著相关的标记位点的等位变异表型效应Fig. 3 Phenotypic effects of major alleles of 13 loci significantly associated with sheath blight resistance

3 讨论

3.1 水稻纹枯病抗病基因(QTL)定位结果比较

目前被精细定位的水稻抗纹枯病QTL仅有2个。Zuo等^{[ 4]}利用染色体片段置换系将 qSB-11^LEQTL精细定位于74 kb区间内, Channamallikarjuna等^{[ 3]}利用重组自交系群体将 qSBR- 11-1精细定位于850 kb区间内, 其余抗纹枯病QTL均为初步定位结果。在将定位结果应用于育种实践以前, 必须验证QTL真实性。由于传统的遗传分离群体的局限性, 研究者通常只能通过设置重复或在不同年份/地点多次试验, 根据结果的重演性来判断QTL的真实性, 费时费力。

本研究采用144个分布于全基因组的多态性标记, 对456份水稻材料组成的自然群体进行纹枯病抗性关联分析。10个抗病标记位点与以往报道的抗病QTL的侧翼标记相同或位于以往报道的抗病QTL区间内, 包括RM267^{[ 2, 5, 6]}、RM190^{[ 6, 16]}、RM6917^{[ 2, 13]}、RM209^{[ 3, 7]}、RM1233^{[ 3, 8, 16]}、RM224^{[ 3, 8]}、RM6297^{[ 2, 11, 12]}、RM6838^{[ 2, 8]}、RM8242^{[ 2]}、RM311^{[ 7]}, 进一步验证了这些QTL的真实性, 暗示这10个抗病标记位点在不同的遗传背景或环境中能够稳定表达, 育种利用价值可能更高。

本研究在第11染色体上关联到3个标记, 其中RM1233和RM224之间0.4 Mb, 已精细定位的 qSB-11^LEQTL位于该区间内^{[ 3, 8]}; 在第6染色体上关联到4个标记, 其中RM190和RM6917两者之间2.3 Mb, RM190为以往已报道的抗病QTL^{[ 6, 16]}的侧翼标记, RM6917位于抗病QTL区间内^{[ 2, 13]}, 说明抗病标记RM190和RM6917真实性较高, 可能是精细定位水稻抗纹枯病基因的目标区域。

3个抗病位点RM1036、RM5371和RM7585是未曾报道的新的抗病基因位点。RM1036距离RG241a-RZ397区间的抗纹枯病QTL^{[ 12]}约3.0 Mb, RM5371距离RM30-RM439区间的抗纹枯病QTL^{[ 7]}约1.4 Mb, RM7585距离Y1065Le-RZ69x区间的抗纹枯病QTL^{[ 2]}约1.8 Mb。这3个标记经过进一步验证将有可能成为水稻抗病性分子辅助选择新的有效标记。

表2 13个抗性等位变异在456份水稻种质资源中的分布 Table 2 Distribution of the 13 putative resistant alleles among 456 rice accessions

表3 10份优异的抗病种质材料纹枯病病级及含有的抗性等位变异 Table 3 Distribution of sheath blight disease ratings and putative resistant alleles among the ten resistant accessions

3.2 水稻纹枯病抗性遗传改良

采用传统育种手段对由数量基因控制的病害的抗性改良, 难度较大。分子标记辅助育种已被认为是抗病育种的一个可行途径^{[ 29]}。但迄今未见抗纹枯病QTL定位成果应用于分子辅助选择育种。本研究通过对13个与纹枯病抗性显著相关的标记位点的等位变异分析发现, 每个位点上有多个等位变异, 每个等位变异效应不同。极显著相关性表明( r = -0.502, P<0.0001), 含有的抗性等位变异数量越多, 供试水稻材料对纹枯病的抗性也越高。这些结果表明, 利用分子标记辅助选择, 聚合不同位点的抗性等位变异, 可以提高水稻纹枯病抗性。因此, 聚合不同的遗传背景中能稳定表达的RM267-159、RM190-118、RM6917-154、RM209-153、RM1233-160、RM224-120、RM6297-149、RM6838-104抗性等位变异, 可能是提高水稻纹枯病抗性水平的一个有效途径。

不同水稻品种对纹枯病的抗性存在明显的差异, 但至今未发现免疫和高抗的品种。目前研究中的抗纹枯病水稻亲本多局限于少数几个公认的抗病材料如“特青”或“Jasmine 85”等。而事实证明, 育种中对少数抗性亲本材料的广泛使用, 造成推广品种遗传背景狭窄、作物病虫害种类演变, 重要病虫害持续发生或流行^{[ 30]}。因此迫切需要挖掘新的抗病种质材料, 发现新的抗病基因或QTL, 以拓宽水稻纹枯病抗性遗传背景。本研究发现27份水稻材料含有5个或更多的抗性等位变异且抗性显著大于抗性对照特青, 它们是优异的抗病种质材料, 可以作为水稻抗病育种的供体亲本加以利用。

4 结论

发现13个标记位点与纹枯病抗性显著关联, 单个位点可解释表型变异的1.84%~8.42%; 附近, 3个标记位点(RM1036、RM5371和RM7585)是未曾报道的新的抗病相关位点。

The authors have declared that no competing interests exist.

作者已声明无竞争性利益关系。The authors have declared that no competing interests exist.

Reference

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2006

10.229

0.0

Savary

, Teng

P S

, Willocquet

, Nutter

F W

. Quantification and modeling of crop losses: a review of purposes. Annu Rev Phytopathol, 2006, 44: 89-112

INRA, UMR Santé Végétale, BP81, Villenave d'Ornon 33883, France. ssavary@inra.bordeaux.fr

This review considers the cascade of events that link injuries caused by plant pathogens on crop stands to possible (quantitative and qualitative) crop losses (damage), and to the resulting economic losses. To date, much research has focused on injury control to prevent this cascade of events from occurring. However, this cascade involves a complex succession of components and processes whereby knowledge on crop loss generates entry points for management. Proposed here is a framework linking different types of knowledge on crop loss to a range of decision categories, from tactical to strategic short- or long-term. Important advances in this field are now under way, including a probabilistic treatment of the injury-damage relationship, or analyses of the sources of uncertainty attached to some components of the decision process. Management of injury profiles, rather than individual injuries, and shifts in dimensionality of crop losses are anticipated to contribute to the design of sustainable agricultural systems, and address global issues concerning food security and food safety.

PMID: 16480337

... hn)侵染引起的一种世界性水稻病害, 造成水稻巨大的产量损失和品质降低^[1] ...

2005

1.513

0.0

... 水稻对纹枯病的抗性属于典型的数量性状^[2], 利用传统的遗传分离群体定位水稻纹枯病抗性QTL, 操作繁琐, 耗时耗力 ...

... 虽然国内外利用传统的遗传分离群体已定位了30多个水稻抗纹枯病QTL ^{[2,3,4,5,6,7,8,9,10,11,12]}, 但迄今为止, 仍然没有一个抗纹枯病基因被克隆, 除少数几个抗纹枯病QTL被精细定位外^[3,4], 大多数为初步定位结果^{[2,3,4,5,6,7,8,9,10,11,12]} ...

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

... 10个抗病标记位点与以往报道的抗病QTL的侧翼标记相同或位于以往报道的抗病QTL区间内, 包括RM267 ^[2,5,6]、RM190 ^[6,16]、RM6917 ^[2,13]、RM209 ^[3,7]、RM1233 ^[3,8,16]、RM224 ^[3,8]、RM6297 ^[2,11,12]、 ...

... RM6838 ^[2,8]、RM8242 ^[2]、RM311 ^[7], 进一步验证了这些QTL的真实性, 暗示这10个抗病标记位点在不同的遗传背景或环境中能够稳定表达, 育种利用价值可能更高 ...

... 3 Mb, RM190为以往已报道的抗病QTL^[6,16]的侧翼标记, RM6917位于抗病QTL区间内^[2,13], 说明抗病标记RM190和RM6917真实性较高, 可能是精细定位水稻抗纹枯病基因的目标区域 ...

... 4 Mb, RM7585距离Y1065Le-RZ69x区间的抗纹枯病QTL^[2]约1 ...

2009

3.251

0.0

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

... Zuo等^[4]利用染色体片段置换系将qSB-11^LEQTL精细定位于74 kb区间内, Channamallikarjuna等^[3]利用重组自交系群体将qSBR-11-1精细定位于850 kb区间内, 其余抗纹枯病QTL均为初步定位结果 ...

... 4 Mb, 已精细定位的qSB-11^LEQTL位于该区间内^[3,8] ...

2013

3.658

0.0

Zuo

S M

, Yin

Y J

, Pan

C H

, Chen

Z X

, Zhang

Y F

, Zhu

L H

, Pan

X B

. Fine mapping of qSB-11^LE, the QTL that confers partial resistance to rice sheath blight. Theor Appl Genet, 2013, 126: 1257-1272

Abstract

Sheath blight (SB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. No major resistance genes to SB have been identified so far. All discovered loci are quantitative resistance to rice SB. The qSB-11^LE resistance quantitative trait locus (QTL) has been previously reported on chromosome 11 of Lemont (LE). In this study, we report the precise location of qSB-11^LE. We developed a near isogenic line, NIL-qSB11^TQ, by marker-assisted selection that contains susceptible allele(s) from Teqing (TQ) at the qSB-11 locus in the LE genetic background. NIL-qSB11^TQ shows higher susceptibility to SB than LE in both field and greenhouse tests, suggesting that this region of LE contains a QTL contributing to SB resistance. In order to eliminate the genetic background effects and increase the accuracy of phenotypic evaluation, a total of 112 chromosome segment substitution lines (CSSLs) with the substituted segment specific to the qSB-11^LE region were produced as the fine mapping population. The genetic backgrounds and morphological characteristics of these CSSLs are similar to those of the recurrent parent LE. The donor TQ chromosomal segments in these CSSL lines contiguously overlap to bridge the qSB-11^LE region. Through artificial inoculation, all CSSLs were evaluated for resistance to SB in the field in 2005. For the recombinant lines, their phenotypes were evaluated in the field for another 3 years and during the final year were also evaluated in a controlled greenhouse environment, showing a consistent phenotype in SB resistance across years and conditions. After comparing the genotypic profile of each CSSL with its phenotype, we are able to localize qSB-11^LE to the region defined by two cleaved-amplified polymorphic sequence markers, Z22-27C and Z23-33C covering 78.871 kb, based on the rice reference genome. Eleven putative genes were annotated within this region and three of them were considered the most likely candidates. The results of this study will greatly facilitate the cloning of the genes responsible for qSB-11^LE and marker-assisted breeding to incorporate qSB-11^LE into other rice cultivars.

<li>1.Key Lab of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou, 225009, People’s Republic of China</li><li>2.Key Lab for Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People’s Republic of China</li><li>3.National Plant Gene Research Center, Institute of Genetics and Development Biology, Chinese Academy of Science, Beijing, 100101, People’s Republic of China</li>

... C418和特青是抗病对照, Lemont是感病对照, 武育粳3号较感纹枯病^[4,17,19] ...

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

2003

3.658

0.0

Che

K P

, Zhan

Q C

, Xing

Q H

, Wang

Z P

, Jin

D M

, He

D J

, Wang

. Tagging and mapping of rice sheath blight resistant gene. Theor Appl Genet, 2003, 106: 293-297

1.Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China 2.Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

2009

2.968

0.0

Liu

, Jia

, Correa-Victoria

F J

, Prado

G A

, Yeater

K M

, McClung

, Correll

J C

. Mapping quantitative trait loci responsible for resistance to sheath blight in rice. Phytopathology, 2009, 99: 1078-1084

Rice Research and Extension Center, University of Arkansas, 2900 Hwy 130E, Stuttgart, AR 72160, USA.

Rice sheath blight (ShB), caused by the soilborne pathogen Rhizoctonia solani, annually causes severe losses in yield and quality in many rice production areas worldwide. Jasmine 85 is an indica cultivar that has proven to have a high level of resistance to this pathogen. The objective of this study was to determine the ability of controlled environment inoculation assays to detect ShB resistance quantitative trait loci (QTLs) in a cross derived from the susceptible cv. Lemont and the resistant cv. Jasmine 85. The disease reactions of 250 F(5) recombinant inbred lines (RILs) were measured on the seedlings inoculated using microchamber and mist-chamber assays under greenhouse conditions. In total, 10 ShB-QTLs were identified on chromosomes 1, 2, 3, 5, 6, and 9 using these two methods. The microchamber method identified four of five new ShB-QTLs, one on each of chromosomes 1, 3, 5, and 6. Both microchamber and mist-chamber methods identified two ShB-QTLs, qShB1 and qShB9-2. Four of the ShB-QTLs or ShB-QTL regions identified on chromosomes 2, 3, and 9 were previously reported in the literature. The major ShB-QTL qShB9-2, which cosegregated with simple sequence repeat (SSR) marker RM245 on chromosome 9, contributed to 24.3 and 27.2% of total phenotypic variation in ShB using microchamber and mistchamber assays, respectively. qShB9-2, a plant-stage-independent QTL, was also verified in nine haplotypes of 10 resistant Lemont/Jasmine 85 RILs using haplotype analysis. These results suggest that multiple ShB-QTLs are involved in ShB resistance and that microchamber and mist-chamber methods are effective for detecting plant-stage-independent QTLs. Furthermore, two SSR markers, RM215 and RM245, are robust markers and can be used in marker-assisted breeding programs to improve ShB resistance.

PMID: 19671010

... 目前这一新方法已被成功地应用于水稻纹枯病抗病基因表达和QTL定位研究^[6,9] ...

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

2008

0.0

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

... 0 Mb, RM5371距离RM30-RM439区间的抗纹枯病QTL^[7]约1 ...

2008

0.0

1.667

Xie

X W

, Xu

M R

, Zang

J P

, Sun

, Zhu

L H

, Xu

J L

, Zhou

Y L

, Li

Z K

. Genetic background and environmental effects on expression of QTL for sheath blight resistance in reciprocal introgression lines of rice. Acta Agron Sin, 2008, 34: 1885-1893 (in Chinese with English abstract)

Genetic background and environmental effects of QTL for sheath blight resistance to the isolate RH-9 (Rhizoctonia solani kuhn) were revealed using the reciprocal introgression line populations derived from the cross of Lemont/Teqing. Lemont is highly susceptible while Teqing resistant to RH-9. The relative lesion height (a ratio of lesion height to plant height, RLH) of TQ-ILs was normally distributed whereas that of LT-ILs was apparently inclined to the susceptible parent, Lemont. Total 10 main-effect QTLs and 13 epistatic QTLs affecting sheath blight resistance were mapped under different years and genetic backgrounds. Among them, six main-effect QTLs detected in 2006 were all verified in 2007, suggesting these QTLs had reliable performance across years. QSh4 was the only one QTL expressed under the reciprocal backgrounds and Teqing allele at this locus decreased RLH, suggesting the improvement of resistance level. QSh10a detected in the TQ-ILs and located in the region of RM216–RM311 on the chromosome 10 and QSh10b detected in the LT-ILs in the neighboring region of RM222–RM216 were not the same gene but existed tight linkage as regards to different gene directions in different backgrounds. Most QTLs identified in TQ-ILs were not expressed in LT-ILs, indicating there was evident genetic background effect. By comparative mapping, 8 QTLs detected in this study were located in the same or near regions that associated with sheath blight resistance identified in the previous studies, suggesting these main-effect QTLs could be applied in rice breeding for sheath blight resistance by marker-assisted selection. As indicated in this study, it is an effective way to further improve sheath blight resistance by selecting the QTL stably expressed in different backgrounds or pyramiding different main-effect QTLs.

1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences / National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China; 2 International Rice Research Insititute, DAPO Box 7777, Metro Manila, Philippines

利用水稻纹枯病菌强致病菌系RH-9人工接种Lemont导入到特青背景的213个近等基因导入系(TQ-ILs)群体和特青导入到Lemont背景的195个近等基因导入系(LT-ILs)群体，定位和分析了水稻抗纹枯病数量性状座位(quantitative trait loci, QTL)及其表达的环境与遗传背景效应。亲本Lemont对RH-9表现为高度感病，特青表现为中等抗病。人工接种后TQ-ILs群体的相对病斑高度(病斑高度与株高比)呈连续正态分布，LT-IL群体则明显偏向感病亲本Lemont。在不同年份和遗传背景下检测到影响纹枯病相对病斑高度的主效QTL 10个和互作QTL 13个，其中2006年在TQ-IL群体定位到的6个主效QTL在2007年均得到验证，表明这些QTL具有较好年度间的重复性。QSh4是唯一在双向导入系背景下表达的QTL，该位点特青等位基因降低相对病斑高度，提高抗性水平。在TQ-ILs群体中定位到位于第10染色体RM216~RM311区间的QSb10a与在LT-IL群体中定位到的位于相邻区间RM222~RM216的QSb10b的基因作用方向不同，推断这两个QTL存在紧密连锁关系。绝大多数在TQ-IL群体中表达的主效及互作QTL在LT-ILs群体中不表达，表明水稻抗纹枯病QTL具有明显的遗传背景效应。通过比较作图，本研究定位到的其中8个QTL在以往不同群体中同样被检测到，这些主效QTL对通过分子标记辅助选择(marker-assisted selection, MAS)培育水稻抗纹枯病育种可能具有应用价值。研究指出，标记辅助选择在不同遗传背景中能稳定表达的QTL或通过聚合不同抗病QTL是进一步提高水稻纹枯病抗性水平的一个有效途径。

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

... 4 Mb, 已精细定位的qSB-11^LEQTL位于该区间内^[3,8] ...

2009

0.0

... 目前这一新方法已被成功地应用于水稻纹枯病抗病基因表达和QTL定位研究^[6,9] ...

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

2009

0.0

1.667

, Cheng

L R

, Xu

M R

, Zhou

, Zhang

, Sun

, Zhou

Y L

, Zhu

L H

, Xu

J L

, Li

Z K

. QTL mining for sheath blight resistance using the backcross selected introgression lines for grain quality in rice. Acta Agron Sin, 2009, 35: 1729-1737 (in Chinese with English abstract)

QTLs for disease scale (DS), relative lesion height (RH) and plant height (PH) were mapped using the four introgression lines selected against grain quality from the four introgression populations between two elite varieties, IR64 and Teqing as recurrent parents and two tall varieties, Tarom Molaii and Binam with high grain quality and sheath blight resistance (SBR) as donors. DS had high significant positive correlation with RH, and both of them were significantly negatively correlated with PH. DS, RH and PH presented wide segregations even in the relative small (28–60) introgression populations, including some semidwarf plants segregated with overparent SBR. Ten, eight, eight and six QTLs for the three traits were identified in IR64/Tarom Molaii, Teqing/Tarom molaii, IR64/Binam and Teqing/Binam, respectively by one way ANOVA analysis. The two donor alleles at most QTLs reduced DS and RH as well as increased PH. No any a common QTL for each of the three traits was detected in the populations of the same donor in the two different background, indicating there was a obvious genetic background effect on expression of SBR- and PH-QTLs. QTLs linked to the same marker loci between PH and DS, and PH and RH accounted for 38% and 52% of total QTLs for the two traits, respectively, indicating SBR had tight relationship with PH and both of them shared some linked loci. As compared with the previous QTL mapping results of grain quality in the same populations, most QTLs for grain quality and SBR distributed in different chromosome regions and showed independently inherited. Efficiency, influencing factors and its application in breeding of QTL mapping for non-target traits using introgression lines selected against the target trait were deeply discussed, and importance of selective introgression lines in QTL mining and breeding use was also emphasized.

1Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement，Chinese Academy of Agricultural Sciences，Beijing 100081，China；2International Rice Research Institute，DAPO Box7777，Metro Manila，Philippines

将优质、抗纹枯病的高秆供体Tarom Molaii和Binam导入半矮秆IR64和特青背景，培育品质性状回交选择构建的4个导入系群体IR64/Tarom Molaii、特青/Tarom Molaii、IR64/Binam和特青/Binam，定位了影响水稻抗纹枯病病级(disease scale, DS)、相对病斑高度(relative lesion height, RH)和株高(plant height, PH)的QTL。结果表明，4个导入系群体的DS与RH高度相关，两者与PH呈显著负相关。导入系后代各性状均呈现超亲分离，出现抗性明显优于双亲的抗病个体，其中40%左右属半矮秆抗病类型。采用单向方差分析，在这4个群体中分别定位到10、8、8和6个影响3个性状的QTL，多数基因座上降低DS和RH即增强抗病性同时增加株高的等位基因均来自两个供体。未在同一供体两个不同背景下检测到影响3个性状的相同QTL，表明抗纹枯病QTL表达有明显的遗传背景效应。PH与DS及PH与RH被定位在同一个显著标记位点的QTL数分别占两个性状QTL总数的38%和52%，表明水稻纹枯病抗性与株高关系密切，两者存在许多连锁位点。与以往相同群体品质性状QTL的定位结果相比，发现品质性状QTL与抗纹枯病QTL大多分布在染色体的不同区域，彼此独立遗传。对利用目标性状选择导入系定位非目标性状QTL的效果、影响因素及育种应用进行了探讨，强调了目标性状选择导入系对非目标性状QTL发掘及育种应用的重要性。

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

2013

2.455

0.0

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

2002

0.0

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

... RM1036距离RG241a-RZ397区间的抗纹枯病QTL^[12]约3 ...

2002

0.0

Han

Y P

, Xing

Y Z

, Chen

Z X

, Gu

S L

, Pan

X B

, Chen

X L

, Zhang

Q F

. Mapping QTLs for horizontal resistance to sheath blight in an elite rice restorer line, Minghui63. Acta Genet Sin, 2002, 29: 565-570 (in Chinese with English abstract)

Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai 200040, China.

HS2 and HS3 are important elements of human beta-globin locus control region (LCR). To study the effect of HS2, HS3, and HS2-HS3 on human beta-globin gene expression, a series of expression cassettes were constructed, in which the reporter gene encoding the enhanced green fluorescent protein (EGFP) was driven by the beta-globin promotor and under the control of HS2, HS3, and HS2-HS3. These constructs were transfected transiently into MEL and K562 cell lines mediated with liposome and their expression was measured with FACS as well as semi-quantitative RT-PCR method. The results showed that 3.2-kb HS2 could significantly enhance the activity of beta-globin promotor in MEL and K562 cells, while 3-kb HS3 could do only in MEL cells. There was no synergistic function in transient expression in the cassettes with the combination of HS2 and HS3 in MEL and K562 cells.

PMID: 12143302

... 与连锁分析相比, 关联分析可以利用具有丰富遗传多样性的自然群体为材料, 无需构建专门的作图群体, 并可实现同时检测自然群体同一座位的多个等位基因, 对QTL定位的广度和精度也相对较高^[13] ...

2009

1.513

0.0

... 鉴于这些优势, 关联分析被广泛应用于发掘植物数量性状基因的研究^[14,15,16], 成为植物遗传学研究的热点 ...

... 参考Breseghello等^[14]和文自翔等^[24]的方法计算标记位点等位变异的表型效应 ...

1995

3.658

0.0

Z K

, Pinson

S R M

, Marshetti

M A

, Stansel

J W

, Park

W D

. Characterization of quantitative trait loci (QTLs) in cultivated rice contributing to field resistance to sheath blight (Rhizoctonia solani). Theor Appl Genet, 1995, 91: 374-381

Texas A&M University System Agricultural Research and Extension Center, Imes Rd, Box 999, 77713, Beaumont, TX, USA.

'Lemont' and 'Teqing' are both semidwarf rice varieties that differ in heading date by only 6 days. However, when 'Lemont' and 'Teqing' are crossed there is transgressive segregation for both heading date (HD) and plant height (PH). By testing 2418 F4 lines with 113 well-distributed RFLP markers, we identified and mapped chromosomal regions that were largely responsible for this transgressive segregation. QHd3a, a QTL from 'Lemont' that gives 8 days earlier heading, was identified on chromosome 3 approximately 3 cM from the marker RG348. Another QTL with a large effect, QHd8a, which gives 7 days earlier heading, was identified on chromosome 8 of 'Teqing' between RG20 and RG1034. Along with a QTL, QHd9a with a phenotypic effect of 3.5 days, these genomic regions collectively explain 76.5% of the observed phenotypic variance in heading date. Four QTLs which altered plant height from 4 to 7 cm were also mapped; these collectively explain 48.8% of the observed phenotypic variation in plant height. None of the QTLs for plant height mapped to chromosome 1, the location of the semidwarf gene sd-1. All three of the HD loci mapped to approximately the same genomic locations as PH QTLs, and in all cases, there was a reduction in height of approximately 1 cm for every day of earlier heading. The correspondence between the HD and some of the PH loci suggests that genes at these chromosome locations may have pleiotropic effects on both HD and PH. The observed heterosis in the F1 plants for HD can be largely explained by the dominance for earliness of the identified HD loci and distribution of earlier heading alleles in the parents. However, overdominance observed at one of the PH QTL may, at least in part, be responsible for the observed heterosis in PH.

PMID: 24169788

... 鉴于这些优势, 关联分析被广泛应用于发掘植物数量性状基因的研究^[14,15,16], 成为植物遗传学研究的热点 ...

... 水稻拥有非常丰富的种质资源, 是进行关联分析的理想材料^[15], 但利用关联分析方法进行中国水稻稻种资源对纹枯病抗性基因定位的研究目前未见报道 ...

2007

11.808

0.0

Mackay

, Powell

. Methods for linkage disequilibrium mapping in crops. Trends Plant Sci, 2007, 12: 57-63

Linkage disequilibrium (LD) mapping in plants detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. It offers greater precision in QTL location than family-based linkage analysis and should therefore lead to more efficient marker-assisted selection, facilitate gene discovery and help to meet the challenge of connecting sequence diversity with heritable phenotypic differences. Unlike family-based linkage analysis, LD mapping does not require family or pedigree information and can be applied to a range of experimental and non-experimental populations. However, care must be taken during analysis to control for the increased rate of false positive results arising from population structure and variety interrelationships. In this review, we discuss how suitable the recently developed alternative methods of LD mapping are for crops.

... 鉴于这些优势, 关联分析被广泛应用于发掘植物数量性状基因的研究^[14,15,16], 成为植物遗传学研究的热点 ...

... ^[16] ...

... 结果发现, 有13个标记位点在MLM (Q+K)或MLM (PCA+K)任一模型中被检测到与供试群体纹枯病病级显著关联(PP[2,3,4,5,6,7,8,9,10,11,12,16] ...

... ^[16] ...

2006

4.389

0.0

Breseghello

, Sorrells

M E

. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L. ) cultivars. Genetics, 2006, 172: 1165-1177

Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA.

Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. In this study, association mapping was performed on a selected sample of 95 cultivars of soft winter wheat. Population structure was estimated on the basis of 36 unlinked simple-sequence repeat (SSR) markers. The extent of LD was estimated on chromosomes 2D and part of 5A, relative to the LD observed among unlinked markers. Consistent LD on chromosome 2D was <1 cM, whereas in the centromeric region of 5A, LD extended for approximately 5 cM. Association of 62 SSR loci on chromosomes 2D, 5A, and 5B with kernel morphology and milling quality was analyzed through a mixed-effects model, where subpopulation was considered as a random factor and the marker tested was considered as a fixed factor. Permutations were used to adjust the threshold of significance for multiple testing within chromosomes. In agreement with previous QTL analysis, significant markers for kernel size were detected on the three chromosomes tested, and alleles potentially useful for selection were identified. Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection.

PMID: 16079235

... 至今虽然已研发了一些较有效的大田成株期纹枯病菌接种和抗性鉴定的方法, 但其工作量大、周期长, 难以用于大规模且农艺性状差别大的自然群体的接种鉴定^[17] ...

... C418和特青是抗病对照, Lemont是感病对照, 武育粳3号较感纹枯病^[4,17,19] ...

... 9级^[17] ...

... 43, 品种抗感性与前人描述基本一致^[17,25] ...

2010

35.209

0.0

Huang

X H

, Wei

X H

, Sang

, Zhao

, Feng

, Zhao

, Li

C Y

, Zhu

C R

, Lu

, Zhang

Z W

, Li

, Fan

D L

, Guo

Y L

, Wang

A H

, Wang

, Deng

L W

, Li

W J

, Lu

Y Q

, Weng

Q J

, Liu

K Y

, Huang

, Zhou

T Y

, Jing

Y F

, Li

, Lin

, Buckler

E S

, Qian

, Zhang

Q F

, J

, Han

. Genome-wide association studies of 14 agronomic traits in rice land races. Nat Genet, 2010, 42: 961-967

National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

PMID: 20972439

... 苗期微室接种鉴定法(micro-chamber method, MCM)由Jia等^[18]于2007年建立, 以水稻幼苗为接种对象, 试验周期短, 环境相对可控, 结果具有更好的重复性和可靠性 ...

... 参考Jia等^[18]的苗期微室法接种鉴定 ...

2012

3.73

0.0

Jia

L M

, Yan

W G

, Zhu

C S

, Agrama

H A

, Jackson

, Yeater

, Li

X B

, Huang

B H

, Hu

B L

, Mcclung

, Wu

D X

. Allelic analysis of sheath blight resistance with association mapping in rice. PLoS One, 2012, 7(3): e32703

State Key Lab of Rice Biology, Institute of Nuclear-Agriculture Sciences, Zhejiang University, Hangzhou, China.

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = -0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice.

PMID: 22427867

... C418和特青是抗病对照, Lemont是感病对照, 武育粳3号较感纹枯病^[4,17,19] ...

2009

0.0

... 25软件^[20]统计标记位点的等位变异及其频率和多态信息含量PIC ...

2009

0.0

Wang

Z B

, Zuo

S M

, Li

, Chen

X J

, Chen

Z X

, Zhang

Y F

, Pan

X B

. Rapid identification technology of resistance to rice sheath blight in seedling stage. Acta Phytopath Sin, 2009, 39: 174-182 (in Chinese with English abstract)

以抗感反应不同的5个水稻品种为试验材料,在人工气候箱、控温室中进行水稻苗期抗纹枯病接种试验,并与田间相应的成株期抗性试验进行比较,研究水稻苗期快速鉴定技术.结果表明:85%的相对湿度为纹枯病菌侵染危害水稻苗期植株的适宜湿度;苗期5个水稻品种对纹枯病抗性差异极显著,可将其分为相对感病(Lemont、武育粳3号)和相对抗病(YSBR1、Jasmine 85、特青)2大类;接种叶龄对发病程度有显著的影响,5个品种在四叶期接种时的平均病级显著高于五叶期接种的平均病级;苗期水稻品种『日J抗感差异小于田间鉴定试验结果,但两者间品种抗感趋势基本一致.苗期快速鉴定技术可用于大规模水稻品种(组合)的抗性筛选或初步鉴定.

... 2软件^[21]完成供试材料的遗传结构分析 ...

2007

2.455

0.0

... 用SPAGeDi软件^[22]计算个体间亲缘关系系数Kinship ...

2009

0.0

... 1软件^[23]的GLM (general linear model)和MLM (mixed linear model)模型, 分别以各材料Q值、Q+Kinship值和PCA+ Kinship值作为协变量进行关联分析 ...

2009

0.0

Chen

X J

, Wang

, Zuo

S M

, Wang

Z B

, Chen

Z X

, Zhang

Y F

, Zhou

E X

, Guo

Z J

, Huang

S W

, Pan

X B

. Screening of varieties and isolates for identifying interaction between host and pathogen of rice sheath blight. Acta Phytopath Sin, 2009, 39: 514-520 (in Chinese with English abstract)

经过近十年的病原菌接种试验,从国内外数百份水稻种质中,筛选出了抗病水平不同的5个代表品种Lemont、武育粳3号、Jasmine85、C418和YSBR1,作为水稻纹枯病菌致病力的鉴别品种.从江苏、广东、广西、海南、云南、湖南、福建等省采集、分离的水稻纹枯病菌中,初步筛选出致病力有差异的30个菌株,于温室苗期接种上述5个品种,确定了不同致病力的5个代表菌株C30、GD-118、E67、YN-7和YN-3.将选出的品种和菌株在江苏扬州和浙江富阳进行大田成株期抗性和致病力分析,结果表明:品种的抗病性和菌株的致病力都存在极显著差异,分别属于5个和3个不同的显著性级别,均可暂时作为鉴定材料使用.据以上结果,初步建立了一套可供水稻纹枯病菌致病力检测和寄主抗病性鉴定的鉴别体系.本文还讨论了建立水稻纹枯病鉴别体系的必要性、可行性和需要进一步开展的工作.

Abstract：

Five rice cultivars (YSBR1 ,C418,Jasmine85,Wuyujing3 and Lemont) with different levels of resistance to Rhizoctonia solani identified and screened from worldwide rice collections were selected to identify the pathogenicity of different isolates. Several hundred strains of R. solani had been isolated and purified from Jiangsu,Guangdong,Guangxi,Hainan, Yunnan,Hunan and Fujian Province. Thirty isolates with different path-ogenicity were selected to inoculate the five identification cultivars at the seedling stage in the greenhouse. Five isolates with obvious discrepancy of pathogenicity, C30,GD-118,E67, YN-7 and YN-3, were selected ulti-mately. The obtained cultivars and strains for identification were verified through field experiments at rice adult stage in Yangzhou of Jiangsu Province and Fuyang of Zhejiang Province. The results indicated that both the cultivars and isolates were divided significantly to five resistance grades and three pathogenicity grades respectively, so both of which could be used as identification materials. An identification system to the isolate pathogenity and the host resistance for rice sheath blight was preliminarily setup. The necessity and feasibility about the identification system, and the further work were also discussed in the paper.

... 参考Breseghello等^[14]和文自翔等^[24]的方法计算标记位点等位变异的表型效应 ...

2005

5.323

0.0

... 43, 品种抗感性与前人描述基本一致^[17,25] ...

2005

6.275

0.0

Evanno

, Regnaut

, Goudet

. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol, 2005, 14: 2611-2620

Department of Ecology and Evolution, Biology building, University of Lausanne, CH 1015 Lausanne, Switzerland.

The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

PMID: 15969739

... 被认为是引起假阳性的最主要因素^[26], 而加入群体结构和亲缘关系控制的混合线性模型MLM (Q+K)及加入主成分分析和亲缘关系控制的混合线性模型MLM (PCA+K)均能够较好地去除由群体分层引起的假阳性^[27,28] ...

2002

2.384

0.0

2007

5.323

0.0

Bradbury

P J

, Zhang

, Kroon

D E

, Casstevens

T M

, Ramdoss

, Buckler

E S

. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23: 2633-2635

United States Department of Agriculture-Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA. pjb39@cornell.edu

Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.

PMID: 17586829

2008

0.0

... 分子标记辅助育种已被认为是抗病育种的一个可行途径^[29] ...

2008

0.0

1.667

Wen

Z X

, Zhao

T J

, Zheng

Y Z

, Liu

S H

, Wang

C E

, Wang

, Gai

J Y

. Association analysis of agronomic and quality traits with SSR markers in Glycine max and Glycine soja in China: II. Exploration of elite alleles. Acta Agron Sin, 2008, 34: 1339-1349 (in Chinese with English abstract)

On the basis of our previous results of SSR loci associated with the 16 traits, alleles of loci significantly associated with the traits were analyzed further in the present paper. The phenotypic allele effect was estimated through comparison between the average phenotypic value over accessions with the specific allele and that of accessions with “ allele”, and then the average positive (negative) allele effect (AAE) of a locus was calculated over the estimated phenotypic effects of all positive (negative) alleles. The results showed that a set of elite alleles, loci and their carrier materials were screened out. Among the elite alleles existed in Glycine max and Glycine soja, some were consistent, some inconsistent and some complementary. The phenotypic effects of posi-tive (negative) alleles were different from each other, and therefore, the average positive (negative) effects of a locus were also different from each other, indicating the potential of genetic recombination for breeding purposes. A same marker locus could associate with multiple traits with its alleles performed in their own way in direction and size, and the covariation of a same allele performed in two related traits might be the genetic basis of their phenotypic correlation. In summary, the results implied that association mapping could offer further genetic information complementary to the family-based linkage mapping for the im-provement of breeding procedures. In addition, further detailed information on elite alleles and phenotypic effects of the 16 traits were shown in the text.

Soybean Research Institute of Nanjing Agricultural University / National Center for Soybean Improvement / National Key Laboratory for Crop Ge-netics and Germplasm Enhancement, Nanjing 210095, Jiangsu, China

在前文研究已检出与农艺品质性状显著关联的SSR位点的基础上, 本文进一步对与性状关联位点的等位变异作解析, 通过将携带某等位变异的所有材料表型均值与携带无效等位基因( allele)材料表型均值做比较, 估计等位变异的潜在表型效应增量(减量), 进一步利用该信息估计位点增效(减效)等位变异的平均效应, 鉴别出一批农艺品质性状优异位点、等位变异及携带优异等位变异的载体材料。发现在栽培及野生种质中检出的优异等位变异有同、有异、有互补性。发现关联位点正、负效应等位变异均值间有差异, 可根据育种目标性状选择要求, 选取适合的位点及相应等位变异。同一标记位点可与多性状关联, 其等位变异在不同性状间各有其表型效应的方向和大小; 等位变异在相关性状效应上方向、大小的异同解释了性状间正、负相关的遗传原因。关联作图得到的信息可以弥补家系连锁法QTL定位信息的不足, 并直接利用等位变异信息进行亲本选拔、组合选配及后代等位条带辅助选择以提高育种成效。

... 而事实证明, 育种中对少数抗性亲本材料的广泛使用, 造成推广品种遗传背景狭窄、作物病虫害种类演变, 重要病虫害持续发生或流行^[30] ...

2009

0.0

2009

0.0

1.667

Zuo

S M

, Wang

Z B

, Chen

X J

, Zhang

Y F

, Chen

X J

, Chen

Z X

, Pan

X B

. Evaluation of resistance of a novel rice germplasm YSBR1 to sheath blight. Acta Agron Sin, 2009, 35: 608-614 (in Chinese with English abstract)

A novel rice line YSBR1 with resistance to sheath blight (SB) was identified from the progenies of a cross between varieties of japonica and indica. The resistance of YSBR1 to SB was evaluated with multiple replications in the field and greenhouse and inhibition rate of embryo root growth by SB-toxin was investigated also. The results indicated that the resistance of YSBR1 to SB was significantly higher than that of other germplasms tested, and was stable and reliable; the average SB disease score of YSBR1 was 2.39±0.23 and reached “resistant” grade based on a “0–9” SB disease rating system. Line YSBR1 has an appropriate growth period duration and an improved plant type, with semi-dwarf plant (102±4.32 cm), slightly rolled and erect leaves. These results suggested that line YSBR1 has potentially high value for study on genetics and can be useful for improvement of resistance to SB in rice breeding.

Key Laboratory of Plant Functional Genomics of Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province,Yangzhou University, Yangzhou 225009,China

从籼粳交后代群体中筛选到一份抗纹枯病水稻新种质YSBR1。多年的大田和温室接种鉴定以及立枯丝核菌毒素对水稻胚根伸长抑制率试验结果均表明，YSBR1的抗性水平极显著高于其他参试品种(系)，且稳定、可靠，在大田接种试验中的纹枯病平均病级为2.39±0.23级(按0~9级评价标准)，达“抗病”水平。YSBR1的株高为(102±4.32) cm，叶片稍内卷而挺拔，株形优良，生育期适中，在水稻抗纹枯病遗传育种中可有较大研究价值和利用前景。

2003

39.06

0.0

Cardon

L R

, Palmer

J L

. Population stratification and spurious allelic association. Lancet, 2003, 361: 598-604

Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, UK. Ion.cardon@well.ox.ac.uk

Great efforts and expense have been expended in attempts to detect genetic polymorphisms contributing to susceptibility to complex human disease. Concomitantly, technology for detection and scoring of single nucleotide polymorphisms (SNPs) has undergone rapid development, extensive catalogues of SNPs across the genome have been constructed, and SNPs have been increasingly used as a means for investigation of the genetic causes of complex human diseases. For many diseases, population-based studies of unrelated individuals--in which case-control and cohort studies serve as standard designs for genetic association analysis--can be the most practical and powerful approach. However, extensive debate has arisen about optimum study design, and considerable concern has been expressed that these approaches are prone to population stratification, which can lead to biased or spurious results. Over the past decade, a great shift has been noted, away from case-control and cohort studies, towards family-based association designs. These designs have fewer problems with population stratification but have greater genotyping and sampling requirements, and data can be difficult or impossible to gather. We discuss past evidence for population stratification on genotype-phenotype association studies, review methods to detect and account for it, and present suggestions for future study design and analysis.

PMID: 12598158

2006

35.209

0.0

J M

, Pressoir

, Briggs

W H

, Bi

I V

, Yamasaki

, Doebley

J F

, McMullen

M D

, Gaut

B S

, Nielsen

D M

, Holland

J B

, Kresovich

, Buckler

E S

. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet, 2006, 38: 203-208

Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA.

As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping.

PMID: 16380716

2007

4.389

0.0

2010

0.0

2010

0.0

2000

0.0

2000

0.0