普通菜豆基因组SSR标记开发及在豇豆和小豆中的通用性分析

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陈明丽, 王兰芬, 武晶, 张晓艳, 杨广东, 王述民. 普通菜豆基因组SSR标记开发及在豇豆和小豆中的通用性分析. 作物学报, 2014, 40(5): 924-933[CHEN Ming-Li, WANG Lan-Fen, WU Jing, ZHANG Xiao-Yan, YANG Guang-Dong, WANG Shu-Min. Development of Genomic SSR Markers in Common Bean and Their Transfera-bility in Cowpea and Adzuki Bean. 作物学报, 2014, 40(5): 924-933] 复制到剪切板

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作物学报编辑部

普通菜豆基因组SSR标记开发及在豇豆和小豆中的通用性分析

陈明丽¹, 王兰芬¹, 武晶¹, 张晓艳², 杨广东³, 王述民^1,^*

¹中国农业科学院作物科学研究所, 北京100081

² 青岛市农业科学研究院蔬菜所, 山东青岛266100

³黑龙江省农业科学院克山分院, 黑龙江克山161606

^*通讯作者(Corresponding author): 王述民, E-mail:wangshumin@caas.cn, Tel: 010-62175628

第一作者联系方式: E-mail:sscmlss_cool@126.com

收稿日期:2014-03-04

基金:本研究由中国农业科学院科技创新工程和国家科技支撑计划项目(2013BAD01B05-2-4)资助;

摘要

分子标记具种属间通用性可提高其利用效率, 并降低标记开发成本。本研究基于Roche 454超高通量测序技术获得普通菜豆基因组测序结果, 共开发了560个普通菜豆基因组SSR标记。利用2份普通菜豆品种对标记进行初步筛选, 有421个标记能够有效扩增。用新开发的标记分析16份豇豆和16份小豆的通用性。结果显示, 185个普通菜豆基因组SSR标记在豇豆中能有效扩增, 通用性比率为43.9%; 161个SSR标记在小豆中能有效扩增, 通用性比率为38.2%; 在豇豆和小豆中都能获得有效扩增条带的标记共138个; 并且普通菜豆基因序列SSR标记在豇豆和小豆中的通用性比率高于基因间序列SSR标记。通用性标记的多态性分析表明, 豇豆和小豆的多态性比率分别为34.0%和24.8%; 且豇豆和小豆中基因间标记的多态性都比基因内标记的多态性高。上述通用性标记为豇豆属作物的多样性评价、连锁图谱的构建及基因定位等方面的研究提供了便利。

关键词: 普通菜豆; 豇豆属; SSR标记; 通用性

Development of Genomic SSR Markers in Common Bean and Their Transfera-bility in Cowpea and Adzuki Bean

CHEN Ming-Li¹, WANG Lan-Fen¹, WU Jing¹, ZHANG Xiao-Yan², YANG Guang-Dong³, WANG Shu-Min^1,^*

¹Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China

²Institute of Vegetables, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China

³Keshan Branch, Heilongjiang Academy of Agricultural Sciences, Keshan 161606, China

Fund:

Abstract

Transferability analysis of molecular markers has significantly improved their development efficiency and reduced their development cost. A total of 560 novel SSR markers were successfully developed based on common bean genomic sequences, and 421 (75.2%) of those markers generated effective amplification bands from two accessions of the cultivated common bean. TwoVigna species, cowpea and adzuki bean were used to test the transferability and polymorphism of new genomic markers. The results indicated that the transferability rate of common bean genomic-SSR in cowpea and adzuki bean was 43.9% and 38.2%, and the ratio of polymorphism SSR markers in the crops was 34.0% and 24.8%, respectively. A total of 138 common bean genomic-SSR primers were detected to be highly transferable between two species ofVigna. In addition, the diversity of transferability gene-SSR markers was higher for cowpea and adzuki bean than that of intergenic regions-SSR. These transferable markers are useful for further genetic diversity analysis, genetic linkage map construction, quantitative trait loci annotation, genetic evolution and marker-assisted selection inVigna species because of their multi-allelic nature, reproducibility, co-dominant inheritance, high abundance in genome.

Keyword: Common bean; GenusVigna; SSR markers; Transferability

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普通菜豆、豇豆及小豆均是我国的主要栽培食用豆种。普通菜豆属于豆科(Leguminosae), 蝶形花亚科(Papilioni-deae), 菜豆族(Phaseoleae)菜豆属( Phaseolus)^{[ 1]}。豇豆^{[ 2]}和小豆^{[ 3]}属豆科(Leguminosae), 蝶形花亚科(Papilionideae), 菜豆族(Phaseoleae), 豇豆属( VignaL.)。豇豆属含有2个亚属, 豇豆属于 Vigna亚属, 小豆属于 Ceratoropis亚属。

豇豆和小豆在中国栽培历史悠久, 全国各地都有种植。中国被认为是豇豆的起源中心或次级起源中心之一, 目前除西藏自治区外, 其他各地都有豇豆生产^{[ 4]}; 小豆原产中国, 在中国华北、东北、黄河及长江中下游地区广泛种植^{[ 5]}。豇豆和小豆在我国农产品出口, 饮食改善以及作物种植结构优化等方面具有重要作用^{[ 6]}。但是, 与其他豆科模式作物如普通菜豆和苜蓿相比, 豇豆^{[ 7]}和小豆^{[ 8]}公开发表的分子标记数目极少。

分子标记在许多作物的遗传研究中起重要作用。SSR标记因其在基因组中分布广泛且具有共显性遗传、可重复性、多态性丰富等特点而被认为是最好的分子标记之一, 广泛应用于种质资源的多样性分析、遗传连锁图谱构建、基因定位及标记辅助育种等研究^{[ 9]}。SSR标记在近缘植物乃至远缘植物基因组间有一定的通用性^{[ 10]}。目前, 许多物种间SSR标记通用性研究已取得较大进展。张扬勇等^{[ 11]}根据拟南芥叶绿体全基因组序列开发89个叶绿体基因组SSR标记, 并分析了标记在甘蓝中的通用性; Wang等^{[ 12]}研究发现禾本科作物小麦、玉米和高粱中的SSR标记在海滨雀稗属作物中的通用性比率分别为67.5%、49.0%和66.8%, 多态性达51.5%。Hu等^{[ 13]}发现黄瓜EST-SSR标记在甜瓜、西瓜、南瓜和葫芦中的具有很高通用性, 通用性比率为92.9%、57.1%、53.6%和60.7%。王丽侠等^{[ 14]}分析187个小豆SSR标记在绿豆中的通用性表明, 约75%的小豆SSR标记可在绿豆中有效扩增。钟敏等^{[ 15]}分析1205个新开发绿豆基因组SSR标记的通用性表明其在豇豆、小豆和饭豆中的通用性比率分别为50.0%、73.3%和81.6%; 多态性比率分别为4.1%、1.7%和1.5%。但与其他物种相比, SSR标记通用性在豆科作物中研究较少, 需进一步探讨不同豆科作物间标记的通用性, 以提高标记的利用效率, 促进遗传研究水平较低的物种的分子遗传学研究。本研究通过分析基于普通菜豆基因组序列开发的SSR标记在豇豆属作物豇豆和小豆中的通用性, 以期增加豇豆、小豆的分子标记, 进而加速豇豆属的基因组学研究。

1 材料与方法

1.1 试验材料

用于检测普通菜豆SSR标记有效性的普通菜豆地方品种红芸豆(统一编号: F0002322)和京豆(统一编号: F0000777); 用于SSR标记通用性分析的16份小豆材料和16份豇豆材料均由中国农业科学院作物科学研究所提供。16份小豆材料来源于中国11个省市, 16份豇豆材料来源于中国8个省市(表1)。

表1 小豆和豇豆品种资源名称及来源 Table 1 Names and origins of adzuki bean and cowpea

1.2 DNA提取与检测

采用天根生化科技(北京)有限公司植物基因组DNA提取试剂盒(离心柱型)提取植物基因组DNA。用1%琼脂糖凝胶电泳检测DNA质量, 紫外分光光度计检测浓度和纯度。

1.3 引物开发

依据普通菜豆基因组序列信息, 利用SSR Locator软件查找SSR位点并设计引物^{[ 16]}。查找SSR位点参数设置: 二核甘酸重复10次, 三核苷酸重复5次。设定引物长度18~22 bp; 引物序列的GC含量40%~60%, 且下游引物GC含量差异小; 引物退火温度在55~60℃之间; 扩增片段长度在100~300 bp之间。引物均由Invitrogen公司合成。

1.4 PCR扩增反应

PCR总体积15 μL, 含50 ng基因组DNA, 10×PCR缓冲液1.5 μL (含1.5 mmol L^-1MgCl₂), 0.25 mmol L^-1dNTPs, 上下游引物各0.25 μmol L^-1和1 U Taq DNA聚合酶。反应程序为 95℃ 5 min; 95℃ 45 s, 50~60℃ 45 s, 72℃ 45 s, 35个循环; 最后72℃延伸5 min。反应在T100 Thermal Cycler (Bio-Rad Research, USA)扩增仪上进行。SSR扩增产物经6%的聚丙烯酰胺非变性凝胶在60 W恒定功率下电泳 70 min, 用NaOH快速银染法染色后读取条带^{[ 17]}。

1.5 标记多态性分析

利用Popgen32^{[ 18]}软件分析标记多态性信息含量(PIC)、等位基因数( N_a)、观察杂合度( H_o)和期望杂合度( H_e)。

2 结果与分析

2.1 普通菜豆基因组SSR标记开发及筛选

利用SSR Locator软件, 共开发560个菜豆基因组SSR标记。选2份普通菜豆红芸豆和京豆对SSR标记进行初步筛选, 确定有421个SSR标记在菜豆中能够稳定扩增出清晰条带, 有效扩增率为75.2%; 421个有效扩增标记中, 有93个标记在2份材料中表现多态性, 多态性比率为22.1%。

表2 普通菜豆基因内SSR标记和基因间序列SSR标记在豇豆和小豆中的通用性和多态性分布 Table 2 Transferability and polymorphism of gene-SSR markers and intergenic region-SSR for cowpea and adzuki bean

421个普通菜豆SSR标记的基因组序列与菜豆全基因组序列(http://www.phytozome.net/)比对分析显示, 213个标记属于基因内SSR标记, 208个标记属于基因间序列SSR标记(表2)。213个基因内SSR标记分布于普通菜豆11条染色体上, 平均每个染色体上19个标记。Pv03染色体上标记数量最多, 有30个SSR标记, 其次是Pv02和Pv01染色体, 标记数分别为26个和25个。染色体Pv04和Pv05上标记数量最少, 都只有11个(表3)。

表3 213个普通菜豆基因序列SSR标记在染色体上的分布 Table 3 Distribution of 213 gene-SSR markers on chromosome in common bean

2.2 普通菜豆基因组SSR标记的通用性

分析421个普通菜豆SSR标记在16份豇豆和16份小豆中的通用性显示, 185个菜豆SSR标记在豇豆中能够有效扩增, 标记在豇豆中的通用性比率为43.9%。其中112个标记属于普通菜豆基因内SSR标记, 比率为52.6%; 有73个标记属于普通菜豆基因间序列SSR标记, 比率为35.1% (表2)。161个标记在小豆中能获得有效扩增条带, 标记在小豆中的通用性比率为38.2%。161个通用性标记中, 有95个标记属于普通菜豆基因内SSR标记, 比率为44.6%, 有66个标记属于普通菜豆基因间序列SSR标记, 比率为31.7% (表2)。普通菜豆SSR标记在豇豆属物种豇豆和小豆中通用性存在差异, 在豇豆中的通用性比率高于在小豆中的通用性比率。SSR标记绝大多数在2个物种中能同时得到有效扩增, 2个物种间均能获得有效扩增条带的标记共有138个, 其中基因内的SSR标记达到85个, 基因间序列SSR标记有53个。47个标记只能在豇豆中扩增, 23个标记特异在小豆中扩增。

2.3 SSR标记的多态性

在SSR标记通用性分析的基础之上, 进一步研究了普通菜豆基因组SSR标记在16份豇豆和16份小豆中的多态性(图1和图2)。豇豆中可有效扩增的185个标记中, 有63个标记表现多态, 多态性比率为34.0%, 其中有36个标记属于普通菜豆基因内SSR标记, 比率为32.1%, 27个标记属于普通菜豆基因间序列SSR标记, 比率为37.0% (表2)。PIC值变化在0.110~0.671, 平均PIC值为0.305, 标记的等位基因数量在2~6之间, 平均为2.54; 期望杂合度在0.121~0.706之间, 平均期望杂合度为0.322; 有11个标记位点表现不同程度的杂合性。标记BMg409、BMg497、BMg538、BMg568和BMg569表现较高的杂合度, 观察杂合度均大于0.5, 标记BMg317、BMg445、BMg449、BMg492、BMg567和BMg661观察杂合度小于0.5 (见附表)。

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	图1 普通菜豆SSR标记在16份豇豆中的扩增图谱Fig. 1 Amplification bands of common bean SSR markers in cowpea

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	图2 普通菜豆SSR标记在16份小豆中的扩增图谱Fig. 2 Amplification bands of common bean SSR markers in adzuki bean

小豆中有效扩增的161个标记中, 40个标记表现出多态, 多态性比率为24.8%, 其中23个属于普通菜豆基因内SSR标记, 比率为24.2%, 17个属于普通菜豆基因间序列SSR标记, 比率为25.8% (表2)。PIC变化在0.059~0.668, 平均PIC值为0.359, 标记的等位基因数在2~5之间, 平均值为2.8。期望杂合度在0.063~0.734之间, 平均期望杂合度为0.389; 多数多态性标记位点观察杂合度为0, 仅有标记BMg384和BMg445位点观察杂合度大于0, 分别为0.063和0.133 (见附表)。22个普通菜豆SSR标记在豇豆和小豆中存在多态性, 其中13个属于基因内SSR标记, 9个属于基因间序列SSR标记。

3 讨论

分子标记开发的关键是如何高效获得基因组序列或表达的序列标签(EST)序列, 而新一代测序技术可以快速获得海量的序列数据, 极大程度提高了挖掘、验证和评估分子标记的效率^{[ 19]}。小麦^{[ 20]}、水稻^{[ 21]}、甘薯^{[ 22]}、黄瓜^{[ 23]}、西葫芦^{[ 24]}等作物依据基因组序列开发了大量分子标记。豆科作物在这方面的研究也取得一定的进展, Tangphatsornruang等^{[ 25]}利用Roche 454超高通量组测序技术获得470 024条绿豆基因组序列, 并检测到1493个SSR位点用于标记开发。Kaur等^{[ 26]}对小扁豆特异组织进行转录组测序, 获得1.38 ×10⁶个EST, 并开发了2393个小扁豆EST-SSR标记用于后续研究。Garg等^{[ 27]}和Dutta等^{[ 28]}分别利用组装的鹰嘴豆和木豆转录组序列开发了大量功能标记。本研究正是利用Roche 454测序数据, 从中开发SSR标记, 丰富了普通菜豆的遗传标记。

SSR序列在相近的物种间具有一定的保守性, 因而SSR标记在近缘物种间能够通用。标记通用性研究可以为相近物种提供更多的遗传信息, 方便了物种内、种间遗传学与基因组学等方面的研究^{[ 29]}。SSR标记通用性比率高低与所属物种之间亲缘关系密切相关。Gupta等^{[ 30]}随机选取41个豆科模式生物蒺藜状苜蓿SSR标记, 分析显示, 其在豆科植物中的通用性(53%~71%)明显高于非豆科植物(33%~44%)。同科不同属间SSR标记通用性比率明显比同属不同种间通用性低。本研究中普通菜豆与豇豆和小豆是同科不同属作物, 通用性比率为43.9% (豇豆)和38.2% (小豆), 明显低于同属作物绿豆与豇豆和小豆的通用性比率, 后者分别为50.0% (豇豆)和73.3% (小豆)^{[ 15]}。

SSR序列不仅存在于基因序列中, 而且存在于基因间序列中, 由于在物种间基因序列的保守性高于基因间序列的保守性, 因此, 基因内SSR标记在物种间通用性一般高于基因间序列SSR标记。文明富等^{[ 31]}研究木薯419对EST-SSR引物和182对基因组SSR引物在麻疯树和橡胶树通用性发现, 木薯EST-SSR在麻疯树和橡胶树中的通用性比率分别为55.85%和38.90%, 明显高于木薯基因组SSR在麻疯树和橡胶树通用性比率37.36%和26.37%; Varshney等^{[ 32]}分析大麦的EST-SSR和G-SSR标记在近缘物种小麦中的通用性, 发现EST-SSR标记的通用性比率高于G-SSR标记。在本研究中普通菜豆基因内SSR标记在豇豆和小豆中的通用性比率分别为52.6%和35.1%; 高于普通菜豆基因间序列SSR标记在豇豆(44.6%)和小豆(31.7%)中的通用性比率。

多态性分子标记在生物多样性、遗传多样性、物种鉴定等研究中具有广泛的应用价值。标记多态性比率, 多态性标记平均PIC值和平均 H_e值都可以用来度量群体的遗传多样性。标记多态性比率, 平均PIC值及平均 H_e值越高, 其群体遗传多样性就越丰富; 反之, 其遗传多样性就越低^{[ 33, 34]}。本研究结果显示普通菜豆基因组SSR标记在16份豇豆和16份小豆中的多态性比率分别为34.0%和24.8%, 多态性标记平均PIC值分别为0.305和0.359, 平均期望杂合度为0.322和0.389, 说明所选用的群体多样性偏低。可能是因为所选取的豇豆和小豆材料数量偏少, 且都是中国栽培种, 起源单一, 材料间的亲缘关系较近。此外, 分子标记多态性高低也与序列所在的位置有一定的关系, 基因内的序列因其保守性较高, 多态性会相对较低, 而基因间序列因其保守性较差, 多态性会相对较高。本文中在豇豆和小豆中基因间标记的多态性都比基因内标记的多态性高。

物种间的遗传关系^{[ 35]}。综合分析SSR标记的通用性和多态性, 可以看出豇豆略高于小豆, 普通菜豆与豇豆的亲缘关系较小豆近。而Sumanasinghe等^{[ 36]}研究表明, 菜豆属的普通菜豆与Ceratotropis亚属小豆的亲缘关系比普通菜豆与 Vigna亚属豇豆的亲缘关系近。本研究中SSR标记基于通用性结果分析的亲缘关系与此正好相反, 主要是因为本研究用于分析的分子标记仅是基因组标记的小部分, 并不能准确地反应物种间基因组信息。只有依据全基因组的序列开发数目更多、类型更加丰富的标记, 才能准确地分析物种的亲缘与进化关系。

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	附表豇豆和小豆中通用性SSR标记信息及在豇豆和小豆中多样性评价Supplemental table Information and diversity asscssments of transferability SSR markers in cowpea and adzuki bean

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	附表(续) 豇豆和小豆中通用性SSR标记信息及在豇豆和小豆中多样性评价Supplemental table(Continued) Information and diversity asscssments of transferability SSR markers in cowpea and adzuki bean

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	附表(续) 豇豆和小豆中通用性SSR标记信息及在豇豆和小豆中多样性评价Supplemental table(Continued) Information and diversity asscssments of transferability SSR markers in cowpea and adzuki bean

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	附表(续) 豇豆和小豆中通用性SSR标记信息及在豇豆和小豆中多样性评价Supplemental table(Continued) Information and diversity asscssments of transferability SSR markers in cowpea and adzuki bean

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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[8]	Han O K, Kaga A, Isemura T, Wang X W, Tomooka N, Vaughan D A. A genetic linkage map for adzuki bean [Vigna angularis (Willd. ) Ohwi & Ohashi]. Theor Appl Genet, 2005, 111: 1278-1287 [Cited within: 1] [JCR: 3.658]
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[15]	钟敏, 程须珍, 王丽侠, 王素华, 王小宝. 绿豆基因组SSR 引物在豇豆属作物中的通用性. 作物学报, 2012, 38: 223-230 Zhong M, Cheng X Z, Wang L X, Wang S H, Wang X B. Transferability of mungbean genomic-SSR markers in other Vigna species. Acta Agron Sin, 2012, 38: 223-230 (in Chinese with English abstract) [Cited within: 2] [CJCR: 1.667]
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[36]	Sumanasinghe V A, Tomooka N, Fukuoka S. Phylogenetic relationships of the subgenus Ceratotropis based on rand om ampliﬁed polymorphic DNA. J Nat Sci Coun Sri Lanka, 1997, 25: 73-82 [Cited within: 1]

1991

0.0

... 普通菜豆属于豆科(Leguminosae), 蝶形花亚科(Papilioni-deae), 菜豆族(Phaseoleae)菜豆属(Phaseolus)^[1] ...

2006

0.0

... 豇豆^[2]和小豆^[3]属豆科(Leguminosae), 蝶形花亚科(Papilionideae), 菜豆族(Phaseoleae), 豇豆属(Vigna L ...

1997

0.0

... 豇豆^[2]和小豆^[3]属豆科(Leguminosae), 蝶形花亚科(Papilionideae), 菜豆族(Phaseoleae), 豇豆属(Vigna L ...

2012

0.0

... 中国被认为是豇豆的起源中心或次级起源中心之一, 目前除西藏自治区外, 其他各地都有豇豆生产^[4] ...

1982

0.0

... 小豆原产中国, 在中国华北、东北、黄河及长江中下游地区广泛种植^[5] ...

2002

0.0

... 豇豆和小豆在我国农产品出口, 饮食改善以及作物种植结构优化等方面具有重要作用^[6] ...

2011

3.251

0.0

Andargie

, Pasquet

R S

, Gowda

B S

, Muluvi

G M

, Timko

M P

. Construction of a SSR-based genetic map and identification of QTL for domestication traits using recombinant inbred lines from a cross between wild and cultivated cowpea (V. unguiculata (L. ) Walp. ). Mol Breed, 2011, 28: 413-420

Cowpea (Vigna unguiculata (L.) Walp.) is a grain legume commonly grown and consumed in many parts of the tropics and subtropics. A genetic linkage map was constructed using simple sequence repeat (SSR) markers and a recombinant inbred (RI) population of159 individuals derived from a cross between the breeding line 524B, a California Blackeye, and 219-01, a perennial wild cowpea from Kenya. Out of 912 primer combinations predicted to amplify SSRs in cowpea, 639 reliably produced amplification products in PCR assays and 202 (31.6%) were polymorphic between the two parents. These polymorphic SSRs were used to construct a genetic map consisting of 11 linkage groups (LGs) spanning 677 cM, with an average distance between markers of 3 cM. Agronomic traits related to domestication (seed weight, pod shattering) were analyzed together with the genotypic data. Six quantitative trait loci (QTL) for seed size were revealed with the phenotypic variation ranging from 8.9 to 19.1%. Four QTL for pod shattering were identified with the phenotypic variation ranging from 6.4 to 17.2%. The QTL for seed size and pod shattering mainly cluster in two areas of LGs 1 and 10, facilitating the use of marker-assisted selection to eliminate undesirable wild phenotypes in breeding activities involving introgression of traits from wild germplasm. The generation of an SSR-based molecular map and additional trait-linked markers also contributes to the expanding tool kit available to cowpea breeders, especially in Africa.

1.Molecular Biology and Biotechnology Department, International Center of Insect Physiology and Ecology, Nairobi, Kenya 2.Department of Biology, University of Virginia, Charlottesville, VA 22901, USA 3.IRD, UR072, LEGS, BP1, 91198 Gif-sur-Yvette Cedex, France 4.Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya

... 但是, 与其他豆科模式作物如普通菜豆和苜蓿相比, 豇豆^[7]和小豆^[8]公开发表的分子标记数目极少 ...

2005

3.658

0.0

Han

O K

, Kaga

, Isemura

, Wang

X W

, Tomooka

, Vaughan

D A

. A genetic linkage map for adzuki bean [Vigna angularis (Willd. ) Ohwi & Ohashi]. Theor Appl Genet, 2005, 111: 1278-1287

To make progress in genome analysis of azuki bean (Vigna angularis) a genetic linkage map was constructed from a backcross population of (V. nepalensis x V. angularis) x V.angularis consisting of 187 individuals. A total of 486 markers—205 simple sequence repeats (SSRs), 187 amplified fragment length polymorphisms (AFLPs) and 94 restriction fragment length polymorphisms (RFLPs) —were mapped onto 11 linkage groups corresponding to the haploid chromosome number of azuki bean. This map spans a total length of 832.1 cM with an average marker distance of 1.85 cM and is the most saturated map for a Vigna species to date. In addition, RFLP markers from other legumes facilitated finding several orthologous linkage groups based on previously published RFLP linkage maps. Most SSR primers that have been developed from SSR-enriched libraries detected a single locus. The SSR loci identified are distributed throughout the azuki bean genome. This moderately dense linkage map equipped with many SSR markers will be useful for mapping a range of useful traits such as those related to domestication and stress resistance. The mapping population will be used to develop advanced backcross lines for high resolution QTL mapping of these traits.

1.National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Japan 2.Winter Cereal and Upland Crop Division, Honam Agricultural Research Institute, NICS, Rural Development Administration, #381 Songhak-dong, Iksan 570-080, Seoul, Korea 3.Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN 37996, USA

... 但是, 与其他豆科模式作物如普通菜豆和苜蓿相比, 豇豆^[7]和小豆^[8]公开发表的分子标记数目极少 ...

2014

3.251

0.0

... SSR标记因其在基因组中分布广泛且具有共显性遗传、可重复性、多态性丰富等特点而被认为是最好的分子标记之一, 广泛应用于种质资源的多样性分析、遗传连锁图谱构建、基因定位及标记辅助育种等研究^[9] ...

2013

2.196

0.0

Singha

R K

, Jenab

S N

, Khana

, Yadava

, Banarjeea

. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene, 2013, 524: 309-329

Indian Institute of Sugarcane Research (ICAR), Rai Bareli Road, Lucknow-226002, U.P., India. ikrps@yahoo.com

Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5'UTR and in the ORF (about 27%) and a low frequency was observed in the 3'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in sugarcane but also enriched the microsatellite marker resources in sugarcane.

PMID: 23587912

... SSR标记在近缘植物乃至远缘植物基因组间有一定的通用性^[10] ...

2011

1.44

0.0

... 张扬勇等^[11]根据拟南芥叶绿体全基因组序列开发89个叶绿体基因组SSR标记, 并分析了标记在甘蓝中的通用性 ...

2006

1.593

0.0

Wang

M L

, Chen

Z B

, Bakley

N A

, Newman

M L

, Kim

, Raymer

, Pederson

G A

. Characterization of seashore paspalum (Paspalumm vaginatum Swartz) germplasm by transferred SSRs from wheat, maize and sorghum. Genetic Resour Crop Evol, 2006, 53: 779-791

One hundred and thirty SSR markers from wheat, maize and sorghum were screened for the transferability to Paspalum. The transfer rate was 67.5, 49.0 and 66.8% respectively. This would be a very efficient approach for DNA marker development for species which are not well studied molecularly. The polymorphism level for transferred SSR markers was 51.5% within species (Paspalum vaginatum) and 87.1% among Paspalum species. The high level of polymorphism is directly related to the high degree of heterozygosity maintained by its way of reproduction, i.e. self-incompatibility. Forty transferred polymorphic SSR markers were selected and used for characterization and evaluation of seventy-three Paspalum accessions. In total, 209 polymorphic bands were detected from these 40 SSR markers, with an average of five polymorphic bands per marker. The Paspalum accessions clustered into three major groups. Two very similar dendrograms can be generated from either 109 or 209 polymorphic bands. This led us to determine that 18 of the transferred SSR markers were sufficient for genetically differentiating the investigated germplasm accessions. The number of SSR markers required for germplasm characterization and evaluation is discussed. This is the first report of the transfer of SSR markers from major field crops to newly emerged environmental turfgrasses.

1.USDA-ARS Plant Genetic Resources Conservation Unit 1109 Experiment Street Griffin GA 30223 USA 1109 Experiment Street Griffin GA 30223 USA 2.University of Georgia Department of Crop and Soil Sciences 1109 Experiment Street Griffin GA 30223 USA 1109 Experiment Street Griffin GA 30223 USA

... Wang等^[12]研究发现禾本科作物小麦、玉米和高粱中的SSR标记在海滨雀稗属作物中的通用性比率分别为67 ...

2010

2.277

0.0

... Hu等^[13]发现黄瓜EST-SSR标记在甜瓜、西瓜、南瓜和葫芦中的具有很高通用性, 通用性比率为92 ...

2009

0.0

1.667

王丽侠, 程须珍, 王素华, 刘长友, 梁辉. 小豆SSR引物在绿豆基因组中的通用性分析. 作物学报, 2009, 35: 816-820

Wang

L X

, Cheng

X Z

, Wang

S H

, Liu

C Y

, Liang

. Transferability of SSR from adzuki bean to mungbean. Acta Agron Sin, 2009, 35: 816-820 (in Chinese with English abstract)

SSR (Simple sequence repeat) has been a popular tool in genetic studies. However, only a few SSR markers are available in mungbean (Vigna radiata L.). Adzuki bean (Vigna angularis L.) is a close relative of mungbean. In the study reported in this paper, we tested the transferability of adzuki bean SSR markers into mungbean. A total of 187 sets of SSR primers were tested and about 75% of them generated repeatable and clear products in mungbean, indicating a high homology between these two genomes. Of the transferable SSRs, 28 sets of primers generated polymorphic products among 60 mungbean genotypes with a total of 81 alleles detected. The average PIC (polymorphic information content) value is 0.36. Based on the SSR fingerprints, the 60 accessions can be divided into different groups agreeing well with their geographical origins. The exotic accessions were well separated from the local genotypes, indicating the former could be important sources for broadening the mungbean gene pool. The present study identified useful SSR markers for mungbean research, which will undoubtedly accelerate the genetic study of this crop.

Institute of Crop Science,Chinese Academy of Agricultural Sciences,Beijing 100081,China

分析了187对小豆SSR引物在绿豆基因组中的可转移性, 以期为绿豆分子遗传育种研究提供分析工具。结果表明，约75%的小豆SSR引物可在绿豆中有效扩增，但不同小豆连锁群SSR引物的可转移率存在差异。多态性分析发现80对引物中有29对在60份绿豆种质中可以检测到多态性, 等位变异数从2~7不等，平均为2.9, PIC指数从0.02~0.69，平均为0.36。UPGMA聚类及主坐标分析表明, 尽管同一省份的种质不能紧密聚在一起，但大多在聚类图上成簇状分布，说明相同来源的绿豆种质具有相似的遗传背景；此外，国外及我国边远地区的绿豆种质在遗传背景上与内部省份间存在明显差异。这些多态性SSR不仅可以有效用于绿豆分子遗传学研究，还可以用于不同来源绿豆种质资源的辅助鉴别。

... 王丽侠等^[14]分析187个小豆SSR标记在绿豆中的通用性表明, 约75%的小豆SSR标记可在绿豆中有效扩增 ...

2012

0.0

1.667

钟敏, 程须珍, 王丽侠, 王素华, 王小宝. 绿豆基因组SSR 引物在豇豆属作物中的通用性. 作物学报, 2012, 38: 223-230

Zhong

, Cheng

X Z

, Wang

L X

, Wang

S H

, Wang

X B

. Transferability of mungbean genomic-SSR markers in other Vigna species. Acta Agron Sin, 2012, 38: 223-230 (in Chinese with English abstract)

Cowpea (Vigna unguiculata L. Walp.), mungbean (V. radiata L. Wilczek), rice bean [V. umbellate (Thunb.) Ohwi & Ohashi] and adzuki bean (V. angularis Willd. Ohwi and Ohashi) are major food legumes in China. At present, SSR markers for genetic analysis of these legumes are much limited. Transferability analysis of primers has the vital significance to reduce their development cost and improve their development efficiency. In this study, 1 205 SSRs primers were tested for their transferability and polymorphism by PCR amplification with the genomic DNA of four Vigna species, cowpea, adzuki bean, mungbean and rice bean. The results indicated that the transferability rate of mungbean genomic-SSR in cowpea, adzuki bean and rice bean was 50.0%, 73.3%, and 81.6%, and the ratio of polymorphism SSR primers in these crops was 4.1%, 1.7%, and 1.5%, whereas 32.0% in mungbean. A total of 469 mungbean genomic-SSR primers were detected to be highly transferable among different species of Vigna. The transferability of mungbean genomic-SSR was higher in adzuki bean and rice bean than in cowpea. These transferable markers are useful for further genetic and breeding studies in these species.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China?

分子标记的种间通用性可降低其开发成本，提高利用效率，也有助于促进遗传研究较薄弱物种的分子遗传学研究。本文选取绿豆、小豆、豇豆及饭豆材料各3份, 分析1 205对新开发的绿豆基因组SSR引物在这些材料中的扩增效果，结果显示绿豆基因组SSR引物在豇豆、小豆和饭豆中的通用性比率分别为50.0%、73.3%和81.6%；多态性比率分别为4.1%、1.7%和1.5%；在4个种间均通用的引物469对。这些通用性SSR引物将有助于这4种食用豆类在多样性评价、连锁图谱的构建、基因定位及比较基因组学等方面的研究。

... 钟敏等^[15]分析1205个新开发绿豆基因组SSR标记的通用性表明其在豇豆、小豆和饭豆中的通用性比率分别为50 ...

... 3% (小豆)^[15] ...

2008

0.0

... 3 引物开发依据普通菜豆基因组序列信息, 利用SSR Locator软件查找SSR位点并设计引物^[16] ...

2009

0.0

高东, 杜飞, 朱有勇. 低背景、高分辨率PAGE简易银染法. 遗传, 2009, 31: 668-672

Gao

, Du

, Zhu

Y Y

. Low-background and high-resolution contracted silver-stained method in polyacrylamide gels electrophoresis. Hereditas (Beijing), 2009, 31: 668-673 (in Chinese with English abstract)

The disadvantage of time-consuming and fussy steps of conventional silver-stained method for polyacrylamide gels is evident, and has become the choke point in its application. In this paper, a low-background and high-resolution con-tracted silver-stained method for polyacrylamide gels was established. Compared with the conventional banding method, this contracted method has fewer steps and needs fewer reagents, in particular, lower NaOH concentration. It is rapid and economic, especially for mass silver-staining.

The National Center for Agricultural Biodiversity, Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Key laboratory of Plant Pathology, Yunnan Agricultural University, Kunming 650201, China

聚丙烯酰胺凝胶电泳银染一直存在耗时长、步骤繁琐等缺陷, 是其批量应用的瓶颈。文章报道了一种低背景、高分辨率的PAGE简易银染方法, 该法在降低NaOH浓度和批量显带方面进行了有益的探索, 建立了节省时间、节约试材, 对批量显带尤为实用的简易银染法。

... SSR扩增产物经6%的聚丙烯酰胺非变性凝胶在60 W恒定功率下电泳 70 min, 用NaOH快速银染法染色后读取条带^[17] ...

0.0

... 5 标记多态性分析利用Popgen32^[18]软件分析标记多态性信息含量(PIC)、等位基因数(N_a)、观察杂合度(H_o)和期望杂合度(H_e) ...

2011

41.063

0.0

Davey

J W

, Hohenlohe

P A

, Etter

P D

, Boone

J Q

, Catchen

J M

, Blaxter

M L

. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet, 2011, 12: 499-510

Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK. john.davey@ed.ac.uk

The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target. These new methods -- which include reduced-representation sequencing using reduced-representation libraries (RRLs) or complexity reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA sequencing (RAD-seq) and low coverage genotyping -- are applicable to both model organisms with high-quality reference genome sequences and, excitingly, to non-model species with no existing genomic data.

PMID: 21681211

... 3 讨论分子标记开发的关键是如何高效获得基因组序列或表达的序列标签(EST)序列, 而新一代测序技术可以快速获得海量的序列数据, 极大程度提高了挖掘、验证和评估分子标记的效率^[19] ...

2011

3.658

0.0

Trebbi

, Maccaferri

, De

Heer P

, Sørensen

, Giuliani

, Salvi

, Sanguineti

, Massi

, Van

der-Vossen E

, Tuberosa

. High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf. ). Theor Appl Genet, 2011, 123: 555-569

Keygene NV, Applied Research, Agro Business Park 90, 6708, PW, Wageningen, The Netherlands. trebbida@msu.edu

We describe the application of complexity reduction of polymorphic sequences (CRoPS(®)) technology for the discovery of SNP markers in tetraploid durum wheat (Triticum durum Desf.). A next-generation sequencing experiment was carried out on reduced representation libraries obtained from four durum cultivars. SNP validation and minor allele frequency (MAF) estimate were carried out on a panel of 12 cultivars, and the feasibility of genotyping these SNPs in segregating populations was tested using the Illumina Golden Gate (GG) technology. A total of 2,659 SNPs were identified on 1,206 consensus sequences. Among the 768 SNPs that were chosen irrespective of their genomic repetitiveness level and assayed on the Illumina BeadExpress genotyping system, 275 (35.8%) SNPs matched the expected genotypes observed in the SNP discovery phase. MAF data indicated that the overall SNP informativeness was high: a total of 196 (71.3%) SNPs had MAF >0.2, of which 76 (27.6%) showed MAF >0.4. Of these SNPs, 157 were mapped in one of two mapping populations (Meridiano × Claudio and Colosseo × Lloyd) and integrated into a common genetic map. Despite the relatively low genotyping efficiency of the GG assay, the validated CRoPS-derived SNPs showed valuable features for genomics and breeding applications such as a uniform distribution across the wheat genome, a prevailing single-locus codominant nature and a high polymorphism. Here, we report a new set of 275 highly robust genome-wide Triticum SNPs that are readily available for breeding purposes.

PMID: 21611761

... 小麦^[20]、水稻^[21]、甘薯^[22]、黄瓜^[23]、 ...

2002

4.425

0.0

McCouch

S R

, Teytelman

, Xu

, Lobos

K B

, Clare

, Walton

, Fu

, Maghirang

, Li

, Xing

, Zhang

, Kono

, Yano

, Fjellstrom

, DeClerck

, Schneider

, Cartinhour

, Ware

, Stein

. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L. ). DNA Res, 2002, 9: 199-207

Plant Breeding Dept, Cornell University, Ithaca, NY 14853-1901, USA. SRM4@cornell.edu

A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker loci, have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7% (174) of the loci. The majority (92%) of primer pairs were developed in regions flanking perfect repeats > or = 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Additional information based on genetic mapping and "nearest marker" information provided the basis for locating a total of 1825 (81%) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), followed by poly(AT) (15%) and poly(CCG) (8%) motifs. AT-rich microsatellites had the longest average repeat tracts, while GC-rich motifs were the shortest. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.

PMID: 12597276

... 小麦^[20]、水稻^[21]、甘薯^[22]、黄瓜^[23]、 ...

2010

4.397

0.0

Wang

Z Y

, Fang

B P

, Chen

J Y

, Zhang

X J

, Luo

Z X

, Huang

L F

, Chen

X L

, Li

Y C

. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genom, 2010, 11: 726-739

Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 PR China.

The tuberous root of sweet potato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweet potato root for gene discovery and molecular marker development.

PMID: 21182800

... 小麦^[20]、水稻^[21]、甘薯^[22]、黄瓜^[23]、 ...

2010

2.277

0.0

... 小麦^[20]、水稻^[21]、甘薯^[22]、黄瓜^[23]、 ...

2011

4.397

0.0

Blanca

, Cañizares

, Roig

, Ziarsolo

, Nuez

, Picó

. Transcriptome characterization and high throughput SSRs and SNPs discovery in cucurbita pepo (Cucurbitaceae). BMC Genom, 2011, 12: 104-118

<li>1.Institute for the Conservation and Breeding of Agricultural Biodiversity, Universidad Politécnica de Valencia (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain</li>

... 西葫芦^[24]等作物依据基因组序列开发了大量分子标记 ...

2009

4.354

0.0

Tangphatsornruang

, Somta

, Uthaipaisanwong

, Chanprasert

, Sangsrakru

, Seehalak

, Sommanas

, Tragoonrung

, Srinives

. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L. ) Wilczek). BMC Plant Biol, 2009, 9: 137

National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd,, Klong 1, Klong Luang, Pathumthani 12120, Thailand. somvong.tra@biotec.or.th.

Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean.

PMID: 19930676

... 豆科作物在这方面的研究也取得一定的进展, Tangphatsornruang等^[25]利用Roche 454超高通量组测序技术获得470 024条绿豆基因组序列, 并检测到1493个SSR位点用于标记开发 ...

2011

2.277

0.0

Kaur

, Cogan

N O

, Pembleton

L W

, Shinozuka

, Savin

K W

, Materne

, Forster

J W

. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics, 2011, 12: 265

<li>1.Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, 1 Park Drive, Bundoora, Victoria, 3083, Australia</li><li>2.Department of Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, Victoria, 3401, Australia</li><li>3.La Trobe University, Bundoora, Victoria, 3086, Australia</li>

... Kaur等^[26]对小扁豆特异组织进行转录组测序, 获 ...

2011

4.425

0.0

Garg

, Patel

R K

, Tyagi

A K

, Jain

. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res, 2011, 18: 53-63

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.

Chickpea ranks third among the food legume crops production in the world. However, the genomic resources available for chickpea are still very limited. In the present study, the transcriptome of chickpea was sequenced with short reads on Illumina Genome Analyzer platform. We have assessed the effect of sequence quality, various assembly parameters and assembly programs on the final assembly output. We assembled ~107million high-quality trimmed reads using Velvet followed by Oases with optimal parameters into a non-redundant set of 53 409 transcripts (≥100 bp), representing about 28 Mb of unique transcriptome sequence. The average length of transcripts was 523 bp and N50 length of 900 bp with coverage of 25.7 rpkm (reads per kilobase per million). At the protein level, a total of 45 636 (85.5%) chickpea transcripts showed significant similarity with unigenes/predicted proteins from other legumes or sequenced plant genomes. Functional categorization revealed the conservation of genes involved in various biological processes in chickpea. In addition, we identified simple sequence repeat motifs in transcripts. The chickpea transcripts set generated here provides a resource for gene discovery and development of functional molecular markers. In addition, the strategy for de novo assembly of transcriptome data presented here will be helpful in other similar transcriptome studies.

PMID: 21217129

... Garg等^[27]和Dutta等^[28]分别利用组装的鹰嘴豆和木豆转录组序列开发了大量功能标记 ...

2011

4.354

0.0

Dutta

, Kumawat

, Singh

B P

, Gupta

D K

, Singh

, Dogra

, Gaikwad

, Sharma

T R

, Raje

R S

, Band hopadhya

T K

, Datta

, Singh

M N

, Bashasab

, Kulwal

, Wanjari

K B

, Varshney

R K

, Cook

D R

, Singh

N K

. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L. ) Millspaugh]. BMC Plant Biol, 2011, 11: 17

<li>1.National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110 012, New Delhi, India</li><li>2.Department of Molecular Biology and Biotechnology, University of Kalyani, 741235, Kalyani, WB, India</li><li>3.Division of Genetics, Indian Agricultural Research Institute, 110012, New Delhi, India</li><li>4.Indian Institute of Pulses Research, 208024, Kanpur, UP, India</li><li>5.Institute of Agricultural Sciences, Banaras Hindu University, 221005, Varanasi, UP, India</li><li>6.University of Agricultural Sciences, 580005, Dharwad, Karnataka, India</li><li>7.Panjabrao Deshmukh Krishi Vidyapeeth, 444 104, Krishinagar, Akola, Maharasthra, India</li><li>8.International Crops Research Institute for the Semi-Arid Tropics, 502324, Patancheru, AP, India</li><li>9.Department of Plant Pathology, University of California, 95616-8680, Davis, CA, USA</li>

... Garg等^[27]和Dutta等^[28]分别利用组装的鹰嘴豆和木豆转录组序列开发了大量功能标记 ...

2011

0.0

... 标记通用性研究可以为相近物种提供更多的遗传信息, 方便了物种内、种间遗传学与基因组学等方面的研究^[29] ...

2009

1.668

0.0

... Gupta等^[30]随机选取41个豆科模式生物蒺藜状苜蓿SSR标记, 分析显示, 其在豆科植物中的通用性(53%~71%)明显高于非豆科植物(33%~44%) ...

2011

0.0

1.667

文明富, 陈新, 王海燕, 卢诚, 王文泉. 木薯基因组SSR和EST-SSR在麻疯树和橡胶树中的通用性分析. 作物学报, 2011, 37: 74-78

Wen

M F

, Chen

, Wang

H Y

, Lu

, Wang

W Q

. Transferability analysis of cassava EST-SSR and genomic-SSR markers in jatropha and rubber tree. Acta Agron Sin, 2011, 37: 74-78 (in Chinese with English abstract)

Euphorbiaceae family includes abundant economic species, such as rubber tree, cassava, castor bean and Jatropha. Cassava (Manihot esculenta Crantz) ranks in the sixth food crop in the world. In China, cassava is also an important tropical economic crop. The genomic-SSRs derived from cassava genome, and EST-SSRs derived from expressed sequence tags (ESTs). In this study, the transferability of 419 pairs of EST-SSR primer and 182 pairs of genomic-SSR primer from cassava was tested in five Jatropha lines and two rubber tree lines. The result showed that the transferability rate of cassava EST-SSR in Jatropha and rubber tree was 55.85% and 38.90%, and the transferability rate of cassava genomic-SSR in Jatropha and rubber tree was 37.36% and 26.37%, respectively. The transferability EST-SSR was higher for cssava than for genomic-SSR. Meanwhile, the transferability of cassava EST-SSR and genomic-SSR was higher in Jatropha than in rubber tree. These results suggested that the cassava SSR can be used for comparative mapping, gene tagging and QTL mapping among cassava, Jatropha and rubber tree.

Institute of Tropical Bioscience & Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China

利用木薯的419对EST-SSR引物和182对基因组SSR引物在5个麻疯树品系和2个橡胶树品系中进行通用性分析。结果显示，木薯EST-SSR在麻疯树和橡胶树中的通用性比例分别为55.85%和38.90%，而木薯基因组SSR在麻疯树和橡胶树中的通用性比例分别为37.36%和26.37%。由此推测，EST-SSR的通用性高于基因组SSR。此外，木薯EST-SSR和基因组SSR的通用性在麻疯树中高于在橡胶树中。本研究发掘的通用性SSR引物可以用于木薯、麻疯树和橡胶树间的比较作图、基因发掘和QTL定位研究。

... 文明富等^[31]研究木薯419对EST-SSR引物和182对基因组SSR引物在麻疯树和橡胶树通用性发现, 木薯EST-SSR在麻疯树和橡胶树中的通用性比率分别为55 ...

2005

2.922

0.0

... Varshney等^[32]分析大麦的EST-SSR和G-SSR标记在近缘物种小麦中的通用性, 发现EST-SSR标记的通用性比率高于G-SSR标记 ...

1998

3.658

0.0

... 反之, 其遗传多样性就越低^[33,34] ...

2002

0.0

... 反之, 其遗传多样性就越低^[33,34] ...

2005

0.0

... 物种间的遗传关系^[35] ...

1997

0.0

... 而Sumanasinghe等^[36]研究表明, 菜豆属的普通菜豆与Ceratotropis亚属小豆的亲缘关系比普通菜豆与Vigna亚属豇豆的亲缘关系近 ...