长江流域野生拟南芥种群QTL作图平台的建立

doi:10.11983/CBB16120

植物学报 ›› 2016, Vol. 51 ›› Issue (5): 659-666.DOI: 10.11983/CBB16120

长江流域野生拟南芥种群QTL作图平台的建立

康菊清^1,^2,^*(), 孙田舒², 张慧婷², 施逸豪²

¹陕西师范大学生命科学学院, 西安 710119
²北京大学生命科学学院, 北京 100871

收稿日期:2016-05-30 接受日期:2016-07-05 出版日期:2016-09-01 发布日期:2016-09-27
通讯作者: 康菊清
作者简介:
# 共同第一作者
基金资助:
国家自然科学基金青年项目(No.31400203)和陕西省自然科学基础研究计划青年人才项目(No.2016JQ3030)

Quantitative Trait Loci Mapping Platform of Natural Populations of Arabidopsis thaliana along the Yangtze River in China

Juqing Kang^1,2*, Tianshu Sun², Huiting Zhang², Yihao Shi²

¹College of Life Science, Shaanxi Normal University, Xi’an 710119, China
²College of Life Sciences, Peking University, Beijing 100871, China

Received:2016-05-30 Accepted:2016-07-05 Online:2016-09-01 Published:2016-09-27
Contact: Kang Juqing
About author:
# Co-first authors

摘要/Abstract

摘要： 对模式植物的研究不仅能揭示众多具有普遍规律的生物现象, 而且能为其它植物物种, 特别是与人类生活紧密相关的经济植物提供具有借鉴与参考意义的研究方法。QTL遗传作图是寻找那些影响不同地域植物自然变异等位基因的传统且有效的工作方法。对不同分化时长和不同遗传背景的植物种群, 有针对性地开发特异的分子标记, 一直是QTL遗传作图工作的重要内容。该研究利用二代测序技术得到的全基因组重测序结果, 根据其中鉴定到的结构变异(SV)多态性设计引物, 开发了针对分化时间短、多态性位点少的中国长江流域野生拟南芥(Arabidopsis thaliana)种群的QTL作图分子标记平台, 得到了有效适用的结果, 该方法不仅在模式植物拟南芥中适用, 而且也适用于其它植物。

Abstract: Studies on model plants have not only explored the mechanism of many life phenomenology but also provide research methods for other plants, especially economic plants. Quantitative trait loci (QTL) mapping is an effective method for identifying the alleles contributing to natural variation among populations that might be involved in adaptation in different environments. Exploring enough effective markers for specific mapping populations overcoming the differences of diverging time and genetic background was always the important and challenging part in these works. Here we explored efficient mapping markers by using SVs based on resequencing data of populations of Arabidopsis thaliana along the Yangtze River, a plant group that recently diverged and lacks sufficient genetic diversities. This research approach combining next-generation sequencing and traditional QTL mapping to identify the genetic basis of natural variation is effective for Arabidopsis and for other plants.

康菊清, 孙田舒, 张慧婷, 施逸豪. 长江流域野生拟南芥种群QTL作图平台的建立. 植物学报, 2016, 51(5): 659-666.

Juqing Kang, Tianshu Sun, Huiting Zhang, Yihao Shi. Quantitative Trait Loci Mapping Platform of Natural Populations of Arabidopsis thaliana along the Yangtze River in China. Chinese Bulletin of Botany, 2016, 51(5): 659-666.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB16120

https://www.chinbullbotany.com/CN/Y2016/V51/I5/659

图/表 7

表1 4个长江流域野生拟南芥种群的基本信息

Table 1 Location information of the 4 populations of Arabidopsis along the Yangtze River

Populations	Location	Latitude (N)	Longitude (E)	Altitude (m)
AHqsx	Qianshanxian, AnHui	30º44'46''	117º37'26''	150
CQtlx	Tongliangxian, ChongQing	29º49'24''	106º03'23''	263
JXjjs	Jiujiangshi, JiangXi	29º35'41''	115º54'44''	80
SXcgx	Chengguxian, ShaanXi	32º55'56''	107º12'39''	607

图1 长江流域4个野生拟南芥种群个体重测序数据中SVs分布的维恩图种群个体框内的数字为相应的个体在重测序结果中检测到的SVs数目

Figure 1 Venn diagram of the SVs in the resequencing data among 4 populations of Arabidopsis along the Yangtze River The number in the different boxes represent the total number of unique or shared SVs in each population or between/ among relevant populations respectively.

图2 基于SVs多态性设计的243个分子标记在拟南芥基因组上的定位每条染色体上的白色标识为每一个分子标记所在的基因座位

Figure 2 243 markers designed in Arabidopsis thaliana ge- nome based on SVs The white bar on chromosomes is the loci where the marker located

图3 琼脂糖凝胶电泳检测CQtlx、SXcgx和Col生态型中PCR扩增产物片段的长度 Ctl: 种群CQtlx; Scg: 种群SXcgx

Figure 3 The size difference of PCR products among population CQtlx, SXcgx and Col Ctl: Population CQtlx; Scg: Population SXcgx

图4 64个CQtlx-SXcgx分子标记在基因组上的定位每条染色体上的白色标识为每一个分子标记所在的基因座位

Figure 4 64 markers for CQtlx-SXcgx mapping population of Arabidopsis The white bar on chromosomes is the loci where the marker located

图5 拟南芥CQtlx-SXcgx QTL遗传作图平台的应用举例 CQtlx: F2作图群体(CQtlx × SXcgx)中母方杂交亲本CQtlx5; SXcgx: F2作图群体(CQtlx × SXcgx)中父方杂交亲本SXcgx42; 1-46: F2作图群体的不同个体

Figure 5 Application example of CQtlx-SXcgx QTL mapping CQtlx: Female parents for F2 mapping population (CQtlx × SXcgx); SXcgx: Male parents for F2 mapping population (CQtlx × SXcgx); 1-46: The different individuals from the F2 mapping population

表2 拟南芥重测序检测SVs的PCR扩增和琼脂糖电泳后的验证结果

Table 2 Confirmation and statistic of SVs in resequencing data of Arabidopsis

SVs’ number called in resequencing data		Total number	In CQtlx5	In SXcgx42	Shared among populations	Unique in one population
SVs’ number called in resequencing data		246*	122	209	85	161
Verified results by PCR	CQtlx vs Col	SVs’ number verified	Predicted in resequencing data	Not predicted in resequencing data	False positive	False negative
	CQtlx vs Col	116*	85	31	30.33%	26.72%
	SXcgx vs Col	SVs’ number verified	Predicted in resequencing data	Not predicted in resequencing data	False positive	False negative
	SXcgx vs Col	134*	128	6	35.89%	4.47%
	CQtlx vs SXcgx	SVs’ number verified	Predicted in resequencing data	Not predicted in resequencing data	False positive	False negative
	CQtlx vs SXcgx	76*	70	6	56.52%	7.89%

参考文献 21

1	种康, 王台, 钱前, 王小菁, 左建儒, 顾红雅, 姜里文, 陈之端, 白永飞, 杨淑华, 孔宏智, 陈凡, 萧浪涛 (2015). 2014年中国植物科学若干领域重要研究进展. 植物学报 50, 412-459.
2	康菊清 (2010). 中国野生拟南芥种群冷胁迫响应的分化及其分子机制. 博士论文. 北京: 北京大学. pp. 7.
3	邢光南, 赵团结, 盖钧镒 (2008). 关于Mapmaker/Exp遗传作图中标记分群和排序操作技术的讨论. 作物学报 34, 217-223.
4	张艺能, 周玉萍, 陈琼华, 黄小玲, 田长恩 (2014). 拟南芥开花时间调控的分子基础. 植物学报 49, 469-482.
5	Alonso-Blanco C, Aarts MG, Bentsink L, Keurentjes JJ, Reymond M, Vreugdenhil D, Koornneef M (2009). What has natural variation taught us about plant development, physiology, and adaptation?Plant Cell 21, 1877-1896.
6	Alonso-Blanco C, Bentsink L, Hanhart CJ, Blankestijn- de Vries H, Koornneef M (2003). Analysis of natural allelic variation at seed dormancy loci of Arabidopsis tha- liana.Genetics 164, 711-729.
7	Alonso-Blanco C, El-Assal SE, Coupland G, Koornneef M (1998). Analysis of natural allelic variation at flowering time loci in the Landsberg erecta and Cape Verde Islands ecotypes of Arabidopsis thaliana.Genetics 149, 749-764.
8	Alonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, Salinas J, Martinez-Zapate JM (2005). Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis.Plant Physiol 139, 1304-1312.
9	Alonso-Blanco C, Koornneef M (2000). Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics.Trends Plant Sci 5, 22-29.
10	Alonso-Blanco C, Koornneef M, van Ooijen JW (2006). QTL analysis.Methods Mol Biol 323, 79-99.
11	Cheo TY, Lu L, Yang G (2001). Brassicaceae. In: Wu ZY, Raven PH, eds. Flora of China. Beijing, China and St. Louis, USA: Science Press and Missouri Botanical Garden Press. pp. 120-121.
12	Collard B, Jahufer M, Brouwer J, Pang E (2005). An introduction to markers, quantitative trait loci (QTL) map- ping and marker-assisted selection for crop improvement: the basic concepts.Euphytica 142, 169-196.
13	He F, Kang DM, Ren YF, Qu LJ, Zhen Y, Gu HY (2007). Genetic diversity of the natural populations of Arabidopsis thaliana in China.Heredity 99, 423-431.
14	He F, Kang J, Zhou X, Su Z, Qu L, Gu H (2008). Variation at the transcriptional level among Chinese natural popu- lations of Arabidopsis thaliana in response to cold stress.Chin Sci Bull 53, 2989-2999.
15	Hou X, Li L, Peng Z, Wei B, Tang S, Ding M, Liu J, Zhang F, Zhao Y, Gu H, Qu LJ (2010). A platform of high- density INDEL/CAPS markers for map-based cloning in Arabidopsis.Plant J 63, 880-888.
16	Kang JQ, Zhang HT, Sun TS, Shi YH, Wang JQ, Zhang BC, Wang ZH, Zhou YH, Gu HY (2013). Natural variation of C-repeat-binding factor (CBFs) genes is a major cause of divergence in freezing tolerance among a group of Ara- bidopsis thaliana populations along the Yangtze River in China.New Phytol 199, 1069-1080.
17	Koornneef M, Alonso-Blanco C, Vreugdenhil D (2004). Naturally occurring genetic variation in Arabidopsis tha- liana.Annu Rev Plant Biol 55, 141-172.
18	Mitchell-Olds T, Willis JH, Goldstein DB (2007). Which evolutionary processes influence natural genetic variation for phenotypic traits?Nat Rev Genet 8, 845-856.
19	Weigel D (2012). Natural variation in Arabidopsis: from molecular genetics to ecological genomics.Plant Physiol 158, 2-22.
20	Weigel D, Nordborg M (2005). Natural variation in Ara- bidopsis. How do we find the causal genes? Plant Physiol 138, 567-568.
21	Yin P, Kang J, He F, Qu LJ, Gu H (2010). The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences.BMC Plant Biol 10, 22.

长江流域野生拟南芥种群QTL作图平台的建立

Quantitative Trait Loci Mapping Platform of Natural Populations of Arabidopsis thaliana along the Yangtze River in China

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