Chin Bull Bot ›› 2016, Vol. 51 ›› Issue (5): 659-666.doi: 10.11983/CBB16120

Previous Articles     Next Articles

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

Juqing Kang1,2*, Tianshu Sun2, Huiting Zhang2, Yihao Shi2   

  1. 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:2016-09-27 Published:2016-09-01
  • Contact: Kang Juqing E-mail:kangjq@snnu.edu.cn
  • About author:

    # Co-first authors

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.

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

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."

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"

Figure 3

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

Figure 4

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

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"

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
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
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
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
76* 70 6 56.52% 7.89%
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.
No related articles found!
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
[1] ZHANG Shu-Qiu LIU Xin LOU Cheng-Hou. Regulation of Carbon Metabolism in Guard Cellsin the Stomatal Movement[J]. Chin Bull Bot, 2000, 17(04): 345 -351 .
[2] Qian Wu, Shuai Shao, Shanshan Li, Huijin Zhang, Liangsheng Wang. Composition of Flavonoids in Lotus Pollen[J]. Chin Bull Bot, 2015, 50(6): 721 -732 .
[3] . [J]. Chin Bull Bot, 2000, 17(06): 572 .
[4] GAO Shu-Min LU Guo-Yi. Adavances in Research on Somatic Embryogenesisof Garlic(Allium sativum]L.)[J]. Chin Bull Bot, 2000, 17(04): 338 -344 .
[5] Zhu Zhi-qing and Sun Jing-san. Plant Regeneration from Inflorescence Callus of Haynaldia villosa and Hordeum brevisubulatum[J]. Chin Bull Bot, 1984, 2(23): 69 -70 .
[6] Bai Song;Lu Fang-chi;Bai Bao-zhang;Li Xiu-kun;Liu Zhi-qing and Chen Wen-rong. Effects of Copper on Tuber Yield and Physiological and Biochemical Characteristcs of potato[J]. Chin Bull Bot, 1996, 13(01): 58 -59 .
[7] TU Jie SHEN Wen-BiaoYE Mao-Bing XU Lang-Lai. The Effects of Exogenous Nitric Oxide Donor on The Metabolismof Hydrogen Peroxide in Detached Wheat Leaves[J]. Chin Bull Bot, 2002, 19(03): 336 -341 .
[8] Wu Chong-ming and Tu You-you. Study on Chemical Constituents of Artemisia gmelinii[J]. Chin Bull Bot, 1985, 3(03): 34 -37 .
[9] Yang Chun-yu and Wang Hui-qin. Retrospect and prospect for the plant Cytotaxonomy in China[J]. Chin Bull Bot, 1985, 3(06): 1 -6 .
[10] WANG Yu-Hua YANG Qing CHEN Min. Sugar Sensing and Signaling in Plants[J]. Chin Bull Bot, 2004, 21(03): 273 -279 .