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

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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
  • About author:

    # Co-first authors


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
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%
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