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Comparative Study
. 2016 Jul 8:6:29345.
doi: 10.1038/srep29345.

Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

Xinxin Zhao  1 , Linkai Huang  1 , Xinquan Zhang  1 , Jianping Wang  2 , Defei Yan  1 , Ji Li  1 , Lu Tang  1 , Xiaolong Li  3 , Tongwei Shi  3
Affiliations
Comparative Study

Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

Xinxin Zhao et al. Sci Rep. .

Abstract

Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits-heading date (HD) and flowering time (FT)-were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20-27.00% of the total phenotypic variation, with the LOD ranging from 3.85-12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya'an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass.

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Figures

Figure 1
Figure 1. Distribution of SLAF and SSR markers on seven linkage groups.
The linkage group number is shown on the x-axis, and genetic distances (cM) are shown on the y-axis.
Figure 2
Figure 2. Frequency distributions of orchardgrass heading times and flowering times.
The x-axis indicates the days to heading and flowering. The left y-axis indicates the number of individuals, and the right y-axis reflects the frequency distribution.
Figure 3
Figure 3. QTL analysis of heading date and flowering time in linkage group 3 (LG3).
Logarithm of odds (LOD; blue) and percentage of phenotypic variance explained (Expl%; red) curves for heading time and flowering time of orchardgrass markers (x-axis) in LG3. The gray line indicates the threshold LOD score of 2.5.
See this image and copyright information in PMC

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