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High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species

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White cypress pine (Callitris glaucophylla) is a drought-tolerant evergreen conifer, which is a member of the Australian C. columellaris species complex. The complex is comprised of five closely related morphospecies that occur in a wide range of bioclimatic regions in Australia. Ecological genomics of the complex provides an opportunity to identify markers associated with environmental adaptation and is expected to broaden our understanding of its speciation process. We adopted a single-tree linkage mapping approach combined with high-throughput restriction site associated DNA (RAD) sequencing and expressed sequence tag-simple sequence repeat (EST-SSR) genotyping to set up a baseline genetic map for C. glaucophylla. The generated linkage map consisted of 4284 markers positioned on 11 linkage groups, corresponding to the haploid chromosome number of Callitris (2n = 22). The spatial distribution of markers was uneven compared to random expectation with significant clustering in central positions of some linkage groups, which may be associated with recombination cold spots of pericentromere regions. Allelic segregation was shown to be distorted in particular regions of four linkage groups, where selection may have operated on viability genes, leaving allelic distortion in surrounding linked markers. We then tested RAD single nucleotide polymorphisms (RAD-SNP) marker recovery and transferability of the linkage map to population genomic data collected for a related species, Callitris gracilis. Of the linkage map markers, 1257 markers (ca. 30 %) were recovered in independent RAD sequencing of population samples of C. glaucophylla. Genetic diversity and differentiation evaluated using mapped markers reflected ascertainment bias slightly; a decrease in Hs (absolute difference of −0.018) for a related species (C. gracilis) and an increase in F ST between C. glaucophylla and C. gracilis (+0.018) were detected. Although care should be taken given such biases in cross-species transfer, this study demonstrated that the RAD-SNP-based linkage map is essentially useful when combined with population genomic analysis of this conifer lineage.

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We are grateful to NSW State Forests, NSW Department of Environment and Climate Change, Queensland Department of Environment and Resource Management, SA Department of Environment and Heritage, Victorian Department of Sustainability and Environment, the Australian Wildlife Conservancy, and many private landholders for help with site selection and permission to sample on their land. We thank Lynda D. Prior for collecting population samples, N. Nakahama and Y. Unno for their assists in genotyping EST-SSRs and a preliminary analysis, M. Yamasaki for his insightful discussions on statistical analysis, and Y. Moriguchi for kindly providing unpublished data. RAD-sequencing experiment was conducted using Joint Usage/Research Program of Center for Ecological Research, Kyoto University. Funding was provided by Japan Society for the Promotion of Science Grant-in-Aid for JSPS Fellows (13 J06059), Grant-in-Aid for Scientific Research (JSPS KAKENHI 24248028 and 26850098), and the Environment Research and Technology Development Fund of the Ministry of the Environment (4-1403).

Data archiving statement

Raw RAD sequence data is deposited at DDBJ Sequence Read Archive (DRA) with accession numbers of DRA003554 (submission), PRJDB3893 (BioProject), SAMD00029742 (BioSample), DRX031648 (Experiment), and DRR035015 (Run). Details of each sequence read file can be found in supplementary material 4.

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Correspondence to Shota Sakaguchi.

Additional information

Communicated by W. Ratnam

This article is part of the Topical Collection on Germplasm Diversity

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1

Oligonucleotide sequences used as adaptor and index primers in RAD-sequencing library construction. (DOC 31 kb)

Supplementary material 2

Description of RAD reference assembly of Callitris columellaris species complex, which includes information of the individual samples used for Miseq (Illumina, San Diego, USA) sequencing and analysis protocol for short read assembly. (DOC 38 kb)

Supplementary material 3

Information of genetic markers mapped on the linkage groups. (CSV 889 kb)

Supplementary material 4

Information of RAD-sequencing read files. (CSV 9 kb)

Supplementary figure 1

(a) Distribution of Callitris columellaris species complex. Ranges for C. glaucophylla (GD lineage in Sakaguchi et al. (2013)) and C. gracilis are colored by ochre and pink, respectively. The locality where the seed samples for linkage map construction were collected is indicated by a black square on the smaller map. Superimposed are pie charts illustrating the two genetic clusters, corresponding to the two species, which were detected by STRUCTURE analysis. (b) A split network for 31 individuals of C. glaucophylla and C. gracilis analyzed in this study. Genetic membership estimated from STRUCTURE analysis is placed on the tips. A genetically intermediate individual is indicated by a green triangle. (GIF 134 kb)

High-resolution image (EPS 4065 kb)

Supplementary figure 2

Graphical results of GAM analysis of genetic marker segregation. Partial effects of genomic position are shown for each linkage group, expressed as fitted loess functions with 95 % boot-strapped confidence intervals (gray in color). Ticks in the x-axis represent the location of observations along the predictor. (GIF 127 kb)

High-resolution image (EPS 1231 kb)

Supplementary figure 3

Relationship between marker positions estimated from genotype data sets with and without imputation and error correction procedures. (GIF 97 kb)

High-resolution image (EPS 763 kb)

Supplementary figure 4

Distribution of genetic marker density calculated based on different bin widths (1, 5, 10 cM). Expected probability curves are estimated using a Poisson distribution (blue) and a negative binomial distribution (red) (GIF 78 kb)

High-resolution image (EPS 722 kb)

Supplementary table 1

Results of GAM analysis of genetic marker segregation for each linkage group, as a function of missing rate in genotype data and map position. (DOCX 27 kb)

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Sakaguchi, S., Sugino, T., Tsumura, Y. et al. High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species. Tree Genetics & Genomes 11, 121 (2015).

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