High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra

BMC Genomics

Research Article

Arpita Konar¹  Jeanne Romero-Severson¹  Rebecca Bullis¹  Lauren Fiedler¹  Melissa T. Stephens¹  Olivia Choudhury²  Scott Emrich²  John E. Carlson³  Margaret E. Staton⁴  Scott Schlarbaum⁵  Jacqueline M. Kruser⁶  Oliver Gailing⁷  Mark V. Coggeshall⁸ 

[1] Department of Biological Sciences, University of Notre Dame, 46556, Notre Dame, IN, USA;Department of Computer Science and Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA;Department of Ecosystem Science and Management, Penn State, University Park, 16802, State College, PA, USA;Department of Entomology and Plant Pathology, University of Tennessee, 37996, Knoxville, TN, USA;Department of Forestry, Wildlife and Fisheries, University of Tennessee, 37996, Knoxville, TN, USA;Internal Medicine, Northwestern Memorial Hospital, 60611, Chicago, IL, USA;School of Forest Resources and Environmental Science, Michigan Technological University, 49931, Houghton, MI, USA;School of Natural Resources, University of Missouri-Columbia, 65211, Columbia, MO, USA;Hardwood Tree Improvement and Regeneration Center, USDA Forest Service Northern Research Station, 47907, West Lafayette, IN, USA;

关键词: Quercus rubra;    Sequencing depth;    ddRADseq;    Dense linkage mapping;   

DOI  :  10.1186/s12864-017-3765-8

 received in 2016-07-19, accepted in 2017-05-04,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundRestriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The statistical inference of linear order must be as accurate as possible for the correct ordering of sequence scaffolds and contigs to chromosomal locations. Accurate maps also facilitate the discovery of chromosome segments containing allelic variants conferring resistance to the biotic and abiotic stresses that threaten forest trees worldwide. We used ddRADseq for genetic mapping in the tree Quercus rubra, with an approach optimized to produce a high-quality map. Our study design also enabled us to model the results we would have obtained with less depth of coverage.ResultsOur sequencing design produced a high sequencing depth in the parents (248×) and a moderate sequencing depth (15×) in the progeny. The digital normalization method of generating a de novo reference and the SAMtools SNP variant caller yielded the most SNP calls (78,725). The major drivers of map inflation were multiple SNPs located within the same sequence (77% of SNPs called). The highest quality map was generated with a low level of missing data (5%) and a genome-wide threshold of 0.025 for deviation from Mendelian expectation. The final map included 849 SNP markers (1.8% of the 78,725 SNPs called). Downsampling the individual FASTQ files to model lower depth of coverage revealed that sequencing the progeny using 96 samples per lane would have yielded too few SNP markers to generate a map, even if we had sequenced the parents at depth 248×.ConclusionsThe ddRADseq technology produced enough high-quality SNP markers to make a moderately dense, high-quality map. The success of this project was due to high depth of coverage of the parents, moderate depth of coverage of the progeny, a good framework map, an optimized bioinformatics pipeline, and rigorous premapping filters. The ddRADseq approach is useful for the construction of high-quality genetic maps in organisms lacking a reference genome if the parents and progeny are sequenced at sufficient depth. Technical improvements in reduced representation sequencing (RRS) approaches are needed to reduce the amount of missing data.

【 授权许可】

CC BY   
© The Author(s). 2017