Author
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ENDELMAN, JEFF - University Of Wisconsin |
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Jansky, Shelley |
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Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only Publication Acceptance Date: 11/6/2014 Publication Date: 1/10/2015 Citation: Endelman, J., Jansky, S.H. 2015. Genotyping-by-sequencing of a diploid potato F2 population [abstract]. Plant and Animal Genome Conference. Paper No. P0840. Interpretive Summary: Technical Abstract: Genotyping-by-sequencing, or GBS, is an attractive technology for genome-wide markers because of its low per-sample cost and lack of ascertainment bias. To investigate its feasibility for potato, we used GBS at 96-plex to genotype a diploid F2 population created from the inbred lines DM (S. tuberosum Group Phureja) and M6 (S. chacoense). Of the 908K unique sequence tags identified, 60% aligned to unique positions in the DM reference genome. After filtering for read depth and segregation distortion, there were 8654 putative SNPs. From this set, linkage analysis identified 104 SNPs for which the linkage group was different than the chromosome in the reference genome. These discrepancies may be the result of alignment error, or they may represent errors in the anchoring of some superscaffolds in the reference genome. The final curated marker set was used to map yellow flesh color to the region 40–50 Mb on chromosome 3, which contains the previously identified gene CHY2 encoding a beta-carotene hydroxylase. We also mapped an unusual trait expressed in DM: the formation of secondary tubers instead of sprouts at the tuber eyes. A recessive locus for this trait was clearly identified at 48–50 Mb on chromosome 5. Our results demonstrate that GBS is a viable alternative to SNP arrays for diploid potato, but further research is needed to determine a suitable multiplexing level for autotetraploids. |
