Protocol detail

Integrating Genetic Linkage Maps for Perennial Ryegrass Genome Assembly

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Marker sequences from the Illumina GoldenGate assay (as presented in the S3 File) and from the previously developed transcriptome map [31 (link)] were aligned to the perennial ryegrass genome [25 (link)] using BLAT [38 (link)]. Only sequences that aligned to a single genomic location were retained. These were then used as markers to integrate the information from both genetic linkage maps for ordering scaffolds from the genome assembly. This was done using ALLMAPS [39 (link)] and equal weighting was applied to both maps. The chain file with the anchored scaffolds is presented in S4 File.

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Paina C., Byrne S.L., Studer B., Rognli O.A, & Asp T. (2016). Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass. PLoS ONE, 11(3), e0152004.

Publication 2016

GoldenGate assay

Assay Genetic linkage Genome Maps Ryegrass Transcriptome

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Variable analysis

independent variables

Marker sequences from the Illumina GoldenGate assay
Marker sequences from the previously developed transcriptome map

dependent variables

Ordering of scaffolds from the genome assembly

control variables

Only sequences that aligned to a single genomic location were retained
Equal weighting was applied to both maps

controls

No positive or negative controls were explicitly mentioned.

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