Chris Grassa
c.j.grassa@gmail.com

2014-11-29



The Fasta file (TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.fasta) includes HA412 v0.2 reference sequence matching the manuscript reference (TranscriptomeRef_mar30.fa) transcriptome. Each header is made up of comma-separated values describing the sequence placement on the genetic map. The fields are ordered:

1) Scaffold ID
2) Scaffold nATCG
3) Scaffold Length
4) Linkage Group
5) centiMorgan estimate
6) segregation pattern ID - anchored low
7) segregation pattern ID - anchored high
8) segregation pattern ID - lower bounds
9) segregation pattern ID - upper bounds

The reference genome of sunflower line HA412 was sequenced using 454 technology and assembled with CABOG. 

Our core mapping population (1) are ninth generation RILs of single seed decent from an F1 produced by the cross of lines RHA280 x RHA801. The genomes of one individual from each parental line plus ninety three RILs were sequenced using Illumina technology and genotyped against the reference (2).

Complete segregation patterns were ordered using MSTmap. CentiMorgan positions are reported as raw recombination fractions between adjacent markers. Incomplete segregation patterns of reference scaffolds for which only a subset of RILs were genotyped were compared to the framework map in forward and reverse directions. The best match in each direction was recorded as the upper and lower bounds of placement on the framework map, following the method described by Bowers et. al (3).

1. Tang, S., J. K. Yu, M. B. Slabaugh, D. K. Shintani, and S. J. Knapp, 2002 Simple sequence repeat map of the sunflower genome. Theor. Appl. Genet. 105: 1124-1136.

2. Renaut, S., et al. "Genomic islands of divergence are not affected by geography of speciation in sunflowers." Nature communications 4 (2013): 1827.

3. Bowers, John E., et al. "Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses." G3: Genes| Genomes| Genetics2.7 (2012): 721-729.