Arabidopsis Bay-0 × Sha SFP Haplotype Map with 211 RILs



Supplemental Data to the paper:

Marilyn A.L. West, Kyunga Kim, Daniel J. Kliebenstein, Hans van Leeuwen, Richard Michelmore, R.W. Doerge, Dina A. St.Clair 2007. Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript Level Variation in Arabidopsis. Genetics, 175: 1441-1450, PubMed link PubMed - National Library of Medicine.



Background

This high-resolution haplotype map contains 540 SFP markers plus the 38 microsatellite core markers from the Bay-0 × Shahdara RIL population (Loudet et al. 2002). The methods for the SFP detection, genotyping and map construction are as described previously (West et al. 2006, PubMed link PubMed - National Library of Medicine; http://elp.ucdavis.edu/data/analysis/sfp_map/sfp_map.html). The SFPscan algorithm was used for SFP detection and genotyping.





Calculation of genetic distances


Table 1. Characteristics of an integrated genetic map derived from the Bay-0 × Shahdara RIL population (211 RILs).
Markers1 Size (cM) Marker density (cM) Maximum gap (cM)
Linkage Group 1 150 (141+9) 102.5 0.73 3.88
Linkage Group 2 102 (95+7) 70.5 0.74 3.48
Linkage Group 3 118 (112+6) 77.6 0.69 3.04
Linkage Group 4 101 (93+8) 77.1 0.83 4.23
Linkage Group 5 145 (137+8) 94.5 0.69 8.70
All linkage groups 578 (540+38) 422.2 0.73 8.70
1 Between parentheses the number of our SFP markers, and microsatellite markers (Loudet et al. 2002), respectively.



Data Visualization


Order of the markers according to genetic maps constructed with JoinMap (Van Ooijen and Voorrips, 2001):
CheckMatrix heat map of linkage values Graphical genotype map of RILs Circular map of linkage between markers1
Linkage
Group 1
Linkage
Group 2
Linkage
Group 3
Linkage
Group 4
Linkage
Group 5
1For the circular maps a linkage cutoff value of 0.9 was used.



Order of the markers according to the physical order of the genes in the Columbia genome:
CheckMatrix heat map of linkage values Graphical genotype map of RILs Circular map of linkage between markers1
All five
linkage
groups
1For the circular maps a linkage cutoff value of 0.9 was used.



Data files

Table 2. Data files of haplotypes and genetic distances of the high-resolution map of the Bay-0 × Shahdara RIL population (211 RILs).
Haplotypes1 Genetic Distances (cM)2
Linkage Group 1 SFP578map_At1_genotypes.txt SFP578map_At1_jm.txt
Linkage Group 2 SFP578map_At2_genotypes.txt SFP578map_At2_jm.txt
Linkage Group 3 SFP578map_At3_genotypes.txt SFP578map_At3_jm.txt
Linkage Group 4 SFP578map_At4_genotypes.txt SFP578map_At4_jm.txt
Linkage Group 5 SFP578map_At5_genotypes.txt SFP578map_At5_jm.txt
All linkage groups SFP578map_all_genotypes.txt SFP578map_all_phys.txt3
1 First column contains marker ID's. First row contains column numbers, second row contains Loudet's RIL numbers. "A" is the Shahdara genotype, "B" is the Bay-0 genotype, and "-" is missing data.
2 Genetic distances calculated with JoinMap 3.0 (Van Ooijen and Voorrips, 2001). First column contains marker ID's; second column contains genetic distances (cM).
3 Physical distances. First column contains marker ID's; second column contains physical distances (Mb).






References

Loudet, Chaillou, Camilleri, Bouchez and Daniel-Vedele, 2002. Bay-0 x Shahdara recombinant inbred lines population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics, vol 104 (6-7), pp 1173-1184. http://www.inra.fr/qtlat/BayxSha/index.htm.

Van Ooijen, J.W. & R.E. Voorrips, 2001. JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, the Netherlands. http://www.kyazma.nl/index.php/mc.JoinMap.

Marilyn A.L. West, Hans van Leeuwen, Alexander Kozik, Daniel J. Kliebenstein, R.W. Doerge, Dina A. St.Clair, Richard W. Michelmore 2006. High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Research, PubMed link PubMed - National Library of Medicine.



Last modified: September 19, 2007.

email to: hvanleeuwen@ucdavis.edu Hans van Leeuwen (Data analysis, SFP detection and marker development, Web design)

email to: mlwest@ucdavis.edu Marilyn West (microarray experiments)

email to: akozik@atgc.org Alexander Kozik (MadMapper and CheckMatrix software)