16.marker.66-74

Genetic maps of three populations were used to establish a consensus map suitable for guiding the construction of superscaffolds and pseudomolecules. Each linkage map consisted of a “full” dataset including all the segregating markers mapped in each population and a “bin” data set, consisting of markers representing unique recombination events.

This is the "bin" data set map, the "full" data set map can be found here.

The F₂ population 70349, consisting of 187 individuals, resulted from an original cross between P4201 [58262⊗] (an inbred line with purple outer phloem and yellow xylem storage roots and purple petioles) and B6320 [96'606-4] (an inbred with orange roots and green petioles derived from the European open-pollinated cultivars Nantes and Camberley). The 70349 genetic map included 894 co-dominant markers (482 bins) with known sequence information.

Genetic maps of three populations were used to establish a consensus map suitable for guiding the construction of superscaffolds and pseudomolecules. Each linkage map consisted of a “full” dataset including all the segregating markers mapped in each population and a “bin” data set, consisting of markers representing unique recombination events.

This is the "bin" data set map, the "full" data set map can be found here.

The F₄ population 70796, consisting of 150 individuals, resulted from an original cross between B493 (an inbred with orange roots) and QAL (a wild carrot with white branching roots collected in Wisconsin-USA). The 70796 genetic map included 920 co-dominant markers (304 bins) with known sequence information.

Genetic maps of three populations were used to establish a consensus map suitable for guiding the construction of superscaffolds and pseudomolecules. Each linkage map consisted of a “full” dataset including all the segregating markers mapped in each population and a “bin” data set, consisting of markers representing unique recombination events.

This is the "bin" data set map, the "full" data set map can be found here.

The F₂ population Br1091×HM1, consisting of 138 individuals, resulted from an original cross between Brasília, a Brazilian open pollinated variety that led to the discovery of M. javanica resistance, and Homs (a Syrian open pollinated variety, with purple roots). The Br1091×HM1 genetic map included 843 co-dominant markers (367 bins) with known sequence information.

To independently verify the order of superscaffolds along the nine pseudomolecules, F₂ population 85036, consisting of 84 individuals (unpublished data), was used to generate a linkage map including GBS SNP markers. Sequencing and library preparation was carried out at the Biotechnology Center, UW-Madison (WI, USA). DNA was quantified using Quantus PicoGreen ds DNA Kit (Life Technologies, Grand Island, NY) and normalized to 10ng/μl. 50 ng of DNA was used for each GBS reaction. GBS libraries were prepared as described by Elshire et al., with minimal modification and half-sized reactions.

The resulting reads were analyzed using TASSEL version 4.3.11 with paired-end data preprocessed for TASSEL compatibility with bb.tassel (https://github.com/dsenalik/bb). SNPs were called using documented GBS pipeline procedures, with non-default parameter of mintagoccurrence=2. A total of 85,178 SNPs were obtained. Only sequences containing SNPs that unambiguously aligned to the carrot genome assembly were kept (18,007 SNPs). Finally, SNPs scored as heterozygous but with an allele ratio A:B far from 1:1 were eliminated if the ratio was < 0.3 or > 3.0, where A and B were the two alleles for a given SNP, leaving 516 high quality markers for linkage mapping.

Mapping was carried out with JoinMap 4.0. Population-specific locus genotype scores were then integrated into one dataset in each Linkage Group (LG) using the Combine Groups for Mapping Integration Module, followed by locus ordering by the Regression Mapping Module of JoinMap. The following parameters were used for the calculation: Kosambi's mapping function, LOD ≥ 3.0, REC frequency ≤0.4, goodness of fit jump threshold for removal of loci = 5.0, number of added loci after which a ripple is performed = 1, and third round = yes. Markers in common were used as anchor points. The order of markers across the linkage map was verified using CheckMatrix (http://www.atgc.org/XLinkage). Markers that were inconsistently placed due to false double recombination events were removed. The resulting map covered 450 cM and included 394 markers. At LOD > 10, with less than 10% missing data for marker and genotype, 394 markers were grouped into nine linkage groups.

Genetic maps of three populations were used to establish a consensus map suitable for guiding the construction of superscaffolds and pseudomolecules. Each linkage map consisted of a “full” dataset including all the segregating markers mapped in each population and a “bin” data set, consisting of markers representing unique recombination events.

This is the "full" data set map, the "bin" data set map can be found here.

Before merging the data from each population for map integration, the co-linearity of common markers was inspected using MapChart 2.2, and markers that were inconsistent were removed. In total, the three linkage maps shared 567 markers in the full dataset and 228 markers in the bin dataset. Both the “full” set and the “bin” dataset were used to generate a “full” and a “bin” integrated map using JoinMap 4.0 software. Population-specific locus genotype scores were then integrated into one dataset in each Linkage Group (LG) using the Combine Groups for Mapping Integration Module, followed by locus ordering by the Regression Mapping Module of JoinMap. The following parameters were used for the calculation: Kosambi's mapping function, LOD ≥ 3.0, REC frequency ≤0.4, goodness of fit jump threshold for removal of loci = 5.0, number of added loci after which a ripple is performed = 1, and third round = yes. Markers in common were used as anchor points. The integrated maps resulted in 2,073 markers for the full dataset and 918 markers for the bin dataset, covering 622 cM and 616 cM, respectively.

The maps that were used to generate this integrated map are:

• 70349 NG full map
• 70796 NG full map
• 80592 NG full map