PMC:5118429 / 10830-12647 JSONTXT

{"project":"2_test","denotations":[{"id":"27920797-24755649-33226429","span":{"begin":64,"end":68},"obj":"24755649"},{"id":"27920797-24078685-33226432","span":{"begin":750,"end":754},"obj":"24078685"}],"text":"As the current rainbow trout refrence genome (Berthelot et al., 2014) is fragmented into sequence scaffolds and true chromosome sequences are not yet available as a reference for genetic analyses like GWAS, we generated a new dense linkage map which was used as a genetic map reference in this study (Table S1). The 57K SNP Axiom® Trout Genotyping Array (Palti et al., 2015a) was used to genotype (GeneSeek, Inc., Lincoln, NE) 2464 samples collected across 46 full-sib families from a commercial Norwegian population and 10 full-sib families from the NCCCWA odd-year breeding population. Following quality control of raw genotype data as previously described (Palti et al., 2015a), linkage mapping was performed with Lep-MAP software (Rastas et al., 2013). First, SNPs were assigned to linkage groups with the “SeparateChromosomes” command using increasing LOD thresholds until the observed number of linkage groups corresponded with the haploid chromosome number in this species. Additional SNPs were subsequently added to the groups with the “JoinSingles” command at a more relaxed LOD threshold, and finally SNPs were ordered in each linkage group with the “OrderMarkers” command. Numerous iterations were performed to optimize error and recombination parameters. A total of 47,839 SNPs were mapped to 29 linkage groups, with an average of 1650 SNPs per group. The number of SNPs assigned to each group ranged from 754 to 2934. The total distances covered by the male and female maps were 2214 cM and 4248 cM, respectively. In all 13 chromosomes, known to have homologous pairing with at least one other chromosome arm, female/male recombination ratios were \u003e2.0; whereas, in non-duplicated chromosomes, the female/male recombination ratio ranged from 1.0 to 2.0, with the exception of chromosomes Omy15 and Omy21."}

{"project":"MyTest","denotations":[{"id":"27920797-24755649-33226429","span":{"begin":64,"end":68},"obj":"24755649"},{"id":"27920797-24078685-33226432","span":{"begin":750,"end":754},"obj":"24078685"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"As the current rainbow trout refrence genome (Berthelot et al., 2014) is fragmented into sequence scaffolds and true chromosome sequences are not yet available as a reference for genetic analyses like GWAS, we generated a new dense linkage map which was used as a genetic map reference in this study (Table S1). The 57K SNP Axiom® Trout Genotyping Array (Palti et al., 2015a) was used to genotype (GeneSeek, Inc., Lincoln, NE) 2464 samples collected across 46 full-sib families from a commercial Norwegian population and 10 full-sib families from the NCCCWA odd-year breeding population. Following quality control of raw genotype data as previously described (Palti et al., 2015a), linkage mapping was performed with Lep-MAP software (Rastas et al., 2013). First, SNPs were assigned to linkage groups with the “SeparateChromosomes” command using increasing LOD thresholds until the observed number of linkage groups corresponded with the haploid chromosome number in this species. Additional SNPs were subsequently added to the groups with the “JoinSingles” command at a more relaxed LOD threshold, and finally SNPs were ordered in each linkage group with the “OrderMarkers” command. Numerous iterations were performed to optimize error and recombination parameters. A total of 47,839 SNPs were mapped to 29 linkage groups, with an average of 1650 SNPs per group. The number of SNPs assigned to each group ranged from 754 to 2934. The total distances covered by the male and female maps were 2214 cM and 4248 cM, respectively. In all 13 chromosomes, known to have homologous pairing with at least one other chromosome arm, female/male recombination ratios were \u003e2.0; whereas, in non-duplicated chromosomes, the female/male recombination ratio ranged from 1.0 to 2.0, with the exception of chromosomes Omy15 and Omy21."}