Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping
The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted b...
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doaj-97fc40172fba4eb39e7e48c2a09288532021-07-02T02:02:43ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-04-01741177118910.1534/g3.116.03755611Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage MappingBrandon SchlautmanGiovanny Covarrubias-PazaranLuis Diaz-GarciaMassimo IorizzoJames PolashockEdward GrygleskiNicholi VorsaJuan ZalapaThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.http://g3journal.org/lookup/doi/10.1534/g3.116.037556centromere regiongenetic mapsimple sequence repeatsingle nucleotide polymorphismVaccinium |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Brandon Schlautman Giovanny Covarrubias-Pazaran Luis Diaz-Garcia Massimo Iorizzo James Polashock Edward Grygleski Nicholi Vorsa Juan Zalapa |
spellingShingle |
Brandon Schlautman Giovanny Covarrubias-Pazaran Luis Diaz-Garcia Massimo Iorizzo James Polashock Edward Grygleski Nicholi Vorsa Juan Zalapa Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping G3: Genes, Genomes, Genetics centromere region genetic map simple sequence repeat single nucleotide polymorphism Vaccinium |
author_facet |
Brandon Schlautman Giovanny Covarrubias-Pazaran Luis Diaz-Garcia Massimo Iorizzo James Polashock Edward Grygleski Nicholi Vorsa Juan Zalapa |
author_sort |
Brandon Schlautman |
title |
Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping |
title_short |
Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping |
title_full |
Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping |
title_fullStr |
Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping |
title_full_unstemmed |
Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping |
title_sort |
construction of a high-density american cranberry (vaccinium macrocarpon ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping |
publisher |
Oxford University Press |
series |
G3: Genes, Genomes, Genetics |
issn |
2160-1836 |
publishDate |
2017-04-01 |
description |
The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. |
topic |
centromere region genetic map simple sequence repeat single nucleotide polymorphism Vaccinium |
url |
http://g3journal.org/lookup/doi/10.1534/g3.116.037556 |
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