A consensus ‘Honeycrisp’ apple (Malus × domestica) genetic linkage map from three full-sib progeny populations

Clark, Matthew D.; Schmitz, C.; Rosyara, Umesh R.; Luby, James J.; Bradeen, James M.

doi:10.1007/s11295-014-0709-1

Cited by 28 publications

(17 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This might be the case between the genotypes used for the draft genome sequence and the parents used in this study and might explain the differences observed between the genetic and physical map found. Undoubtedly, a consensus genetic map for cassava could be helpful in this regard, as has been performed for other species with high heterozygosity level such as grapevine and apple [ 78 , 79 ]. Other explanations might be that some of the markers identifying these scaffolds are not properly mapped or because of errors during assembly of the reads, that are still present in the draft genome sequence.…”

Section: Discussionmentioning

confidence: 99%

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

et al. 2015

View full text Add to dashboard Cite

BackgroundCassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome.ResultsA high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs.ConclusionsThis is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1397-4) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Genetic maps were constructed in JOINMAP 4.1 software (Van Ooijen 2006 , 2011 ) using 165 progeny from a cross between ‘FL_08-10’ × ‘12.115-10’ and 91 progeny from ‘Winter Dawn’ × ‘Treasure.’ The markers were curated to achieve consistent performance across the germplasm, to maximize polymorphism and to exclude markers with fraction values of observed (oDR) and expected (eDR) double recombination singletons > 0.05 (Clark et al 2014 ). Subgenomes and orientations of linkage groups were assigned according to van Dijk et al ( 2014 ) as the maps share many common markers with those described in Bassil et al ( 2015 ) and Mangandi et al ( 2017 ).…”

Section: Methodsmentioning

confidence: 99%

FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry

et al. 2018

View full text Add to dashboard Cite

Optimal strategies for genetic improvement in crops depend on accurate assessments of the genetic architecture of traits. The overall objective of the present study was to determine the genetic architecture of anthracnose fruit rot (AFR) resistance caused by the fungus Colletotrichum acutatum in the University of Florida strawberry ( Fragaria × ananassa ) breeding germplasm. In 2016–2017, 33 full-sib families resulting from crosses between parents with varying levels of AFR resistance were tested. In 2017–2018, six full-sib families resulting from putative heterozygous resistant parents and homozygous susceptible parents were tested. Additionally, a validation population consisting of 77 advanced selections and ten cultivars was tested in the second season. Inoculation was performed using a mixture of three local isolates of the C. acutatum species complex. Phenotypes were scored weekly, and genotyping was performed using the IStraw35 Affymetrix Axiom ® SNP array. A pedigree-based QTL analysis was performed using FlexQTL™ software. A major resistance locus, which we name FaRCa1 , was detected in both seasons with a peak located at 55–56 cM on LG 6B and explaining at least 50% of the phenotypic variation across trials and seasons. The resistant allele exhibited partial dominance in all trials. The FaRCa1 locus is distinct from the previously discovered Rca2 locus, which mapped to LG 7B. While Rca2 is effective against European isolates from pathogenicity group 2, FaRCa1 appears to confer resistance to isolates of pathogenicity group 1. Electronic supplementary material The online version of this article (10.1007/s00122-018-3263-7) contains supplementary material, which is available to authorized users.

show abstract

“…These three projects utilized the Illumina® Infinium® genotyping platform. To date, these arrays have been used for the generation of linkage maps [ 4 , 6 - 11 ], evaluation of the quality of physical maps [ 12 ], fine mapping and validation of quantitative trait loci (QTL) [ 9 , 13 ], elucidation of marker-trait associations [ 10 , 14 ], genome-wide association studies [ 15 ], genomic selection studies [ 16 ], validation of pedigrees and verification of trueness to type of breeding lines and accessions [ 17 ], and for design of the future generation of arrays [ 18 ]. Thus, these three arrays have had broad utility for the Rosaceae genomics and genetics research and breeding communities.…”

Section: Introductionmentioning

confidence: 99%

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

et al. 2015

View full text Add to dashboard Cite

BackgroundA high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.ResultsAbout 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM.ConclusionsThe Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1310-1) contains supplementary material, which is available to authorized users.

show abstract

A consensus ‘Honeycrisp’ apple (Malus × domestica) genetic linkage map from three full-sib progeny populations

Cited by 28 publications

References 27 publications

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

Contact Info

Product

Resources

About