Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Publication Overview
TitleDevelopment of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
AuthorsAntanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ
TypeJournal Article
Journal NameBMC genomics
Volume13
Year2012
Page(s)203
CitationAntanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC genomics. 2012; 13:203.

Abstract

BACKGROUND A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny. RESULTS Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the 'Golden Delicious' genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the 'Golden Delicious' pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence. CONCLUSIONS We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the 'Golden Delicious' reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.
Features
This publication contains information about 2,546 features:
Feature NameUniquenameType
RosBREEDSNP_SNP_TC_2260844_Lg7_01946_MAF10_684526_exon1RosBREEDSNP_SNP_TC_2260844_Lg7_01946_MAF10_684526_exon1genetic_marker
RosBREEDSNP_SNP_TC_226288_Lg14_01888_MAF20_1628548_exon1RosBREEDSNP_SNP_TC_226288_Lg14_01888_MAF20_1628548_exon1genetic_marker
RosBREEDSNP_SNP_TC_22729723_Lg11_00743_MAF40_MDP0000397218_exon1RosBREEDSNP_SNP_TC_22729723_Lg11_00743_MAF40_MDP0000397218_exon1genetic_marker
RosBREEDSNP_SNP_TC_2334882_Lg9_02134_MAF40_1632164_exon2RosBREEDSNP_SNP_TC_2334882_Lg9_02134_MAF40_1632164_exon2genetic_marker
RosBREEDSNP_SNP_TC_23407280_Lg6_01556_MAF20_MDP0000306342_exon1RosBREEDSNP_SNP_TC_23407280_Lg6_01556_MAF20_MDP0000306342_exon1genetic_marker
RosBREEDSNP_SNP_TC_23529831_Lg2_02155_MAF30_1642317_exon3RosBREEDSNP_SNP_TC_23529831_Lg2_02155_MAF30_1642317_exon3genetic_marker
RosBREEDSNP_SNP_TC_23537758_Lg2_02155_MAF10_MDP0000250217_exon1RosBREEDSNP_SNP_TC_23537758_Lg2_02155_MAF10_MDP0000250217_exon1genetic_marker
RosBREEDSNP_SNP_TC_23880804_Lg8_RosCOS3331_MAF10_MDP0000806017_exon1RosBREEDSNP_SNP_TC_23880804_Lg8_RosCOS3331_MAF10_MDP0000806017_exon1genetic_marker
RosBREEDSNP_SNP_TC_23899418_Lg1_RosCOS1602_MAF20_MDP0000283296_exon1RosBREEDSNP_SNP_TC_23899418_Lg1_RosCOS1602_MAF20_MDP0000283296_exon1genetic_marker
RosBREEDSNP_SNP_TC_2399839_Lg5_02457_MAF50_1676520_exon2RosBREEDSNP_SNP_TC_2399839_Lg5_02457_MAF50_1676520_exon2genetic_marker
RosBREEDSNP_SNP_TC_24102468_Lg3_01728_MAF40_1669728_exon1RosBREEDSNP_SNP_TC_24102468_Lg3_01728_MAF40_1669728_exon1genetic_marker
RosBREEDSNP_SNP_TC_24105196_Lg3_01728_MAF40_MDP0000168162_exon2RosBREEDSNP_SNP_TC_24105196_Lg3_01728_MAF40_MDP0000168162_exon2genetic_marker
RosBREEDSNP_SNP_TC_2414010_Lg17_MDP0000291802_MAF20_MDP0000291802_exon9RosBREEDSNP_SNP_TC_2414010_Lg17_MDP0000291802_MAF20_MDP0000291802_exon9genetic_marker
RosBREEDSNP_SNP_TC_24622707_Lg5_01304_MAF50_1627174_exon3RosBREEDSNP_SNP_TC_24622707_Lg5_01304_MAF50_1627174_exon3genetic_marker
RosBREEDSNP_SNP_TC_24710442_Lg15_02859_MAF40_365356_exon1RosBREEDSNP_SNP_TC_24710442_Lg15_02859_MAF40_365356_exon1genetic_marker
RosBREEDSNP_SNP_TC_24800426_Lg14_02673_MAF40_1646305_exon1RosBREEDSNP_SNP_TC_24800426_Lg14_02673_MAF40_1646305_exon1genetic_marker
RosBREEDSNP_SNP_TC_25009893_Lg12_02228_MAF30_509994_exon3RosBREEDSNP_SNP_TC_25009893_Lg12_02228_MAF30_509994_exon3genetic_marker
RosBREEDSNP_SNP_TC_25205098_Lg6_258116_MAF20_258116_exon2RosBREEDSNP_SNP_TC_25205098_Lg6_258116_MAF20_258116_exon2genetic_marker
RosBREEDSNP_SNP_TC_2521511_Lg15_02844_MAF30_219496_exon1RosBREEDSNP_SNP_TC_2521511_Lg15_02844_MAF30_219496_exon1genetic_marker
RosBREEDSNP_SNP_TC_2558984_Lg15_02844_MAF40_1625529_exon6RosBREEDSNP_SNP_TC_2558984_Lg15_02844_MAF40_1625529_exon6genetic_marker
RosBREEDSNP_SNP_TC_25896512_Lg3_01642_MAF30_MDP0000239694_exon1RosBREEDSNP_SNP_TC_25896512_Lg3_01642_MAF30_MDP0000239694_exon1genetic_marker
RosBREEDSNP_SNP_TC_25900349_Lg3_01642_MAF50_1642190_exon4RosBREEDSNP_SNP_TC_25900349_Lg3_01642_MAF50_1642190_exon4genetic_marker
RosBREEDSNP_SNP_TC_26371625_Lg15_01850_MAF50_1639406_exon1RosBREEDSNP_SNP_TC_26371625_Lg15_01850_MAF50_1639406_exon1genetic_marker
RosBREEDSNP_SNP_TC_26829691_Lg11_01361_MAF50_1663355_exon1RosBREEDSNP_SNP_TC_26829691_Lg11_01361_MAF50_1663355_exon1genetic_marker
RosBREEDSNP_SNP_TC_26990664_Lg5_02251_MAF30_12707_exon1RosBREEDSNP_SNP_TC_26990664_Lg5_02251_MAF30_12707_exon1genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Apple-MM-F1