Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps. In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map. The ‘Draper’ map comprises 12 linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/11032Keywords: Vaccinium corymbosum, Tetraploid Map, Genotyping by sequencing, Autotetraploi

Fine-mapping and validation of the genomic region underpinning pear red skin colour

Crop genetics: What makes a pear red? Researchers in New Zealand have produced a map of genetic variants linked with red skin color in pears, opening the door to identifying the genes responsible. Satish Kumar and others at the New Zealand Institute for Plant and Food Research Limited measured the skin color of 550 hybrid pear seedlings and sequenced their genomes. Combining these data produced a map of 7,500 variants throughout the genome and identified those associated with red skin color. The most significant variant accounted for about 15% of the color variation. Further analysis of that genomic region revealed several genes which might be related to red skin color. The genomic map produced by this study will improve breeding efficiency by making it possible to screen seedlings for fruit color, but further research is necessary to characterize the candidate genes

Additional file 2: Figure S1. of Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Alignment of linkage groups from ‘Louise Bonne de Jersey’ (LBJ) and ‘Old Home’ (OH) pears with the maps of ‘Moonglow’ (Moon) and PEAR1 (Montanari et al., 2013). The markers are named using the NCBI dbSNP accessions and their positions are indicated in centiMorgan. Microsatellite markers mapped in the ‘Moonglow’ x PEAR1 population are underlined. The linkage group (LG) numbering system is consistent with the apple LG numbering. Identified QTLs are shown with blue symbols coming from OH and brown symbols from LBJ. The Dw1 flanking marker Hi01c04 (underlined and red) mapped to LG5 of OH. (PDF 306 kb

Additional file 1: Table S1. of Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Pearson correlation (first cell) and P-value (second cell) of all the traits measured over four years in the ‘Old Home’ x ‘Louise Bonne de Jersey’ OHxLBJ segregating pear population. Branches: branches per tree; Height: total tree height; Inflorescence: inflorescences per tree; Nodes: nodes per tree; Spurs: spurs per tree; TCAtrunk: trunk cross-sectional area 20 cm above graft unit; TCAroot: TCA of rootstock; TCAsec: TCA secondary growth of the main axis; TCAtert: TCA tertiary growth of the main axis. (PDF 164 kb

McCallumConstructionSNPandSSRSupplementaryMaterial2.xlsx

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps. In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map. The ‘Draper’ map comprises 12 linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.Keywords: Genotyping by sequencing, Autotetraploid, Vaccinium corymbosum, Tetraploid Ma

McCallumConstructionSNPandSSRSupplementaryMaterial3.pdf

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps. In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map. The ‘Draper’ map comprises 12 linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.Keywords: Vaccinium corymbosum, Tetraploid Map, Autotetraploid, Genotyping by sequencin

McCallumConstructionSNPandSSRSupplementaryMaterial1.pdf

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps. In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map. The ‘Draper’ map comprises 12 linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.Keywords: Genotyping by sequencing, Autotetraploid, Vaccinium corymbosum, Tetraploid Ma

McCallumConstructionSNPandSSR.pdf

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps. In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map. The ‘Draper’ map comprises 12 linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.Keywords: Autotetraploid, Genotyping by sequencing, Vaccinium corymbosum, Tetraploid Ma

Alignment of LG9 from four parental maps P128R068T003, ‘Moonglow’, P202R137T052 and ‘Old Home’.

<p>The lines between the maps each show markers in common with two other parents.</p