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A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

View Article: PubMed Central - PubMed

ABSTRACT

Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.

No MeSH data available.


Frequency distribution of informative meiosis (in percentage) in the initial set of individual SNP markers (light gray bars) and the final set of HaploBlock (HB) together with remaining individual SNP markers (dark gray bars). The graph highlights the different amount of informative meiosis carried by individual SNPs and the more informative HB markers. SNP markers carried a maximum of 50% of the total information when being completely bi-allelic, as expected, and a maximum of 60% when being tri-allelic in some families when accounting for -alleles and signal intensity differences. However, the latter is true only for a small proportion (0.1%) of the SNPs, while the majority of SNPs is informative for 20–40% of the individuals. On the contrary, the majority of HB markers (+remaining single SNP) are informative for 40–80% of the individuals across all families and even 8.6% of the HBs is fully informative (100%).
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fig2: Frequency distribution of informative meiosis (in percentage) in the initial set of individual SNP markers (light gray bars) and the final set of HaploBlock (HB) together with remaining individual SNP markers (dark gray bars). The graph highlights the different amount of informative meiosis carried by individual SNPs and the more informative HB markers. SNP markers carried a maximum of 50% of the total information when being completely bi-allelic, as expected, and a maximum of 60% when being tri-allelic in some families when accounting for -alleles and signal intensity differences. However, the latter is true only for a small proportion (0.1%) of the SNPs, while the majority of SNPs is informative for 20–40% of the individuals. On the contrary, the majority of HB markers (+remaining single SNP) are informative for 40–80% of the individuals across all families and even 8.6% of the HBs is fully informative (100%).

Mentions: The final integrated data set consisted of a single BC-type population of 3 172 individuals, including the genotypic information of 2837 HB makers and 976 individual SNPs. The overall proportion of missing information was massively reduced from 78% of the initial set of 15 812 SNP markers to 54% of the final (HB+individual SNPs) integrated data set (Figure 2), thus retaining the complete genetic information of the larger SNP data set.


A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species
Frequency distribution of informative meiosis (in percentage) in the initial set of individual SNP markers (light gray bars) and the final set of HaploBlock (HB) together with remaining individual SNP markers (dark gray bars). The graph highlights the different amount of informative meiosis carried by individual SNPs and the more informative HB markers. SNP markers carried a maximum of 50% of the total information when being completely bi-allelic, as expected, and a maximum of 60% when being tri-allelic in some families when accounting for -alleles and signal intensity differences. However, the latter is true only for a small proportion (0.1%) of the SNPs, while the majority of SNPs is informative for 20–40% of the individuals. On the contrary, the majority of HB markers (+remaining single SNP) are informative for 40–80% of the individuals across all families and even 8.6% of the HBs is fully informative (100%).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120355&req=5

fig2: Frequency distribution of informative meiosis (in percentage) in the initial set of individual SNP markers (light gray bars) and the final set of HaploBlock (HB) together with remaining individual SNP markers (dark gray bars). The graph highlights the different amount of informative meiosis carried by individual SNPs and the more informative HB markers. SNP markers carried a maximum of 50% of the total information when being completely bi-allelic, as expected, and a maximum of 60% when being tri-allelic in some families when accounting for -alleles and signal intensity differences. However, the latter is true only for a small proportion (0.1%) of the SNPs, while the majority of SNPs is informative for 20–40% of the individuals. On the contrary, the majority of HB markers (+remaining single SNP) are informative for 40–80% of the individuals across all families and even 8.6% of the HBs is fully informative (100%).
Mentions: The final integrated data set consisted of a single BC-type population of 3 172 individuals, including the genotypic information of 2837 HB makers and 976 individual SNPs. The overall proportion of missing information was massively reduced from 78% of the initial set of 15 812 SNP markers to 54% of the final (HB+individual SNPs) integrated data set (Figure 2), thus retaining the complete genetic information of the larger SNP data set.

View Article: PubMed Central - PubMed

ABSTRACT

Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.

No MeSH data available.