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

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.

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…The optical mapping then allowed us to produce scaffolds with a N50 of 5.5 Mb, which, in association with a high-density integrated linkage map, yielded highly contiguous pseudomolecules. In this new apple genome, we followed a newer convention 23 in which the orientation of Chr10 and Chr05 became aligned by the inversion of Chr05. We chose to invert Chr05 because it is the least frequently reported of the two in previous genetic studies on quantitative trait loci (QTL), gene discovery and characterization.…”

“…This consensus map was then used for the hybrid assembly with the corrected scaffolds, which, together with single-nucleotide polymorphism (SNP) markers derived from a high-density genetic linkage map 23 , allowed the construction of the 17 pseudochromosomes (Supplementary Table 2 and Supplementary Note). To estimate the genome size, we calculated different k-mer frequency distributions of the Illumina reads.…”

“…An integrated multiparental genetic linkage map of apple 23 that was composed of 15,417 SNP markers was used to organize and orientate the scaffolds into chromosomesized sequences. The probe sequences of the 15,417 markers 64 were mapped onto the genome using BWA-MEM.…”

“…This assembly resulted from a combination of short High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development 1 1 0 0 VOLUME 49 | NUMBER 7 | JULY 2017 Nature GeNetics A r t i c l e s (Illumina) and long sequencing reads (PacBio), along with scaffolding based on optical maps (BioNano) and a high-density integrated genetic linkage map 23 . This chromosome-scale assembly was complemented by a detailed de novo annotation of genes based on RNA sequencing (RNA-seq) data, TE annotation and small RNA alignments.…”

The red bayberry genome and genetic basis of sex determination

“…The red bayberry genome size is small and simple (around 320 Mb), being diploid with intermediate heterozygosity. The female and male independent assemblies, reciprocal sequence comparison at micro level in contigs and an efficient mapping approach (Di Pierro et al ., ), led to high quality of assembly, with an extended total and oriented size of the female pseudochromosome of 280 Mb (87%) and 264 Mb (82%) of the male (Table ). Due to genetic diversity of two parents, 65% of haplotype blocks (HB) in the linkage map was heterozygous (Figure S3), which is helpful to define HB and anchor scaffolds in right position and orientation.…”