Abstract
BackgroundGenomic analysis technologies can promote efficient fruit tree breeding. Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Furthermore, High-resolution genetic map construction and accurate QTL detection can significantly narrow down the putative candidate genes associated with important plant traits.ResultsWe genotyped 162 offspring in the F1 ‘Spadona’ x ‘Harrow Sweet’ pear population using GBS. An additional 21 pear accessions, including the F1 population’s parents, from our germplasm collection were subjected to GBS to examine diverse genetic backgrounds that are associated to agriculturally relevant traits and to enhance the power of SNP calling. A standard SNP calling pipeline identified 206,971 SNPs with Asian pear (‘Suli’) as the reference genome and 148,622 SNPs with the European genome (‘Bartlett’). These results enabled constructing a genetic map, after further stringent SNP filtering, consisting of 2036 markers on 17 linkage groups with a length of 1433 cM and an average marker interval of 0.7 cM. We aligned 1030 scaffolds covering a total size of 165.5 Mbp (29%) of the European pear genome to the 17 linkage groups. For high-resolution QTL analysis covering the whole genome, we used phenotyping for vegetative budbreak time in the F1 population. New QTLs associated to vegetative budbreak time were detected on linkage groups 5, 13 and 15. A major QTL on linkage group 8 and an additional QTL on linkage group 9 were confirmed. Due to the significant genotype-by-environment (GxE) effect, we were able to identify novel interaction QTLs on linkage groups 5, 8, 9 and 17. Phenotype–genotype association analysis in the pear accessions for main genotype effect was conducted to support the QTLs detected in the F1 population. Significant markers were detected on every linkage group to which main genotype effect QTLs were mapped.ConclusionsThis is the first vegetative budbreak study of European pear that makes use of high-resolution genetic mapping. These results provide tools for marker-assisted selection and accurate QTL analysis in pear, and specifically at vegetative budbreak, considering the significant GxE and phenotype-plasticity effects.
Highlights
Genomic analysis technologies can promote efficient fruit tree breeding
The aim of this study was to construct high-resolution genetic maps for better detection and mapping of main genotype effect and Genotype-by-environment interaction (GxE) quantitative trait locus (QTL) associated with traits of relevance to agriculture in our F1 population, and to enable the development of genomic tools to select low-chilling requirement (CR) pear genotypes with stable phenotype plasticity over various climatic conditions
Single-nucleotide polymorphism (SNP) calling and genetic map construction The Genotyping by sequencing (GBS) generated a total of 222 million reads with an average of 1.21 million reads per sample; 206,971 SNPs were detected in the Pyrus× bretschneideri genome (Asian pear) and 148,622 in the P. communis genome
Summary
Genotyping by sequencing (GBS) enables generating efficient data for high-quality genetic map construction and QTL analysis in a relatively accessible way. Genotyping by sequencing (GBS) [1] has enabled generating high-quality SNP data for genome-wide association studies (GWAS), genetic relatedness studies, high-quality genetic map construction and accurate quantitative trait locus (QTL) detection [2]. This high-throughput technology detects SNP markers that are spread at very high density over the whole genome, enabling the identification of genetic variance between closely related genotypes within a family [3], and can be used to estimate genetic relatedness of species and cultivars. To date, a large proportion of the genome scaffolds are unplaced due to short scaffold sequences and lack of high-resolution genetic maps [6]
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