Abstract
The allelic diversity of primitive germplasm of fruit crops provides a useful resource for introgressing novel genes to meet consumer preferences and environmental challenges. Pre-breeding facilitates the identification of novel genetic variation in the primitive germplasm and expedite its utilisation in cultivar breeding programmes. Several generations of pre-breeding could be required to minimise linkage drag from the donor parent and to maximise the genomic content of the recipient parent. In this study we investigated the potential of genomic selection (GS) as a tool for rapid background selection of parents for the successive generation. A diverse set of 274 accessions was genotyped using random-tag genotyping-by-sequencing, and phenotyped for eight fruit quality traits. The relationship between ‘own phenotypes’ of 274 accessions and their general combining ability (GCA) was also examined. Trait heritability influenced the strength of correspondence between own phenotype and the GCA. The average (across eight traits) accuracy of predicting own phenotype was 0.70, and the correlations between genomic-predicted own phenotype and GCA were similar to the observed correlations. Our results suggest that genome-assisted parental selection (GAPS) is a credible alternative to phenotypic parental selection, so could help reduce the generation interval to allow faster accumulation of favourable alleles from donor and recipient parents.
Highlights
Growing demand for nutrient-rich foods, increasing biotic and abiotic risks in fruit production, and evolving consumer preferences require development of novel cultivars
Pre-breeding of fruit crops germplasm using recurrent selection is very rare[3], so most efforts have focussed on introgression of major genes using a PBC strategy where foreground selection is carried out using marker assisted selection (MAS) and the resistant seedlings are planted in the orchard for fruit quality and other trait evaluation[4,5]
Single nucleotide polymorphisms (SNPs) were subsequently discarded using these criteria: more than 10% missing data; minor allele frequency (MAF) < 5%; and SNPs separated by one bp
Summary
Growing demand for nutrient-rich foods, increasing biotic and abiotic risks in fruit production, and evolving consumer preferences require development of novel cultivars. Introduction of novel genes/traits from exotic germplasm have been achieved through two main strategies[1]: firstly, prebreeding of primitive/exotic germplasm using recurrent selection, using enriched germplasm as a source for crossing with elite lines; and secondly, backcrossing or pseudo-backcrossing (PBC) for introgression of known major genes from the donor into elite lines or commercial. Pre-breeding of fruit crops germplasm using recurrent selection is very rare[3], so most efforts have focussed on introgression of major genes (e.g. disease resistance) using a PBC strategy where foreground selection is carried out using marker assisted selection (MAS) and the resistant seedlings are planted in the orchard for fruit quality and other trait evaluation[4,5]. Transgenic plants are still regulated in many countries, so this strategy cannot be used for commercial cultivar breeding at the moment
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