Abstract
Interspecific pear (Pyrus spp.) hybrid populations are often used to develop novel cultivars. Pear cultivar breeding is a lengthy process because of long juvenility and the subsequent time required for reliable fruit phenotyping. Molecular techniques such as genome-wide association (GWA) and genomic selection (GS) provide an opportunity to fast-forward the development of high-value cultivars. We evaluated the genetic architecture of 10 pear fruit phenotypes (including sensory traits) and the potential of GS using genotyping-by-sequencing of 550 hybrid seedlings from nine interrelated full-sib families. Results from GWA suggested a complex polygenic nature of all 10 traits as the maximum variance explained by each marker was less than 4% of the phenotypic variance. The effect-size of SNPs for each trait suggested many genes of small effect and few of moderate effect. Some genomic regions associated with pear sensory traits were similar to those reported for apple – possibly a result of high synteny between the apple and pear genomes. The average (across nine families) GS accuracy varied from 0.32 (for crispness) to 0.62 (for sweetness), with an across-trait average of 0.42. Further efforts are needed to develop larger genotype-phenotype datasets in order to predict fruit phenotypes of untested seedlings with sufficient efficiency.
Highlights
Pear is currently grown commercially in almost every continent of the world
Despite sensory traits being primary selection criteria for developing new cultivars, there appears to be no report of genome-wide association (GWA) and genomic selection (GS) for pear sensory traits – something that hinders the acceleration of breeding cycles
Using genomic relationship matrix (GRM) in mixed-model equations would provide improved estimation of h2 compared to the pedigree-based relationships[10]
Summary
Pear is currently grown commercially in almost every continent of the world. The number of catalogued species in the genus Pyrus varies according to different studies, but commercial breeding has mainly focussed on three species: P. communis (European pear), and two Asian pears namely P. pyrifolia and P. x bretschneideri[1]. Breeding programmes in New Zealand and elsewhere have combined Asian and European pears to develop crisp, juicy and highly flavoured hybrid cultivars. New genomic technologies offer the possibility of accelerating and increasing efficiencies and effectiveness of breeding programmes for new pear cultivars. Despite sensory traits being primary selection criteria for developing new cultivars, there appears to be no report of GWA and GS for pear sensory traits – something that hinders the acceleration of breeding cycles. The main objectives of this study were to conduct GWA to find the candidate genomic regions for pear fruit traits including sensory eating quality traits, and evaluate the potential of GS using a hybrid population derived from crosses between Asian and European pears
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