Marker-trait associations and genomic predictions of interspecific pear (Pyrus) fruit characteristics

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.

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“…The genomic regions with high occurrence of ROH have been shown to contain important genes associated with phenotypes in humans (Ceballos et al, 2018;Clark et al, 2019) and livestock species (Purfield et al, 2012;Kim et al, 2013;Biscarini et al, 2014). Overlap of ROH islands with marker-trait associations identified in this study, as well as with the previously published QTLs for pear fruit/tree phenotypes (De Franceschi and Dondini, 2019;Kumar et al, 2019), adds to the robustness of ROH mapping as a complementary strategy for GWA studies in outbred fruit crops.…”

Inheritance of Rootstock Effects in Avocado (Persea americana Mill.) cv. Hass

“…Despite SSRs’ utility, these markers will be limited when trying to assess the genomic architecture of complex traits ( Hirschhorn and Daly, 2005 ) or when calibrating marker-based infinitesimal Genomic Selection models ( Kumar et al, 2012 , 2015 , 2019 ; Muranty et al, 2015 ; Crossa et al, 2017 ). To reveal the rootstock-mediated genomic architecture of key traits, genome-wide association ( Khan and Korban, 2012 ) has to assume some allelic variants are in linkage disequilibrium (LD) ( Blair et al, 2018 ) with causal variants ( Hirschhorn and Daly, 2005 ; Morris and Borevitz, 2011 ; Tam et al, 2019 ) that impact scion’s phenotype ( Minamikawa et al, 2017 ).…”

Turbocharging introgression breeding of perennial fruit crops: a case study on apple

“…GS would be a more efficient strategy for background selection, especially for complex traits, as favourable alleles from the donor and recipient lines can be targeted across the whole genome. Accuracy of GS studies in apple and pear cultivar breeding were encouraging 13,[31][32][33] , but the current applications of GS in perennial fruit crops are generally aimed at skipping Stage 1 seedling evaluation so that candidates for Stage 2 evaluation can be identified based on GEBV-hence reducing the cultivar development timeline by at least five years 13 . Although, the candidates selected for Stage 2 testing could also be used as parents of the next generation, it is suspected that their worthiness as parents could be compromised mainly because of recombination events.…”