Fine-mapping and validation of the genomic region underpinning pear red skin colour

Abstract

Red skin colour is an important target trait in various pear breeding programmes. In this study, the genetic control of red skin colour was investigated in an interspecific population derived using the descendants of the red sport European pear cultivar ‘Max Red Bartlett’ (MRB) and the red-blushed Chinese pear cultivar ‘Huobali’. Approximately 550 seedlings from nine families were phenotyped for red skin over-colour coverage (Ocolcov) and the intensity of red over-colour (Ocolint) on a 0–9 scale, and genotyped using genotyping-by-sequencing. Genome-wide association analyses were conducted using 7500 high-quality single nucleotide polymorphisms (SNPs). Genomic regions on linkage groups (LG) 4 and 5 were found to be associated, and the best SNP (S578_25116) on LG4 accounted for ~15% of phenotypic variation in Ocolcov and Ocolint. The association of S578_25116 with Ocolcov and Ocolint was successfully validated in a sample of ~200 European and Asian pear accessions. The association with red skin at locus S578_25116 was not present in Asian pear accessions, suggesting its close proximity to the MRB’s Cardinal gene. Several putative candidate genes, including MYB transcription factors (PCP027962 and PCP027967), were identified in the quantitative trait locus region on LG4 and await functional validation.

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

“…Our results suggest that the response from MAS in most pear fruit phenotypes would be small – hence GS could be a better selection tool. MAS would still be useful for traits controlled by major genes, such as pear red skin colour 36 .…”

“…An interspecific pear breeding programme at Plant & Food Research Limited (PFR) New Zealand was initiated in 1986 using commercial cultivars of European, Chinese and Japanese pear as parents. Second-generation populations were created in 1996 using the best selections produced from the first-generation hybrid families as parents 36 . A subset of the third-generation families created during 2007–08 using best seedlings from the second-generation were used for this study.…”

“…A subset of the third-generation families created during 2007–08 using best seedlings from the second-generation were used for this study. A total of 12 second-generation selections were used as parents to create nine families and details of mating design and relatedness among the 12 parents were reported earlier 36 .…”

“…As described earlier by Kumar et al . 36 , a random subset of seedlings that reached a minimum height after growing in a field nursery for 1 year were propagated and planted in PFR’s orchard in Motueka during 2011. Fruit were harvested during the fruiting season in 2015 and 2016 and a random sample of six fruit from each seedling was stored for 28 days at 3 °C, then a further 1 day at 20 °C before evaluation 36 .…”

“…36 , a random subset of seedlings that reached a minimum height after growing in a field nursery for 1 year were propagated and planted in PFR’s orchard in Motueka during 2011. Fruit were harvested during the fruiting season in 2015 and 2016 and a random sample of six fruit from each seedling was stored for 28 days at 3 °C, then a further 1 day at 20 °C before evaluation 36 . Sensory traits including firmness (FIRM), crispness (CRISP), juiciness (JUIC), sweetness (SWET), sourness (SOUR) and flavour intensity (FINT) were evaluated on a scale from 0 (=lowest) to 9 (=highest) by two trained assessors, and one overall score for each trait was given to each seedling.…”