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Article|14 Jan 2019|OPEN
Fine-mapping and validation of the genomic region underpinning pear red skin colour
Satish Kumar1 , , Chris Kirk2 , Cecilia Hong Deng3 , Claudia Wiedow2 , Mengfan Qin4 , Richard Espley3 , Jun Wu4 and Lester Brewer,5
1The New Zealand Institute for Plant and Food Research Limited, Hawkes Bay Research Centre, Havelock North, New Zealand
2The New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
3The New Zealand Institute for Plant and Kumar et al. Horticulture Research (2019) 6:29 Page 6 of 7 Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
4Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
5The New Zealand Institute for Plant and Food Research Limited, Motueka Research Centre, Motueka, New Zealand
*Corresponding author. E-mail: satish.kumar@plantandfood.co.nz

Horticulture Research 6,
Article number: 29 (2019)
doi: https://doi.org/10.1038/s41438-018-0112-4
Views: 1070

Received: 30 Jul 2018
Revised: 08 Nov 2018
Accepted: 15 Nov 2018
Published online: 14 Jan 2019

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.