Development and validation of an SNP-based new set of markers useful for early selection for Sharka disease in apricot (P. armeniaca)

P. Lambert, C. Confolent, G. Roch, N. Dlalah, A. Remay, A. Bernole, V. Decroocq, C. Auvinet, J.M. Audergon
Sharka disease, due to the Plum pox virus, is a major threat to apricot trees. Most of the accessions world-wide and particularly those cultivated in Western Europe and the Mediterranean area are susceptible to the disease. A few resistance sources have been identified to date in cultivars developed in the US from a basis of Central Asian germplasm, all of these sharing the same genomic region associated with resistance to sharka in chromosome 1. Based on this, Simple sequence repeats (SSR) markers framing the MATH genes possibly responsible for the resistance have been developed in this region and a set of 2 SSRs (PGS1.21 and PGS1.24) and an indel (ZP002) was selected for identifying and discarding susceptible individuals at the plantlet stage of the apricot breeding process. However SSR markers could be difficult to implement by small teams due to the investment in hands-on time and equipment. As a consequence we turned to single nucleotide polymorphisms (SNP) to develop an alternative set of markers that could be cheaper and more easily implemented. Taking advantage of the numerous apricot genomic-sequences available at the UGAFL, we identified resistant/susceptible SNP/indel haplotypes and developed a set of three primer triplets (SP353, SP870, and SP871) based on the competitive allele-specific PCR (KASP™) technique by LGC genomics. This set was validated using a wide range of apricot accessions from different geographic origins and genetic backgrounds, concurrently with the original set of three SSRs. The new set gave similar results as the SSR-based set, was more convenient and, as a result, is now routinely used for early selection of apricot seedlings in our breeding programs.
Lambert, P., Confolent, C., Roch, G., Dlalah, N., Remay, A., Bernole, A., Decroocq, V., Auvinet, C. and Audergon, J.M. (2020). Development and validation of an SNP-based new set of markers useful for early selection for Sharka disease in apricot (P. armeniaca). Acta Hortic. 1290, 47-52
DOI: 10.17660/ActaHortic.2020.1290.9
https://doi.org/10.17660/ActaHortic.2020.1290.9
marker-assisted selection, Plum pox virus, haplotype, SSR, resistance, KASP¿
English

Acta Horticulturae