Introgressing blue mold resistance into elite apple germplasm by rapid cycle breeding and foreground and background DNA-informed selection

Authors: LUO, FEIXIONG - Washington State University; Norelli, John; HOWARD, NICHOLAS - University Of Minnesota; Wisniewski, Michael; FLACHOWSKY, HENRYK - Julius Kuhn Institute; VIOLA-HANKE, MAGDA - Julius Kuhn Institute; PEACE, CAMERON - Washington State University

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2020
Publication Date: 2/7/2020
Citation: Luo, F., Norelli, J.L., Howard, N., Wisniewski, M.E., Flachowsky, H., Viola-Hanke, M., Peace, C. 2020. Introgressing blue mold resistance into elite apple germplasm by rapid cycle breeding and foreground and background DNA-informed selection. Tree Genetics and Genomes. https://doi.org/10.1007/s11295-020-1419-5.
DOI: https://doi.org/10.1007/s11295-020-1419-5

Interpretive Summary: Apple blue mold is a serious postharvest disease of apple that causes significant economic losses. A source of blue mold resistance was previously identified in an accession of wild apple germplasm (Malus sieversii – PI 613981) and a genetic marker was subsequently identified in a mapping population (GMAL4593) representing a cross between PI-613981 x ‘Royal Gala’). Utilizing this source of resistance, however, requires that the resistant germplasm is introgressed with germplasm that has other commercially acceptable traits, such as good fruit size and taste. The present study utilized a rapid cycle breeding approach to combine the rapid cycle breeding trait (early flowering) with the resistant germplasm to establish resistant germplasm that was also early-flowering. Molecular markers were used to select offspring that would carry both traits. Genetic marker information was also used to select germplasm that carried more ‘Royal Gala’ genetic information than PI 613981 genetic information. Ideal candidates were selected using the genome-wide marker information and will now be used to further introgress the blue mold resistance trait into high-quality apple germplasm. Overall, the study demonstrates the ability to find sources of disease resistance into wild germplasm and integrate the trait into high-quality germplasm in an efficient and timely manner using a combination of the rapid cycle breeding system and genome-wide markers for fruit quality traits.

Technical Abstract: Apple blue mold causes significant postharvest economic losses worldwide. A blue mold resistance locus, qM-Pe3.1, was previously identified on chromosome 3 with the resistance allele source being Malus sieversii PI 613981, a wild accession with inferior fruit quality. Introgression of the resistance allele into elite breeding germplasm is difficult. Success of introgression and the effect of PI 613981 genome on fruit quality cannot be phenotypically evaluated until fruiting that takes approximately five years from seed. Here, introgression of the qM-Pe3.1 resistance allele was realized by rapid cycle breeding and supported with DNA-based diagnostic information. The transgenic line T1190, constitutively expressing the BpMADS4 early-flowering gene, was used to hasten fruiting of seedlings via the rapid cycle breeding approach. Of 141 secondgeneration [(‘Gala’× PI 613981) × T1190] offspring, 75 carried BpMADS4 according to a diagnostic DNA test. Another DNA test was developed and used to detect the qMPe3.1 resistance allele in offspring (foreground selection). Forty-three BpMADS4-carrying offspring were detected with the qM-Pe3.1 resistance allele. DNA tests for other trait loci were used to identify other desirable alleles and 6874 genome-wide SNP markers (from the apple 20K Illumina SNP array) were used to identify undesirable genomic segments of PI 613981 (background selection). Three individuals were identified with favorable recombination close to qM-Pe3.1 and less than 25% of M. sieversii, best suited for the elimination of unadapted DNA segments in subsequent generations. The introgression of qM-Pe3.1, in combination with marker-assisted foreground and background selection, successfully advanced promising germplasm in readiness for the next generation.