Marker-assisted backcross breeding for development of pepper varieties (Capsicum annuum) containing capsinoids

Capsinoids have similar biological effects as capsaicinoids, including anticancer and anti-obesity properties. The Capsicum chinense ‘SNU11-001’ variety of pepper was previously reported to contain high levels of capsinoids due to a mutation in the putative aminotransferase (pAMT) gene, which leads to production of the capsinoid precursor vanillyl alcohol. Here, to develop Capsicum annuum pepper varieties with high capsinoid contents, marker-assisted backcrossing was performed during backcross breeding. For foreground selection, plants carrying the pAMT/pamt genotype were selected from BC₁F₁ and BC₂F₁ populations using SCAR markers derived from the unique pamt mutation of ‘SNU11-001.’ To obtain background selection markers, 412 single nucleotide polymorphism (SNP) markers were screened to identify SNP markers polymorphic between the ‘Shinhong’ paternal lines and ‘SNU11-001.’ Of the 412 SNP markers, 204 polymorphic SNP markers evenly distributed in pepper genome were selected. BC₁F₁ and BC₂F₁ plants carrying the pAMT/pamt genotype were subjected to background selection using these SNP markers. Multiple genotypes were analyzed using a high-throughput genotyping system. As a result, one BC₁F₁ plant 84 % similar to the recurrent parent and seven BC₂F₁ plants showing more than 96 % recovery of the recurrent parent genotype were selected. Genetic backgrounds of the selected BC₂F₁ plants were evaluated using the genotype-by-sequencing (GBS) method to confirm the background selection results from the SNP marker set. GBS results showed that the recovery rate and positions of introgressed segments were well matched between two methods, demonstrating MABC can be successfully performed with only ~200 SNP markers.