Genetic analysis of callus formation in a diversity panel of 96 rose genotypes

• Published in: Plant cell, tissue and organ culture Vol. 142; no. 3; pp. 505 - 517
• Main Authors: Nguyen, Thi Hong Nhung, Winkelmann, Traud, Debener, Thomas
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.09.2020; Springer Nature B.V
• Subjects: Acetic acid; Biomedical and Life Sciences; Callus; Chromosome 3; Chromosomes; Dichlorophenoxyacetic acid; Explants; Genetic analysis; Genetic factors; Genome-wide association studies; Genomes; Genotypes; Growth regulators; Hydrolase; Life Sciences; Original Article; Phenotypic variations; Plant Genetics and Genomics; Plant growth; Plant Pathology; Plant Physiology; Plant Sciences; Polyglutamine; Proteins; Quantitative trait loci; S-Formylglutathione hydrolase; Single-nucleotide polymorphism; Trinucleotide repeat diseases; Callus induction; Genome-wide association study (GWAS); SNP markers
• ISSN: 0167-6857; 1573-5044
• DOI: 10.1007/s11240-020-01875-6

In a diversity panel of 96 rose genotypes, variation in the capacity to form calluses on leaf explants in vitro was investigated, and a genome-wide association study (GWAS) was performed to identify genetic factors associated with callus formation. Calluses were induced from wounded in vitro leaflets on two media differing in their plant growth regulator composition. Significant differences between genotypes were observed in callus size on the first callus-inducing medium (CIM1, containing 10.7 µM naphthylene acetic acid) using a 0–4 scale, as well as on a second callus-inducing medium (CIM2, containing 4.5 µM dichlorophenoxyacetic acid and 2 µM 6-(γ,γ-dimethylallylaminopurine)) with callus size scales of 0.82–4. GWAS utilizing the WagRhSNP 68K SNP array for callus size induced on either CIM1 or CIM2 enabled the identification of 26 and 13 significantly associated SNPs, respectively. Among these SNPs, we found the SNPs Rh12GR_12098_1092Q (uncharacterized gene) and RhMCRND_2903_1233Q in a gene encoding a pentatricopeptide repeat-containing protein were associated with callus size on CIM1, with large effects being observed between alleles. Two SNPs, RhK5_5473_763P ( S -formylglutathione hydrolase) and Rh12GR_37799_568Q (polyglutamine binding protein, WW domain binding protein), were associated with callus size on CIM2 with large effect sizes. The markers associated with callus size on CIM1 form a large cluster on chromosome 3 and minor clusters on other chromosomes and provide the first preliminary indications of candidate genes responsible for the observed phenotypic variation. Key message Callus formation in rose is strongly genotype dependent and varies continuously among 96 genotypes. A major QTL associated to callus size was located on chromosome 3.