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

Abstract

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.

Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses

“…Very few publications have recently reported markers derived from association studies that are based on a larger number of unrelated genotypes and therefore have a much broader genetic base and use a large number of molecular markers covering the genome [ 17 , 19 , 25 , 26 ].…”

“…For roses, a number of genomes [ 14 , 15 ] have been published, and the WagRhSNP 68k Axiom SNP array [ 16 ], providing 68,893 SNPs, allows high-density marker analyses and the identification of candidate genes. GWAS has been used to determine QTL associated with anthocyanin and carotenoid contents of petals in roses [ 17 ], with adventitious shoot regeneration [ 18 ], with petal numbers [ 14 ] and the genetic analysis of callus formation [ 19 ]. In the current paper, we present markers on QTL for petal number, petal length and fragrance evaluated in the same rose panel used in previous studies by Schulz et al [ 17 ] and Nguyen et al [ 18 , 19 ].…”

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

“…to identify SNPs within and between rose varieties. SNPs, which detected variation among tetraploid roses, were selected for constructing the WagRh SNP 68K Axiom ® genotyping array, which has since been used to genotype 96 ornamental rose cultivars for use in several GWAS [ 155 , 156 , 157 , 158 ].…”

“…Ornamentals: An association panel with 96 mostly tetraploid roses was investigated for a number of commercially important traits. Carefully conducted experiments were performed to provide data for concentration of anthocyanins and carotenoids in the rose petals [ 155 ], the capacity of leaf petioles to generate adventitious shoots [ 157 ], the capacity to form roots in vitro and in vivo [ 156 ], and the capacity to form calluses on leaf explants in vitro [ 158 ]. This rose panel was also genotyped with the WagRhSNP 68K Axiom ® SNP array, and several GWAS were performed.…”

“…Some of these SNPs were located in genes with homology to root-related genes. In the study on callus formation, a large cluster of markers was found on chromosome 3 and minor clusters on other chromosomes [ 158 ]. A rose APETALA2/TOE homologue was identified as a major regulator of petal number on chromosome 3 using genetic information acquired in the process of developing a high-quality genome sequence in diploid rose [ 190 ].…”