Details
| Original language | English |
|---|---|
| Pages (from-to) | 505-517 |
| Number of pages | 13 |
| Journal | Plant Cell, Tissue and Organ Culture |
| Volume | 142 |
| Issue number | 3 |
| Early online date | 7 Jul 2020 |
| Publication status | Published - Sept 2020 |
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.
Keywords
- Callus induction, Genome-wide association study (GWAS), Rosa x hybrida, SNP markers
ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- Horticulture
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In: Plant Cell, Tissue and Organ Culture, Vol. 142, No. 3, 09.2020, p. 505-517.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Genetic analysis of callus formation in a diversity panel of 96 rose genotypes
AU - Nguyen, Thi Hong Nhung
AU - Winkelmann, Traud
AU - Debener, Thomas
N1 - Funding information: Open Access funding provided by Projekt DEAL. This study was carried out with financial support from the Vietnamese Government and the Department of Molecular Plant Breeding, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany. Open Access funding provided by Projekt DEAL. This study was carried out with financial support from the Vietnamese Government and the Department of Molecular Plant Breeding, Institute of Plant Genetics, Leibniz Universit?t Hannover, Hannover, Germany.
PY - 2020/9
Y1 - 2020/9
N2 - 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.
AB - 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.
KW - Callus induction
KW - Genome-wide association study (GWAS)
KW - Rosa x hybrida
KW - SNP markers
UR - http://www.scopus.com/inward/record.url?scp=85087623962&partnerID=8YFLogxK
U2 - 10.1007/s11240-020-01875-6
DO - 10.1007/s11240-020-01875-6
M3 - Article
AN - SCOPUS:85087623962
VL - 142
SP - 505
EP - 517
JO - Plant Cell, Tissue and Organ Culture
JF - Plant Cell, Tissue and Organ Culture
SN - 0167-6857
IS - 3
ER -