Strigolactone pathway genes and plant architecture: association analysis and QTL detection for horticultural traits in chrysanthemum

Abstract

Chrysanthemums are important ornamental plants with abundant phenotypic diversity. Especially in cut-flower breeding, shoot branching is important for the success of new varieties. To assess the genetic regulation of shoot branching and other horticultural important traits, we phenotyped and genotyped two types of chrysanthemum populations: a genotype collection of 86 varieties and a biparental F1-population (MK11/3) of 160 individuals. Using two different statistical approaches, a genome-wide association analysis and a single marker ANOVA, with AFLP marker data and candidate gene markers for shoot branching, we tried to identify markers correlated to the traits of interest. As expected for the outcrossing hexasomic chrysanthemums most of the phenotypic traits showed a continuous variation in both populations. With the candidate gene approach we identified 11 significantly associated marker alleles for all 4 strigolactone pathway genes BRC1, CCD7, CCD8 and MAX2 regulating shoot branching in the genotype collection. In the MK11/3 we detected seven markers for all candidate genes except MAX2 explaining a large proportion of the variation. Using anonymous AFLP markers in the GWA with the 86 genotypes and the single locus analysis with the F1-population we could detect 15 and 17 additional marker-trait associations, respectively. Our analyses indicate a polygenic inheritance of the shoot branching in the chrysanthemum, with a fundamental role of the strigolactone pathway genes BRC1, CCD7, CCD8 and MAX2 and we identified 50 associated markers to all traits under study. These markers could be used in the selection of the parental plants for breeding chrysanthemums to enrich them for positive alleles influencing plant architecture traits.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

“…In recent years, genome-wide association studies (GWASs) based on linkage disequilibrium have been shown to represent a powerful tool for detecting important QTLs or genes underlying complex traits in the sequenced genomes of rice 14 , Arabidopsis thaliana 15 , and maize 16 and the unsequenced genomes of wheat 17 and roses 18 . In chrysanthemums, GWASs have been used to identify favorable alleles and to explore the pattern of inheritance for a number of horticultural and WT traits based on gel-based markers 7,19,20 . However, the low marker density exhibited in the traditional molecular marker system limits the detection power of GWASs.…”

A SNP-enabled assessment of genetic diversity, evolutionary relationships and the identification of candidate genes in chrysanthemum

“…In chrysanthemum, Klie et al (2016) have used GWAS to identify a number of AFLP markers and candidate gene-related alleles associated with shoot branching traits and Li et al (2016) have uncovered considerable dominant markers linked to certain plant and inflorescence traits. The present attempt was based on a large collection of SNP assays, so was more informative than the Li et al (2016) study, which worked with a very limited number of gel-based markers.…”

“…This approach has been used to dissecting genetic basis of quantitatively inherited traits in a number of plant species (Huang et al 2010; Kump et al 2011; Morris et al 2013; Zhang, Song, et al 2014). The use of GWAS to date in chrysanthemum has been restricted to the genetic analysis of a few horticultural traits (Klie et al 2016; Li et al 2016). …”

Current achievements and future prospects in the genetic breeding of chrysanthemum: a review

“…Several candidate genes related to waterlogging tolerance and inflorescence-related traits were recently identified based on the above-mentioned SNP sets in a similar way 99,100 . Using another method, Klie et al 101 were able to identify 11 markers significantly associated with four strigolactone pathway genes regulating shoot branching in chrysanthemum by utilizing the candidate gene approach, which also provided insight into some potential candidate genes.…”