Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.)

Abstract

Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.

Combining ability, heterosis, genetic distance and their intercorrelations for waterlogging tolerance traits in chrysanthemum

“…The Euclidean distance was calculated from the seven traits using SPSS 20.0 software (http://www-01.ibm.com), and it was treated as a measure of multivariate phenotypic distance (PD). Nei's (1972) genetic distance was calculated based on 707 informative markers (371, 49, and 406 generated from 39 SRAP, 7 SCoT and 31 EST-SSR, respectively) as reported by Li et al (2016) (GD) and 80 markers significantly associated with WT (QTL-GD) (P B 0.05, Table S1 and S2) according to a mixed linear model from a previous association mapping study . The dendrograms were constructed from the three distance matrixes using the unweighted pair group method with the arithmetic averages (UPGMA) method of cluster analysis in NTSYS-pc v2.1 software (Rohlf 1998).…”

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

“…During the past 1,600 years of breeding activity, chrysanthemums have developed some major cultivated types, i.e. traditional (TC) types, spray cut (SCC) types, disbud cut (DCC) types, potted and ground-cover (PGC) types, wild chrysanthemums (WC), diverse in plant architecture and inflorescence traits (Li and Shao 1990; Zhang, Dai, et al 2014; Li et al 2016). Specifically, the DCC type bears a single, large flower per stem, typically produced by removing side bud prior to flowering; and the SCC type bear several small flowers per stem, which were often more densely packed than those borne by the DCC type.…”

“…In a panel of 480 Chinese traditional chrysanthemum cultivars, however, the UPGMA (unweighted pair-group method with arithmetic means) clustering, based on genomic SSR-derived Nei’s genetic distances mostly was consistent with the horticultural classification (Zhang, Dai, et al 2014). A latest research in cut chrysanthemum failed to reflect known variation in either provenance or inflorescence type (Li et al 2016). Despite an enormous amount of research effect into genetic characterization of modern chrysanthemum, the phylogenetic relationships harbored in various cultivated types and the wild progenitors remain obscure as yet.…”

“…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 status and prospects of chrysanthemum genomics

“…다형성을 보이는 204개의 allele 중에서 42개의 allele 이 19종류의 표현형과 연관되었고, 몇몇 allele은 여러 형질 에 동시에 연관되었다 . 한편, 159 품종의 국 화를 대상으로 꽃차례(inflorescence)와 식물체 구조의 형질 11종을 조사하고, SRAP, start codon targeted (SCoT), expressed sequence tag-simple sequence repeat (EST-SSR) 표지를 이용하 여 유전형을 분석하였다 (Li et al 2016). 그 결과 707개의 allele 중에서 54개가 형질과 높은 연관성이 있었다 (Li et al 2016).…”