High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum \xd7 morifolium Ramat.)

Xuebin Song,Chengyan Deng,Yingying Li,Yuhui Xu,Kang Gao,Huaigen Xin,Guangxun Fan,Silan Dai,Fan Zhang,He Huang

doi:10.1038/s41438-020-0333-1

Xuebin Song, Chengyan Deng + Show 8 more

Open Access

https://doi.org/10.1038/s41438-020-0333-1

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Abstract

Flower type is an important and extremely complicated trait of chrysanthemum. The corolla tube merged degree (CTMD) and the relative number of ray florets (RNRF) are the two key factors affecting chrysanthemum flower type. However, few reports have clarified the inheritance of these two complex traits, which limits directed breeding for flower-type improvement. In this study, 305 F1 hybrids were obtained from two parents with obvious differences in CTMD and RNRF performance. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, we constructed a high-density genetic linkage map with an average map distance of 0.76 cM. Three major QTLs controlling CTMD and four major QTLs underlying RNRF were repeatedly detected in the 2 years. Moreover, the synteny between the genetic map and other Compositae species was investigated, and weak collinearity was observed. In QTL regions with a high degree of genomic collinearity, eight annotated genes were probed in the Helianthus annuus L. and Lactuca sativa L. var. ramosa Hort. genomes. Furthermore, 20 and 11 unigenes were identified via BLAST searches between the SNP markers of the QTL regions and the C. vestitum and C. lavandulifolium transcriptomes, respectively. These results lay a foundation for molecular marker-assisted breeding and candidate gene exploration in chrysanthemum without a reference assembly.

Highlights

Flower type is an important quality trait of all ornamental plants[1,2]
Compared with the framework linkage map constructed based on SSR, SRAP and AFLP markers, the above markers added more than 10,000 markers, and the average map distance was reduced by 9.93 cM17
This study provides a foundation of selective molecular markers for marker-assisted breeding and the gene mapping and map cloning of QTLs for corolla tube merged degree (CTMD) and relative number of ray florets (RNRF) in chrysanthemum

Summary

Introduction

Flower type is an important quality trait of all ornamental plants[1,2]. Flower-type variation is extremely abundant in chrysanthemum due to the presence of ray and disc florets with complex and varied shapes in the chrysanthemum capitulum. Compared with the framework linkage map constructed based on SSR, SRAP and AFLP markers, the above markers added more than 10,000 markers, and the average map distance was reduced by 9.93 cM (compared to 10.82 cM with the shortest average distance between markers)[17] This strategy is advantageous for the construction of maps in highly heterozygous ornamental plants without reference genomes. Based on this technology, ultrahigh-density genetic maps with an average map distance of less than 1 cM have been successfully constructed for Paeonia suffruticosa[18], Osmanthus fragrans[19] and Prunus mume[14]. SNP markers obtained from the whole genome can promote the subsequent analysis of population evolution and fine mapping[22]

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