Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis.

Xiaopeng Fu,Xiaoni Zhang,Qijian Wang,Shaozong Yang,Shengnan Lin,Mohammed Bendahmane,Xiuli Yan,Manzhu Bao,Fabrizio Costa

doi:10.1093/jxb/erz558

Xiaopeng Fu, Xiaoni Zhang + Show 7 more

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https://doi.org/10.1093/jxb/erz558

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Abstract

The double flower is a highly important breeding trait that affects the ornamental value in many flowering plants. To get a better understanding of the genetic mechanism of double flower formation in Dianthus chinensis, we have constructed a high-density genetic map using 140 F2 progenies derived from a cross between a single flower genotype and a double flower genotype. The linkage map was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with 2353 single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping analysis was conducted for 12 horticultural traits, and major QTLs were identified for nine of the 12 traits. Among them, two major QTLs accounted for 20.7% and 78.1% of the total petal number variation, respectively. Bulked segregant RNA-seq (BSR-seq) was performed to search accurately for candidate genes associated with the double flower trait. Integrative analysis of QTL mapping and BSR-seq analysis using the reference genome of Dianthus caryophyllus suggested that an SNP mutation in the miR172 cleavage site of the A-class flower organ identity gene APETALA2 (DcAP2L) is responsible for double flower formation in Dianthus through regulating the expression of DcAG genes.

Highlights

Genetic linkage maps play important roles in genetic and genomic studies, and provide an essential foundation for quantitative trait locus (QTL) mapping and map-based cloning. Bernatzky and Tanksley (1986) constructed the first linkage map for tomato which contains 84 restriction fragment length polymorphisms (RFLPs)
Quantitative trait locus (QTL) mapping of the flower type phenotype and other horticultural traits was conducted, and candidate genes were selected by integrative analysis of QTL mapping and Bulked segregant RNA-seq (BSR-seq). This map helps the identification of DcAP2L as a candidate gene associated with the double flower type.We report that an single nucleotide polymorphisms (SNPs) in the miR172 target site of DcAP2L is likely to be associated with double flower formation in D. chinensis
Caryophyllales are valued as pentamerous ornamental plants (Decraene et al, 1998) and are typically considered as a representative plant for the study of the transition between pentamerous and trimerous flower forms (Soltis et al, 2003)

Summary

Introduction

Genetic linkage maps play important roles in genetic and genomic studies, and provide an essential foundation for quantitative trait locus (QTL) mapping and map-based cloning. Bernatzky and Tanksley (1986) constructed the first linkage map for tomato which contains 84 restriction fragment length polymorphisms (RFLPs). Bernatzky and Tanksley (1986) constructed the first linkage map for tomato which contains 84 restriction fragment length polymorphisms (RFLPs). Genetic maps were developed and used in a wide range of ornamental plant species, such as petunia (Strommer et al, 2000), rose (Debener and Mattiesch, 1999), azalea (Keyser et al, 2010), and chrysanthemum (Zhang et al, 2010). Single nucleotide polymorphisms (SNPs) became the main genetic markers to construct highresolution linkage maps after the emergence of next-generation sequencing (NGS). Restriction site-associated sequencing (RAD-seq) is widely used for genotyping and polymorphism identification (Davey and Blaxter, 2011). Several related methods for library construction have been developed, 1916 | Wang et al

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