Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).

Yan Xu,Chaotian Xie,Dehua Ji,Long Huang,Changsheng Chen,Hongkun Zheng

doi:10.1186/s12870-015-0604-4

Yan Xu, Chaotian Xie + Show 4 more

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https://doi.org/10.1186/s12870-015-0604-4

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Abstract

BackgroundPyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis.ResultsIn total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM.ConclusionsThe first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical map and will assist in the process of assembling the P. haitanensis genome sequence. This will have a positive impact on breeding programs that aim to increase the production and quality of P. haitanensis in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0604-4) contains supplementary material, which is available to authorized users.

Highlights

Pyropia haitanensis is one of the most economically important mariculture crops in China
This study presents the first example of quantitative trait locus (QTL) detection for economic traits in a double haploid (DH) population of P. haitanensis using a high-density linkage map and phenotypic data, these phenotypic data were obtained under only one environment
In this study, the SLAF-seq approach was used for largescale marker discovery and genotyping to develop a high-density genetic linkage map of P. haitanensis from a DH population of 100 lines

Summary

Introduction

Pyropia haitanensis is one of the most economically important mariculture crops in China. SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis. Pyropia/Porphyra is one of the most important marine macroalgae in terms of both its global distribution and economic importance. Farming and processing of Pyropia have generated the largest seaweed industries in East Asian countries, such as China, Japan, and South Korea [3, 4]. In China, two major cultivars, Pyropia yezoensis Ueda and Pyropia haitanensis Chang et Zheng, are distributed in North China and South China, respectively. P. haitanensis, as a typical warm, temperate zone species originally found in the south of China, has been extensively cultured in Fujian, Zhejiang and Guangdong Provinces of China for more than 50 years. Its output accounts for about 75 % of the total production of cultivated Pyropia in China [4, 5]

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