Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing.

Tifeng Shan,Jing Li,Shaojun Pang,Li Su,Xia Li

doi:10.1186/s12864-015-2184-y

Abstract

BackgroundUndaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida.ResultsA total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region.ConclusionsA high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2184-y) contains supplementary material, which is available to authorized users.

Highlights

Undaria pinnatifida is an important economic brown alga in East Asian countries
With the reduction of sequencing cost brought by advanced generation sequencing approach, Single nucleotide polymorphism (SNP) are becoming the first choice for construction of high-density genetic linkage map, in which the average marker interval can reach < 1 cM, providing more accurate foundation for discovery of functional genes and analysis of genome structure [48]
4626 Specific length amplified fragment (SLAF) and one simple sequence repeat (SSR) markers were assigned to 30 linkage group (LG), which equals the chromosome number identified by Yabu et al [41]

Summary

Introduction

Undaria pinnatifida is an important economic brown alga in East Asian countries. Undaria pinnatifida (Harv.) Suringar is an important economic macroalga that has been used as sea vegetable for a long history in East Asian countries [1]. Despite the economic and ecological importance and nutritional value, the genetic study of U. pinnatifida lags far behind that of S. japonica, for which the draft genome sequence has recently been sequenced and characterized [8]. A genetic linkage map is a basic and robust tool for genetic and genomic research, which can provide a foundation for identification of genomic loci linked to phenotypic variants, mapping of quantitative traits loci (QTL) and even anchoring genomic sequence scaffolds [11,12,13]. There has been no genetic linkage map for U. pinnatifida

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