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 sequencingReportar como inadecuado




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 - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Genomics

, 16:902

Plant genomics

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.

KeywordsGenetic map SNP Undaria pinnatifida Laminariales Sex determination AbbreviationsSLAFSpecific length amplified fragment

QTLQuantitative trait loci

SSRSimple sequence repeat

AFLPAmplified fragment length polymorphism

SRAPSequence-related amplified polymorphism

SNPSingle nucleotide polymorphism

RRLReduced representation library

RADRestriction site-associated DNA

GBSGenotyping by sequencing

LGLinkage group

PESProvasoli enriched seawater

PCRPolymerase chain reaction

LODLogarithm of odds

SDRSex determining region

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-2184-y contains supplementary material, which is available to authorized users.

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Autor: Tifeng Shan - Shaojun Pang - Jing Li - Xia Li - Li Su

Fuente: https://link.springer.com/







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