Construction of high-density genetic linkage maps and mapping of growth-related quantitative trail loci in the Japanese flounder (Paralichthys olivaceus).

Wentao Song,Lei Wang,Changwei Shao,Xiaolin Liao,Jing Zhang,Songlin Chen,Renyi Pang,Jian Sun,Fengtao Gao,Yongsheng Tian,Yuze Niu,Yongwei Zhao,Zhanjiang Liu

doi:10.1371/journal.pone.0050404

Wentao Song, Lei Wang + Show 11 more

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https://doi.org/10.1371/journal.pone.0050404

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Abstract

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS.

Highlights

Genetic linkage mapping has become a critically important tool in many areas of genetic research
Genetic Markers To obtain microsatellite markers useful for linkage analysis, we examined the segregation patterns of 4600 markers in the mapping family
Segregation Analysis Segregation distortion from expectation under Mendelian inheritance was found in 625 (38%) of 1624 microsatellite markers. These markers are normally excluded from linkage analysis, the independence LOD score, one of the grouping parameters provided by JoinMap4.0, allows these markers to be included

Summary

Introduction

Genetic linkage mapping has become a critically important tool in many areas of genetic research. Genetic linkage maps based on microsatellite markers have been produced for economically important fish species, including salmon [2], tilapia [3], European sea bass [4], rainbow trout [5], sea bream [6], Barramundi [7], catfish [8], grass carp [9], Japanese flounder [10] and Asian sea bass [11]. The QTL for growth, disease resistance and stress response have been mapped in only a few species to date, such as disease resistance in rainbow trout [14] and Japanese flounder [15], body weight in salmon [16] and European seabass [17], cold tolerance in tilapia [18], and color variation in the guppy [19]

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