Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder

Abstract

A genetic linkage map of Japanese flounder was constructed using 165 doubled haploids (DHs) derived from a single female. A total of 574 genomic microsatellites (type II SSRs) and expressed sequence tag (EST)-derived markers (EST-SSRs) were mapped to 24 linkage groups. The length of linkage map was estimated as 1270.9 centiMorgans (cM), with an average distance between markers of 2.2 cM. The EST-SSRs were used together with type II SSR markers to construct the Japanese flounder genetic linkage map which will facilitate identify quantitative trait locus (QTL) controlling important economic traits in Japanese flounder. Thus, twelve skeletal traits at 2 years of age were measured for all DHs. Forty-one QTLs were detected on 14 linkage groups and totally account for a small proportion of phenotypic variation (4.5 to 17.3%). Most of QTLs detected distribute on linkage groups 5 (9 QTLs), 8 (9 QTLs), 9 (5 QTLs) and 20 (4 QTLs), in which, some QTLs perform the pleiotropy.

Bayesian Analysis for Genetic Architectures of Body Weights and Morphological Traits Using Distorted Markers in Japanese Flounder Paralichthys olivaceus

“…Except for the growth traits associated with body weights, few growth and morphological traits have been mapped in Japanese flounder (Liu et al 2013;Song et al 2012). In this DH population, Liu et al (2013) detected main-effect QTLs for six morphological traits and six skeletal traits by using interval mapping.…”

“…In this DH population, Liu et al (2013) detected main-effect QTLs for six morphological traits and six skeletal traits by using interval mapping. Of the detected QTLs, few were found by using Bayesian model selection with either the uncorrected aa represents the epistatic effect corresponding to additive by additive interaction conditional probabilities of QTL genotypes or the corrected one.…”

“…Herein, the genotype indicators are estimated using conditional probabilities of QTL genotypes on the flanking distorted markers. According to the results by interval mapping (Liu et al 2013), the expected numbers of main-effect QTLs and epistatic QTLs are set to 4 and 5, respectively, so that upper bound of QTLs is 9 þ 3 ffiffi ffi 9 p ¼ 18 (Yi et al 2005). A total of 2.1×10 6 rounds are ran to implement MCMC algorithm for each trait, first 10,000 rounds of which, as burn-in, are discarded to ensure proper mixing of the Markov chain.…”

“…Finally, 458 genetic markers are used to construct genetic linkage map (Liu et al 2013). The linkage map spans 1214.7 cM and on average, interval between adjacent unique marker loci is 2.65 cM long.…”

“…As a kind of Bayesian mapping methodology, Bayesian model selection approach has been developed based on a composite space representation of the problem (Yi et al 2005, which provides an efficient and relatively simple way of identifying epistatic QTLs for complex traits. In order to identify the QTLs for growth and morphological traits in Japanese flounder, a doubled haploids (DHs) population is constructed by mitotic gynogenesis (Liu et al 2013). It was found that nearly half of the genotyped markers segregate distortedly.…”