QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio)

Lv et al. BMC Genetics (2016) 17:65 DOI 10.1186/s12863-016-0370-9 RESEARCH ARTICLE Open Access QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio) Weihua Lv1,2, Xianhu Zheng2, Youyi Kuang2, Dingchen Cao2, Yunqin Yan1* and Xiaowen Sun2* Abstract Background: Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. Results: We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sibpair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in markerassisted selection. Conclusion: A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp. Keywords: Cyprinus carpio, Growth-related traits, Linkage maps, QTL, Multiple families Background The common carp (Cyprinus carpio) is one of the most widespread freshwater teleost species in the world. It has been domesticated as an important food fish in over 100 countries worldwide with global production exceeding 3.79 million tons in 2012, according to the Food and Agriculture Organization [1]. This globally important aquaculture species is used as a model in many research * Correspondence: ; 1 College of Life Science, Northeast Agricultural University, Harbin 150030, China 2 Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China areas, e.g., ecology, physiology, and evolution. Significant progress has been made in common carp genetics and genome research over the last decade. The current genomic resources available for common carp include polymorphic genetic markers [2, 3], genetic linkage maps [4–6], QTLs [7–10], cDNA microarrays [11], bacterial artificial chromosome libraries [12, 13], and physical maps [14]. Furthermore, A draft sequence of the common carp genome has been assembled [15], which provides reference sequences for genomic and comparative genomic studies of all common carp strains and other Cyprinidae species. All of these resources, which are available online (http://www.carpbase.org), lay the foundation © 2016 Lv et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Lv et al. BMC Genetics (2016) 17:65 for future studies on the genetic mechanisms of economic traits in common carp and related species. Growth is an economically important trait in the fish farming industry because it is directly related to fish production. An improvement in growth rate increases benefits for aquaculture companies because it decreases the raising time at farm facilities, leading to lower costs and higher harvests [16]. Growth-related traits such as body weight, total length, standard length, body depth, and body thickness are quantitative traits influenced by both environmental factors and multiple genes with relatively small effects according to the infinitesimal model [17]. Traditional selective breeding techniques are valuable in achieving improved fish growth [18], but the genetic gain can be increased far faster with MAS [19]. More recently, there has been an increasing number of studies that identify QTLs for growth-related traits in food fish species [20–22]. Most have been carried out in salmonids (e.g., Atlantic salmon [23, 24], rainbow trout [25], and coho salmon [26]), tilapia [27], sea bass [28, 29], and turbot [30, 31] as well as in common carp, involving backcross [32] and F1 [9, 33, 34] populations. However, all of these common carp QTL studies were limited to a single segregating family and small population size (~46–190 samples). In our previous study, through comparing the distribution and variation of QTLs in four half-sib families, we found that the major QTLs for growth-related traits were not fixed either between or among families. The study also revealed that both major and minor genes differ in their genetic performance. Therefore, we concluded that the major genes are undergoing change and remain unfixed in these families [35]. Further investigation is needed to identify shared and overlapping QTLs in either populations or families to understand quantitative genetic variation. In the present work, we conducted a genome scan for QTLs that affect body weight, total length, and body thickness in eight full-sib families containing 522 individuals from a breeding population. The objectives of this current study were: 1) to locate QTLs on linkage groups, 2) to identify which QTLs are either common or specific to all families, 3) to detect common and overlapping QTLs for the three growth-related traits, and 4) to explore the genetic architecture of growth-related traits. Results Phenotypic variation (...truncated)