Evaluation of 1-stage and 2-stage selection in yellow perch I: Genetic and phenotypic parameters for body weight of F1 fish reared in ponds using microsatellite parentage assignment

ArticleinJournal of Animal Science 90(1):27-36 · August 2011with6 Reads
DOI: 10.2527/jas.2011-3902 · Source: PubMed
Two selection methods, 1-stage selection (OSS) and 2-stage selection (TSS), for improving efficiency and profitability of selective breeding of yellow perch were evaluated, through examining the genetic and phenotypic parameters for BW of F(1) fish using microsatellite parentage assignment in this study. Approximately 94% of the sampled yellow perch progeny were assigned to single parental pairs using 8 microsatellite markers, which confirmed the applicability of the communal rearing technique in yellow perch breeding. Within OSS, the genetic correlation between 1-yr-BW and 2-yr-BW was high (0.98), indicating that the growth of yellow perch recorded at yr 1 could predict their growth for yr 2. Also mean family BW and family EBV for BW between yr 1 and 2 were found to be significantly correlated, suggesting yr 1 fast-growing yellow perch families continued to be the fast growing families in yr 2. Two-year random fish undergoing TSS were significantly heavier (P < 0.01) than those undergoing OSS. In addition, top males and females with TSS were heavier (P < 0.01) than those with OSS. Based on these results we concluded that the TSS was more desirable and effective for yellow perch breeding compared with OSS in terms of improving selection efficiency and reducing costs.
    • The results from the MCMC Bayesian and REML analysis were varied in all traits in this study, and this might be caused by different tolerances of the whole sample size, unequal family sizes, and common environmental factors in different models and analyses. Although REML is thought to be robust against unbalanced design in their simulation (Lim et al. 2010), more research of environmental factors, unequal family sizes, and sample size could result in some bias in the estimates of the genetic parameters (Falconer and Mackay 1996; Fishback et al. 2002; Wang et al. 2008; Cao et al. 2012 ). Although the heritabilities were different between the two methods, all the growth traits were moderate to high heritabilites, as has been the case in the other fish species (Fishback et al. 2002; Liu et al. 2014) and also in our previous studies of M. amblycephala (Luo et al. 2014; Zeng et al. 2014).
    [Show abstract] [Hide abstract] ABSTRACT: Blunt snout bream, Megalobrama amblycephala, is an herbivorous freshwater fish and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system. The objective of the study is to estimate the genetic parameters for growth, body shape, and gonad traits for M. amblycephala at 1 yr of age. The phenotypic analysis showed that coefficients of variation for gonad traits had large variation relative to the other traits analyzed, and there was no sexual dimorphism by comparing growth and body shape in M. amblycephala. Based on restricted maximum likelihood and Markov chain Monte Carlo Bayesian methods using the animal model, the heritabilities of body weight (0.423–0.504), body length (0.309–0.678), body height (0.408–0.599), and dressed weight (0.359–0.643) were moderate and high, while the other traits, including conditional factor (0.029–0.199), body shape coefficient (0.095–0.405), edible ratio (0.073–0.207), gonad weight (0.018–0.170), and gonadosomatic index (0.050–0.222), had moderate or low heritabilities. High genetic and phenotypic correlations were found among growth traits, but not between growth traits and body shape or gonad traits except dressed weight. Based on our results, it could be efficient to combine the selection on body weight for fast growth and nonearly sexual maturity varieties of M. amblycephala breeding.
    Full-text · Article · Feb 2016
    • Therefore, selection for increased weight can be indirectly performed on length, which is much easier to measure in the field on a large number of fish (Vandeputte et al., 2004), and usually has a lower coefficient of variation, as found in our study, thus being more repeatable than weight (Friars et al., 1995). In addition, the length traits will be more accurate, with less influence from the volume of gonads, especially during the breeding season (Cao et al., 2011). Thus, the improvement for growth traits of grass carp can be achieved using an indirect selection method based on SL that is more practical and labor-saving for our ongoing selective breeding program.
    [Show abstract] [Hide abstract] ABSTRACT: The aim of this study was to estimate the growth trait parameters in grass carp, Ctenopharyngodon idella, which is one of the major freshwater aquaculture species in China. The heritability, genetic and phenotypic correlations were estimated for body weight, standard length, body height and body thickness measurements of 10 and 18 month old fish. Analyses were performed on a total of 41 and 104 full-sib families of grass carp including 937 and 2454 individuals at 10 (first spring) and 18 months (second winter) of age, respectively. The families were reconstructed using the molecular pedigree based on twelve microsatellite loci, and 97.6% of the offspring were unambiguously assigned to single parent pairs. Unbalanced contributions to progeny were found among families and parents (P b 0.01). Variance components and genetic parameters were estimated using the restricted maximum-likelihood algorithm with animal models. For all growth traits across two stages of grass carp, the common environment/maternal effect in proportion to phenotypic variance was very low (0.00–0.06), and not significant (P N 0.05). The heritability estimates for growth traits ranged from 0.24 to 0.38, and were significantly different from zero (P b 0.01). These results indicated that the breeding population had considerable additive genetic variation in growth traits, and the ongoing selective breeding program should produce considerable genetic improvement in the growth traits of the grass carp. High genetic and phenotypic correlations were found among growth traits (0.81–0.99, P b 0.01). These data indicate that selection for improved standard length will have a favorable effect on body weight in grass carp which is the key economic parameter for production yield. High and positive genetic correlations between growth traits at 10 and 18 months of age were also detected in grass carp (0.87–0.95, P b 0.01), which indicated that individuals with higher growth performance at 10 months also grew to be better at 18 months. The results showed that genetic differences in growth traits among grass carp progeny could be determined earlier by measuring indicator traits predictive of long-term genetically determined growth. Statement of relevance: Our article comply with the Policy Statement for submission of manuscripts to the Genetic Section. In this study, we aim to estimate the genetic parameters of growth traits in grass carp, Ctenopharyngodon idella, which is one of the major freshwater aquaculture species in China. The heritability, genetic, and phenotypic correlations were estimated for growth traits of grass carp at 10 and 18 months. Our study is an essential report on the quantitative genetic analysis of growth traits in sub-adult grass carp. This paper has not been submitted to any other journal for publication. The authors can confirm that the study has no actual or potential conflicts of interest to report. All authors have read and agreed the contents of the manuscript and consent to its publication.
    Full-text · Article · Jan 2016
    • Moreover, growth traits in yellow perch may be somewhat heritable. One study in a relatively small number of full-sib families estimated heritabilities between 0.075 and 0.14 for length and weight, respectively (Cao et al. 2012), while other studies have shown strong family effects and genotype by environment interactions for growth during the first 2 years of life (Wang et al. 2009aWang et al. , 2011). In the closely related percid walleye (Sander vitreus Mitchill), heritability of length and weight ranged from 0.30 to 0.93 (Kapuscinski et al. 1996).
    [Show abstract] [Hide abstract] ABSTRACT: Size-selective harvest of fish stocks can lead to maturation at smaller sizes and younger ages, which may depress stock productivity and recovery. Such changes in maturation may be very slow to reverse, even following complete fisheries closures. We evaluated temporal trends in maturation of five Great Lakes stocks of yellow perch (Perca flavescens Mitchill) using indices that attempt to disentangle plastic and evolutionary changes in maturation: age at 50% maturity and probabilistic maturation reaction norms (PMRNs). Four populations were fished commercially throughout the time series, while the Lake Michigan fishery was closed following a stock collapse. We documented rapid increases in PMRNs of the Lake Michigan stock coincident with the commercial fishery closure. Saginaw Bay and Lake Huron PMRNs also increased following reduced harvest, while Lake Erie populations were continuously fished and showed little change. The rapid response of maturation may have been enhanced by the short generation time of yellow perch and potential gene flow between northern and southern Lake Michigan, in addition to potential reverse adaptation following the fishing moratorium. These results suggest that some fish stocks may retain the ability to recover from fisheries-induced life history shifts following fishing moratoria.This article is protected by copyright. All rights reserved.
    Full-text · Article · Jun 2015
    • Therefore, microsatellite-based parentage identification approach could be a better alternative to overcome these defects imposed by physical tags as it can be retrospectively used after the growth phase of fish has been evaluated. It has been demonstrated that the accuracy of parentage assignment was usually very high even estimated with few microsatellite loci (Castro et al. 2007; Gheyas et al. 2009; Cao et al. 2012). In this study for golden mandarin fish, performed with seven microsatellite loci, the allocation success rate was 91.6 % in parentage identification with known parental andTable 3 Number of alleles (k), number of individuals (n) genotyped, observed heterozygosities [H (O)], expected heterozygosities [H (E)], polymorphic information content (PIC), probabilities of exclusion based either on the genotype of no parent known (Excl 1) or one parent known (Excl 2) for 325 S. scherzeri at seven microsatellite loci HW = Conformance to Hardy–Weinberg expectations, NS = P [ 0.05, ** P \ 0.01 filial information and 89.5 % in pedigree analysis in mixed families.
    [Show abstract] [Hide abstract] ABSTRACT: Retaining pedigree information and genetic diversity in each generation is essential but difficulty in selective breeding of aquaculture species. In this study, simulations and real data analysis were performed to examine the power of microsatellite markers in parentage determination of golden mandarin fish (Siniperca scherzeri). Simulations based on allele frequency data from the population of golden mandarin fish showed that the power of six loci to exclude false parents was higher than 95 % and that of seven loci over 97 %. When marker data from seven loci were combined, the accuracy of assignment to one true parental pair was up to 91.6 % with known parental and filial information. The marker panel tested in mixed families, 89.5 % of progeny was correctly assigned to their parental pairs. The mismatches caused by scoring errors at microsatellites loci were the major reason for the discrepancies between simulations and real data analysis. Taking these results into considerations, it was concluded that microsatellite markers can be used as a tool, alternative to physical tagging, to maintain pedigree information in selection programs of golden mandarin fish.
    Full-text · Article · Apr 2014
    • Some researchers presented that selection for weight is performed on length because length is much easier to measure in the field on a large number of fish (Vandeputte et al. 2004) and usually BL has a lower coefficient of variation therefore being more repeatable than BW (Friars, Bailey & O'Flynn 1995). In addition, female BW during breeding season is increased due to the larger volume of gonads (Cao et al. 2011), and therefore BL can be a better indication of meat yield than BW in some instances. In this sense, Friars et al. (1995) have demonstrated the usefulness of fork length instead of weight in genetic selection indexes for S. salar both at commercial and sexual maturity size.
    [Show abstract] [Hide abstract] ABSTRACT: Blunt snout bream (Megalobrama amblycephala) is an herbivorous freshwater fish species native to China and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system with high economic value. The genetic parameter estimates for important economic traits are needed for its selective breeding. The aim of this study was to estimate the heritabilities for its growth-related traits and explore the genetic and phenotypic correlations among the traits using microsatellite-based pedigree approach. Offspring from a mass-spawning of 92 broodstocks (42 sires and 50 dams) were reared in a communal pond and nine microsatellites were used to identify the parents of each sampled offspring. Of 749 offspring randomly selected, 708 (94.53%) could be assigned directly to a single parental pair, which was used for heritability estimates. Data were analysed using the method of restricted maximum likelihood (REML) using animal model and the results showed that the heritabilities of body weight, body length, total length and body height were 0.65, 0.53, 0.53 and 0.50, respectively. High genetic correlations were found among these four traits. According to these results, selection for growth seems to be feasible in M. amblycephala and the other growth traits will be heightened accordingly with the selection based on body length.
    Full-text · Article · Feb 2013
  • [Show abstract] [Hide abstract] ABSTRACT: During the past years, breeding programs for aquaculture have shown fast development. Globally, economically highly relevant species have experienced implementation of large scale breeding programs and it is impossible to imagine life today without them as they significantly improve production and profitability of enterprises. However, there are still many aquatic species cultured that rely on wild broodstock and for which there is no breeding program. The reasons for not having breeding programs are diverse: the knowledge to execute a breeding program is often not available, and more importantly, breeding programs are considered expensive. Costs for separate family rearing systems, testing environments, extensive tagging etc. are often limiting. Farming of percids is a new sector where pioneering farmers have to develop rearing systems, reproduction methodology, fish feeds, etc., all at the same time. Especially in such cases, low-cost methods are required to get their business up and running. For this reason, many farms consider the foundation of a basic breeding program as their least concern, only to reduce costs. However, we argue that there are good reasons to start with selective breeding at the very start of an aquaculture enterprise. In the next chapters, the principles of selective breeding programs will be described. This includes a basic description of the concept of estimating the heritable components of the phenotypic appearance of fish. Next the most commonly used selection methods and their implication for percids will be discussed. The potential traits for selection that should be relevant in percid culture are reviewed. Some insights into the optimisation of breeding programs and an overview of basic breeding program management will be presented. We present an outline of how to maintain genetic diversity within cultured stocks, with a special focus on limiting rates of inbreeding while selecting. Finally, some insights on how to manage costs and benefits of breeding programs are discussed.
    Chapter · Jan 2015 · Aquaculture International
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