Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis

Nguyen, Nguyen Hong; Phuthaworn, Chontida; Knibb, Wayne

doi:10.1016/j.ygeno.2019.11.014

Cited by 31 publications

(25 citation statements)

References 36 publications

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“…Our result is consistent with the published information in other shrimp populations, such as c 2 = 0.02-0.03 in the study of Castillo-Juarez et al [18]. The low common full-sib variance estimates in this study can be explained, because carcass and quality traits are less affected by the c 2 than growth-related traits [38]. The inclusion of the c 2 effects in our statistical models avoided an overestimation of the heritability estimated here.…”

Section: Common Full-sib Effectssupporting

confidence: 93%

Prospects for Genetic Improvement in Objective Measurements of Body Colour in Pacific Whiteleg Shrimp (Litopenaeus vannamei)

Giang

Knibb

Muu

et al. 2019

JMSE

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Body colour, together with growth and survival, are traits of commercial importance in Pacific whiteleg shrimp (Litopenaeus vannamei). However, heritability estimates for objective measurements of body colour are not available in Whiteleg shrimp species, including L. vannamei. Further, the effect of genotype by environment interactions (G × E) on this trait (i.e., the objective measures of body colour) and its genetic associations with growth are not known in this species. The present study presented the first attempt at understanding the genetic architecture of this complex character (body colour) that is of economic significance to the shrimp aquaculture sector world-wide. Specifically, we investigated the quantitative genetic basis of shrimp colour, while using the measurement tool (colorimeter) for a Whiteleg shrimp population reared in two contrasting environments. A total of 5464 shrimp had the objective measurements of body colour (lightness, yellowness, and redness) and growth trait records (weight, length and width). They were the offspring of 204 dams and 197 sires. The restricted maximum likelihood mixed model analysis showed that there were heritable additive genetic components for all of the measurements of shrimp colour, with the heritability (h2) ranging from 0.11–0.55. The h2 estimates for redness and yellowness traits differed between the two environments (h2 = 0.66–0.82 in Khanhhoa vs. 0.00–0.03 in Haiphong). However, the heritability for colour traits was moderate (0.11–0.55) when the two environments were combined. There is existence of (co)-genetic variances between the studied traits. The genetic correlations of body traits with redness or yellowness colour of the shrimp were moderate and positive (a*: 0.13–0.32 for redness and b*: 0.19–0.40 for yellowness). The effect of G × E interactions on shrimp colours could be important, as the genetic correlations for these traits between the two environments were low (−0.41 to 0.16). Our results showed that the genetic improvement for body colour can be achieved through direct selection and the increased redness colour is also expected to have favorable impacts on growth traits. Breeding programs to improve shrimp colour should account for the effects of environmental factors.

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Section: Common Full-sib Effectssupporting

confidence: 93%

Prospects for Genetic Improvement in Objective Measurements of Body Colour in Pacific Whiteleg Shrimp (Litopenaeus vannamei)

Giang

Knibb

Muu

et al. 2019

JMSE

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“…Interestingly, the gBLUP mixed model analysis obtained a close-to-one genetic correlation between body weight and length, which is consistent with the REML analysis [1]. This is also observed in a different study in banana shrimp in which the genetic correlations estimated from SNPs data had similar signs and direction to those obtained from pedigree and phenotype analysis [26]. These results suggest that genotyping by sequencing can provide informative markers to understand genetic relationships among complex traits in fish and aquaculture species.…”

Section: Genetic Parameterssupporting

confidence: 85%

“…Thus, when resources are permitted, a greater number of barramundi fish should be sequenced to improve the accuracy of genomic prediction, especially for the resistance to Streptococcus iniae. Published information reporting the genomic prediction accuracy is low to moderate (0.36 to 0.71) for a range of infectious diseases in fish species, namely resistance to amoebic gill disease in Atlantic salmon [21], resistance to infectious pancreatic necrosis virus in rainbow trout [22,23], resistance to viral nervous necrosis in European sea bass [24] or resistance to photobacteriosis in gilthead sea bream [25] or Hepatopancreatic parvovirus (HPV) disease in white shrimp [26]. When taken together, these results suggest the potential application of genomic selection to improve quantitative traits in Asian seabass.…”

Section: Genomic Predictionmentioning

confidence: 99%

Genome-Wide Marker Analysis for Traits of Economic Importance in Asian Seabass Lates calcarifer

Nguyen

Khang

2021

JMSE

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To date, it is not known whether animal breeding values in Asian seabass (Lates calcarifer) can be estimated using single nucleotide polymorphisms (SNPs) generated from new high-throughput genotyping by sequencing platforms. The principal aim of the present study was to assess the genomic prediction accuracy for growth traits, survival, cannibalism, and disease resistance against Streptococcus iniae in this species L. calcarifer. Additionally, this study attempted to identify markers associated with the five traits studied as well as to understand if the genotype data can be used to estimate genetic parameters for these complex traits. The genomic best linear unbiased prediction (gBLUP) method was used to analyze 11,084 SNPs and showed that the prediction accuracies for growth traits (weight and length) were high (0.67–0.75). By contrast, these estimates for survival were low (0.25). Multi-locus mixed model analyses identified four SNPs significantly associated with body weight (p < 5 × 10−8 or −log10p> = 5). There were, however, no significant associations detected for other traits. Similarly, the SNP heritability was moderate, while the estimates for other traits were approximated to zero and not significant. Genetic correlations between body weight and standard length were close to unity. Collectively, the results obtained from this study suggest that genotyping by sequencing platforms can provide informative DNA markers to conduct genome-wide association analysis, estimation of genetic parameters, and evaluation of genomic prediction accuracy for complex traits in Asian seabass.

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“…It can exploit within family variability more accurately than pedigree information and has been widely shown to be more efficient by improving predictive accuracy and increasing genetic gain relative to conventional selection methods [12]. To date, prediction accuracies have been reported in several fish and shrimp species, ranging from 0.16 to 0.83 for growth, carcass and meat quality traits, and disease resistance [15][16][17][18][19][20][21]. In molluscs, genomic selection is less common, but has been used to evaluate growth traits [22], disease resistance [23] in the Pacific oyster Crassostrea gigas, and pearl quality traits in the Pearl oyster Pinctada maxima [24].…”

Section: Introductionmentioning

confidence: 99%

“…An understanding of the relationship between genotyping costs and genomic prediction accuracy is necessary to find an appropriate balance between the two that will allow commercial adoption of genomic selection in the oyster breeding program. DArT-Seq has been used for genomic selection in other aquaculture species where a whole genome sequence is not available such as the banana shrimp [16] and yellowtail kingfish [15]. However, no studies to date have reported the use of DArT-Seq to evaluate prediction accuracy of genomic selection in a mollusc species.…”

Section: Introductionmentioning

confidence: 99%

Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology

Gondro

Nguyen

et al. 2021

Genes

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Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species.

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Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis

Cited by 31 publications

References 36 publications

Prospects for Genetic Improvement in Objective Measurements of Body Colour in Pacific Whiteleg Shrimp (Litopenaeus vannamei)

Prospects for Genetic Improvement in Objective Measurements of Body Colour in Pacific Whiteleg Shrimp (Litopenaeus vannamei)

Genome-Wide Marker Analysis for Traits of Economic Importance in Asian Seabass Lates calcarifer

Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology

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