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One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1–4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.

The black-lipped pearl oyster, Pinctada margaritifera , produces the largest and most valuable coloured pearls in the world. Cultured pearl size remains one of the most important quality traits. Despite the great geographical area covered by pearl farms in the atolls of French Polynesia, little is known about the influence of grow-out site effects on pearl size attained. To explore the genetic and environmental impact on the size of pearls as well as the genetic × environment interaction, a uniform experimental graft was designed on two contrasting macro-geographical lagoons. Five biparental families of donor oysters were grafted and then reared at both sites. After 18 months of culture, phenotypic parameters corresponding to pearl size, i.e. nacre weight and thickness, were recorded among the harvested pearls. The expression of Pif-177 gene, a biomarker encoding protein in the aragonite nacreous layer, was analysed in the corresponding pearl sac. The results show a family effect for nacre weight and thickness on both sites, with family F058 producing the heaviest and thickest nacre, and F805 the lightest and thinnest. By contrast, inter-site comparison revealed no significant site effects for these two parameters. In addition, grow-out location did not modify the relative gene expression of Pif-177 in the pearl sac between donor families in either culture site. Both nacre weight and thickness were positively correlated with the level gene expression of Pif-177. These results suggest that pearl size parameters were not affected by the environment in the present study and this is supported by the relative gene expression of Pif-177 observed. This knowledge constitutes an initial step in the study of pearl size trait inheritance, which will be helpful in the near future for the diffusion of genetically selected donor oyster lines produced by hatchery systems throughout production sites.

Pinctada margaritifera is an economically important marine bivalve species for cultured pearl production in French Polynesian aquaculture. In order to evaluate the influence of donor oyster age on pearl quality traits, experiments were conducted over 6 years using both grafts and surgreffe operations. At harvest, 6 pearl quality traits were recorded and compared: surface defects, luster, grade, darkness level, and visual color. Analyzing the quality traits of pearls harvested in the initial graft process and those of pearls obtained from surgreffe experiments allowed a comparison of the influence of pearl sac cells originating from the initial mantle graft, which aged together with their recipient oysters. The results demonstrated a significant decrease between these successive grafts in luster, grade (A-B-C,) darkness level, and green color – traits that are of major importance in the pearl market. The duplicated graft experiment allowed the comparison of donor oyster families at 2 and 5 years old, where a mantle graft was inserted into recipient oysters aged 2.5 years old. The results showed the same tendencies to a lesser extent, with 1) an improved pearl grade, predominantly through a most important rate of 0 surface defect category, and 2) a green / grey ratio in favor of the younger donor. A comparison between the graft-surgreffe and the duplicated graft experiments also highlighted: 1) the indirect role played by the younger recipient oysters, which must be optimized for optimal pearl quality realization, and 2) the complex interplay between donor and recipient oysters.

Grafting associates two distinct genotypes, each of which maintains its own genetic identity throughout the life of the grafted organism. Grafting technology is well documented in the plant kingdom, but much less so in animals. The pearl oyster, Pinctada margaritifera, produces valuable pearls as a result of the biomineralisation process of a mantle graft from a donor inserted together with a nucleus into the gonad of a recipient oyster. To explore the respective roles of donor and recipient in pearl formation, a uniform experimental graft was designed using donor and recipient oysters monitored for their growth traits. At the same time, phenotypic parameters corresponding to pearl size and quality traits were recorded. Phenotypic interaction analysis demonstrated: 1) a positive correlation between recipient shell biometric parameters and pearl size, 2) an individual donor effect on cultured pearl quality traits. Furthermore, the expressions of biomineralisation biomarkers encoding proteins in the aragonite or prismatic layer showed: 1) higher gene expression levels of aragonite-related genes in the large donor phenotype in the graft tissue, and 2) correlation of gene expression in the pearl sac tissue with pearl quality traits and recipient biometric parameters. These results emphasize that pearl size is mainly driven by the recipient and that pearl quality traits are mainly driven by the donor.

Cultured pearl nacre deposition rate in Pinctada margaritifera oysters was studied to examine its influence on Tahitian classification grade and colour and to further our understanding of using selected donor oysters produced in a hatchery system for the improvement of these traits. A large-scale grafting experiment using 150 farmed donor oysters was realised in Rangiroa atoll (French Polynesia). After 18 months of culture, 874 pearls were harvested and 7 pearls quality traits were recorded: (1) nacre deposition rate assessed by nacre thickness and weight, (2) classification grade, lustre and surface defects, and (3) colour assessed by pearl colour darkness level and visual colour categories. Nacre deposition rate significantly influence pearl grade, surface defects, darkness level and colour categories, but not the lustre. Grade A pearls had the thickest and heaviest nacre on average, compared with grade D pearls and rejects. In addition, pearls without any surface defect had thicker and heavier nacre. Pearls with low darkness were the thinnest and the lightest. Pearls of aubergine–peacock secondary colours were the thickest and the heaviest. These results highlight the importance of rapid nacre deposition rate for increasing the production of grade A pearls, with less surface defects and dominance of a black tone colour. Fast nacre deposition may, however, have a negative impact on other pearl quality traits, such as pearl lustre. This study demonstrates the importance of examining relationships between pearl quality traits in a way that provides solid information that can be directly used for breeding and genetic selection programmes.

Ageing is defined as the progressive decline in tissue and organ functions over time. This study aims to evaluate the ageing effect on cultured pearl quality phenotypes (including size and quality traits) in the graft-recipient animal model: Pinctada margaritifera. For this, eight uniform grafting experiments were designed using two hatchery-produced pearl oyster families as donors, which were followed through time, between 7 and 30 months in age. For each age category, 20 donors were studied for each culture site giving a total of 2400 grafted oysters. Several phenotypic measurements were made: 1) donor family growth performance from shell size records, 2) pearl size and corresponding quality traits, and 3) expression of some genes related to biomineralization processes on both the mantle graft and on pearl sac tissues. Results showed that: 1) donor age has an impact on pearl size, with grafts coming from the youngest donors yielding the biggest pearls; and 2) grafts from donors between 12 and 18 months in age produced pearls of the highest quality (grade and surface quality), a result supported by an analysis where the level of expression for a panel of genes associated with biomineralization was greatest in donors within the 12 to 18 months age group. These results indicate that donors aged between 12 and 18 months have high potential for biomineralisation and nacre deposition, and likely produce larger and higher quality cultured pearls than older donors.

Premise of the study: We developed nuclear microsatellite primers to explore the genetic diversity, population genetic structure, and evolutionary history of the fonio (Digitaria exilis), an understudied cereal cultivated in West Africa. o Methods and Results: We used a microsatellite-enriched library approach to isolate and characterize 38 nuclear primer pairs (31 di-, five tri-, and two tetranucleotide repeats), of which 21 were polymorphic and exhibited a clear pattern in 36 accessions from West Africa. The number of alleles per locus ranged from two to 22, with a mean of 4.71, and expected heterozygosity ranged from 0.03 to 0.93. o Conclusions: The developed set of 21 polymorphic SSR markers will provide tools for population and evolutionary genetics studies of the cultivated fonio. (Resume d'auteur)