Blay Carole, Haffray Pierrick, Bugeon Jérôme, D'Ambrosio Jonathan, Dechamp Nicolas, Collewet Guylaine, Enez Florian, Petit Vincent, Cousin Xavier, Corraze Geneviève, Phocas Florence, Dupont-Nivet Mathilde
Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
SYSAAF, Station LPGP-INRAE, Rennes, France.
Front Genet. 2021 Feb 22;12:639223. doi: 10.3389/fgene.2021.639223. eCollection 2021.
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 () 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 (, , , , and ) 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.
水产养殖业的首要任务之一是对鱼类经济重要性状进行遗传改良，比如与加工和品质相关的性状。然而，由于缺乏来自足够大量动物群体的此类性状数据，遗传评估的准确性受到了阻碍。因此，本研究的目标有三个：（i）使用三种不同的表型分析技术[有创和无创：基于微波、数字图像分析和磁共振成像（MRI）]来估计虹鳟（）生长、产量和品质相关性状的遗传参数，（ii）检测与这些性状相关的数量性状基因座（QTL），以及（iii）识别这些QTL区域内存在的候选基因。我们的研究收集了1379条鱼的生长数据、产量相关性状（体重、肥满度、鱼头产量、胴体产量、去头去内脏胴体产量）和品质相关性状（总脂肪、皮下脂肪组织中的脂肪百分比、鱼肉中的脂肪百分比、鱼肉颜色）；然后使用57K SNP Axiom Trout基因分型芯片获得了所有鱼的基因型数据。所检测的14个性状中，大多数性状的遗传力估计值为中度到高度，范围从0.12到0.67。大多数性状显然是多基因的，但我们的全基因组关联研究（GWAS）在8号染色体上鉴定出两个基因组区域，它们解释了几个性状（体重、肥满度、皮下和总脂肪含量、胴体和去头去内脏胴体产量）高达10%的遗传变异（两个QTL的累积效应）。对于鱼肉颜色性状，六个QTL解释了1 - 4%的遗传变异。在这些区域内，我们鉴定出了几个与脂肪生成或类胡萝卜素代谢有关的基因（、、、、和），因此它们是进一步功能验证的良好候选基因。最后，在用于表型分析的三种技术中，MRI在脂肪含量和分布测量方面显示出特别的前景，而基于数字图像分析的方法在量化颜色相关性状方面非常有用。这项工作提供了新的见解，可能有助于虹鳟商业育种计划的发展，特别是在产量和鱼肉品质性状的遗传改良以及使用有创和/或无创技术预测此类性状方面。
