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Testing strategies for genomic selection in aquaculture breeding programs

机译:水产养殖育种计划中基因组选择的测试策略

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Genomic selection is a selection method where effects of dense genetic markers are first estimated in a test population and later used to predict breeding values of selection candidates. The aim of this paper was to investigate genetic gains, inbreeding and the accuracy of selection in a general genomic selection scheme for aquaculture, where the test population consists of sibs of the candidates. The selection scheme started after simulating 4000 generations in a Fisher-Wright population with a size of 1000 to create a founder population. The basic scheme had 3000 selection candidates, 3000 tested sibs of the candidates, 100 full-sib families, a trait heritability of 0.4 and a marker density of 0.5Ne/M. Variants of this scheme were also analysed. The accuracy of selection in generation 5 was 0.823 for the basic scheme when the sib-testing was performed every generation. The accuracy was hardly reduced by selection, probably because the increased frequency of favourable alleles compensated for the Bulmer effect. When sib-testing was performed only in the first generation, in order to reduce costs, accuracy of selection in generation 5 dropped to 0.304, the main reduction occurring in the first generation. The genetic level in generation 5 was 6.35σa when sib-testing was performed every generation, which was 72%, 12% and 9% higher than when sib-testing was performed only in the first generation, only in the first three generations or every second generation, respectively. A marker density above 0.5Ne/M hardly increased accuracy of selection further. For the basic scheme, rates of inbreeding were reduced by 81% in these schemes compared to traditional selection schemes, due to within-family selection. Increasing the number of sibs to 6000 hardly affected the accuracy of selection, and increasing the number of candidates to 6000 increased genetic gain by 10%, mainly because of increased selection intensity. Various strategies were evaluated to reduce the amount of sib-testing and genotyping, but all resulted in loss of selection accuracy and thus of genetic gain. Rates of inbreeding were reduced by 81% in genomic selection schemes compared to traditional selection schemes for the parameters of the basic scheme, due to within-family selection.
机译:基因组选择是一种选择方法,其中首先在测试群体中估算致密遗传标记的作用,然后用于预测选择候选物的育种值。本文的目的是研究水产养殖的通用基因组选择方案中的遗传增益,近交和选择的准确性,其中测试种群由候选同胞组成。选择方案是在模拟规模为1000的Fisher-Wright人口中创建4000个世代后创建的。基本方案有3000个选择候选者,3000个经过测试的同胞,100个完整同胞科,性状遗传力0.4和标记密度0.5Ne / M。还分析了该方案的变体。对于基本方案,每代进行同胞测试时,第5代选择的准确性为0.823。通过选择很难降低准确性,这可能是因为有利的等位基因频率的增加补偿了布尔默效应。当仅在第一代中进行同胞测试时,为了降低成本,第5代中的选择精度降至0.304,主要降低发生在第一代中。每一代进行同胞测试时,第五代的遗传水平为6.35σa,比仅在第一代,仅在前三代或每一代中进行同胞测试时的遗传水平高72%,12%和9%。第二代。高于0.5Ne / M的标记密度几乎不会进一步提高选择的准确性。对于基本计划,由于家庭内部的选择,与传统选择计划相比,这些计划的近交率降低了81%。同胞数增加到6000几乎不会影响选择的准确性,而候选数增加到6000则遗传增益增加了10%,这主要是因为选择强度增加了。对各种策略进行了评估,以减少同胞测试和基因分型的数量,但所有策略均导致选择准确性下降,从而导致遗传增益下降。与传统选择方案相比,由于家庭内部选择,与传统选择方案相比,基因组选择方案的近交率降低了81%。

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