Effect of genotyping strategies on the sustained benefit of single-step genomic BLUP over multiple generations.
Effect of genotyping strategies on the sustained benefit of single-step genomic BLUP over multiple generations.
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DOI：
10.1186/s12711-022-00712-y
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发表时间：
2022-03-18
期刊：
影响因子：
--
通讯作者：
Pong-Wong R
中科院分区：
文献类型：
--
作者：
Sánchez-Mayor M;Riggio V;Navarro P;Gutiérrez-Gil B;Haley CS;De la Fuente LF;Arranz JJ;Pong-Wong R
单步基因组最佳线性无偏预测（ssGBLUP）允许在单个分析中包含来自基因分型和未基因分型个体的信息。这避免了对所有候选物进行基因分型的需要，具有降低总体成本的潜在益处。本研究的目的是评估使用ssGBLUP评估时，基因分型策略的效果、基因分型候选者的比例以及对待基因分型候选者进行排序的基因分型标准。进行模拟研究，假设在几个离散世代中进行选择，其中对一部分候选人进行基因分型，并使用ssGBLUP进行评估。所比较的设想是：（i）由其方案定义的用于选择待基因分型的候选人的三种基因分型策略（随机：随机选择候选者; TOP：对具有最佳基因分型标准的候选者进行基因分型;和EXTREME：对具有最佳和最差标准的候选者进行基因分型）;（ii）八个比例的基因分型候选者（p）;和（iii）两个基因分型标准，用于将待基因分型的候选者分级（候选者自身的表型或估计的育种值）。比较的标准是累积增益和基因组估计育种值（GEBV）的可靠性。具有最大累积增益的基因分型策略是TOP，其次是RANDOM，EXTREME在低p时表现为RANDOM，在高p时表现为TOP。然而，GEBV的可靠性用RANDOM高于TOP。增益趋势和可靠性之间的这种差异是由于TOP方案对具有更大被选择机会的候选人进行基因分型。当对待基因分型的候选者进行排名的选择标准的准确性增加时，用TOP获得的额外增益增加。当只有一部分候选人要进行基因分型时，使遗传增益最大化的最佳策略是TOP，因为它优先考虑更有可能被选择的候选人的基因分型。然而，具有最大GEBV可靠性的策略并没有实现最大的增益，因此可靠性不能被认为是用于确定使遗传增益最大化的方案的绝对和充分的标准。在线版本包含补充材料，可通过10.1186/s12711-022-00712-y获得。
Single-step genomic best linear unbiased prediction (ssGBLUP) allows the inclusion of information from genotyped and ungenotyped individuals in a single analysis. This avoids the need to genotype all candidates with the potential benefit of reducing overall costs. The aim of this study was to assess the effect of genotyping strategies, the proportion of genotyped candidates and the genotyping criterion to rank candidates to be genotyped, when using ssGBLUP evaluation. A simulation study was carried out assuming selection over several discrete generations where a proportion of the candidates were genotyped and evaluation was done using ssGBLUP. The scenarios compared were: (i) three genotyping strategies defined by their protocol for choosing candidates to be genotyped (RANDOM: candidates were chosen at random; TOP: candidates with the best genotyping criterion were genotyped; and EXTREME: candidates with the best and worse criterion were genotyped); (ii) eight proportions of genotyped candidates (p); and (iii) two genotyping criteria to rank candidates to be genotyped (candidates’ own phenotype or estimated breeding values). The criteria of the comparison were the cumulated gain and reliability of the genomic estimated breeding values (GEBV). The genotyping strategy with the greatest cumulated gain was TOP followed by RANDOM, with EXTREME behaving as RANDOM at low p and as TOP with high p. However, the reliability of GEBV was higher with RANDOM than with TOP. This disparity between the trend of the gain and the reliability is due to the TOP scheme genotyping the candidates with the greater chances of being selected. The extra gain obtained with TOP increases when the accuracy of the selection criterion to rank candidates to be genotyped increases. The best strategy to maximise genetic gain when only a proportion of the candidates are to be genotyped is TOP, since it prioritises the genotyping of candidates which are more likely to be selected. However, the strategy with the greatest GEBV reliability does not achieve the largest gain, thus reliability cannot be considered as an absolute and sufficient criterion for determining the scheme which maximises genetic gain. The online version contains supplementary material available at 10.1186/s12711-022-00712-y.
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3.3
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