Subsampling and DNA pooling can increase gains through genomic selection in switchgrass

Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross-validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the ...基因组选择（Genomic selection, GS）可加速多年生作物的育种周期，例如能源草柳枝稷（Panicum virgatum L.）。通过对训练群体（training population, TP）的DNA样本进行混合测序、仅对TP的表型极端个体进行测序，或是对候选群体（candidate population, CP）样本进行混合测序，可降低GS的测序成本。本研究在三个育种群体中，针对春季活力与开花期两个性状，对上述三种策略进行了模拟。仅对TP表型分布中最极端的50%个体进行测序时，以交叉验证（cross-validation）衡量的预测精度损失小于5%。当测序的TP DNA混合样本数量逐步减少时，预测精度也会随之下降，但仅由两个表型差异显著的DNA样本构建的TP，其相对于单个TP测序的平均预测精度仍保留了80%以上。新型分组检测方法允许每份测序的DNA样本同时筛选超过1个CP个体，但会带来预测精度的损失。为了确定……