Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA.
International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
Genetics. 2021 Nov 5;219(3). doi: 10.1093/genetics/iyab122.
Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).
不同的作物既有杂交品种，也有克隆繁殖品种。育种者通常采用亲本截断选择，并投入大量时间、土地和资金来评估杂交后代，以寻找特殊的基因型。我们开发并测试了适合任意纯合度水平生物体的基因组交配选择标准，其中全同胞后代是未来的亲本和/或品种的直接关注点。我们扩展了交叉方差和协方差方差预测，以包括显性效应，并根据提出的亲本的单倍型、标记效应和重组频率预测杂交的多变量选择指数遗传方差。我们将预测的平均值和方差组合为亲本和品种开发的有用性标准。我们提出了一个关于木薯（Manihot esculenta）的实证研究，木薯是一种热带主要根作物。我们评估了使用交叉验证预测 462 个木薯家系的多变量遗传分布（平均值、方差和性状协方差）的潜力，包括加性和总价值。大多数方差（89%）和协方差（70%）预测准确性估计值大于零。杂交的有用性可以通过预测与实际成员表现之间的良好对应关系来准确预测，这些成员是育种者选择作为新亲本和候选品种的进步的。我们还使用了方向显性模型来量化大多数性状的显著近交衰退。我们预测了 306 个亲本的 47083 个可能的杂交，并与之前测试的杂交进行了对比，以展示交配选择如何揭示种质中的新潜力。我们使育种者能够考虑杂交产生未来亲本（具有最高育种值的后代）和品种（具有最高自身表现的后代）的潜力。
