McElroy Michel S, Navarro Alberto J R, Mustiga Guiliana, Stack Conrad, Gezan Salvador, Peña Geover, Sarabia Widem, Saquicela Diego, Sotomayor Ignacio, Douglas Gavin M, Migicovsky Zoë, Amores Freddy, Tarqui Omar, Myles Sean, Motamayor Juan C
Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
MARS, Incorporated c/o United States Department of Agriculture - Agricultural Research Service, Miami, FL, United States.
Front Plant Sci. 2018 Mar 20;9:343. doi: 10.3389/fpls.2018.00343. eCollection 2018.
Cacao () is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches' broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: and , respectively. Resistant cultivars are the most effective long-term strategy to address diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao.
可可树是一种全球重要的作物，其产量受到病害的严重限制。两种最具破坏性的病害，即扫帚病（WBD）和霜霉病（FPRD），分别由一对相关真菌引起。抗性品种是应对这些病害的最有效长期策略，但要高效培育出抗性强且高产的新品种，就需要在田间试验前采用可靠的种质筛选方法。标记辅助选择（MAS）和基因组选择（GS）为预测新基因型的表现提供了两条潜在途径，有可能提高单位时间的选择增益。为了测试这两种方法的有效性，我们对厄瓜多尔三个相关的可可种群进行了全基因组关联研究（GWAS）和GS，这些种群使用15K单核苷酸多态性（SNP）微阵列进行基因分型，以评估扫帚病感染的三个指标（营养扫帚、垫层扫帚和番荔枝荚）、霜霉病的一个指标（丛梗孢荚）以及两个生产力性状（荚果总鲜重和健康荚果百分比）。GWAS在每个种群中都产生了几个与抗病性相关的SNP，但在其他种群中没有一个与相同性状显著相关。基因组选择，使用一个种群作为训练集来估计其余两个种群（由不同家族组成）的表型，在不同性状间有所不同，从平均预测准确率0.46（营养扫帚）到0.15（丛梗孢荚），并且在训练种群之间也有所不同。模拟结果表明，仅使用GWAS标记选择幼苗与随机选择相比没有改善，但GS显著改善了选择过程。我们的结果表明，这里发现的GWAS标记在不同种质间的预测性不足，无法用于MAS，但在GS框架中使用所有标记在加速可可树抗病性方面具有很大潜力。
