Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato (Solanum tuberosum).
Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato (Solanum tuberosum).
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DOI：
10.1534/g3.118.200273
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发表时间：
2018-07-02
期刊：
影响因子：
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通讯作者：
de Los Campos G
中科院分区：
文献类型：
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作者：
Enciso-Rodriguez F;Douches D;Lopez-Cruz M;Coombs J;de Los Campos G
马铃薯（Solanum tuberosum）是一种主要的粮食作物，被认为是全球碳水化合物的主要来源之一。晚疫病（致病疫霉）和普通疮痂病（疥疮链霉菌）是马铃薯种植面临的两个主要生产限制。以前的研究已经确定了一些晚疫病和普通赤霉病的抗性基因，但是，这些基因只能解释这些疾病的遗传力的一小部分。基因组选择已被证明是许多主要作物育种价值预测的有效方法（例如，玉米和小麦）。然而，该技术在马铃薯育种中很少受到关注。我们提出了第一个基因组选择研究涉及晚疫病和普通疮痂病在四倍体马铃薯。我们的数据涉及4，110（单核苷酸多态性，SNP）和表型田间评价晚疫病（n= 1，763）和普通赤霉病（n= 3，885）分别在7年和9年收集。我们报告了中等高的基因组遗传力估计值（晚疫病和普通赤霉病分别为0.46 ± 0.04和0.45 ± 0.017）。基因型与年份互作的程度晚疫病高，普通赤霉病低。我们的预测精度评估表明，四倍体马铃薯育种的基因组预测的适用性。对于这两个性状，我们发现超过90%的遗传方差可以用加性模型捕获。对于常见结痂，使用加性模型实现了最高的预测准确度。对于晚疫病，小，但统计上显着的收益，实现了使用模型，占加性和显性效应的预测精度。使用全基因组回归模型，我们确定了位于先前报道的晚疫病热点区域的SNP，与系统性抗病反应相关的基因，以及位于普通赤霉病WRKY转录因子的新位点。
Potato (Solanum tuberosum) is a staple food crop and is considered one of the main sources of carbohydrates worldwide. Late blight (Phytophthora infestans) and common scab (Streptomyces scabies) are two of the primary production constraints faced by potato farming. Previous studies have identified a few resistance genes for both late blight and common scab; however, these genes explain only a limited fraction of the heritability of these diseases. Genomic selection has been demonstrated to be an effective methodology for breeding value prediction in many major crops (e.g., maize and wheat). However, the technology has received little attention in potato breeding. We present the first genomic selection study involving late blight and common scab in tetraploid potato. Our data involves 4,110 (Single Nucleotide Polymorphisms, SNPs) and phenotypic field evaluations for late blight (n=1,763) and common scab (n=3,885) collected in seven and nine years, respectively. We report moderately high genomic heritability estimates (0.46 ± 0.04 and 0.45 ± 0.017, for late blight and common scab, respectively). The extent of genotype-by-year interaction was high for late blight and low for common scab. Our assessment of prediction accuracy demonstrates the applicability of genomic prediction for tetraploid potato breeding. For both traits, we found that more than 90% of the genetic variance could be captured with an additive model. For common scab, the highest prediction accuracy was achieved using an additive model. For late blight, small but statistically significant gains in prediction accuracy were achieved using a model that accounted for both additive and dominance effects. Using whole-genome regression models we identified SNPs located in previously reported hotspots regions for late blight, on genes associated with systemic disease resistance responses, and a new locus located in a WRKY transcription factor for common scab.