Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis.
Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis.
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DOI：
10.1111/nph.12621
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发表时间：
2014-03
期刊：
影响因子：
--
通讯作者：
Jensen E
中科院分区：
文献类型：
--
作者：
Slavov GT;Nipper R;Robson P;Farrar K;Allison GG;Bosch M;Clifton-Brown JC;Donnison IS;Jensen E
对粮食和能源的需求不断增加，要求作物育种的有效性、速度和灵活性发生重大变化。因此，本研究的目的是评估全基因组关联研究（GWAS）和基因组选择（即从全基因组标记中预测表型）的潜力，以指导基础植物科学并加速能源草芒属的育种。我们通过对 138 个芒草基因型中的限制性位点相关 DNA (RAD) 标签进行测序，生成了超过 100 000 个单核苷酸变异 (SNV)，并将 SNV 与现场试验中测量的 17 个性状的表型数据相关联。在幼稚的 GWAS 分析中，群体结构和相关性的混淆是严重的，但混合线性模型可以强有力地控制这些影响，并使我们能够检测到达到全基因组显着性的多重关联。全基因组预测准确度往往为中等到高（平均值为 0.57），但不同性状之间的差异很大。正如预期的那样，预测能力随着绘图群体的规模线性增加，但当用于预测的标记数量超过 10 000–20 000 时达到稳定水平，并且在跨子群体进行交叉验证时趋于下降，但仍然显着。我们的结果表明，在芒草育种计划中立即实施基因组选择可能是可行的。
Increasing demands for food and energy require a step change in the effectiveness, speed and flexibility of crop breeding. Therefore, the aim of this study was to assess the potential of genome-wide association studies (GWASs) and genomic selection (i.e. phenotype prediction from a genome-wide set of markers) to guide fundamental plant science and to accelerate breeding in the energy grass Miscanthus. We generated over 100 000 single-nucleotide variants (SNVs) by sequencing restriction site-associated DNA (RAD) tags in 138 Micanthus sinensis genotypes, and related SNVs to phenotypic data for 17 traits measured in a field trial. Confounding by population structure and relatedness was severe in naïve GWAS analyses, but mixed-linear models robustly controlled for these effects and allowed us to detect multiple associations that reached genome-wide significance. Genome-wide prediction accuracies tended to be moderate to high (average of 0.57), but varied dramatically across traits. As expected, predictive abilities increased linearly with the size of the mapping population, but reached a plateau when the number of markers used for prediction exceeded 10 000–20 000, and tended to decline, but remain significant, when cross-validations were performed across subpopulations. Our results suggest that the immediate implementation of genomic selection in Miscanthus breeding programs may be feasible.
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影响因子：
3.7
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3.7
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