A RARSeq based Association mapping study was performed in a population of 104 Elaeis oleifera x E. guineensis hybrids of five origins with the aim of finding functional markers associated to six productive and 19 oil quality traits. For this purpose mRNA of each genotype was isolated and double stranded cDNA was synthesized. Following digestion with two restriction enzymes and adapter ligation, a size selected pool of barcoded amplicons was produced and sequenced using Illumina MiSeq. The obtained sequences were processed with a "snakemake" pipeline, filtered and missing values were imputed. For all traits except two significant effects of the origin was observed. Genetic diversity analyses revealed high variability within origins and an excess of heterozygosity in the population. Two GLM models with Q matrix or PCA matrix as covariates and two MLM models incorporating in addition a Kinship matrix were tested for genotype-phenotype associations using GAPIT software. Using unadjusted p values (< 0.01) 78 potential associations were detected involving 25 SNP and 20 traits. When applying FDR multiple testing with p < 0.05, 25 significant associations remained involving eight SNP and six quality traits. Four SNP were located in genes with a potential relevant biological meaning.

中文翻译：

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使用 RARSeq 检测与种间油棕杂交种的生产和油质量性状相关的重要 SNP

一项基于 RARSeq 的关联作图研究在 104 个来自五个来源的油棕 x E. guineensis 杂种群体中进行，目的是找到与 6 个生产性状和 19 个油质性状相关的功能标记。为此目的，分离每个基因型的mRNA并合成双链cDNA。在用两种限制性内切酶消化和接头连接后，产生了大小选择的条码扩增子库，并使用 Illumina MiSeq 进行测序。获得的序列用“蛇形”管道处理，过滤和缺失值被估算。除了两个显着的起源影响外，所有性状都被观察到。遗传多样性分析揭示了起源内的高度可变性和种群中过多的杂合性。使用 GAPIT 软件测试了具有 Q 矩阵或 PCA 矩阵作为协变量的两个 GLM 模型和另外包含亲属矩阵的两个 MLM 模型的基因型-表型关联。使用未调整的 p 值 (< 0.01) 检测到 78 个潜在关联，涉及 25 个 SNP 和 20 个性状。当应用 p < 0.05 的 FDR 多重测试时，25 个显着关联仍然涉及 8 个 SNP 和 6 个质量特征。四个 SNP 位于具有潜在相关生物学意义的基因中。25 个重要的关联仍然涉及 8 个 SNP 和 6 个质量特征。四个 SNP 位于具有潜在相关生物学意义的基因中。25 个重要的关联仍然涉及 8 个 SNP 和 6 个质量特征。四个 SNP 位于具有潜在相关生物学意义的基因中。