NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain.
NEIKER Tecnalia, Campus Agroalimentario De Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain.
Plant Sci. 2020 Feb;291:110366. doi: 10.1016/j.plantsci.2019.110366. Epub 2019 Dec 3.
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.
基于 RARSeq 的关联作图研究在五个起源的 104 个油棕杂种群体中进行，目的是找到与六个生产力和 19 个油质性状相关的功能标记。为此，从每个基因型中分离出 mRNA，并合成双链 cDNA。用两种限制酶消化和接头连接后，产生了大小选择的带条形码扩增子池，并使用 Illumina MiSeq 进行测序。获得的序列通过“snakemake”管道进行处理，进行过滤和缺失值插补。除了两个性状外，其他所有性状都观察到了起源的显著影响。遗传多样性分析显示，各起源内部具有高度的变异性，且群体中存在杂合过度。使用 GAPIT 软件，使用包含 Q 矩阵或 PCA 矩阵作为协变量的两个 GLM 模型和另外包含亲缘关系矩阵的两个 MLM 模型，测试基因型-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 FDR 多重检验（p<0.05）时，仍有 25 个显著关联，涉及 8 个 SNP 和 6 个质量性状。四个 SNP 位于具有潜在相关生物学意义的基因中。
