Functional QTL mapping and prediction of 3D height measured from a robotic field scanalyzer in wheat

We provided the raw phenotypic data (FA_data_raw.RData), and individual-TP BLUPs, B-spline bases, and the first functional PCs from the 5, 10, and 26 TPs (phenotypic_traits.RData). The rqtl package input files for scenarios R1, R5, and R9 are also provided (CSP_ph17_5t_R1, CSP_ph17_10t_R5, and CSP_ph17_R9). The additive genomic relationship matrix is available as VanRaden_matrixCSP.RData. The codes provided are (1) factor analytic model, (2) smoothing and dimensionality reduction, QTL scanning using (3) individual-TP and (4) functional mapping, (5) power simulations, genomic prediction (6) with and (7) without including covariates as fixed effects.

本数据集提供原始表型数据（FA_data_raw.RData），以及来自5、10、26个训练群体（Training Population，TP）的个体-训练群体最佳线性无偏预测值（Best Linear Unbiased Prediction，BLUPs）、B样条基函数，还有首项功能主成分（functional Principal Components），相关内容均保存于phenotypic_traits.RData文件中。
此外，还提供了适配情景R1、R5、R9的rqtl软件包输入文件，具体为CSP_ph17_5t_R1、CSP_ph17_10t_R5与CSP_ph17_R9。
加性基因组亲缘关系矩阵以VanRaden_matrixCSP.RData文件形式提供。
本次提供的代码涵盖以下模块：(1) 因子分析模型；(2) 平滑与降维分析；(3) 基于个体-训练群体的数量性状位点（Quantitative Trait Locus，QTL）扫描，以及(4) 采用功能作图法的QTL扫描；(5) 统计功效模拟；(6) 纳入协变量作为固定效应的基因组预测，(7) 不纳入协变量作为固定效应的基因组预测。