Fig 1.
Flowchart illustrating polygenic QTL mapping using the PEPIS.
The PEPIS is divided into two parts: sub-pipeline 1, used for the six polygenic kinship matrix calculations, and sub-pipeline 2, used for the six polygenic component ratio estimations and further genome scanning for main and epistatic genetic effects.
Table 1.
Summary of parallel strategy in the PEPIS for increasing analysis speed.
Fig 2.
(A) Data submission and (B) Results return.
Fig 3.
Pie charts illustrating the polygenic structure of the quantitative traits of rice.
(A) YIELD, (B) KGW, (C) GRAIN, and (D) TILLER.
Fig 4.
Plot of main-effect LRT results for quantitative traits with the markers/bins distributed across the complete rice genome.
(A) YIELD, (B) KGW, (C) GRAIN, and (D) TILLER. Dashed lines distinguish the 12 chromosomes and corresponding marker/bin numbers for the complete rice genome.
Fig 5.
Two-dimensional illustration of epistatic-effect LRTs for quantitative traits with marker/bin pairs distributed across the complete rice genome.
(A)YIELD, (B) KGW, (C) GRAIN, and (D) TILLER.