Fig 1.
Visualization of phenotypic performance (A) Individual environment boxplot for grain yield. The y-axis is grain yield in t ha1 and the x-axis represents environments. The mid line in the box represent the median, the lower and upper horizontal lines of the box represent 25 and 75 percentiles, respectively. The lower whisker represents the 25th percentile minus 1.5 × inter-quartile range (IQR) and the upper whisker is the 75th percentile plus 1.5 × IQR. (B) Entry-mean heritability (C) Percentage of phenotypic variance explained (PVE), genotype and genotype x environment components (D) Genetic correlation between grain yield and agronomic traits.
Table 1.
Summary of consistent QTL for yield, yield components and agronomic traits.
Fig 2.
Genomewide scan for multi-trait QTL for grain yield and agronomic traits.
The upper graph is the QTL profile plot with the y-axis representing the log of likelihood, -log (P), for declaring significance of QTL. The red horizontal line represents the threshold corrected for the number of independent tests using Li and Ji [38]. The lower profile is the genomewide heat map of significant QTL across environments. The y-axis is the traits and the x-axis represents the chromosomes. The light blue to blue color indicates the high value allele originates from CO9602932 and the yellow-red color indicates the high value allele originates from TAM 111.
Table 2.
Multitrait QTL detected using data pooled across environments.
Fig 3.
Interactions and pleiotropic patterns based on markers linked to significant QTL from multi-environment and multi-trait QTL analysis.
(A) Eigentraits (ET) generated through singular value decomposition of phenotypic data. The first three ET explained approximately 90% of the phenotypic variation and were used for combined analysis of pleiotropy and epistasis (CAPE). The legend indicates the direction of variance among traits. For instance, for ET1, kernel spike-1 (KPS) and thousand kernel weight (TKW) vary in opposite direction compared to grain yield (GY) and spike m-2 (SPM). (B) Interaction patterns from CAPE with main effects (brown and blue) depicted on the concentric rings and interactions depicted by color-coded arrow lines within the plot. Brown arrow line represents enhancing effect whereas blue arrow line indicates repressing effect.
Table 3.
Significant marker-to-trait influences based on a subset of markers in combined analysis of pleiotropy and epitasis.