Fig 1.
Diagram of key features of rare allele linkage scan compared to genome wide association study tests for quantitative trait loci.
Fig 2.
Distribution of representative traits plant height (PLHT, a Vegetative/Flowering Time trait), lateral branch length (LBLN, an Environmental Response trait), and total grain weight per plant (TGWP, a Reproductive trait) among outcross and selfed progenies in teosinte and maize.
The coefficient of inbreeding (δ) represents inbreeding depression as the mean proportional decline in trait values due to one generation of self-fertilization.
Table 1.
List of 18 teosinte-maize landrace comparable traits and the corresponding acronyms, units and trait groups. From Yang et al. (2019).
Fig 3.
Predicted segregating mutational burden per parent in the parents of maize and teosinte populations.
(A) Total number of sites heterozygous or homozygous for segregating deleterious alleles per individual parent, (B) Mean burden per site per parent based on genomic evolutionary rate profiling (GERP) score under a model of partial recessivity, including only sites segregating within the parent’s population, (C) Total burden per parent based on GERP scores, (D) Derived allele frequency spectrum for maize and teosinte populations. A total of 293,720 and 362,145 variants with GERP scores are segregating within maize and teosinte, respectively.
Fig 4.
Variation in outbred and selfed progeny breeding values among parents in teosinte and maize.
Mean values for self-fertilized S1 progenies (Y-axis) and outbred progenies (X-axis) scaled to the outbred population mean for each parent. Each trait is plotted in a different color. The 1:1 line is plotted in black, deviations from this line in the vertical direction correspond to the inbreeding depression for a single parent’s selfed progenies compared to their outcrossed siblings.
Fig 5.
Rare allele linkage scan for five traits in maize landrace and teosinte populations.
Each column represents one chromosome; linkage map cM positions are displayed on the x-axis. Each row represents LOD scores of linkage scan for one trait. Each founder parent is represented by a different color and the two different haplotypes of each parent are distinguished by solid vs. dashed lines. Red solid line indicates the whole-genome LOD significance threshold.
Fig 6.
The proportion of trait variance due to rare allele scan QTL (red color) and polygenic background effects (blue color) for each of 18 traits measured in maize and teosinte populations.
The number of rare allele scan QTL detected for each population and trait is indicated on top of bars.
Fig 7.
Segregation distortion whole genome scan results plotted as -log10p-valueof the chi-square test for agreement to expected 1:2:1 segregation at each genome region (cM position) for (A) three selfed families in maize, and (B) eleven selfed families in teosinte; each family scan is plotted on a different row. Blue arrows indicate significant segregation distortion regions.
Fig 8.
Percent inbreeding depression of individual families related to the parental rare allele load (RAL) measured genome-wide and within QTL CI for affected traits in maize and teosinte.
Only traits for which a significant (P < 0.05) correlation was observed within one of the populations are displayed.