Figure 2. Plant height and seeds weight scaling in wild and cultivated
barley. A. pattern of scaling in wild barley, landrace and cultivars. B.
Kolmogorov-Smirnov plot showing the phenotypic distribution of plant
height in in wild barley, landrace and cultivars. C. Kolmogorov-Smirnov
plot showing the phenotypic distribution of seeds weight in in wild
barley, landrace and cultivars.
Both barley cultivars and landraces show a positive plant height and
seeds weight scaling with r = 0.422, p = 0.0001 for
cultivars (N=3390), and r = 0.230, p = 0.0001 for
landraces (N5740), respectively (Figure 2A). However, plant height and
seeds weight scaling is not evident in wild barley (N=292) withr = 0.0368 and p = 0.5233) (Figure 2A), which is probably
due to relatively small number of wild barley samples in the analysis.
Significant difference between phenotypic distribution in wild barley,
landrace and cultivar were observed. Kolmogorov-Smirnov test for equal
distribution for plant height between cultivar and landrace returned a D
= 0.128 and p = 0.0001, and a D = 0.127, p = 0.0001 for
seeds weight. Domestication led to a shift to shorter status, from a
median of 107.9 cm in wild barley to 98.8 cm in landraces and 102.2 cm
in cultivars (Figure 2B). Meanwhile, the shift of plant height to
shorter status was accompanied by a shift to smaller seeds, as it would
be expected from a positive plant height and seeds weight scaling.
Median seeds weight decreased from 46.5 g in wild barley to 45.3 g in
landraces and 43.5 g in cultivars (Figure 2C).
With the filtrations, a total of 133,588 SNPs were obtained for the
12,828 samples. Wild barley has a relatively higher genomic diversity
(nucleotide diversity π = 0.0673, N = 292) than both landraces (π =
0.0535, N = 5740) and cultivars (π = 0.0485, N = 3390). Plant height is
highly heritable with SNP-based heritability
hSNP2 of 0.603 ± 0.095, while SNPs
explained less variation in seeds weight with
hSNP2 of 0.322 ± 0.100. Plant height
and seeds weight are genetically correlated (r G = 0.272 ± 0.020,p < 0.0001). Barley accessions with closer genetic
relatedness tend to have similar plant height and to have similar seeds
weight, as indicated by the phylogenetic signal lambda of 0.822 andp < 0.001, while by the lambda of 0.853 and p< 0.001 for seeds weight. Generalised least-squares fit by
REML indicate that the two traits are phylogenetically correlated
(p < 0.001), implying that the two traits tend to vary
correlated toward the similar direction of the phenotypic spectrum.
Genome-wide association studies revealed 314 SNPs, or 0.23% of the
133,588 SNPs in total, associated with plant height, and 190 (0.14%)
with seeds weight. Among them, eight SNPs are associated with both
traits (Figure 2). The eight SNPs, forming two clusters in chromosome 2H
and 5H (Figure 2), can be traced to at least three functional genes
(Table 1), with two genes in cluster 1 (an Expansin B3 gene and an
Elongation Factor G gene), and one gene in cluster 2 (Vacuolar protein
sorting-associated protein 18 gene).