Discussion
The offspring size at independence has been shown to be correlated with
adult size across plant species (Moles et al., 2004) and animals
(McMahon & Bonner, 1983; Rollinson et al., 2019). Here we show that the
size scaling law holds within domesticated crop species when examining
the plant height and seeds weights within 12,828 globally collected
barley samples. The observed correlation across species between adult
size and offspring size at independence (seeds weight in the case of the
plant) has been hypothesized as the result of evolutionary coordination
between the two traits (Moles et al., 2005; Rees & Venable, 2007, 2009;
Westoby et al., 2009), though Grubb et al. (2005) argued for a
biomechanically constrained mechanism shaping size scaling. Despite the
mechanisms underlying size scaling remain debated from a theoretical
perspective (Niklas, 2004), the size components – plant height and
seeds weight – are undoubtedly under natural selection or artificially
selection in the case of crop plants (Gross & Beckage, 2012). It is a
logical hypothesis that the correlation between the two traits has a
genetic basis. Using a large dataset with high-density genome-wide SNP
map and phenotypes for barley, we demonstrated that two genetic
mechanisms might be involved in shaping the plant height and seeds
weight scaling. Both plant height and seeds weight are complex traits
and are influenced by multiple genes. Multiple genes with significance
in plant growth and development assert pleiotropic effects on both plant
height and seeds weight contribute to the positive correlation of the
two traits. Meanwhile, many of the genes influencing either plant height
or seeds weight are closely linked in the chromosome, leading to
co-inheritance of the two traits, also contributing to the trait
correlation in barley. Together, our results provide direct empirical
evidence to the hypothesis that the size scaling in plant has a genetic
basis and it may be the result of shared genetic factors controlling
both traits.
The plant height and seeds weight scaling hold for the domesticated
barley, in both landraces and cultivars, despite thousands of years of
domestication and breeding targeting the two traits in opposite
directions. Barley breeding tends to select varieties with shorter and
stiffer for protection against lodging and benefit of yield improvement
(Langridge, 2014). Indeed, we observed an average shorter plant in
landrace and cultivar than in wild barley. On the other hand, larger and
plump barley grains are favoured as plump kernels could produce more
beer from a given weight of malts (Gupta et al., 2010). Larger seeds
would also be a selection goal as they could contribute to yield
improvement. However, we observed averagely smaller seeds in both
landrace and cultivars than in the wild barley. It seems that plant
height and seed weight scaling is genetically constrained and less
influenced by direct artificial selection.
The evolution of seeds weight (size) in domestication has been
hypothesised be affected by both artificial and natural selection (Milla
et al., 2015). However, a comparative study (Kluyver et al., 2013)
failed to support the natural selection mechanism that proposes larger
seeds were selected in agricultural habitats to allow more effective
germination and larger vigorous seedlings with greater fitness (Turnbull
& Rees, 1999; Purugganan, 2019). Our results of shared genetic factors
controlling the two traits open an alternative hypothesis that the
evolution of seed weight in domestication may have been constrained by
the selection in plant height (size). Except for major cereal crops,
domestication tended to increase aboveground plant size in many crops
(Milla et al., 2017), likely as a consequence of selecting larger
vegetative part for human consumption. Therefore, larger seeds may have
been selected indirectly as the consequence of selecting for larger
non-seed part as the two traits are genetically correlated. For cereal
crops such as barley, rice and wheat, shorter plant with stiffer stem is
advantageous as it resists lodging and increases the relative proportion
of photosynthesis product allocating to seeds output. With cereal
varieties having shorter plant is selected for improving grain yield,
seeds adversely become smaller because of the genetic constrains.
Despite current researches believe that genetic architecture of size
scaling and more broadly trait correlations, in general, are polygenic
(Saltz et al., 2017). Gardner & Latta (2007) reviewed genetic
correlations among quantitative traits and found that an average
of only two QTLs (quantitative trait locus) were shared between two
correlated traits. The traditional method identifying causal QTLs for a
trait, such as GWAS, may have limits because those methods usually rely
on linkage decay among causal and non-causal variants to detect
associations, and therefore cannot directly establish the number of
causal variants (Gianola et al., 2015), which consequently underestimate
the pleiotropic genetic variants underlying trait correlations (Saltz et
al., 2017). Indeed, using regular GWAS analysis, we identified eight
SNPs in two clusters (two QTLs) possibly have pleiotropic effects on
plant height and seeds weight in barley. The advanced method in
deciphering the genetic architecture of trait correlation, e.g. common
factor analysis within the genomic SEM framework, allow us to identify
SNPs that may be pleiotropic on influencing plant height and seeds
weight, highlighting the power of advancement of analytical methodology.
At least three genes have been revealed to likely play an important role
in structuring plant height and seeds weight scaling in barley, an
expansins gene, an elongation factor G gene, and an Hsp90 organizing
protein gene. It is known that these genes have a function for diverse
traits related to plant growth and development. In barley, transcripts
of these genes could be found in both grain and shoot
(https://ics.hutton.ac.uk/barleyrtd/index.html). Expansins enable
the local sliding of wall polymers by reducing adhesion between adjacent
wall polysaccharides, and has an important role in cell wall
re-modelling after cytokinesis. Expansins are required in plant
physiological development aspects from germination to fruiting. It is
known that expansins influence seed development and seed size, also
increase plant height, root mass, number and size of leaves in plants
(Chen et al., 2001; Ma et al., 2013; Bae et al., 2014). Elongation
factor (EF ) G protein promotes tRNA translocation on the
ribosome (Stark, 2000). Liu et al. (2016) reported that overexpressed an
EF gene (MaEF1A ) greatly enhanced plant height, root length, and
both rachis and silique length by promoting cell expansion and
elongation. Hsp90 organizing protein mediates nuclear-encoded
chloroplast preproteins binding to HSP90 prior to chloroplast sorting
(Odunuga et al., 2004). Hsp90 is extensively involved in plant growth
and development and has a function for diverse traits such as hypocotyl
elongation, leaf size, seed mass (Sangster et al., 2008; Delker & Quint
2011). These previous molecular biology studies suggest that the plant
height and seed weight scaling may be co-ordinated through
multi-functioning genes involved in plant growth and development.
The extensive research into crop genetic improvement has led to the
accumulation of extensive data resources from genomics to phenotypes,
which offers unprecedented opportunity to explore fundamental biological
questions at the molecular and cellular level. Our results on the
genomic mechanism underlying size scaling demonstrated the promise of
using crop plants as a model organism in the research of plant biology.
On the other hand, allometric relationships between traits can constrain
phenotypic variation (Vasseur et al., 2018), which opens promising
avenues for crop species with a perspective of targeting optimal crosses
based on allometric relationships in parental lines (Garnier & Navas.,
2012). For example, a pleiotropic genetic variant with desirable effects
on two correlated traits would have direct benefit in plant breeding
(Gross & Beckage 2012). In conclusion, plant height and seeds weight
scaling could be formed through pleiotropic effect of many genes
conferring an effect on both traits, and by the genetic linkage of genes
with multiple functions in plant growth and development. Plant height
and seed weight scaling is genetically constrained and less influenced
by direct artificial selection, which could pose a serious challenge in
crop breeding when targeting correlated traits in opposite direction.
Though we here only examined plant height and seeds weight scaling
within a species, it could be speculated that similar genomic basis may
exist to explain the often observed allometric scaling across diverse
species. The recent advances at cellular to molecular levels of
organization, genomic analysis and large scale phenotyping, and research
into heritability and genetic basis of size scaling could open a new
venue for a grand unifying theory on allometric scaling in plants.