4.2 Non-random association and interactions between DOC
loci and chloroplastic RpoC1
Since its establishment, the Barley1K infrastructure has been an
instrumental research tool to explore landscape genomics (Hubneret al. , 2009; Hübner et al. , 2013; Chang et al. ,
2022) , plant biotic and abiotic interactions (Sade et al ., 2012;
Dakhiya et al. 2017; Alegria Terrazas et al. 2020; Dakhiya
& Green 2023), and more recently as reference for the whole barley Pan
genome (Jayakodi et al. 2020). Here, we extend the use of the B1K
by 1) developing a more dedicated genotyping platform for the wild
barley to allow GWAS and 2) start exploring the chloroplast variation
and its possible relationship with fitness traits. At first glance, the
results obtained in this study could not directly be translated to crop
improvement, mainly since, as we show here, adaptation strategies in the
wild and agricultural set up are different (biomass vs reproductive
output responses to heat, see above). However, the B1K resource bear
genetic attributes that could assist in targeting specific genes and
gene complexes mainly owing to the non-randomness and long years of
recombination within and between nuclear and chloroplastic genomes and
the way natural selection works on these intra and inter-loci
combinations. For the nuclear genome, it is clear that the LD decay is
enormously shorter than that one could find in interspecific populations
(Morrell et al. 2005). DOC3.2 may be a good example for
this “gene discovery” use of the B1K panel for zooming-in on a causal
diversity that otherwise would be delimited to 7.7 Mbp in using the
interspecific population (Prusty et al., 2021).
Here, a closer look on at the
allelic diversity indicates the QTL for amplitude under HT in long days,
which was identified in the previous study, most probably corresponds to
the signal identified at chr3H_67267835. This marker is flanked by the
non-significant markers chr3H_66,838,086 and chr3H_68,838,244,
therefore limiting the source of phenotypic variation to approximately 2
Mbp for this QTL.
For the chloroplast genome per se, and for the allelic combinations with
the nuclear genome, this study shows clearly the rich diversity
repertoire found in this organelle within the wild (Table S7 )
and its relevance to plant adaptation. Moreover, we could identify both
LD and CNI between DOC and the rpoC1 alleles in the B1K panel, where in
an extreme case of the DOC3.2 this locus showed segregation only
among carriers of the RpoC1G1713T . Non-random
association of alleles in the nucleus and cytoplasmic organelles, or
cyto-nuclear LD, is both an important component of a number of
evolutionary processes and a statistical indicator of others (Fieldset al., 2014). We also followed up on the GWAS to examine
inheritance of these CNI intereaction, and, beyond validating the
environment-specific effects of the DOCs , we could also get
indication for preferred homogeneity of the CNI. For example, in the
case of CNI for the DOC5.1 combination of plasmotype and nuclear
alleles from same origin (B1K-05-07 or B1K-50-07, the two parental lines
of the F2) was associated with higher amplitude. This correspond well
with recent study which suggested that increased amplitude under heat is
positively correlated with higher plant vitality (Dakhiya & Green,
2023). In case of cereal evolution, it was hypothesized and in silico
tested that in ancient hybridization, such as the one between the A and
D-genomes of modern wheat there has been biased maintenance of maternal
A-genome ancestry in nuclear genes encoding cytonuclear enzyme complexes
(CECs) (Li et al., 2019). It is tempting to hypothesize that we
observe such scenario in the case of the DOC and rpoC1 loci in the B1K.