After 4 weeks of growth at 16°, pots from each accession were grouped together, to decrease shading of smaller accessions.
The relative reduction in biomass in response to WS was similar in all accessions except T-MI, which had no reduction in growth in response to WS, but was also the smallest accession in the WW treatment.
The large number of these small-fruit accessions in the reference group induced a negative effect for FW.
This subpopulation is the smallest (44 accessions) and the less diverse one, with an average polymorphism information content that is roughly half of the averages observed in the other six subpopulations (Table S6).
Two other core collections which were defined for comparative purposes using the M strategy (CC Powercore and CC MStrat) maintained a greater proportion of alleles (in the case of the Powercore program, with 100% of the alleles in 82 accessions) or equivalent, with a smaller number of accessions (in the case of the MStrat program, with 85.6% of alleles in 51 accessions).
All examined accessions were diploid, thus keeping the number of expected sequences per accession small.
Three sets of small RNA populations (accession number: GSE26368) from N. benthamiana were generated in our previous study using high-throughput sequencing technology [ 30].
However, group 3, with a much smaller number of accessions, but comprised of those with a probable indica genetic background, embodies the highest levels of polymorphism (GD = 0.79 and PIC = 0.76).
Small RNA libraries accession numbers GSM319953 (MILI late), GSM319956 (MILI early) and GSM319957 (MIWI2 early) were retrieved through DeepBase (http://deepbase.sysu.edu.cn/) [ 39] and mapped to the mouse genome (mm9 assembly) using bowtie [ 65].
Consistent with our previous findings, which were based on a smaller collection of accessions [ 26], we found that the copy number of rRNA genes was positively correlated with CR DNA methylation in this larger survey (Fig. 2).
