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The mean survival rates were estimated as best linear unbiased predictors (BLUPs) for each accession across all environments.
Thus, the BLUPs for each accession across the three environments were calculated, and the phenotype-genotype associations were analyzed.
Results were further filtered using software developed in-house, and differences in protein abundance between the samples were derived by summing the total CID events that resulted in a positively identified peptide for a given protein accession across all samples (spectral counting) [ 20].
The BLUP of FT-related traits, including the DTT, DTP and DTS for each accession across three environments, and 43,252 SNPs were selected to perform a phenotype-genotype GWAS, which was implemented in the GAPIT R package [ 58], using mix linear model (MLM) in which the population structure and pair-kinship were treated as covariates [ 38].
The total number of distinct, putative SCN loci detected by MarkerMiner (Fig. 4A) for each clade ranged from 666 (Draba) to 1993 (Lamiales) (mean = 1217, median = 1106, standard deviation = 560), with a mean of 535 loci detected per transcriptome accession across the four test cases (median = 584, standard deviation = 226, range = 0 909; results for individual data sets are reported in Fig. 4B).
Similar(55)
We show that significant variation exists in the shoot and the seed ionomes of 12 A. thaliana accessions across different environments.
Gealy et al. [58] studied the genetic diversity and structure of weedy rice from USA, where geographic differentiation among weedy rice accessions across the country was found.
This produced 20 lists of up- and down-regulated genes both within an individual accession and between accessions across developmental time.
In this work, we conducted proteomic analysis using FN collected from Nicotiana attenuata accessions across the plant's native habitat, the Great Basin Desert, Utah.
Shown are the geographic origins of 144 Arabidopsis accessions across (A ) Europe and Northern Africa, (B ) North America and (C ) Japan, as well as their corresponding GSL haplotypes and chemotypes.
HAPLOVIEW v4.2 [ 39] was used to estimate haplotype block structure in the 203 Chinese semi-winter rapeseed accessions across the 24,994 unique SNPs.
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