Linkage map positioning on E. grandis genome and you can map-built quotes of recombination

Linkage map positioning on E. grandis genome and you can map-built quotes of recombination

Genomic correlates regarding recombination

Pearson’s correlations along windows of 100 kb were calculated between recombination rates and the following genomic features: nucleotide diversity (?w), gene density (measured as the proportion of base pairs of the window falling into coding regions), GC content (%) and distance from the centromere to the tip of each chromosome arm (in kb). As no information exists regarding the exact position of centromeres in the Eucalyptus chromosomes, and no relationship has been yet established between the pseudochromosomes and the chromosomes in cytological observations, all chromosomes were assumed to be metacentric. Correlation significance was assessed by comparing the calculated values with those of 5000 permuted data sets that maintained the chromosomal order of all observations but that shuffled the relative positions of the two variables (Nordborg et al., 2005 ) using the function ‘sample’ in R.

Results

The two linkage charts designed with separate categories of SNPs contains 4396 SNPs to own Elizabeth. grandis and 3991 for E. urophylla, layer equivalent total recombination distances (Fig. 1; Table S1; Notes S1). A total of 192 (dos.3%) nonsyntenic SNPs, was in fact omitted, that is SNPs one to mapped so you can linkage organizations distinct from brand new asked ones centered on their genome condition. New positioning of your own E. grandis charts to the current genome type 1.step 1 shown installation inconsistencies towards the multiple chromosomes, way more somewhat on the chromosomes step one, dos, 4 Leeds hookup online free and you can 8 (Figs step 1, dos, S1). Map-mainly based rates regarding recombination pricing was comparable into a few species, step 3.18 ± 1.1 and you will step 3.55 ± 0.8 cM Mb ?step one (Table S1). New Yards arey charts (Figs dos, S1) revealed a fairly equivalent slope regarding recombination speed round the most of the chromosomes, and just smaller plateaus out of recombination was viewed, such as for instance, towards the chromosomes 4, 9 and you will 10.

The total amount away from genome-large linkage disequilibrium in the Elizabeth. grandis

Pairwise estimates of r 2 were obtained from haplotype probabilities for all pairwise distances among the Infinium SNPs on each chromosome. A total of 21 351 SNPs, an average of 1941 SNPs per chromosome, with pairwise distances varying from 135 bp up to several Mb, were used in the calculations, resulting in nearly two million pairwise estimates of r 2 per chromosome and over 21 million at the genome-wide scale for 72 sampled genomes of E. grandis. Owing to the very large number of estimates of r 2 and because the LD decay curves become an asymptote thereafter, LD decay plots are shown only up to 50 kb distances. Average genome-wide LD was r 2 = 0.131, decaying to < 0.2 within c. 5.7 kb (half-decay within 4.3 kb) while = 0.123, showing a slightly faster decay within c. 4.9 kb (half-decay within 3.7 kb) (Fig. 3). The small difference between raw and corrected r 2 is consistent with the lack of population structure between the two E. grandis provenances as indicated by the low Fst = 0.041 ± 0.06 previously calculated based on 28 658 genome-wide SNPs (Silva-ong the c. 4000 linkage mapped markers in E. grandis and r 2 plotted against the distance in cM. With map resolution of c. 0.3 cM, corresponding to c. 106 kb, no r 2 estimate was larger than 0.2, consistent with the decay observed at c. 4–6 kb (Fig. S2). No impact of the few assembly inconsistencies of the E. grandis genome version 1.1 was seen on the pattern of LD decay and no difference was observed when rarer SNPs with MAF > 0.01 were included in the estimation of r 2 (Fig. S3).

Population-scaled recombination rate during the E. grandis

About three approaches to get genome-greater prices off ? was in fact performed playing with several independent experimental study kits related almost thirteen million SNPs regarding the pooled sequence analysis and over 21 100 Infinium SNPs. Chromosome-certain estimates out-of ? was basically obtained for several genomic screen brands with regards to SNP quantity with LDH during the and H otspotter (Table step one). Estimates was in fact determined around the most of the chromosomes when you look at the 2402 overlapping containers away from 15 SNPs (mean bin proportions, 250 kb; SNP density, 1/16.7 kb) plus in 242 overlapping pots out-of 105 SNPs (suggest container dimensions, 2500 kb; SNP occurrence, 1/ kb). Little type is seen between the two prices and across chromosomes. Prices obtained by H otspotter was overall two times as high since those of LDH at , most likely highlighting different presumptions regarding your LD brand of the one or two estimation steps. Thus, the latest genome-greater quotes away from effective populace models obtained because of the equating ? to help you the latest recombination price c were and twice as highest which have H otspotter . Brand new genome-greater quotes off ? received having Infinium SNPs converged to actually comparable thinking and you can magnitudes into the guess received towards the pooled sequencing study having fun with mlRho and to rates derived from population-height LD (Desk 2). However some amount of sampling prejudice inherent towards means looks become establish when comparing the fresh prices off ? out-of H otspotter and mlRho and have now amongst the prices from LDH during the and you will inhabitants-level LD, the costs did not disagree by the > 30%. Nevertheless, the second several prices are a couple of to three moments smaller compared to the initial a couple of. Most of the prices away from ? has large practical deviations, showing the latest expected genome-greater variation during the recombination, and particularly therefore to your guess from sequencing research, perhaps due to the much bigger number of nucleotides examined.

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