Reflecting the synteny conservation among Prunus maps, we detected many Arabidopsis regions matching to more than one Prunus map region.
On LG6 of the three maps we detected QTLs for flowering time (13.4 20.8% of total variance, 3 years), veraison time (9.0 9.9% of total variance, 2 years), ripening date (10.2 17.2% of total variance, 2 years), flowering-veraison interval (8.2 8.5% of total variance, 2 years) and flowering-ripening interval (9.1 15.3% of total variance, 2 years).
However when using multiple-interval mapping, we detected the same QTL as that observed in families 4 and 11.
Using the QTLMap software developed for linkage analyses by interval mapping, we detected 16 QTL for feed intake, 13 for feed efficiency, 49 for anatomy-related traits, seven for growth, six for body composition and ten for excretion.
Using multiple-interval mapping analysis, we detected 19 significant QTLs for seven traits over two trials (Table 3; Fig. 3).
Based on result of mapping reads, we detected the total of 1,154,063 DNA polymorphisms including 1,024,202 SNPs, 53,180 insertions and 76,681 deletions between the five accessions and the reference genome, with an average density of a SNP per 1.6 kb on Nipponbare.
With an identical mapping approach, we detected fewer modifier QTL (1 and 0 in the FTC and BEPA crosses, respectively).
In a genome-wide association mapping scan we detected eight SNPs (Table 2) significantly associated with genetic variation for Septoria tritici blotch resistance.
However, we did not find any contigs with dominant satellite tandem repeats [ 51] in our physical map, although we detected sequences for the centromeric satellite-like repeat in CTG2884 on 6BS.
In the chrV 4 Mb region in which we had mapped lsy-12, we detected one new variant by SOLiD sequencing, which we validated by Sanger sequencing.
Although the phosphoproteomics method did not detect phosphorylated ERK-1 (Map kinase 1), we detected the phosphorylation of regulators of ERK-1 activation (Table 2).
