Table 4 Number of alleles (A) and gene diversity value (B) observed for eight groups of Vietnamese local varieties Group Locus Average RM2 RM29 RM31 RM60 RM201 RM208 RM225 RM232 RM237 RM241 (Chr. 7) (Chr. 2) (Chr. 5) (Chr. 3) (Chr. 9) (Chr. 2) (Chr. 6) (Chr. 3) (Chr. 1) (Chr.
A significant difference was observed for sex in the Chr 2T, Chr 3, Chr 4, Chr 7T and Chr 13 strains.
The IGF2 DMR includes three CpG dinucleotides upstream of exon 3 (chr 11p15.5; CpG site 1: 2 109 519; CpG site 2: 2 109 516; and CpG site 3: 2 109 500; NCBI Human Genome Build 37.1) [ 35].
Our results show that QTLs on Chr 2T, Chr 3, Chr 4 and Chr 13 have a male-specific effect, and the QTL on Chr 7T has a female-specific effect.
The ranking of chrs from the shortest to the longest based on the sequence of the 'Golden Delicious' apple reference genome sequence is: chr 16, chr 4, chr 17, chr 6, chr 7, chr 14, chr 8, chr 1, chr 12, chr 9, chr 5, chr 10, chr 13, chr 3, chr 11, chr 2 and chr 15.
Quantitative trait locus mapping of these 15 latent factors showed the presence of suggestive QTL on Chr 1, 4, 5, 6, 8 9, 10, 11, 13 and significant QTL on Chr 9 (Factor 3), Chr 10 (Factor 2) and Chr 13 (Factors 1 and 13).
We further divided the supergroup called "Other SUB1-like proteins", which is formed by longer proteins, into three groups: "SUB1-like Chr 2" (SUB1chr2), "SUB1-like Chr 6" (SUB1chr6) and "SUB1-like Chr 9" (SUB1chr9) (Additional file 3: Figure S2).
Three of these QTLs (qj01 1 on chr 1, qj07 2 on chr 2 and qj11_2 on chr11) corresponded to QTLs identified using the GBS data.
Chr 1 in NU5 and Chr 7 in NU7 also indicated non-parental segments.
This occurs due to mutations in NOTCH2 in chr 1p and JAG1 (Jagged 1) in chr 20p [ 71 – 74 ].
Two of these QTLs (q01 1 on chr 1 and q07 2 on chr 2) corresponded to QTLs identified using the GBS data.
