QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers.
Verticillium wilt (VW): Refers to traits (percentage of plants infected or disease severity rating) which allow the plant to resist infection after being inoculated with VW fungus [ 37].
Means of the traits: percentage of explants with buds (B), percentage of explants with shoots (R) and number of shoots per explant with shoots (PR) for the parent genotypes (S. pennellii and S. lycopersicum), F1, F2 and BC1. a B and R are the percentages of explants able to develop buds and shoots, respectively.
For each trait and percentage value of estimation individuals, 100 estimation-testing data sets generated, each time resampling the subset of 285 markers, too.
It turned out that most of the SNPs became non-significant (in particular the SNPs with strong LD with C199) or less significant (Additional file 1: Table S12, taking the trait fat percentage as an example).
The dataset comprised mainly of males used as sires, for each trait the percentage of females in the training and validation sets were: 39 and 50%% for DAG3, 20 and 43 % for DAG8, 30 and 38 % for FEC1, 26 and 32%% for FEC2 and 9 and 27%% for AFEC, respectively.
Expectedly, the actual selected optimal weights are relatively large for the traits fat percentage in cattle and rust resistance in pine, and small for the traits somatic cell score in cattle and PolyUnres in the GSA dataset (Table 3 and Table 4).
Results showed that the stem cuttings pretreated with 2000 mg L−1 indole-3-butyric acid (IBA) in quick-dip method got the best rooting traits (rooting percentage is 86.7%, root number is 23.1 and root length per rooted cutting is 6.4 cm).
However, for specific traits, the percentage of AFLP markers close to genes can be rather small.
For 11 of the 16 traits, the percentage of effects in the same direction was larger than 50%.
