Fig. 2

The genotype analysis view of 2 M markers in the whole genome sequencing. After sequencing and filtering, total 2,060,483 markers were kept in the whole genome. 29 autosomes and 2 sex chromosome were marked as numeric 1 to 31. The odd number of chromosome were painted as goldenrod color. The even number of chromosome were painted as gray color. The genotype and position of neighboring two markers were used to calculate correlation (R, a) and distance (b). The relative distance against R (c) and R² (d) between markers were used to show the linkage level. Every 20 markers were used to calculate average values of R², then the average R² were used to indicate LD-decay of whole population. The frequency of R (e) and distance (f) were used to show the statistical results