Contribution of rare and low-frequency whole-genome sequence variants to complex traits variation in dairy cattle

Table 2 Relative contribution to the proportion of DRP variance explained by variants in different MAF classes for 17 traits

Traits and scenarios	Relative contribution of MAF classes to the explained DRP variance			Total proportion of DRP variance explained
Traits and scenarios	0.001–0.01	0.01–0.05	0.05–0.5	Total proportion of DRP variance explained
YIELD	0.063	0.038	0.899	0.860
MILK	0.015	0.030	0.955	0.872
PROT	0.054	0.038	0.908	0.858
FAT	0.022	0.012	0.966	0.854
MILKORG	0.072	0.003	0.925	0.679
MILKSP	0.005	0.035	0.960	0.719
LONG	0.081	0.141	0.778	0.630
MASTI	0.019	0.000	0.981	0.669
HEALTH	0.125	0.121	0.755	0.514
LEG	0.059	0.149	0.796	0.525
CALV	0.037	0.000	0.963	0.507
BIRTH	0.000	0.020	0.980	0.602
FERT	0.000	0.133	0.867	0.600
BODY	0.088	0.026	0.886	0.568
GROWTH	0.010	0.087	0.903	0.814
TEMP	0.054	0.059	0.887	0.406
NTM	0.031	0.030	0.940	0.847

All the variants were partitioned into seven MAF classes. In this table, we report the proportion of DRP variance explained for three groups of MAF classes (rare: MAF < 0.01, low-frequency: 0.01 ≤ MAF < 0.05 and common: MAF ≥ 0.05). For the group of common variants, the proportion of DRP variance explained was equal to the sum of the proportions of DRP variance explained for classes of variants with MAF: 0.05–0.1; 0.1–0.2; 0.2–0.3; 0.3–0.4 and 0.4–0.5

ISSN: 1297-9686