Table 1.

Proportion of phenotypic variance for five body size traits explained by each chromosome. LG gives the autosome analysed, h ² gives the proportion of phenotypic variance explained by the autosomes analysed, LRT gives the likelihood ratio test statistic. Standard errors for genetic variances are shown within parentheses

LG	Physical length (Mb)	Nr of SNP markers	Foreleg			Hindleg			Metacarpal			Weight			Jaw
			V A	h 2	LRT	V A	h 2	LRT	V A	h 2	LRT	V A	h 2	LRT	V A	h 2	LRT
Whole genome	2452	37 037	11.107 (1.624)	0.255 (0.043)	NA	20.924 (2.91)	0.444 (0.049)	NA	7.928 (1.17)	0.494 (0.057)	NA	2.926 (0.501)	0.312 (0.046)	NA	10.69 (1.46)	0.53 (0.056)	NA
1	276	4138	1.012 (0.81)	0.023 (0.019)	2.093	2.076 (1.48)	0.044 (0.031)	2.722	0.024 (0.465)	0.001 (0.029)	0.002	0.447 (0.279)	0.048 (0.029)	3.833	2.086 (0.757)	0.103 (0.036)	12.829
2	249	3842	0.906 (0.765)	0.021 (0.018)	1.871	2.348 (1.436)	0.05 (0.03)	4.103	0.167 (0.447)	0.01 (0.028)	0.145	0.408 (0.276)	0.043 (0.029)	2.711	0.619 (0.555)	0.031 (0.027)	1.469
3	224	3540	0.085 (0.596)	0.002 (0.014)	0.022	0 (0)	0 (0)	0	0.642 (0.522)	0.04 (0.032)	1.81	0.061 (0.209)	0.006 (0.022)	0.091	0.639 (0.531)	0.032 (0.026)	1.845
4	119	1992	0 (0)	0 (0)	0	0.771 (1.016)	0.016 (0.022)	0.706	0.628 (0.436)	0.039 (0.027)	3.011	0.159 (0.195)	0.017 (0.021)	0.81	0.535 (0.465)	0.027 (0.023)	1.637
5	108	1702	1.38 (0.791)	0.032 (0.018)	4.312	0 (0)	0 (0)	0	1.38 (0.59)	0.085 (0.035)	9.787	0.067 (0.179)	0.007 (0.019)	0.132	0.196 (0.36)	0.01 (0.018)	0.371
6	117	1784	2.067 (0.895)	0.047 (0.021)	9.933	4.737 (1.69)	0.1 (0.034)	17.036	0.745 (0.462)	0.046 (0.028)	4.175	0.659 (0.266)	0.07 (0.027)	14.414	1.046 (0.515)	0.052 (0.025)	8.126
7	100	1653	1.056 (0.698)	0.024 (0.016)	3.492	2.316 (1.254)	0.049 (0.026)	6.328	0.988 (0.489)	0.062 (0.03)	7.753	0 (0)	0 (0)	0	1.036 (0.583)	0.051 (0.028)	4.014
8	91	1535	0.188 (0.476)	0.004 (0.011)	0.186	1.035 (1.019)	0.022 (0.022)	1.343	0.135 (0.316)	0.008 (0.02)	0.217	0.158 (0.172)	0.017 (0.018)	1.307	0.06 (0.348)	0.003 (0.017)	0.028
9	95	1546	0.884 (0.631)	0.02 (0.015)	2.993	2.007 (1.209)	0.043 (0.025)	4.458	0.061 (0.308)	0.004 (0.019)	0.037	0.426 (0.218)	0.046 (0.023)	8.111	1.771 (0.727)	0.087 (0.035)	8.978
10	86	1416	0 (0)	0 (0)	0	1.141 (1.063)	0.024 (0.022)	1.466	0 (0)	0 (0)	0	0.205 (0.202)	0.022 (0.021)	1.21	0.378 (0.404)	0.019 (0.02)	1.061
11	62	853	1.541 (0.739)	0.035 (0.017)	8.991	2.233 (1.231)	0.048 (0.026)	6.206	0.427 (0.339)	0.027 (0.021)	3.136	0 (0)	0 (0)	0	0.991 (0.524)	0.049 (0.026)	6.375
12	79	1218	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.327 (0.372)	0.016 (0.018)	1.032
13	83	1165	0.337 (0.513)	0.008 (0.012)	0.521	1.652 (1.084)	0.035 (0.023)	4.283	0.499 (0.381)	0.031 (0.024)	2.712	0.174 (0.18)	0.018 (0.019)	1.261	0.025 (0.308)	0.001 (0.015)	0.006
14	63	786	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.586 (0.413)	0.036 (0.025)	3.288	0 (0)	0 (0)	0	0.71 (0.503)	0.035 (0.025)	2.015
15	81	1204	0.37 (0.51)	0.008 (0.012)	0.646	0.345 (0.779)	0.007 (0.017)	0.248	0.516 (0.367)	0.032 (0.023)	3.396	0 (0)	0 (0)	0	0 (0)	0 (0)	0
16	72	1091	1.843 (0.849)	0.042 (0.02)	5.959	3.38 (1.502)	0.071 (0.031)	7.585	2.098 (0.66)	0.129 (0.038)	22.814	0.005 (0.119)	0.001 (0.013)	0.002	0 (0)	0 (0)	0
17	72	1032	0.203 (0.478)	0.005 (0.011)	0.193	0 (0)	0 (0)	0	0.042 (0.259)	0.003 (0.016)	0.032	0 (0)	0 (0)	0	0.871 (0.468)	0.043 (0.023)	6.915
18	69	1003	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.109 (0.257)	0.007 (0.016)	0.247	0 (0)	0 (0)	0	0 (0)	0 (0)	0
19	60	846	1.116 (0.634)	0.026 (0.015)	6.397	1.816 (1.092)	0.038 (0.023)	5.25	0.886 (0.448)	0.055 (0.027)	8.642	0.086 (0.151)	0.009 (0.016)	0.382	0 (0)	0 (0)	0
20	51	801	1.052 (0.633)	0.024 (0.015)	4.639	0.693 (0.789)	0.015 (0.017)	1.155	0 (0)	0 (0)	0	0.006 (0.114)	0.001 (0.012)	0.003	0.222 (0.322)	0.011 (0.016)	0.577
21	50	587	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.163 (0.254)	0.008 (0.013)	0.693
22	51	804	0.548 (0.549)	0.013 (0.013)	1.243	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.029 (0.145)	0.003 (0.015)	0.036	0 (0)	0 (0)	0
23	62	741	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.066 (0.142)	0.007 (0.015)	0.249	0.94 (0.532)	0.047 (0.026)	4.655
24	42	439	0.222 (0.35)	0.005 (0.008)	0.646	0.39 (0.626)	0.008 (0.013)	0.619	0.002 (0.2)	0 (0.012)	0	0.013 (0.103)	0.001 (0.011)	0.021	0.095 (0.305)	0.005 (0.015)	0.077
25	45	685	0 (0)	0 (0)	0	0 (0)	0 (0)	0	0.21 (0.282)	0.013 (0.018)	0.8	0.079 (0.143)	0.008 (0.015)	0.355	0.24 (0.322)	0.012 (0.016)	0.739
26	44	634	0.139 (0.441)	0.003 (0.01)	0.08	0.071 (0.718)	0.001 (0.015)	0.007	0.279 (0.338)	0.017 (0.021)	0.763	0.26 (0.186)	0.028 (0.02)	3.243	0.059 (0.263)	0.003 (0.013)	0.057
Sum	2452	37 037	14.948	0.343	NA	27.007	0.572	NA	10.424	0.647	NA	3.31	0.353	NA	13.009	0.645	NA

The first row shows the estimates using a GRM calculated using all SNPs and represent genomic heritability estimates. The last row shows the sum of all the individual chromosome estimates. LRT values in bold indicate that the model where a chromosome effect was fitted in addition to a polygenic effect explained significantly more of the phenotypic variation than a model only including a remaining polygenic effect.