Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

Papachristou, Dimitris; Koutsouli, Panagiota; Laliotis, George P.; Kunz, Elisabeth; Upadhyay, Maulik; Seichter, Doris; Russ, Ingolf; Gjoko, Bunevski; Kostaras, Nikolaos; Bizelis, Iosif; Medugorac, Ivica

doi:10.1186/s12711-020-00560-8

Genetics Selection Evolution

Table 1 Parameters of genetic diversity in the 115 examined cattle breeds with 46,678 SNPs

From: Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

Breed	Nd	nA	\( \overline{nA} \)	mA	\( \overline{mA} \)	H_O	H_E	H_def	npA	\( \overline{npA} \)	nspA	\( \overline{nspA} \)	fpA	F	\( \overline{F} \)	AR	\( \overline{AR} \)	H_o(SNPs)	H_E(SNPs)	Νe₅	\( \overline{{Ne_{5} }} \)	Ne₅₀	Ne₂₀₀₀
Outgroups
YAK	26	9193		1.60		0.232	0.099	− 1.350	79		70		0.406	1.056		1.29		0.030	0.029	54		123
GIR	24	24,111		4.19		0.486	0.464	− 0.049	78		139		0.041	0.647		2.63		0.169	0.169	48		304	3966
NDA	27	32,136		5.58		0.569	0.574	0.009	188		185		0.032	0.334		3.15		0.228	0.230	67		524	2737
Minor Asia
ATER	17	41,775		7.26		0.733	0.725	− 0.011	147		158		0.031	0.106		4.17		0.321	0.317	40		349	4338
ATBC	37	51,955		9.03		0.730	0.746	0.022	294		362		0.015	0.112		4.25		0.322	0.330	96		831	5040
ATSR	17	40,859		7.10		0.713	0.719	0.008	152		185		0.034	0.142		4.12		0.310	0.313	40		337	4274
ATSY	7	29,941		5.20		0.696	0.683	− 0.019	43		64		0.076	0.161		4.08		0.302	0.298	–		–	–
TRG	8	31,406	44,046	5.46	7.65	0.740	0.695	− 0.064	28	191.7	65	234.8	0.069	0.071	0.117	4.10	4.18	0.327	0.308	15	64	125	2952
Greece and Cyprus
CYP	12	27,328		4.75		0.629	0.627	− 0.004	32		55		0.115	0.261		3.41		0.271	0.271	18		119	2753
AGT	6	17,302		3.01		0.593	0.504	− 0.178	17		23		0.206	0.329		2.74		0.244	0.218	–		–	–
CRT	11	12,688		2.20		0.518	0.373	− 0.387	11		8		0.376	0.457		2.02		0.193	0.166	8		53	1753
NSY	7	19,634		3.41		0.608	0.551	− 0.102	11		16		0.188	0.242		2.97		0.268	0.249	–		–	–
GRB	41	49,079		8.53		0.701	0.742	0.056	142		208		0.021	0.108		4.18		0.314	0.334	85		618	4170
KAS	4	17,185		2.99		0.656	0.520	− 0.261	23		19		0.141	0.261		2.99		0.270	0.224	–		–	–
KEA	27	33,145		5.76		0.646	0.622	− 0.038	16		23		0.026	0.150		3.31		0.295	0.284	28		160	2791
PRG	9	26,666		4.63		0.704	0.643	− 0.094	13		31		0.073	0.096		3.58		0.319	0.293	15		109	2950
ROG	9	25,912		4.50		0.723	0.602	− 0.202	20		29		0.100	0.094		3.36		0.321	0.270	15		114	3099
SYK	17	37,037		6.43		0.664	0.698	0.049	67		71		0.050	0.149		3.91		0.300	0.316	29		210	3429
KTR	19	37,105	37,879	6.45	5.89	0.651	0.685	0.050	54	58.6	74	82.6	0.045	0.175	0.178	3.80	3.54	0.292	0.308	26	40	192	3441
South-east Europe
RHS	17	41,278		7.17		0.741	0.734	− 0.009	70		104		0.034	0.058		4.22		0.334	0.332	38		308	3905
MKB	22	45,364		7.88		0.721	0.744	0.031	106		156		0.025	0.076		4.27		0.326	0.337	51		425	3932
SRB	20	44,355		7.71		0.726	0.742	0.021	101		120		0.028	0.063		4.27		0.329	0.337	46		396	4099
PRE	29	44,126		7.67		0.752	0.733	− 0.025	73		92		0.025	0.028		4.12		0.343	0.335	58		420	3933
RMB	17	42,940		7.46		0.757	0.738	− 0.025	105		127		0.032	0.027		4.28		0.343	0.335	40		345	3825
SHB	17	39,748		6.91		0.727	0.724	− 0.004	84		104		0.039	0.062		4.13		0.331	0.329	34		275	3664
DGB	21	36,322		6.31		0.729	0.700	− 0.041	30		41		0.052	0.053		3.86		0.335	0.322	31		228	3398
DBB	25	37,724		6.55		0.725	0.703	− 0.031	34		41		0.038	0.060		3.87		0.334	0.324	34		257	3298
MAB	43	51,066		8.87		0.738	0.745	0.010	148		180		0.013	0.042		4.20		0.339	0.342	97		712	3748
LKB	27	44,381		7.71		0.743	0.729	− 0.020	85		105		0.024	0.034		4.10		0.340	0.333	54		406	3709
SKB	14	35,556		6.18		0.717	0.707	− 0.013	33		48		0.048	0.070		4.00		0.328	0.325	25		205	3312
MNB	19	41,711		7.25		0.731	0.730	− 0.001	65		81		0.032	0.045		4.16		0.336	0.335	41		337	3679
BHB	18	30,993		5.38		0.687	0.642	− 0.070	21		44		0.064	0.113		3.47		0.311	0.291	23		154	3161
HRB	28	48,122	42,800	8.36	7.44	0.745	0.745	0.001	106	82.2	147	106.5	0.020	0.027	0.051	4.26	4.10	0.340	0.341	68	51	583	3916
East Podolian
HRI	28	40,285		7.00		0.709	0.704	− 0.007	25		58		0.039	0.074		3.88		0.323	0.322	49		322	3414
HRP	24	29,711		5.16		0.679	0.639	− 0.063	16		31		0.092	0.129		3.38		0.306	0.289	26		149	2959
UKP	21	31,176	34,188	5.42	5.94	0.689	0.656	− 0.051	27	22.6	38	43.4	0.053	0.109	0.103	3.50	3.61	0.313	0.298	29	36	161	2952
Tyrrhenian
PODO	25	43,858		7.62		0.715	0.731	0.022	75		95		0.023	0.074		4.13		0.325	0.332	56		434	3756
CINI	30	43,242		7.51		0.715	0.727	0.016	44		77		0.025	0.075		4.06		0.325	0.331	60		434	3882
MOSI	29	37,742		6.56		0.690	0.688	− 0.002	26		46		0.021	0.112		3.75		0.312	0.311	51		300	3546
RSIC	24	40,468		7.03		0.739	0.719	− 0.028	21		41		0.024	0.041		4.02		0.337	0.329	45		342	3632
MOSA	28	39,565		6.87		0.719	0.707	− 0.017	22		39		0.037	0.068		3.91		0.325	0.320	53		349	3816
SARD	30	44,722		7.77		0.710	0.726	0.022	76		90		0.021	0.059		4.08		0.326	0.333	66		533	3633
SBRU	10	32,211		5.60		0.697	0.689	− 0.012	15		18		0.050	0.080		3.95		0.319	0.317	21		173	3226
CORS	30	44,708		7.77		0.722	0.724	0.002	120		119		0.022	0.050		4.06		0.331	0.330	67		535	3572
AGER	22	34,676		6.02		0.705	0.688	− 0.025	2		15		0.023	0.072		3.76		0.327	0.320	32		222	2966
MARE	34	37,470		6.51		0.695	0.690	− 0.006	44		47		0.028	0.105		3.74		0.313	0.312	53		294	3367
CHI	12	32,476		5.64		0.702	0.677	− 0.037	21		42		0.042	0.093		3.81		0.320	0.310	24		166	2928
MPIS	15	21,614		3.76		0.639	0.539	− 0.185	7		8		0.152	0.173		2.82		0.286	0.246	15		86	2203
CALV	24	28,886		5.02		0.640	0.617	− 0.036	4		19		0.057	0.172		3.24		0.288	0.280	29		146	2841
MCH	21	37,548		6.52		0.711	0.696	− 0.021	39		50		0.040	0.077		3.86		0.320	0.314	45		282	3311
RMG	18	34,890		6.06		0.677	0.667	− 0.014	158		153		0.032	0.127		3.69		0.307	0.300	34		191	3245
GARF	23	26,502		4.60		0.645	0.618	− 0.044	13		16		0.077	0.156		3.21		0.294	0.283	22		121	2833
PONT	13	25,804		4.48		0.631	0.599	− 0.055	3		18		0.103	0.170		3.20		0.287	0.274	17		104	2466
MODE	23	35,203		6.12		0.705	0.687	− 0.026	27		31		0.045	0.069		3.75		0.324	0.315	35		239	3111
CABA	22	36,019		6.26		0.715	0.693	− 0.031	21		22		0.027	0.052		3.81		0.329	0.319	38		258	3132
REGG	26	38,053		6.61		0.724	0.699	− 0.036	52		56		0.046	0.049		3.83		0.333	0.322	45		293	3503
PMT	16	39,962		6.94		0.737	0.719	− 0.026	171		171		0.033	0.029		4.12		0.339	0.327	36		294	3284
BURL	24	36,125	37,025	6.28	6.43	0.713	0.696	− 0.023	11	45.1	19	55.7	0.047	0.077	0.087	3.81	3.79	0.335	0.327	40	44	267	3014
Alpine
PRDO	23	33,445		5.81		0.685	0.673	− 0.017	15		17		0.038	0.088		3.64		0.314	0.309	38		250	2912
OVAR	31	39,534		6.87		0.731	0.706	− 0.035	30		29		0.035	0.038		3.87		0.335	0.325	48		330	3409
REND	24	33,939		5.90		0.687	0.671	− 0.024	11		23		0.053	0.092		3.63		0.314	0.308	44		233	3181
BPUS	24	38,621		6.71		0.717	0.703	− 0.021	25		31		0.032	0.052		3.88		0.330	0.324	42		321	3335
PUST	24	31,615		5.49		0.701	0.667	− 0.052	16		17		0.059	0.075		3.57		0.321	0.306	32		197	3075
SIC	26	39,920		6.94		0.732	0.714	− 0.025	28		39		0.032	0.035		3.97		0.336	0.328	49		355	3562
PIN	29	38,594		6.71		0.714	0.701	− 0.020	27		39		0.024	0.066		3.84		0.332	0.326	50		309	3408
TGV	50	38,939		6.76		0.700	0.690	− 0.014	36		45		0.023	0.071		3.72		0.322	0.318	67		344	3187
MWF	46	35,855		6.23		0.710	0.675	− 0.053	21		25		0.039	0.058		3.58		0.327	0.311	45		252	3128
OBV	35	36,925		6.42		0.695	0.682	− 0.020	17		26		0.028	0.074		3.68		0.319	0.313	66		333	3390
BBV	50	35,287		6.13		0.656	0.643	− 0.020	10		15		0.010	0.100		3.39		0.301	0.296	65		233	2797
DFV	50	40,079		6.96		0.692	0.684	− 0.013	26		41		0.012	0.075		3.69		0.320	0.316	98		445	3123
FGV	50	37,494		6.51		0.704	0.682	− 0.031	15		36		0.032	0.067		3.65		0.325	0.316	64		311	3148
VOG	18	34,749		6.04		0.721	0.688	− 0.048	12		22		0.039	0.045		3.80		0.331	0.317	33		245	3128
ABO	22	33,385		5.80		0.706	0.666	− 0.061	21		18		0.040	0.054		3.60		0.325	0.306	37		240	3005
MON	28	31,738		5.51		0.691	0.647	− 0.068	11		15		0.065	0.083		3.43		0.318	0.298	36		209	3003
TAR	37	37,339	36,709	6.49	6.38	0.692	0.680	− 0.018	18	20.5	47	30.0	0.022	0.079	0.070	3.66	3.67	0.318	0.314	65	56	342	3228
France
R DBI	29	26,163		4.55		0.606	0.578	− 0.048	25		34		0.174	0.200		2,99		0.277	0.265	28		127	2615
SAL	26	36,384		6.32		0.668	0.667	0.000	26		40		0.043	0.117		3.62		0.305	0.305	58		321	2942
AUB	22	37,489		6.51		0.691	0.685	− 0.008	32		49		0.028	0.079		3.79		0.317	0.314	51		349	2840
LIM	48	42,891		7.45		0.708	0.705	− 0.003	65		75		0.015	0.066		3.85		0.326	0.325	106		563	3274
CHR	39	43,444		7.55		0.720	0.719	− 0.001	67		63		0.018	0.061		3.97		0.335	0.335	88		482	3340
PAR	17	36,898		6.41		0.724	0.701	− 0.033	52		53		0.035	0.044		3.93		0.333	0.322	34		262	3242
BAQ	33	40,280		7.00		0.706	0.700	− 0.009	53		73		0.021	0.065		3.83		0.325	0.322	69		426	3291
GAS	22	37,288	38,387	6.48	6.67	0.699	0.687	− 0.018	49	48.9	65	58.9	0.028	0.071	0.087	3.80	3.73	0.320	0.314	49	67	317	3071
Iberian
MNRQ	30	26,609		4.62		0.637	0.605	− 0.054	28		27		0.173	0.166		3.12		0.292	0.277	29		128	2868
MALL	30	20,486		3.56		0.556	0.521	− 0.067	14		26		0.211	0.276		2.65		0.247	0.236	19		81	2456
NGAN	14	35,429		6.16		0.660	0.702	0.059	56		67		0.053	0.143		3.96		0.301	0.320	28		221	3208
CANA	30	31,527		5.48		0.645	0.614	− 0.051	16		36		0.151	0.158		3.24		0.292	0.279	31		168	2801
MARI	22	30,016		5.21		0.656	0.622	− 0.055	22		42		0.116	0.147		3.30		0.299	0.284	27		148	2686
ALEN	10	29,018		5.04		0.654	0.655	0.001	98		86		0.080	0.166		3.67		0.297	0.294	19		136	3104
BAR	14	32,044		5.57		0.659	0.663	0.006	29		54		0.051	0.145		3.68		0.301	0.302	31		199	2738
MARO	19	35,039		6.09		0.687	0.677	− 0.014	40		65		0.037	0.108		3.73		0.313	0.309	45		265	3147
SYG	11	30,662	29,205	5.33	5.07	0.670	0.667	− 0.004	43	31.3	35	43.2	0.063	0.129	0.169	3.75	3.32	0.305	0.303	20	28	149	2802
North-west Europe
BPN	15	33,384		5.80		0.726	0.689	− 0.054	28		46		0.055	0.047		3.83		0.336	0.319	26		200	3033
NOR	30	34,001		5.91		0.698	0.664	− 0.052	38		61		0.055	0.091		3.55		0.322	0.307	43		234	3072
MAN	20	34,940		6.07		0.683	0.664	− 0.029	23		22		0.032	0.123		3.64		0.320	0.312	44		244	2941
BBB	45	39,395		6.84		0.698	0.690	− 0.010	40		46		0.028	0.103		3.72		0.328	0.325	67		329	3110
LKF	22	31,859		5.53		0.678	0.658	− 0.030	10		25		0.057	0.129		3.54		0.316	0.307	34		187	2810
HF	50	37,888		6.58		0.696	0.685	− 0.016	14		29		0.011	0.127		3.65		0.334	0.329	72		279	2877
GNS	16	28,903		5.02		0.634	0.623	− 0.016	89		65		0.039	0.175		3.36		0.292	0.286	29		159	2606
JSY	49	31,507		5.47		0.624	0.619	− 0.007	20		28		0.020	0.185		3.23		0.287	0.286	74		223	2641
HER	41	36,659		6.37		0.653	0.676	0.034	55		64		0.028	0.229		3.57		0.320	0.332	79		227	2286
SHR	13	25,626		4.45		0.566	0.575	0.016	4		15		0.039	0.300		3.12		0.267	0.274	27		128	2131
KRY	14	27,681		4.81		0.678	0.644	− 0.053	57		67		0.083	0.144		3.46		0.317	0.300	22		131	2698
DXT	16	31,660		5.50		0.625	0.667	0.062	32		26		0.065	0.202		3.64		0.292	0.312	31		185	2841
GLW	40	34,358		5.97		0.635	0.652	0.025	24		36		0.047	0.186		3.45		0.296	0.304	82		275	2744
AAN	48	35,756		6.21		0.659	0.668	0.014	30		42		0.026	0.188		3.53		0.317	0.322	83		249	2617
HGL	27	28,798		5.00		0.606	0.605	− 0.001	33		47		0.045	0.231		3.18		0.281	0.282	57		181	2524
NRC	34	36,853		6.40		0.702	0.686	− 0.023	20		39		0.033	0.101		3.70		0.333	0.325	57		268	3016
SERC	24	35,396		6.15		0.690	0.678	− 0.018	32		35		0.069	0.113		3.68		0.325	0.320	47		239	2839
FJL	22	35,464		6.16		0.700	0.680	− 0.030	67		74		0.083	0.093		3.72		0.319	0.310	42		242	2946
FIAY	42	37,043		6.44		0.686	0.677	− 0.014	19		46		0.018	0.111		3.61		0.323	0.318	65		281	2942
FINE	20	38,958		6.77		0.692	0.711	0.026	78		100		0.048	0.097		3.99		0.317	0.324	41		321	3608
FINW	35	38,966		6.77		0.696	0.693	− 0.004	59		81		0.040	0.095		3.77		0.317	0.316	56		316	3372
FINN	18	32,166		5.59		0.719	0.670	− 0.073	27		42		0.067	0.069		3.64		0.327	0.305	27		190	3140
YARO	20	36,065	34,908	6.27	6.06	0.707	0.686	− 0.029	58	34.9	69	47.0	0.068	0.080	0.142	3.78	3.58	0.324	0.315	39	57	246	3265

Nd, number of genotyped animals; nA and \( \overline{nA} \), total and mean number of observed alleles within subpopulation; mA, nA/5756 (number of blocks); H_O, average observed heterozygosity within subpopulation; H_E, average expected heterozygosity within subpopulation; npA and \( \overline{npA} \), number and mean number of private alleles; nspA and \( \overline{nspA} \), number and mean number of alleles present only in two subpopulations; fpA, average frequency of private alleles, F and \( \overline{F} \), inbreeding coefficient per breed and per group; AR and \( \overline{AR} \), number and mean value of allelic richness; Ho_(SNP) and H_E(SNP), observed and expected heterozygosity within subpopulation by SNPs; Ne₅ and \( \overline{{Ne_{5} }} \), effective population number for five generations back per breed and per group; Ne₅₀ and Ne₂₀₀₀, effective population number for fifty and two thousand generations back

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ISSN: 1297-9686

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