Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

Table 2 Genetic diversity estimated in the whole collection and subgroups

Subgroup	N	4854 HF SNPs						2577 LF SNPs
Subgroup	N	%PL	Na	I	Ho	He	PA	%PL	Na	I	Ho	He	PA
Origin ^a
ARM	71	98.0	1.98	0.478	0.029	0.315	0	45.4	1.45	0.051	0.003	0.022	200
ART	14	83.8	1.84	0.416	0.016	0.273	0	19.6	1.20	0.056	0.002	0.031	50
CHI	26	80.6	1.81	0.390	0.008	0.257	0	27.7	1.28	0.057	0.001	0.028	303
CIM	10	66.3	1.66	0.348	0.003	0.231	0	9.1	1.09	0.032	0.001	0.019	1
FRA	22	92.4	1.92	0.462	0.024	0.306	0	24.6	1.25	0.061	0.003	0.032	86
ITM	16	81.4	1.81	0.423	0.008	0.282	0	12.3	1.12	0.041	0.002	0.023	18
ITT	17	91.7	1.92	0.457	0.020	0.301	0	48.3	1.48	0.131	0.005	0.070	416
USA	4	53.3	1.53	0.320	0.016	0.220	0	6.8	1.07	0.039	0.002	0.026	29
WAN	17	84.7	1.85	0.424	0.008	0.280	0	17.4	1.17	0.048	0.001	0.026	26
Period
1915–1959	6	70.3	1.70	0.382	0.015	0.255	0	10.6	1.11	0.047	0.002	0.029	12
1960–1969	5	61.5	1.62	0.352	0.018	0.239	0	19.6	1.20	0.098	0.006	0.064	33
1970–1979	15	91.0	1.91	0.460	0.022	0.304	0	48.1	1.48	0.137	0.005	0.074	396
1980–1989	22	94.9	1.95	0.474	0.017	0.314	0	23.4	1.23	0.049	0.002	0.024	30
1990–1999	24	95.2	1.95	0.482	0.008	0.320	0	22.7	1.23	0.046	0.001	0.022	32
2000–2009	101	99.8	2.00	0.487	0.015	0.320	0	71.1	1.71	0.067	0.002	0.028	590
2010–2020	24	92.5	1.93	0.459	0.048	0.303	0	19.2	1.19	0.034	0.003	0.016	29
DAPC
Q1	68	99.2	1.99	0.478	0.023	0.315	1	54.2	1.54	0.066	0.003	0.029	313
Q2	41	97.3	1.97	0.450	0.019	0.293	0	35.2	1.35	0.050	0.002	0.022	104
Q3	36	92.0	1.92	0.419	0.014	0.271	0	56.0	1.56	0.108	0.003	0.054	511
Q4	18	70.6	1.71	0.327	0.030	0.212	1	8.2	1.08	0.019	0.002	0.010	6
5	34	83.2	1.83	0.364	0.011	0.234	0	31.2	1.31	0.056	0.001	0.027	297
Total	197	100	2.00	0.503	0.019	0.333	–	100	2.00	0.078	0.002	0.031	–

HF high frequency, LF low frequency, % PL percentage of polymorphic loci, Na average number of alleles, I Shannon’s Information index, Ho observed heterozygosity, He Nei’s gene diversity or heterozygosity, PA number of private alleles
Q1 to Q5 are the sub-population inferred by DAPC
^a ARM Accessions are coded as: modern Argentinian, ART traditional Argentinian, CHI Chile, CIM CIMMYT, FRA France, ITM modern Italian, ITT traditional Italian, USA United States, WAN West Asia/ North Africa region. Accessions from Argentina and Italy were divided into two groups according to the breeding period or year of release (until: ʽtraditional,ʼ and after 1985: ʽmodernʼ)

ISSN: 1471-2164