Assessing genetic diversity and population structure in a <i>Dipteryx alata</i> germplasm collection utilizing microsatellite markers

Guimarães, Rejane Araújo; Miranda, Kássia Marques Corrêa; Mota, Elias Emanuel Silva; Chaves, Lázaro José; Telles, Mariana Pires de Campos; Soares, Thannya Nascimento

doi:10.1590/1984-70332019v19n3a45

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ARTICLE • Crop Breed. Appl. Biotechnol. 19 (03) • Jul-Sep 2019 • https://doi.org/10.1590/1984-70332019v19n3a45 copy

Assessing genetic diversity and population structure in a Dipteryx alata germplasm collection utilizing microsatellite markers

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Dipteryx alata Vogel (Leguminosae) is a native Neotropical tree with a wide distribution in the Brazilian Cerrado that is commonly known as the baru tree. The genetic diversity of 150 D. alata progeny from a germplasm collection was characterized using nine microsatellite markers. Genetic diversity analysis detected 50 alleles ranging from 2 to 14 alleles per locus. The genetic differentiation among populations (θ _p = 0.097) suggests moderate genetic structuring and high genetic differentiation among progenies (θ _s = 0.169). The intrapopulation index (f = 0.122) indicates the presence of low endogamy. The effective population size (N_e = 96) shows that the germplasm collection has sufficient representativeness for use as a base population for breeding programmes. These results are useful for the exploitation of the genetic resources of D. alata for future conservation efforts and breeding programmes.

Keywords:
Baru; cerrado; ex situ conservation; effective size; genetic resources

Locus	Repeat motif	T_a ( °C)	A	A _e	H _e	H _o
DaE06	(AAAT)₄	58	3	1.19	0.162	0.102
DaE12	(ATTTTT)₃	58	3	1.24	0.194	0.133
DaE34	(GA)₁₅	58	9	4.23	0.764	0.469
DaE63	(TC)₆	52	4	2.54	0.606	0.315
Bm164	(GT)₉ (GA)₂₁	52	8	1.47	0.322	0.241
DaE41	(CA)₅	60	14	5.22	0.800	0.711
DaE46	(TTA)₅	54	4	3.18	0.686	0.612
DaE20	(AG)₈	54	3	1.74	0.424	0.291
DaE67	(GATACA)₄	62	2	1.31	0.238	0.181
Average			5.5	2.457	0.467	0.339

Population	Origin	Population code	A	A _e	H _e	H _o	f
1	Cocalinho-MT	CMT	2.185	2.17	0.357	0.333	0.080
2	Água Boa-MT	ABMT	2.166	2.15	0.380	0.355	0.076
3	Pirenópolis-GO	PGO	1.907	2.01	0.311	0.262	0.169
4	Sonora-MS	SMS	2.277	2.54	0.442	0.397	0.119
5	Alcinópolis-MS	ALC	2.000	1.83	0.373	0.333	0.121
6	Alvorada-TO	ATO	2.018	2.28	0.410	0.355	0.154
7	São Miguel do Araguaia-GO	SMGO	2.148	2.00	0.391	0.360	0.095
8	Luziânia-GO	LGO	2.000	1.86	0.355	0.293	0.190
9	Icém-SP	ISP	2.074	2.08	0.358	0.318	0.127
10	Monte Alegre de Minas-MG	MAMG	2.000	2.00	0.384	0.315	0.210*
11	Estrela do Norte-GO	ENGO	2.000	2.17	0.347	0.327	0.006
12	Santa Terezinha-GO	STGO	2.092	2.09	0.370	0.381	-0.035
13	Arinos-MG	AMG	2.462	2.75	0.442	0.395	0.120
14	Pintópolis-MG	PMG	1.777	1.64	0.329	0.310	0.069
15	Paraíso-MS	PMS	2.333	2.41	0.409	0.360	0.138
16	Terenos-MS	TRMS	2.203	2.42	0.402	0.375	0.007
17	Camapuã-MS	CMS	2.500	2.42	0.473	0.383	0.216*
18	Indiara-GO	IGO	2.074	1.96	0.385	0.329	0.176*
19	Barra do Garças-MT	BGMT	2.148	2.45	0.369	0.343	0.088
20	Várzea Grande - MT	VGMT	2.462	2.62	0.484	0.420	0.159
21	Jandaia-GO	JGO	2.148	2.09	0.367	0.333	0.106
22	Natividade-TO	NTO	1.740	1.74	0.278	0.276	0.012
23	Arraias-TO	ARTO	1.814	1.88	0.281	0.225	0.224*
24	Aquidauana- MS	AQMS	2.092	2.41	0.386	0.307	0.230*
25	Cárceres- MT	CAMT	2.425	2.81	0.492	0.412	0.190*
Average			2.122	2.46	0.383	0.340	0.122*

Population	N	t_m (SE)	t_s (SE)	t_m-t_s (SE)	r _p
1	24	0.979 (0.006)	0.881 (0.017)	0.097 (0.019)	0.057 (0.019)
2	23	0.987 (0.001)	0.879 (0.016)	0.108 (0.016)	0.087 (0.021)
3	21	0.755 (0.116)	0.843 (0.033)	-0.087 (0.096)	0.063 (0.012)
4	23	0.916 (0.041)	0.844 (0.028)	0.072 (0.050)	0.083 (0.036)
5	23	0.923 (0.044)	0.8584 (0.027)	0.066 (0.034)	0.061 (0.019)
6	23	0.800 (0.078)	0.811 (0.045)	-0.011 (0.073)	0.159 (0.057)
7	24	0.954 (0.032)	0.869 (0.017)	0.085 (0.027)	0.075 (0.029)
8	23	0.945 (0.033)	0.864 (0.033)	0.081 (0.042)	0.053 (0.013)
9	24	0.855 (0.035)	0.840 (0.033)	0.015 (0.040)	0.104 (0.059)
10	24	0.718 (0.048)	0.795 (0.044)	-0.077 (0.047)	0.090 (0.036)
11	23	0.954 (0.033)	0.843 (0.032)	-0.111 (0.039)	0.078 (0.055)
12	23	0.856 (0.043)	0.872 (0.018)	-0.016 (0.037)	0.048 (0.009)
13	24	0.863 (0.041)	0.824 (0.023)	0.039 (0.033)	0.038 (0.008)
14	21	0.855 (0.041)	0.859 (0.021)	-0.004 (0.042)	0.105 (0.029)
15	23	0.891 (0.064)	0.875 (0.027)	0.015 (0.057)	0.043 (0.009)
16	22	0.954 (0.034)	0.832 (0.024)	0.122 (0.037)	0.111 (0.028)
17	24	0.952 (0.033)	0.846 (0.031)	0.105 (0.038)	0.030 (0.006)
18	23	0.898 (0.062)	0.840 (0.028)	0.058 (0.053)	0.144 (0.061)
19	23	0.856 (0.043)	0.840 (0.022)	0.016 (0.044)	0.044 (0.008)
20	22	0.908 (0.064)	0.836 (0.024)	0.073 (0.056)	0.069 (0.022)
21	23	0.881 (0.047)	0.884 (0.014)	-0.003 (0.037)	0.073 (0.036)
22	23	0.750 (0.093)	0.836 (0.038)	-0.086 (0.076)	0.073 (0.015)
23	24	0.897 (0.041)	0.816 (0.041)	0.080 (0.042)	0.121 (0.045)
24	22	0.800 (0.042)	0.030 (0.042)	-0.030 (0.062)	0.044 (0.008)
25	20	0.954 (0.031)	0.785 (0.029)	0.169 (0.039)	0.152 (0.033)

Locus	f	F	θ _s	θ _p	θ _m
DaE06	0.325	0.370	0.067	0.035	0.033
DaE12	0.228	0.312	0.109	0.039	0.073
DaE34	0.280	0.388	0.150	0.069	0.087
DaE63	0.229	0.484	0.331	0.189	0.175
Bm164	0.075	0.256	0.196	0.141	0.064
DaE41	-0.108	0.125	0.211	0.118	0.105
DaE46	0.043	0.110	0.070	0.042	0.029
DaE20	0.220	0.316	0.123	0.095	0.031
DaE67	0.126	0.240	0.131	0.081	0.054
Average	0.129	0.276	0.169	0.097	0.080
Upper CI (95%)	0.239	0.385	0.231	0.134
Lower CI (95%)	0.021	0.177	0.110	0.063

Sample data	Planned collection	Actual collection
N	600	575
S	25	25
M	150	150
θ _p	0.097
θ _s	0.169
F	0.276
N _e	96.9	96.0

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