Microsatellites for detecting inconsistencies in <i>Capsicum</i> cultivars registration in Brazilian database: more than meets the eye

Azevedo, Carlos Diego de O; Rodrigues, Rosana; Sudré, Cláudia P

doi:10.1590/S0102-053620190306

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Research • Hortic. Bras. 37 (3) • Jul-Sep 2019 • https://doi.org/10.1590/S0102-053620190306 copy

Microsatellites for detecting inconsistencies in Capsicum cultivars registration in Brazilian database: more than meets the eye

Microssatélites na detecção de inconsistências no registro de cultivares de Capsicum em banco de dados brasileiro: além do que o olho pode ver

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

In Brazil, cultivars are registered by National Register of Cultivars (RNC), which besides enabling commercialization of cultivar propagative material, also guarantees the producers genetic purity and identity of propagules. However, it is possible that the information about registration and commercialization of some cultivars is inaccurate. This study aims to analyze the use of microsatellite markers to detect inconsistencies in data of Capsicum spp. cultivars obtained from the official database (CultivarWeb). Seven cultivars were evaluated, three of them were through genetic identity analysis (Amarela Comprida, De Cayenne and Cayenne Long Slin) and the others were used as standard for the species C. annuum, C. frutescens and C. chinense. Thirty-three microsatellite loci were polymorphic and presented 76 alleles (an average of 2.3 alleles/locus). Fixation Index (F) showed high homozygosis and estimators of genetic diversity (Ho and I) presented low genetic diversity among cultivars. The molecular analysis, represented in a dendrogram and in Principal Coordinate Analysis Chart (PCOA), showed that the investigated cultivars belong to C. annuum, contrary to what is registered in CultivarWeb, which indicates that such cultivars belong to the species C. frutescens. Thus, the authors recommend that the data in the CultivarWeb should be checked and enhanced.

Keywords:
Capsicum spp.; microsatellites; registered cultivars

Loci	Forward primer (5’-3’)	Reverse primer	Linking group	Source
Hpms 1-1*	F tcaacccaatattaaggtcacttcc	R ccaggcggggattgtagatg	1	Lee et al. 2004
Hpms 1-3	F tgggaaataggatgcgctaaacc	R aactttaagactcaaaatccataacc	9	Lee et al. 2004
Hpms 1-5	F ccaaacgaaccgatgaacactc	R gacaatgttgaaaaaggtggaagac	6	Lee et al. 2004
Hpms 1-41	F gggtatcatccgttgaaagttagg	R caagaggtatcacaacatgagagg	1	Lee et al. 2004
Hpms 1-43	F aaccagcaatcccatgaaaacc	R gggctttggggagaatagtgtg	1	Lee et al. 2004
Hpms 1-62	F catgaggtctcgcatgatttcac	R ggagaaggaccatgtactgcagag	1	Lee et al. 2004
Hpms 1-69	F cggtggcatgtagtttctggag	R aagacatgaaatccacaagttttc	4	Lee et al. 2004
Hpms 1-117	F acccaaatttgccttgttgat	R aatccataaccttatcccataaa	9	Lee et al. 2004
Hpms 1-139	F ccaacagtaggacccgaaaatcc	R atgaaggctactgctgcgatcc	1	Lee et al. 2004
Hpms 1-148	F ggcggagaagaactagacgattagc	R ccacccaatccacatagacg	1	Lee et al. 2004
Hpms 1-155	F acgaggcccaagctgttatgtc	R ttgtcccgactctccattgacc	1	Lee et al. 2004
Hpms 1-165	F ggctatttccgacaaaccctcag	R ccattggtgttttcactgttgtg	4	Lee et al. 2004
Hpms 1-168	F gccccgatcaatgaatttcaac	R tgatttttgggtggagagaaaacc	16	Lee et al. 2004
Hpms 1-172	F gggtttgcatgatctaagcatttt	R cgctggaatgcattgtcaaaga	11	Lee et al. 2004
Hpms 1-173	F tgctgggaaagatctcaaaagg	R atcaaggaagcaaaccaatgc	3	Lee et al. 2004
Hpms 1-214	F tgcgagtaccgagttctttctag	R ggcagtcctgggacaactcg	1	Lee et al. 2004
Hpms 1-216	F tgcttgttgtttttaccctcagc	R agtgaaaggtgggcaacagc	7	Lee et al. 2004
Hpms 1-227	F cgtggcttcaagtatggactgc	R ggggcggaacttttcttatcc	7	Lee et al. 2004
Hpms 1-274	F tcccagacccctcgtgatag	R tcctgctccttccacaactg	7	Lee et al. 2004
Hpms 1-281	F tgaggcagtggtatggtctgc	R cccgagttcgtctgccaatag	1	Lee et al. 2004
Hpms 2-2	F gcaaggatgcttagttgggtgtc	R tcccaaaattaccttgcagcac	11	Lee et al. 2004
Hpms 2-13	F tcacctcataagggcttatcaatc	R tccttaaccttacgaaaccttgg	1	Lee et al. 2004
Hpms 2-21	F tttttcaattgatgcatgaccgata	R catgtcattttgtcattgatttgg	10	Lee et al. 2004
Hpms 2-23	F ccctcggctcaggataaatacc	R ccccagactcccactttgtg	5	Lee et al. 2004
Hpms 2-24	F tcgtattggcttgtgatttaccg	R ttgaatcgaatacccgcaggag	9	Lee et al. 2004
Hpms 2-26	F gggatgtaggaacaaccctaacc	R tgcatcttttcttcatcccctttc	1,3,5	Lee et al. 2004
Hpms 2-45	F cgaaaggtagttttgggcctttg	R tgggcccaatatgcttaagagc	5	Lee et al. 2004
HpmsAT2-14	F tttagggtttccaactcttcttcc	R ctaaccccaccaagcaaaacac	4	Lee et al. 2004
HpmsAT2-20	F tgcactgtcttgtgttaaaatgacg	R aaaattgcacaaatatggctgctg	6	Lee et al. 2004
HpmsCaSIG19	F catgaatttcgtcttgaaggtccc	R aagggtgtatcgtacgcagcctta	7	Lee et al. 2004
HpmshpMADS	F tgctttcaaaacaatttgcatgg	R vgcgtctaatgcaaaacacacattac	1	Lee et al. 2004
CACCEL1	F ctctaataggcaatagctcacatgc	R gcagtctcccagaacgttgtcc	1	Lee et al. 2004
AA840689	F gacaacataggcggacctttgg	R tgctttaggtctacgtccttgcac	3	Lee et al. 2004
AA840692	F tggaagtgattactggaaaccatgc	R ggggtttagtcatggaatcttttgc	3	Lee et al. 2004
AA840721	F cactttgatacgtgaacacttcc	R agtttgcactggtcctgctc	7	Lee et al. 2004
AF242731	F gggctgacggccattaagaac	R cagacagctagaaagagaggaattctg	16	Lee et al. 2004
AF244121	F tacctcctcgccaatccttctg	R ttgaaagttctttccatgacaacc	1,3	Lee et al. 2004
CAN010950	F gattttggtggcagaagaattgg	R tgcactttcgaagcaaacaaacc	1	Lee et al. 2004
AF208834	F tgcaccaaggtccagtaaggttg	R ccaaccaccatggttcatacaag	6	Lee et al. 2004
HpmsE001	F tgccacccataaaattcttaaacca	R tgcaagatcccaaattgaaatga	2	Yi et al. 2006
HpmsE003	F tttctgcaattccccttgttca	R cagcagagccttcagtagcagc	2	Yi et al. 2006
HpmsE004	F tgggaagagaaattgtgaaagca	R caatgccaacaatggcatccta	1	Yi et al. 2006
HpmsE005	F tgcctcagtttcccaaccct	R accaacaccgtaacgcaccc	3	Yi et al. 2006
HpmsE006	F gctgaccgttttcgttttggg	R caaaattcaaccgcaccaaca	4	Yi et al. 2006
HpmsE007	F ccccatttccccttcccata	R gaggggtcatgttgaaggcaa	9	Yi et al. 2006
HpmsE008	F ccccttaacttttaattctagatctgc	R tcgttgttcctccatcacctca	3	Yi et al. 2006
HpmsE009	F tgcacaaacatcatacacctca	R cccatgactgatagtccgggtc	2	Yi et al. 2006
HpmsE010	F ctgtttgccaatcaccatcagg	R gctattttccggcgtgtgagag	3	Yi et al. 2006
HpmsE011	F gcagaagaccaaagccctagca	R tggtttccattgtcactgtatgc	6	Yi et al. 2006
HpmsE012	F aaacgctgaaaaaggcgttgac	R tgcaccaacttcttccatgcac	11	Yi et al. 2006
HpmsE013	F gcgccaagtgagttgaattgat	R caccaatccgcttgctgttgta	10	Yi et al. 2006
HpmsE014	F ctttggaacatttctttggggg	R gcggacgtagcagtaggtttgg	6	Yi et al. 2006
HpmsE015	F ttgtgagggtttgacactggga	R ccgagctcgatgaggatgaact	5	Yi et al. 2006
HpmsE016	F ccaagttcaggcccaggagtaa	R tgcagagaagactcaccagtcc	3	Yi et al. 2006
HpmsE019	F aagtcatcagctgcaaagacca	R ttcaacatgcatccagcttctt	1	Yi et al. 2006
HpmsE020	F cccccgagaggaacagaatcat	R ttccattttggtccagctacca	7	Yi et al. 2006
HpmsE021	F cacactaagcattctgctttcaca	R ggagggaatagtagcggtttgga	1	Yi et al. 2006
HpmsE022	F gcaccagcatcaacatcagcat	R cagcaggtgaaggacttgcaga	1	Yi et al. 2006
HpmsE023	F tttaacacctctctaaccgtcacc	R gcgatttcagcccatcaacaat	11	Yi et al. 2006
HpmsE024	F cgagcctaaccacccaaatcag	R aagggaacggagggacgactac	12	Yi et al. 2006
HpmsE025	F tgagcatcccgttatctcaaatca	R cccaattcttcaggcaatctcc	9	Yi et al. 2006
HpmsE026	F ccaaagtccatcgacgtctcaa	R atcaaatggcaaaccaggagga	1	Yi et al. 2006
HpmsE027	F tggagaattggtgttacatgaagg	R ttcggacccttctccatcactt	1	Yi et al. 2006
HpmsE029	F gatggagaagatcgccgacaag	R tacatcagcaggtttgcctcca	1	Yi et al. 2006
HpmsE030	F gaagcaggggccagagctaga	R gcccccaattctcaaacagaga	3	Yi et al. 2006
HpmsE031	F ccctaaatcaaccccaaattcaa	R cccccattacctgactgcaaaa	10	Yi et al. 2006
HpmsE033	F tggatcctcctttctacttcaaca	R aagggtggtgaaaaggggattt	1	Yi et al. 2006
CAMS-156	F ccctatgctttcacaactcct	R gacgtggttatgacgataggc	10	Minamiyama et al. 2006
CAMS-215	F cgtgggtggtctaggatgat	R gctggcaagtcactctggat	7	Minamiyama et al. 2006
CAMS-311	F ggtgcgctagagatggagag	R tttgagtgttcgggactggt	6	Minamiyama et al. 2006
CAMS-340	F tttatgcccattcacaaaataa	R ggacgaattcaccgagtgc	10	Minamiyama et al. 2006
CAMS-398	F atggtccatggtcagcagat	R gggcagaacagtggatgatt	7	Minamiyama et al. 2006
CAMS-405	F ttcttgggtcccacactttc	R aggttgaaaggagggcaata	11	Minamiyama et al. 2006
CAMS-424	F tccacagcccacagtgtcta	R gcttgtggttccgtgatttt	6	Minamiyama et al. 2006
CAMS-451	F tgcattggtgggctaacata	R gctcttgacacaaccccaat	11	Minamiyama et al. 2006
CAMS-460	F cctttcacttcagcccacat	R accatccgctaagacgagaa	7	Minamiyama et al. 2006
CAMS-606	F gactagtccccgttcaacca	R tttgcgagaagatgcttcag	7	Minamiyama et al. 2006
CAMS-811	F gaagaaacgaaggatgaacaaaa	R cctgtttcctcttcctcagc	9	Minamiyama et al. 2006
CAMS-844	F gcaaagaaaaagaaaagcctga	R ctgcaactgctgcttcattc	1	Minamiyama et al. 2006
CAMS-855	F aagtgtcaaggaaggggaca	R cctaaccacccccaaaagtt	8	Minamiyama et al. 2006

Loci	Na	Ne	I	Ho	F
Hpms 11	2.000	1.508	0.520	0.143	0.576
Hpms 13	2.000	1.690	0.598	0	1.000
Hpms 15	3.000	1.342	0.509	0.143	0.440
Hpms 141	2.000	1.690	0.598	0	1.000
Hpms 143	2.000	1.960	0.683	0	1.000
Hpms 162	2.000	1.849	0.652	0.143	0.689
Hpms 1117	3.000	1.556	0.656	0.143	0.600
Hpms 1139	2.000	1.960	0.683	0.857	-0.750
Hpms 1148	3.000	1.815	0.796	0.286	0.364
Hpms 1173	2.000	1.690	0.598	0	1.000
Hpms 1216	2.000	1.324	0.410	0	1.000
Hpms 1281	2.000	1.690	0.598	0	1.000
Hpms 221	3.000	2.178	0.876	0.857	-0.585
Hpms AT214	2.000	1.690	0.598	0	1.000
Hpms AT220	2.000	1.690	0.598	0	1.000
Hpms hpMADS	2.000	1.690	0.598	0	1.000
AA840692	2.000	1.324	0.410	0	1.000
AF242731	2.000	1.960	0.683	0	1.000
Hpms E003	2.000	1.324	0.410	0	1.000
Hpms E004	2.000	1.690	0.598	0	1.000
Hpms E007	2.000	1.690	0.598	0	1.000
Hpms E009	2.000	1.324	0.410	0	1.000
Hpms E014	3.000	2.333	0.956	0	1.000
Hpms E016	3.000	3.000	1.099	0	1.000
CAMS-215	3.000	1.412	0.566	0.167	0.429
CAMS-340	2.000	1.471	0.500	0	1.000
CAMS-398	3.000	2.178	0.876	0.857	-0.585
CAMS-424	2.000	1.690	0.598	0	1.000
CAMS-451	2.000	1.153	0.257	0.143	-0.077
CAMS-460	2.000	1.324	0.410	0	1.000
CAMS-606	2.000	1.508	0.520	0.143	0.576
CAMS-811	3.000	1.556	0.656	0.286	0.200
CAMS-855	3.000	1.556	0.656	0.143	0.600
Total	76.000	55.811	---	---	---
Average	2.303	1.691	0.611	0.130	0.681

Cultivar	Ap	Private alleles per loci
UENF Campista	16	Hpms 13; Hpms 141; Hpms 143; Hpms 162; Hpms 1148; Hpms 1173; Hpms 1281; Hpms 221; Hpms AT214; Hpms AT220; Hpms hpMADS; AF242731; Hpms E004; Hpms E014; CAMS-398; CAMS-424.
Cascadura Ikeda	15	Hpms 13; Hpms 141; Hpms 162; Hpms 1148; Hpms 1173;Hpms 1281; Hpms 221; Hpms AT214; Hpms AT220; Hpms hpMADS; AF242731; Hpms E004; Hpms E014; CAMS-398; CAMS-424.
Amarela Comprida	16	Hpms 13; Hpms 141; Hpms 162; Hpms 1148; Hpms 1173; Hpms 1281; Hpms 221; Hpms AT214; Hpms AT220; Hpms hpMADS; AF242731; Hpms E004; Hpms E014; CAMS-340; CAMS-398;CAMS-424.
De Cayenne	18	Hpms 13; Hpms 141; Hpms 143; Hpms 162; Hpms 1148;Hpms 1173; Hpms 1281; Hpms 221; Hpms AT214; Hpms AT220; Hpms hpMADS; Hpms E004; Hpms E007; Hpms E014; Hpms E016; CAMS-398; CAMS-424; CAMS-451.
Cayenne Long Slin	17	Hpms 13; Hpms 141; Hpms 143;Hpms 162; Hpms 1148; Hpms 1173; Hpms 1281; Hpms 221; Hpms AT214; Hpms AT220; Hpms hpMADS; Hpms E004; Hpms E007; Hpms E014; Hpms E016; CAMS-398; CAMS-424.
Malagueta	6	Hpms 15; Hpms 1117; CAMS-215; CAMS-398; CAMS-460; CAMS-855.
UENF 2154	8	Hpms 1117; Hpms 1216; Hpms 221; AA840692; Hpms E003; Hpms E009; CAMS-811; CAMS-855.

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