CertiBase: a genetic database for cultivar certification and genetic breeding of pecan in Brazil

This study was aimed at developing a molecular genetic database that allows the certification of the pecan cultivars planted in Brazil, based on reference cultivars from the USA. We used a set of 10 nSSR and 10 cpSSR markers for cultivar identification and characterization. The database developed is an instrument for certification of cultivars, characterization of potential new cultivars, and selection of material for pecan breeding. The CertiBase database is composed of genotypes and haplotypes characterized for 40 reference pecan cultivars, while the CertiBase algorithm for plant identification is implemented in a user-friendly free software. Varietal certification of cultivars will bring more security to the entire production chain, in addition to enabling the characterization of the ancestry of potential new cultivars and establishment of breeding programs of pecan in Brazil.

Keywords:
Carya illinoinensis; germplasm characterization; molecular markers

Authorship

Tales Poletto ^** E-mail: talespoletto@gmail.com

Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Rodovia Admar Gonzaga, 1346, Itacorubi, 88034-000, Florianópolis, SC, Brazil. Universidade Federal de Santa CatarinaBrazilFlorianópolis, SC, Brazil Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Rodovia Admar Gonzaga, 1346, Itacorubi, 88034-000, Florianópolis, SC, Brazil.

https://orcid.org/0000-0002-6162-4445

Igor Poletto

Universidade Federal do Pampa, Campus São Gabriel, Rua Aluízio Barros Macedo, s/n, BR 290, km 423, 97307-020, São Gabriel, RS, BrazilUniversidade Federal do PampaBrazilSão Gabriel, RS, Brazil Universidade Federal do Pampa, Campus São Gabriel, Rua Aluízio Barros Macedo, s/n, BR 290, km 423, 97307-020, São Gabriel, RS, Brazil

Cassiano Eric de Carvalho Marques

Ana Kelly de Sousa Silva

Keith Kubenka

USDA - ARS Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, United StatesUSDA - ARS Southern Plains Agricultural Research CenterUnited StatesUnited States USDA - ARS Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, United States

Warren Chatwin

Oliver Gailing

University of Göttingen, Department of Forest Genetics and Forest Tree Breeding, Buesgenweg 2, 37077 Goettingen, Niedersachsen, GermanyUniversity of GöttingenGermanyGoettingen, Niedersachsen, Germany University of Göttingen, Department of Forest Genetics and Forest Tree Breeding, Buesgenweg 2, 37077 Goettingen, Niedersachsen, Germany

Valdir Marcos Stefenon

* E-mail: talespoletto@gmail.com

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables

Figures (4)
Tables (1)

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Figure 1
Neighbor-joining dendrogram of the pecan cultivars planted in Brazil and the reference cultivars (names followed by -R), based on the Euclidean distance of the combined genetic datasets (nSSR and cpSSR markers). Numbers at nodes are the bootstrap support after 1000 replicates. The inset shows the Probability of Identity (PI) of the SSR markers.

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Figure 2
Allelic patterns of the nuclear marker pm-cin4 for cultivar certification or parental analysis. a) Electropherogram of the North American reference (Barton USA) and one genotype of the Brazilian cultivar Barton, showing a true-to-type pattern. b) Electropherogram of the North American reference and one off-type genotype of the Brazilian cultivar Desirable. The Shawnee cultivar seems to be a parent of the off-type Brazilian genotype since the reference cultivar Shawnee USA holds the allele 158.65, equivalent to allele 158.48 in Desirable BR. The size of the alleles in the electropherogram is larger than registered in the database, due to the 18 bp of the M13-tail used in the PCR amplification (see Material and Methods).

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Figure 3
Molecular characterization of pecan accessions without cultivar definition. a) Neighbor-joining dendrogram based on the Mahalanobis distance of the 40 reference cultivars and the 17 Brazilian accessions without cultivar definition (samples with BG prefix). The mean pairwise distance among all samples (reference cultivars and accessions without cultivar definition) is d = 1.36. b) Staminate flowers of cultivar Barton. c) Pistillate flowers of cultivar Barton. d) Fruits of cultivar Barton. e) Morphological diversity of pecan nuts cultivated in Brazil (from the top: Mahan, Sumner, Choctaw, Pawnee, Desirable, Shoshoni).

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Figure 4
Overall view of the CertiBase software. a) The user must choose the database and the query files (excel sheets) using the “Select” button. b) A search window will open for file choice. c) After uploading both files (database and query sheets), the similarity is computed and presented in the lower part of the window for the three cultivars with the highest similarities to the query plant.

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Table 1
Total number of alleles (A) for nuclear (nSSR) and plastid (cpSSR) SSR markers recorded from 35 accessions representing 11 pecan cultivars planted in Brazil

Figure 1 Neighbor-joining dendrogram of the pecan cultivars planted in Brazil and the reference cultivars (names followed by -R), based on the Euclidean distance of the combined genetic datasets (nSSR and cpSSR markers). Numbers at nodes are the bootstrap support after 1000 replicates. The inset shows the Probability of Identity (PI) of the SSR markers.

Figure 2 Allelic patterns of the nuclear marker pm-cin4 for cultivar certification or parental analysis. a) Electropherogram of the North American reference (Barton USA) and one genotype of the Brazilian cultivar Barton, showing a true-to-type pattern. b) Electropherogram of the North American reference and one off-type genotype of the Brazilian cultivar Desirable. The Shawnee cultivar seems to be a parent of the off-type Brazilian genotype since the reference cultivar Shawnee USA holds the allele 158.65, equivalent to allele 158.48 in Desirable BR. The size of the alleles in the electropherogram is larger than registered in the database, due to the 18 bp of the M13-tail used in the PCR amplification (see Material and Methods).

Figure 3 Molecular characterization of pecan accessions without cultivar definition. a) Neighbor-joining dendrogram based on the Mahalanobis distance of the 40 reference cultivars and the 17 Brazilian accessions without cultivar definition (samples with BG prefix). The mean pairwise distance among all samples (reference cultivars and accessions without cultivar definition) is d = 1.36. b) Staminate flowers of cultivar Barton. c) Pistillate flowers of cultivar Barton. d) Fruits of cultivar Barton. e) Morphological diversity of pecan nuts cultivated in Brazil (from the top: Mahan, Sumner, Choctaw, Pawnee, Desirable, Shoshoni).

Figure 4 Overall view of the CertiBase software. a) The user must choose the database and the query files (excel sheets) using the “Select” button. b) A search window will open for file choice. c) After uploading both files (database and query sheets), the similarity is computed and presented in the lower part of the window for the three cultivars with the highest similarities to the query plant.

Table 1 Total number of alleles (A) for nuclear (nSSR) and plastid (cpSSR) SSR markers recorded from 35 accessions representing 11 pecan cultivars planted in Brazil

nSSR		cpSSR
Marker	N. alleles	Marker	N. alleles
pm-cin4	12	cpCil1	2
pm-ca10	2	cpCil2	2
pm-cin13	5	cpCil4	2
pm-cin20	2	cpCil5	2
pm-cin22	5	cpCil6	1
pm-ga23	5	cpCil7	2
pm-cin27	6	cpCil8	2
pm-ga38	5	cpCil9	2
pm-ga39	4	cpCil10	2
pm-ga41	7	cpCil12	3
Overall mean nSSR	5.3	Overall mean cpSSR	2.0
Total nSSR	53	Total cpSSR	20

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Crop Breeding and Applied Biotechnology Universidade Federal de Viçosa, Departamento de Fitotecnia, 36570-000 Viçosa - Minas Gerais/Brasil, Tel.: (55 31)3899-2611, Fax: (55 31)3899-2611 - Viçosa - MG - Brazil
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CertiBase: a genetic database for cultivar certification and genetic breeding of pecan in Brazil

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[1] * E-mail: talespoletto@gmail.com