Abstract
Genetic redundancy in cassava (Manihot esculenta Crantz) presents a challenge to efficient management of genetic resources. This study aimed to identify and define the genetic structure of duplicates in cassava germplasm from various Embrapa research units, using single-nucleotide polymorphism (SNP) markers. We evaluated 2,371 accessions with 20,712 SNPs. The identification of duplicates was performed based on multilocus genotypes (MLG), adopting a maximum genetic distance threshold of 0.05. The population structure was defined based on discriminant analysis of principal components (DAPC). A total of 1,757 unique and 614 duplicate accessions were identified. The redundancy of the collections ranged from 17 % (Belém, PA – Brazil) to 39 % (Petrolina, PE – Brazil), with an average of 21 %. This redundancy between different research units is probably due to the historical sharing of accessions, as well as collections carried out in the same region, or even to the intense germplasm exchange between farmers with different genotype names. In terms of genetic structure, the 250 principal components explained 88 % of the genetic variation of the SNP markers and defined the hierarchical structure of the duplicate cassava germplasm in 12 groups. Since heterotic groups have not yet been identified for cassava, crosses between accessions of the 12 DAPC groups may be promising. All MLGs were allocated within the same DAPC group, corroborating duplicate analyses yet still revealing high variability between groups that were quite distinct based on the first two discriminant functions. Our results contribute to optimizing the conservation of genetic resources, together with understanding diversity and its use in crop improvement.
Highlights
Cassava (Manihot esculenta Crantz) is native to South America, where Brazil is its probable center of origin and diversity (Olsen, 2004)
Several types of molecular markers have been used in cassava, currently the single-nucleotide polymorphism (SNP) markers are those most commonly used in several molecular studies focused on genomic selection (Oliveira et al, 2012), linkage and mapping of quantitative trait loci (QTL) (Nzuki et al, 2017), and identification of duplicate accessions (Rabbi et al, 2015)
Plant material A total of 2,371 accessions belonging to the Cassava Germplasm Bank (CGB) conserved at Embrapa were analyzed, of which 1,553 accessions belong to Cruz das Almas, BAa (CNPMF, 224 m altitude, 12°40’ S latitude and 39°06’ W longitude); 356 accessions to Belém, PA (CPATU, 12 m altitude, 1°28’ S latitude and 48°27’ W longitude); 327 accessions to Planaltina, Federal District (CPAC, 1,007 m altitude, 15°35’ S latitude and 47°42’ W longitude); and 135 accessions to Petrolina, PE (CPATSA, 370 m altitude, 09°09’ S latitude and 40°22’ W longitude), Brazil
Summary
Cassava (Manihot esculenta Crantz) is native to South America, where Brazil is its probable center of origin and diversity (Olsen, 2004). The Cassava Germplasm Bank (CGB) conserves a wide variety of accessions of this species, with great relevance to future use in several genetic studies and breeding programs. With advances in the molecular biology of cassava, numerous opportunities have arisen to apply this information to increase efficiency in the use of genetic resources and conventional breeding. Several types of molecular markers have been used in cassava, currently the SNP (single-nucleotide polymorphism) markers are those most commonly used in several molecular studies focused on genomic selection (Oliveira et al, 2012), linkage and mapping of quantitative trait loci (QTL) (Nzuki et al, 2017), and identification of duplicate accessions (Rabbi et al, 2015). Along with the phenotypic and passport data, the SNP markers can greatly contribute to a clear and efficient distinction of cassava germplasm
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