Genotypic variation of traits related to quality of cassava roots using affinity propagation algorithm

Abstract

The conservation, sustainable evaluation and use of cassava (Manihot esculenta Crantz) genetic resources are essential to the development of new commercial varieties. This study aimed to evaluate the quality of cassava roots and to estimate genetic variation and clustering in cassava germplasm using the Affinity Propagation algorithm (AP), which is based on the concept of "message passing" between data points. AP finds "exemplars" of each group and members of the input set representative of clusters. The genotypic data of 474 cassava accessions were evaluated over a period of two years for starch yield (StYi), root dry matter (DMC), amylose content (AML), and the level of cyanogenic compounds (CyC). The AP algorithm enabled the formation of nine diversity groups, whose number reflects the high genetic diversity of this germplasm. A high homogeneity of genetic distances was observed within all the groups, except for two groups in which there was a partial overlap caused mainly by a high variation of the CyC trait. In addition, no relationship between the genetic structure and CyC (sweet and bitter cassava) was observed. Analysis of variance of the nine clusters confirmed the presence of differences between the groups. Thus, the results of this study can be used in future breeding programs (hybridization or selection) to introduce new genetic variability into commercial cultivars to avoid problems related to low genetic variation and to improve the quality of cassava roots.

Identification of duplicates in cassava germplasm banks based on single-nucleotide polymorphisms (SNPs)

“…The ability to identify breeding populations with high agronomic performance is an objective in the development of new varieties of cassava (Oliveira et al, 2015). In addition, according to Semagn et al (2012), it is recognized that close groups of diversity tend to increase redundancy in several breeding programs; therefore, their use in crossbreeding may result in a waste of time and resources since crossbreeding low genetic complementarity parents can produce progenies of low performance (Dias et al, 2003;Benin et al, 2012).…”

Phenotypic diversity of starch granules in cassava germplasm

“…This was also observed with other classifications (low and intermediate levels of cyanogenic compounds). Oliveira et al (2015b) used the affinity propagation algorithm to cluster 474 cassava accessions based on the following traits: starch yield, dry matter content, amylose, and cyanogenic compound content in the roots. These authors also reported difficulty in the classification of cassava accessions based exclusively on cyanogenic compound content, due to the large scale of this trait, especially in two groups, and the absence of an association between the genetic structure of accessions and the classification of bitter and sweet cassava.…”

Germplasm of Brazilian winter squash (Cucurbita moschataD.) displays vast genetic variability, allowing identification of promising genotypes for agro-morphological traits

“…As with other species, the usefulness of C. moschata germplasm conserved in banks depends on the level and quality of information associated with it [44, 14, 29, 30, 31]. The samples of C. moschata maintained by BGH-UFV constitute one of the largest collections of this species in Brazil [32].…”

“…In view of this, the FAO’s Second Global Action Plan for Plant Genetic Resources for Food and Agriculture sets out guidelines that provide greater efficiency in the conservation and use of plant germplasm [28]. This is essential information for the management and use of germplasm [14, 29, 30, 31]. Evaluation of the germplasm maintained in banks makes it possible to estimate the magnitude of the genetic and statistical parameters of characteristics of interest, which can provide information on the nature of variability observed for these traits, in addition to elucidating which characteristics or groups of characteristics most contribute to germplasm variability.…”