Title:	A semi-automated SNP-based approach for contaminant identification in biparental Polyploid Populations of tropical forage grasses.
Authors:	MARTINS, F. B. MORAES, A. C. L. AONO, A. H. FERREIRA, R. C. U. CHIARI, L. SIMEÃO, R. M. BARRIOS, S. C. L. SANTOS, M. F. JANK, L. VALLE, C. B. do VIGNA, B. B. Z. SOUZA, A. P. DE
Affiliation:	FELIPE BITENCOURT MARTINS, Center for Molecular Biology and Genetic Engineering ALINE COSTA LIMA MORAES, Center for Molecular Biology and Genetic Engineering ALEXANDRE HILD AONO, Center for Molecular Biology and Genetic Engineering REBECCA CAROLINE ULBRICHT FERREIRA, Center for Molecular Biology and Genetic Engineering LUCIMARA CHIARI, CNPGC ROSANGELA MARIA SIMEAO, CNPGC SANZIO CARVALHO LIMA BARRIOS, CNPGC MATEUS FIGUEIREDO SANTOS, CNPGC LIANA JANK, CNPGC CACILDA BORGES DO VALLE, CNPGC BIANCA BACCILI ZANOTTO VIGNA, CPPSE ANETE PEREIRA DE SOUZA, Center for Molecular Biology and Genetic Engineering UNICAMP.
Date Issued:	2021
Citation:	Frontiers in Plant Science, v.12, article 737919, 2021.
Pages:	19 p.
Description:	Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
NAL Thesaurus:	Principal component analysis
Keywords:	GBS Apomictic clones Self fertilization Half sibling Allele dosage Clustering analysis Shiny
DOI:	https://doi.org/10.3389/fpls.2021.737919
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Artigo em periódico indexado (CPPSE)