Título:	Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urocholoa spp. Tetraploids.
Autoria:	MATIAS, F. I. MEIRELES, K. G. X. NAGAMATSU, S. T. BARRIOS, S. C. L. VALE, C. B. do CARAZZOLLE, M. F. FRITSCHE-NETO, R. ENDELMAN, J. B.
Afiliação:	Filipe Inácio Matias, Universidade de São Paulo - USP/ Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ/Departamento de Genetica KAREM GUIMARAES XAVIER MEIRELES, CNPGC Sheila Tiemi Nagamatsu, Universiade Estadual de Campinas - UNICAMP/Departamento Genética e Evolução SANZIO CARVALHO LIMA BARRIOS, CNPGC Cacilda Borges do Valle, Colaboradora da Embrapa Gado de Corte Marcelo Falsarella Carazzolle, Universiade Estadual de Campinas - UNICAMP/Departamento Genética e Evolução Roberto Fritsche-Neto, Universidade de São Paulo - USP/ Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ/Departamento de Genetica Jeffrey B. Endelman, University of Wisconsin–Madison/Dep. Horticulture.
Ano de publicação:	2019
Referência:	The Plant Genome, v. 12, n. 3, november 2019.
Conteúdo:	Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ~3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Crossvalidation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.
NAL Thesaurus:	Genotype Hybrids Urochloa
Palavras-chave:	Although genotyping-by-sequencing Marker technology
Tipo do material:	Artigo de periódico
Acesso:	openAccess
Aparece nas coleções:	Artigo em periódico indexado (CNPGC)