Genomic Dataset of the Commercial Maize Germplasm in Brazil

Published: 08-10-2019| Version 2 | DOI: 10.17632/j26bcf94wz.2
Contributors:
Roberto Fritsche-Neto,
Luciano Rogério Braatz de Andrade,
Aluizio Borem,
italo granato,
Pedro Patric Pinho Morais,
Gustavo Cesar Sant’Ana

Description

A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Mon- santo® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commer- cial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent geno- mic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Syn- thetic), contributed to the development of the commercial Brazilian germplasms. The hybrids (20) are in the rows and the markers (768) are in the columns. Quality control over data (MAF and Call Rate) was not performed. Genotypes are referred to by nitrogenous bases (eg G / G) and information lost by - / -.

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