SNP genotyping for fast and consistent clustering of maize inbred lines into heterotic groups

Lander Santos De Oliveira,Ivan Schuster,Evandro Novaes,Welison Andrade Pereira

doi:10.1590/1984-70332021v21n1a10

Abstract

Abstract Advances in genotyping technologies have transformed the way breeding programs manage their genetic resources. The identification of single nucleotide polymorphisms (SNPs) can improve understanding of the genetic diversity of maize (Zea mays) inbred lines and their classification into heterotic groups, which is useful in determining certain crosses to obtain hybrids with higher yield performance. The genetic diversity of 293 inbred lines was investigated with 5252 SNPs with minor allele frequency (MAF)>5%. There was an average of 525 SNPs per chromosome. Polymorphism information content (PIC) averaged 0.297. The unweighted pair group method with arithmetic mean analysis (UPGMA) and principal component analysis (PCA) based on the genetic distance matrix revealed four similar clusters and high cophenetic correlation coefficients (0.953 and 0.863, respectively). The results showed consistency between genetic distance-based grouping and the heterotic groups previously established using pedigree and topcross information for the inbred lines studied.

Highlights

Maize (Zea mays) is one of the main crops worldwide, widely used both for human and animal consumption
Unlike primary molecular marker systems, high-density marker genotyping allows simultaneous analysis of markers widely distributed throughout the genome
The magnitude of informativeness of the marker depends on its degree of polymorphism, which is reflected in the genetic diversity among the genotypes under study (Chesnokov and Artemyeva 2015)

Summary

Introduction

Maize (Zea mays) is one of the main crops worldwide, widely used both for human and animal consumption. Brazil is the third largest maize producer in the world, with estimated production of 100 million metric tons in the 2018/19 crop year (CONAB 2020). To meet growing demand for maize worldwide, maize breeding programs have developed high-yielding inbred lines adapted to different environments, which are used as parents in hybrid production (Smith et al 2017). The dramatic increase in the number of inbred lines produced by these programs has made evaluation of the phenotypic performance of all possible hybrid combinations impractical. Classification of inbred lines into heterotic groups has had to be performed in a different way, such as through molecular markers, which has become routine practice in maize breeding programs (Andorf et al 2019). High yielding hybrids can be developed through crosses between inbred lines from different heterotic groups (Souza Júnior 2011)

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