High‐density SNP‐based genetic diversity and heterotic patterns of tropical maize breeding lines

Abstract

Understanding the crop diversity is critical for a successful breeding program, helping to dissect the genetic relationship among lines, and to identify superior parents. This study aimed to investigate the genetic diversity of maize (Zea mays L.) inbred lines and to verify the relationship between genetic diversity and heterotic patterns based on hybrid yield performance. A total of 1,041 maize inbred lines were genotyped-by-sequencing, generating 32,840 quality-filtered single nucleotide polymorphisms (SNPs). Diversity analyses were performed using the neighbor-joining clustering method, which generated diversity groups. The clustering of lines based on the diversity groups was compared with the predefined heterotic groups using the additive genomic relationship matrix and unweighted pair group method with arithmetic mean. Additionally, the genetic diversity of lines was correlated with yield performance of their corresponding 591 single-cross hybrids. The SNP-based genetic diversity analysis was efficient and reliable to assign lines within predefined heterotic groups. However, these genetic distances among inbred lines were not good predictors of the hybrid performance for grain yield, once a low but significant Pearson's correlation (.22, p-value ≤ .01) was obtained between parental genetic distances and adjusted means of hybrids. Thus, SNP-based genetic distances provided important insights for effective parental selection, avoiding crosses between genetically similar tropical maize lines.

Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

“…Generally, high PIC values indicate the effectiveness of markers for linkage analysis when estimating the inheritance between parental lines and the derived hybrids [41], whereas the GD or expected heterozygosity (He) reveals gene diversity for haploid markers and gives information on the proportion of the genetic distance and average heterozygosity within a given population [41,42]. In the present study, an average PIC of 0.25 was obtained, which is comparable to that reported earlier by Dao et al [27] and Zhang et al [28], as well as the 0.24 of Yu et al [43] and 0.29 of Wu et al [44], but higher compared with the results of Adu-Boakyewaa et al [15] and Silva et al [45] who reported average PIC values of 0.19 and 0.17, respectively. The high mean PIC value observed implied that majority of the selected SNPs were informative and polymorphic enough to bring out the differences among the 162 inbred lines studied.…”

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

“…On average, there were 525 SNPs in each chromosome, ranging from 327 in chromosome 10 to 926 in chromosome 1 (Figure 1A). This distribution of SNPs throughout the genome was similar to other studies in maize using this type of marker (Li et al 2018, Guo et al 2019, Leng et al 2019, Silva et al 2020. Unlike primary molecular marker systems, high-density marker genotyping allows simultaneous analysis of markers widely distributed throughout the genome.…”

“…Furthermore, genetic diversity studies are commonly carried out in maize breeding programs in an effort to classify lines into heterotic groups (Wu et al 2016, Leng et al 2019, Silva et al 2020 because parents with high per se performance and genetic divergence from each other are important requirements for manifestation of heterosis (Prasad and Singh 1986). Classification of inbreds into heterotic groups using information on genetic diversity facilitates directed crosses between inbreds from contrasting groups and reduces the number of hybrid crosses made in a breeding program, thus increasing the efficiency of the program and leading to accelerated genetic gains from selection (Reif et al 2005).…”

“…Although this method is simple, it requires detailed pedigree information, which is not always available (Lee et al 2007, Adu et al 2019b, Leng et al 2019. Therefore, the use of molecular markers has become the best method to make inferences regarding genetic diversity among genotypes (Muhammad et al 2017, Scherlosky et al 2018, Adu et al 2019a, Silva et al 2020, without the need for making numerous crosses and evaluating hybrids in the field (Andorf et al 2019). Some molecular markers are highly polymorphic and independent of environmental effects and plant physiological stages.…”

A Genome-Wide Association Study for Fumonisin Contamination Resistance in Tropical Maize

“…The maize diversity panel was comprised two hundred and ve maize inbred lines, from the breeding program of Embrapa (Brazilian Agricultural Research Corporation) Maize and Sorghum, located in Sete Lagoas, state of Minas Gerais, Brazil (Silva et al 2019). During the 2014/2015 crop season, the 205 lines were evaluated in three eld trials conducted in the experimental station of Embrapa Mid-North, located in Teresina, state of Piauí, Brazil.…”