Abstract:Publicly available maize (Zea mays L.) inbred lines with expired Plant Variety Protection certificates (ex‐PVP) constitute the elite germplasm used in hybrids grown by North American farmers during the past half century. A set of 329 ex‐PVP inbreds and eight public reference inbreds was evaluated for genetic diversity using molecular marker and pedigree‐based relationships. The majority of inbreds originated from Dekalb Genetics Corporation, Holden's Foundation Seed, Pioneer Hi‐Bred International, and Syngenta… Show more
“…Principal component analysis (PCA) using these SNPs showed clear separation of the three major maize dent heterotic groups: Stiff Stalk, Iodent, and Non-Stiff Stalk (Figure 4a). The pattern observed in the PCAs are similar to other published results (Romay et al, 2013; van Heerwaarden et al, 2012; White et al, 2020) describing the separation of maize types. The clear separation of maize types from the WGS data gave us confidence in the genotypic data, and provided covariates to use in the GWAS to account for population structure.…”
Maize (Zea mays L.) is a multi-purpose row crop grown worldwide, which overtime has often been bred for increased yield at the detriment of lower composition grain quality. Some knowledge of the genetic factors that affect quality traits has been discovered through the study of classical maize mutants. However, much of the underlying genetic architecture controlling these traits and the interaction between these traits remains unknown. To better understand variation that exists for grain compositional traits in maize, we evaluated 501 diverse temperate maize inbred lines in five unique environments and predicted 16 compositional traits (e.g. carbohydrates, protein, starch) based on the output of near-infrared (NIR) spectroscopy. Phenotypic analysis found substantial variation for compositional traits and the majority of variation was explained by genetic and environmental factors. Correlations and trade-offs among traits in different maize types (e.g. dent, sweetcorn, popcorn) were explored and significant differences and correlations were detected. In total, 22.9-71.1% of the phenotypic variation across these traits could be explained using 2,386,666 single nucleotide polymorphism (SNP) markers generated from whole genome resequencing data. A genome-wide association study (GWAS) was conducted using these same markers and found 70 statistically significant loci for 12 compositional traits. This study provides valuable insights in the phenotypic variation and genetic architecture underlying compositional traits that can be used in breeding programs for improving maize grain quality.
“…Principal component analysis (PCA) using these SNPs showed clear separation of the three major maize dent heterotic groups: Stiff Stalk, Iodent, and Non-Stiff Stalk (Figure 4a). The pattern observed in the PCAs are similar to other published results (Romay et al, 2013; van Heerwaarden et al, 2012; White et al, 2020) describing the separation of maize types. The clear separation of maize types from the WGS data gave us confidence in the genotypic data, and provided covariates to use in the GWAS to account for population structure.…”
Maize (Zea mays L.) is a multi-purpose row crop grown worldwide, which overtime has often been bred for increased yield at the detriment of lower composition grain quality. Some knowledge of the genetic factors that affect quality traits has been discovered through the study of classical maize mutants. However, much of the underlying genetic architecture controlling these traits and the interaction between these traits remains unknown. To better understand variation that exists for grain compositional traits in maize, we evaluated 501 diverse temperate maize inbred lines in five unique environments and predicted 16 compositional traits (e.g. carbohydrates, protein, starch) based on the output of near-infrared (NIR) spectroscopy. Phenotypic analysis found substantial variation for compositional traits and the majority of variation was explained by genetic and environmental factors. Correlations and trade-offs among traits in different maize types (e.g. dent, sweetcorn, popcorn) were explored and significant differences and correlations were detected. In total, 22.9-71.1% of the phenotypic variation across these traits could be explained using 2,386,666 single nucleotide polymorphism (SNP) markers generated from whole genome resequencing data. A genome-wide association study (GWAS) was conducted using these same markers and found 70 statistically significant loci for 12 compositional traits. This study provides valuable insights in the phenotypic variation and genetic architecture underlying compositional traits that can be used in breeding programs for improving maize grain quality.
“…Cluster analysis, principal component analysis, and model-based clustering placed the majority of the lines in the BSSS or NSSS heterotic groups and subgroups as expected according to pedigree information (Mikel and Dudley, 2006;Nelson et al, 2008;Mikel, 2011;Beckett et al, 2017;White et al, 2020). However, there were a few exceptions: PHJ40, PHAA0, and PHRE1 were declared BSSS by Mikel and Dudley (2006), but our results from model-based clustering assigned them to NSSS.…”
Section: Genetic Structure Of Ex-pvp Linessupporting
The use of temperate maize inbreds with expired plant variety protection in tropical maize breeding programs could enhance the combining ability for grain yield among tropical heterotic groups. We used DNA markers from the DArTseq genotyping-by-sequencing platform to investigate the genetic structure of lines with expired U.S. Plant Variety Protection (ex-PVP) relative to CIMMYT's maize heterotic groups. Neighbor-joining cluster analysis revealed two major groups: CIMMYT and ex-PVP. The CIMMYT lines clustered according to their pedigree relationships and adaptation, but not according to their heterotic groups. In contrast, ex-PVP lines clustered according to the Stiff Stalk Synthetic (BSSS) and non-Stiff Stalk Synthetic (NSSS) heterotic groups, except for a few lines that were considered to be mixed. The genetic divergence between BSSS and NSSS (F ST = 0.053; P<0.01) was four times as large as the divergence between CIMMYT Tuxpeño and non-Tuxpeño heterotic groups (F ST = 0.013; P = 0.068). Estimates of genetic divergence marginally favored breeding with BSSS in Tuxpeño and NSSS in non-Tuxpeño. However, CIMMYT breeders may still exploit the ex-PVP heterotic structure fully only by ensuring that the temperate heterotic groups are placed on opposite sides of the Tuxpeño and non-Tuxpeño heterotic pattern. We also showed how estimates of admixture from model-based clustering could be used to avoid ex-PVP lines of mixed heterotic background when selecting lines to maximize the genetic divergence and combining ability of CIMMYT heterotic groups.
“…The M-Reid + P supergroup: includes M-Reid group (see Result) and many inbreds from the P group, which was developed at 1970s and 1980s by introgressing disease resistance genes from the North American germplasm, in particular, those from Pioneer Hybrids, such as, 78599, P3147, and P3382 into Chinese germplasm. The SS + Iodent + Lan supergroup contains many inbreds developed by US public research organizations, such as, B73 (SS) , Mo17 (Lan) in 70s and 80s and many ex-PVP inbreds introduced after 2000s, such as PH207 (Iodent) 14 , 19 , 43 . Figure 8 Heterotic groups of 490 inbred lines in CSM region.…”
Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.
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