Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

<p>Abstract</p> <p>Background</p> <p>Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays.</p> <p>Results</p> <p>Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ≤ 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays.</p> <p>Conclusions</p> <p>There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.</p

Genetic Variation and Aflatoxin Accumulation Resistance among 36 Maize Genotypes Evaluated in Ghana

Aflatoxins are carcinogenic secondary metabolites produced predominantly by the fungi Aspergillus flavus and parasiticus. The toxin contaminate maize grains and threatens human food safety. Survey in Ghana revealed aflatoxin contamination of maize in excess of 941 ppb which is way beyond WHO and USA approved limits of 15 ppb and 20 ppb respectively. Host plant resistance is considered as the best strategy for reducing aflatoxins. This study was designed to (1) identify and select suitable maize lines that combine aflatoxin accumulation resistance and good agronomic traits under tropical conditions and (2) assess the genetic diversity among the exotic and locally adapted maize genotypes using significant morphological traits. Thirty-six maize genotypes, 19 from Mississippi State University, USA and 17 locally adapted genotypes in Ghana were evaluated for aflatoxin accumulation resistance and good agronomic characteristics across six contrasting environments using a 6x6 lattice design with three replicates. Five plants each per genotype were inoculated with a local strain of Aspergillus flavus inoculum at a concentration of 9 x 107/3.4 ml, two weeks after 50% mid silking. Total aflatoxin in the kernels were determined at harvest using HPLC method. Statistical analysis for agronomic traits and aflatoxin levels were performed using PROC GLM procedure implemented in SAS. The result indicated that genotype by environment interaction was significant (p < 0.05) for aflatoxin accumulation resistance and many other agronomic traits. Five genotypes (MP715, NC298, MP705, MP719, CML287 and TZEEI- 24) consistently displayed stable resistance across the environments and may serve as suitable candidates for developing aflatoxin resistant hybrids. Cluster analysis showed two distinct groups (locally adapted and exotic genotypes), an indication of re-cycled alleles per region. Broad sense heritability estimates for grain yield and aflatoxin accumulation resistance were moderately high, which could permit transfer of traits during hybrid development

Comparison of the performance of synthetic maize varieties created based on either genetic distance or general combining ability of the parents

Synthetics varieties are grown by farmers and used by breeders to select new inbred lines. In countries unable to market hybrids, use of synthetics leads to yield improvements over landraces. Synthetics are derived from intercrossing inbred lines known to possess high general combining ability (GCA) as measured via crossing with testers and phenotyping for yield in multiple environments. Genetic similarity (GS) between lines measured by molecular markers may efficiently estimate GCA. Although the prediction of specific combining ability (SCA) of lines via GS has not been successful, it may have potential to predict the suitability of lines to form a synthetic variety. As this has not been reported, the objective of this research was to compare the performance of four synthetic maize varieties developed using GS calculated between parents using SSR markers with the performance of synthetics developed using GCA based on yield. Synthetics were phenotyped for yield and other agronomic traits in replicated field trials in several environments. The two synthetics formed based on low GS (0.34 and 0.33) performed better than all other synthetics in yield and most agronomic traits. The synthetics formed based on high GS (0.77 and 0.53), performed worst for nearly all traits. The GCA-based synthetics were generally intermediate for all traits. Response of synthetics to environmental variation and efficiencies gained via use of molecular markers in synthetic formation is discussed

A Public Platform for the Verification of the Phenotypic Effect of Candidate Genes for Resistance to Aflatoxin Accumulation and Aspergillus flavus Infection in Maize

A public candidate gene testing pipeline for resistance to aflatoxin accumulation or Aspergillus flavus infection in maize is presented here. The pipeline consists of steps for identifying, testing, and verifying the association of selected maize gene sequences with resistance under field conditions. Resources include a database of genetic and protein sequences associated with the reduction in aflatoxin contamination from previous studies; eight diverse inbred maize lines for polymorphism identification within any maize gene sequence; four Quantitative Trait Loci (QTL) mapping populations and one association mapping panel, all phenotyped for aflatoxin accumulation resistance and associated phenotypes; and capacity for Insertion/Deletion (InDel) and SNP genotyping in the population(s) for mapping. To date, ten genes have been identified as possible candidate genes and put through the candidate gene testing pipeline, and results are presented here to demonstrate the utility of the pipeline

Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers

Maize (Zea mays L) was first introduced into Ghana over five centuries ago and remains the most important cereal staple, grown in all agro-ecologies across the country. Yield from farmers’ fields are low, which is attributed in part to farmer’s preferences and/or reliance on local landraces for cultivation. Efforts are underway to improve some of these landraces for improved productivity. Seeds of maize landraces cultivated in all agro-ecologies were col¬lected for genetic characterization using a bulked fingerprinting technique and 20 SSR markers. In all, 20 popula¬tions of 15 plants each from Ghana and 4 control populations from Latin America were characterized. The cluster analysis grouped the 20 landraces into two major groups corresponding to the vegetation/climatic conditions of the north and south of the country. Genotypes from Ashanti, which is centrally located, fell into both major clus¬ters, which suggest its importance in maize seed distribution in Ghana and also the diverse climate/vegetation. A Structure analyses grouped the genotypes into two major clusters similar to the UPGMA cluster, and populations were not fully distinct according to F statistics. The results suggest that breeders should make performance data available to seed dealers for better productivity

Genetic diversity and population structure of bermudagrass (Cynodon spp.) revealed by genotyping-by-sequencing

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei’s genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs

Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system