Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize.

Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.

Genetic relatedness of previously Plant-Variety-Protected commercial maize inbreds.

The emergence of high-throughput, high-density genotyping methods combined with increasingly powerful computing systems has created opportunities to further discover and exploit the genes controlling agronomic performance in elite maize breeding populations. Understanding the genetic basis of population structure in an elite set of materials is an essential step in this genetic discovery process. This paper presents a genotype-based population analysis of all maize inbreds whose Plant Variety Protection certificates had expired as of the end of 2013 (283 inbreds) as well as 66 public founder inbreds. The results provide accurate population structure information and allow for important inferences in context of the historical development of North American elite commercial maize germplasm. Genotypic data was obtained via genotyping-by-sequencing on 349 inbreds. After filtering for missing data, 77,314 high-quality markers remained. The remaining missing data (average per individual was 6.22 percent) was fully imputed at an accuracy of 83 percent. Calculation of linkage disequilibrium revealed that the average r2 of 0.20 occurs at approximately 1.1 Kb. Results of population genetics analyses agree with previously published studies that divide North American maize germplasm into three heterotic groups: Stiff Stalk, Non-Stiff Stalk, and Iodent. Principal component analysis shows that population differentiation is indeed very complex and present at many levels, yet confirms that division into three main sub-groups is optimal for population description. Clustering based on Nei's genetic distance provides an additional empirical representation of the three main heterotic groups. Overall fixation index (FST), indicating the degree of genetic divergence between the three main heterotic groups, was 0.1361. Understanding the genetic relationships and population differentiation of elite germplasm may help breeders to maintain and potentially increase the rate of genetic gain, resulting in higher overall agronomic performance.

Distinct genetic architectures for male and female inflorescence traits of maize.

We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects.

Genome-wide association study of leaf architecture in the maize nested association mapping population.

US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.

The genetic architecture of maize flowering time.

Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.

The xanthophyll composition of biofortified maize (Zea mays Sp.) does not influence the bioefficacy of provitamin a carotenoids in Mongolian gerbils (Meriones unguiculatus).

Maize has been targeted for biofortification with provitamin A carotenoids through traditional breeding. Two studies were conducted in gerbils to evaluate factors that may affect provitamin A activity. Maize diets had equal theoretical concentrations of vitamin A (VA) assuming 100% bioefficacy. Study 1 ( n = 57) varied the ratio of beta-cryptoxanthin and beta-carotene but maintained the same theoretical VA. Study 2 ( n = 67) varied lutein and zeaxanthin. Other treatments were oil, VA, or beta-carotene doses. Serum and livers were analyzed for VA and carotenoids. In study 1, total liver VA did not differ among the maize groups. In study 2, total liver VA of the VA and maize groups were higher than controls ( P < 0.05). Conversion factors were 2.1-3.3 mug beta-carotene equivalents to 1 mug retinol. Twice the molar amount of beta-cryptoxanthin was as efficacious as beta-carotene and the proportion of beta-cryptoxanthin or xanthophylls did not appreciably change the VA value of biofortified maize.

Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification.

Dietary vitamin A deficiency causes eye disease in 40 million children each year and places 140 to 250 million at risk for health disorders. Many children in sub-Saharan Africa subsist on maize-based diets. Maize displays considerable natural variation for carotenoid composition, including vitamin A precursors alpha-carotene, beta-carotene, and beta-cryptoxanthin. Through association analysis, linkage mapping, expression analysis, and mutagenesis, we show that variation at the lycopene epsilon cyclase (lcyE) locus alters flux down alpha-carotene versus beta-carotene branches of the carotenoid pathway. Four natural lcyE polymorphisms explained 58% of the variation in these two branches and a threefold difference in provitamin A compounds. Selection of favorable lcyE alleles with inexpensive molecular markers will now enable developing-country breeders to more effectively produce maize grain with higher provitamin A levels.

The genetic architecture of response to long-term artificial selection for oil concentration in the maize kernel.

In one of the longest-running experiments in biology, researchers at the University of Illinois have selected for altered composition of the maize kernel since 1896. Here we use an association study to infer the genetic basis of dramatic changes that occurred in response to selection for changes in oil concentration. The study population was produced by a cross between the high- and low-selection lines at generation 70, followed by 10 generations of random mating and the derivation of 500 lines by selfing. These lines were genotyped for 488 genetic markers and the oil concentration was evaluated in replicated field trials. Three methods of analysis were tested in simulations for ability to detect quantitative trait loci (QTL). The most effective method was model selection in multiple regression. This method detected approximately 50 QTL accounting for approximately 50% of the genetic variance, suggesting that >50 QTL are involved. The QTL effect estimates are small and largely additive. About 20% of the QTL have negative effects (i.e., not predicted by the parental difference), which is consistent with hitchhiking and small population size during selection. The large number of QTL detected accounts for the smooth and sustained response to selection throughout the twentieth century.

Dissection of maize kernel composition and starch production by candidate gene association.

Cereal starch production forms the basis of subsistence for much of the world's human and domesticated animal populations. Starch concentration and composition in the maize (Zea mays ssp mays) kernel are complex traits controlled by many genes. In this study, an association approach was used to evaluate six maize candidate genes involved in kernel starch biosynthesis: amylose extender1 (ae1), brittle endosperm2 (bt2), shrunken1 (sh1), sh2, sugary1, and waxy1. Major kernel composition traits, such as protein, oil, and starch concentration, were assessed as well as important starch composition quality traits, including pasting properties and amylose levels. Overall, bt2, sh1, and sh2 showed significant associations for kernel composition traits, whereas ae1 and sh2 showed significant associations for starch pasting properties. ae1 and sh1 both associated with amylose levels. Additionally, haplotype analysis of sh2 suggested this gene is involved in starch viscosity properties and amylose content. Despite starch concentration being only moderately heritable for this particular panel of diverse maize inbreds, high resolution was achieved when evaluating these starch candidate genes, and diverse alleles for breeding and further molecular analysis were identified.

Maize selection passes the century mark: a unique resource for 21st century genomics.

The Illinois Long-Term Selection Experiment for grain protein and oil concentration in maize (Zea mays) is the longest continuous genetics experiment in higher plants. A total of 103 cycles of selection have produced nine related populations that exhibit phenotypic extremes for grain composition and a host of correlated traits. The use of functional genomics tools in this unique genetic resource provides exciting opportunities not only to discover the genes that contribute to phenotypic differences but also to investigate issues such as the response of plant genomes to artificial selection, the genetic architecture of quantitative traits and the source of continued genetic variation within domesticated crop genomes.

Enhancement of vitamin E levels in corn.

Vitamin E is the common name that describes eight naturally occurring compounds possessing alpha-tocopherol activity. These eight vitamin E compounds are collectively termed tocols, and all have antioxidant activity. There is natural variation among different corn breeding lines for levels of tocols. The two predominant isomers present in corn grain are gamma-tocopherol and alpha-tocopherol. Alpha-tocopherol is considered more desirable for human and animal consumption because it has higher biological activity than gamma-tocopherol. Most corn breeding lines naturally have much more gamma-tocopherol than alpha-tocopherol. Therefore a breeding goal is to increase levels of alpha-tocopherol relative to gamma-tocopherol. However, recent research suggests that gamma-tocopherol and compounds metabolized from it have properties important to human health that are unique from properties of alpha-tocopherol. Therefore it may be desirable to not only increase levels of alpha-tocopherol in corn grain, but also levels of gamma-tocopherol. Determination of levels of tocopherols in corn grain is very laborious, requires HPLC analysis and is too time consuming for use in routine commercial corn breeding programs. Therefore we are performing biotechnology enabled molecular marker mapping of chromosomal regions with genes that control levels and ratios of alpha- and gamma-tocopherol. Breeders can use molecular markers we have identified to expediently select for desirable alleles of genes that will improve levels of alpha- and gamma-tocopherol in corn grain, without having to perform laborious HPLC assays. Another biotechnology strategy we have initiated is genetic transformation of corn with the gamma-tocopherol methyl transferase gene to enhance conversion of gamma-tocopherol to alpha-tocopherol and thus increase levels of alpha-tocopherol. This transgenic strategy has been demonstrated in the model plant Arabidopsis, and we are now applying this approach to corn.

Germplasm Ownership: Related Corn Inbreds.

Corn (Zea mays L.) germplasm ownership methods are unwieldy and limit progress. Agronomic performance in hybrids better identifies inbreds for distinctness, i.e., independent varieties (IVs) or for dependency, i.e. essentially derived varieties (EDVs) than do molecular methods alone. Our objectives were to assess hybrid agronomic performance of some popular, closely related inbreds on the basis of molecular methods, and to offer thoughts on developing inbreds and on germplasm ownership. Significant agronomic differences were detected between the following: two hybrids in the same genetic group on the basis of 21 isozymic loci; two closely related inbreds (B73 and LH119) with 88.6% (62/70) RFLP (restriction fragment length polymorphism) similarity; and two closely related inbreds (Mo17 and LH51) with 88.2% (60/68) RFLP similarity. We suggest raising dependency standards for patenting inbreds to 90% or more, allowing the right to use and also paying a small royalty for only 5 yr on EDVs to the owner of the IV, and maintaining a research exemption to provide elite inbreds for developing new inbreds and experimental hybrids to all breeders. This will help maintain genetic gain for corn grain yield and serve the common good.