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

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

Using molecular markers to identify heterotic groups in maize.

<p>Using molecular markers to identify heterotic groups in maize.</p

Summary of proposed heterotic group divisions in maize.

<p>Summary of proposed heterotic group divisions in maize.</p

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

<div><p>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 <i>r</i>² 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 (<i>F</i>_ST), 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.</p></div

Historical U.S. Maize Yields, 1866 to 2015.

<p>Data is separated into three time periods according to the source of corn seed planted for agricultural production. In the first period, from 1866 to 1936, the vast majority of corn grown was of the open-pollinated type. During the second period, from 1937 to 1955, most hybrid corn planted in the U.S. was produced from double crosses. Throughout the third period, from 1956 to 2015, single-cross hybrids were the largest source of corn seed planted for commercial production. A best-fit linear trend is included for each time period. Data was obtained from the USDA National Agricultural Statistical Service [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189277#pone.0189277.ref010" target="_blank">10</a>].</p

Summary of proposed heterotic group divisions in maize.

<p>Summary of proposed heterotic group divisions in maize.</p

Three-dimensional plot of principal component analysis.

<p>Axes labels are abbreviated for principal components 1, 2, and 3, respectively. Colors indicate membership in one of three population sub-groups as determined by phylogenetic cluster analysis.</p

Summary statistics of unmerged genotypic data sets, before filtering and imputing.

<p>Summary statistics of unmerged genotypic data sets, before filtering and imputing.</p