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

Summary of proposed heterotic group divisions in maize.

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

Principal component 1 vs. principal component 2.

<p>Principal component no. 1 (x-axis) vs. principal component no. 2 (y-axis), color annotated by three heterotic group divisions. Colors indicate membership in one of three population sub-groups as determined by phylogenetic cluster analysis.</p

Summary of proposed heterotic group divisions in maize.

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

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

Using molecular markers to identify heterotic groups in maize.

<p>Using molecular markers to identify heterotic groups 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

Candidate genes for SNPs with high <i>F</i>_ST values.

<p>Candidate genes for SNPs with high <i>F</i>_ST values.</p

Summary statistics of merged, filtered, and imputed genotypic data sets.

<p>Summary statistics of merged, filtered, and imputed genotypic data sets.</p