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

Abstract

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.

Fig 1. Historical U.S. Maize Yields, 1866 to 2015.

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 [10].

Fig 2. Plant Variety Protection certificates expired as of 2012, by proprietor.

Proprietor names were abbreviated as follows: Pioneer, Pioneer Hi-Bred International, Inc.; Holden’s, Holden’s Foundation Seeds, Inc.; DEKALB, DEKALB Genetics; Novartis, Novartis Seeds, Inc; United AgriSeeds, United AgriSeeds, Inc.; Advanta, Advanta Technology Limited; and Wilson Hybrids, Wilson Hybrids Inc. Proprietor names are on the x-axis, and the number of inbreds present in this set of 283 is on the y-axis. Above each bar is the value in percent, calculated as the number of PVP inbreds for each respective proprietor divided by 283. Proprietorship was obtained from the Plant Variety Protection certificate for each inbred, accessible in the United States Department of Agriculture Agricultural Research Service Germplasm Network Information Database [48].

Fig 3. Decay of linkage disequilibrium with physical distance.

Decay of linkage disequilibrium (LD) with physical distance between 77,314 pairs of single nucleotide polymorphism (SNP) markers in the ex-PVP and public founder genotypic data set. Physical distance (scaled logarithmically) is on the x-axis and LD, measured in r² is on the y-axis. Individual chromosomes are indicated by line color, with the overall average of all data overlaid as a black trend line.

Fig 4. Principal component 1 vs. principal component 2.

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.

Fig 5. Three-dimensional plot of principal component analysis.

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.

Fig 6. Scree plot of principal component analysis.

The number of principal components (PCs) is on the x-axis and the associated eigenvalues–which indicate the amount of variance yet unexplained–are on the y-axis. The optimal number of principal components to explain the variation found in the genotype is found by visually determining the largest point of inflection, or “elbow” of the non-linear trend line [64].

Fig 7. Percent genetic variance explained by principal component analysis.

The percent of genetic variance explained is on the y-axis and the principle component (PC) number is on the x-axis. Exact values of percent variance explained are included next to the plotted points at PCs 1-5, 8, and 13.

Fig 8. Dendrogram of ex-PVP and public founder inbreds.

Circular dendrogram of ex-PVP and public founder inbreds, divided into three heterotic groups. This dendrogram, shown with relative scaled branch lengths and colored according to generally known maize heterotic groups, is based on a cluster analysis using Ward’s minimum distance variance method on the matrix of Nei’s genetic distance [57, 58]. Scaled branch lengths allow a visual representation of the relative proportion of genetic difference between the three main heterotic groups. Consultation of available pedigrees confirm the accuracy of heterotic group placement for individual inbreds [12, 20, 24, 48, 49, 67]. Note: this tree is presented in a rooted format with the primary purpose of illustrating genetic distance while retaining legible inbred names. While no inference is made about common ancestors, the Stiff Stalk and Iodent/Non-Stiff Stalk portions form an ingroup/outgroup interaction, thus ensuring that the presentation of a tree in rooted format is still an acceptable depiction of the detailed population stratification.

Fig 9. Fixation index values across the genome.

Relative SNP position by chromosome (x-axis) and fixation index (y-axis). Each grey dot represents the fixation index statistic (F_ST) for an individual genetic locus. High F_ST value for a genetic locus may indicate that particular genetic locus contributed to genetic differentiation between heterotic groups. The red trend line represents a moving average across a window of 70 SNPs, or approximately 3570 Mb. This red line is representative, then, of the F_ST values across genomic regions. Peaks observed in the trend line, particularly in chromosomes 1, 4, 7, and 10, may be indicative of lengthy genomic regions contributing to heterosis observed in hybrid crosses between inbreds from different heterotic groups.