Combining datasets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies

Abstract

The identification of genomic regions associated with root traits and the genomic prediction of untested genotypes can increase the rate of genetic gain in maize breeding programs targeting roots traits. Here, we combined two maize association panels with different genetic backgrounds to identify single nucleotide polymorphisms (SNPs) associated with root traits, and used a genome-wide association study (GWAS) and to assess the potential of genomic prediction for these traits in maize. For this, we evaluated 377 lines from the Ames panel and 302 from the Backcrossed Germplasm Enhancement of Maize (BGEM) panel in a combined panel of 679 lines. The lines were genotyped with 232 460 SNPs, and four root traits were collected from 14-day-old seedlings. We identified 30 SNPs significantly associated with root traits in the combined panel, whereas only two and six SNPs were detected in the Ames and BGEM panels, respectively. Those 38 SNPs were in linkage disequilibrium with 35 candidate genes. In addition, we found higher prediction accuracy in the combined panel than in the Ames or BGEM panel. We conclude that combining association panels appears to be a useful strategy to identify candidate genes associated with root traits in maize and improve the efficiency of genomic prediction.

Keywords: Zea mays L; Association mapping; candidate genes; genomic selection; inbred line panel; linkage disequilibrium; population structure.

Fig. 1.

Whole-genome linkage disequilibrium decay in the entire 679 maize lines from the Combined panel. Linkage disequilibrium within and over chromosomes is given in physical distances of 50 kb.

Fig. 2.

Analysis of the population structure of 377 inbred lines from Ames panel (A), 302 DH lines from BGEM panel (B), and 679 maize lines from the Combined panel (C) using SNP markers. fastStructure clustering results obtained at K=4. Each inbred line is represented by a thin bar corresponding to the sum of assignment probabilities to the K cluster. For Ames and BGEM panels, orange and yellow refer to NSS and SS subpopulations, respectively; for the Combined panel the association between colors and subpopulations are as follows: orange, SS from BGEM; yellow, NSS from BGEM; blue, SS from Ames; green, NSS from Ames. Panel A (population structure results from Ames panel) was adapted from Pace et al. (2015b).

Fig. 3.

Manhattan plot showing associations between SNP markers and root traits plotted from the association analysis. Lateral root length (A), primary root length (B), total number of roots (C), and total root length (D) in the Combined panel. The dashed horizontal line depicts the simpleM correction.

Fig. 4.

Accuracy assessment of genome wide studies for five root traits, four genetic models and 11 scenarios. LRL: lateral root length; PRL: primary root length; TRL: total root length; TNR: total number of roots.