Genetic basis of maize kernel oil-related traits revealed by high-density SNP markers in a recombinant inbred line population

Abstract

Background: Maize (Zea mays ssp. mays) is the most abundantly cultivated and highly valued food commodity in the world. Oil from maize kernels is highly nutritious and important for the diet and health of humans, and it can be used as a source of bioenergy. A better understanding of genetic basis for maize kernel oil can help improve the oil content and quality when applied in breeding.

Results: In this study, a KUI3/SC55 recombinant inbred line (RIL) population, consisting of 180 individuals was constructed from a cross between inbred lines KUI3 and SC55. We phenotyped 19 oil-related traits and subsequently dissected the genetic architecture of oil-related traits in maize kernels based on a high-density genetic map. In total, 62 quantitative trait loci (QTLs), with 2 to 5 QTLs per trait, were detected in the KUI3/SC55 RIL population. Each QTL accounted for 6.7% (qSTOL1) to 31.02% (qBELI6) of phenotypic variation and the total phenotypic variation explained (PVE) of all detected QTLs for each trait ranged from 12.5% (OIL) to 52.5% (C16:0/C16:1). Of all these identified QTLs, only 5 were major QTLs located in three genomic regions on chromosome 6 and 9. In addition, two pairs of epistatic QTLs with additive effects were detected and they explained 3.3 and 2.4% of the phenotypic variation, respectively. Colocalization with a previous GWAS on oil-related traits, identified 19 genes. Of these genes, two important candidate genes, GRMZM2G101515 and GRMZM2G022558, were further verified to be associated with C20:0/C22:0 and C18:0/C20:0, respectively, according to a gene-based association analysis. The first gene encodes a kinase-related protein with unknown function, while the second gene encodes fatty acid elongase 2 (fae2) and directly participates in the biosynthesis of very long chain fatty acids in Arabidopsis.

Conclusions: Our results provide insights on the genetic basis of oil-related traits and a theoretical basis for improving maize quality by marker-assisted selection.

Keywords: Gene-based association analysis; Maize; Oil-related traits; QTL mapping.

Fig. 1

The distribution and effects of single QTL identified for 19 oil related traits in KUI3/SC55 RIL population. a Distribution of single QTL on chromosomes. QTL regions across the maize genome are represented by confidence intervals, and LOD values are scaled by color. b Total PVE of single (blue bars) and epistatic (red bars) QTLs for each trait. c Effect size (represented by PVE) and the origin of the increasing alleles of the identified QTLs. Blue and red bars indicate that increasing alleles come from KUI3 and SC55, respectively

Fig. 2

Co-localization of QTLs and known genes for oil-related traits. All 10 maize chromosomes (Chr 1–10) were depicted to scale (Mb, million base pairs). Red region indicated the confidence interval region of QTLs and the black lines indicated the position of genes

Fig. 3

Candidate genes for L28 and L34. a LOD profiles of the identified QTL bins for L28 and GRMZM2G101515 were colocalized with a QTL cluster. The dashed lines show the physical positions of genes. b Candidate-gene association analysis for GRMZM2G101515. The most significant locus is shown in red. The intensity of gray shading indicates the extent of LD (r²) between the most significant locus and the other variants identified in this region. The gene struct.is shown on the x-axis. The black and light-gray shading represents exons and UTRs, respectively. c The linkage disequilibrium (LD) patterns of all identified variants (MAF ≥ 0.05) in genes GRMZM2G101515. d The effect of peak locus for GRMZM2G101515 in an association panel. e LOD profiles of the identified QTL bins for L34 and GRMZM2G022558 were colocalized with a QTL cluster. f Candidate-gene association analysis for GRMZM2G022558. g The linkage disequilibrium (LD) patterns of all identified variants (MAF ≥ 0.05) in genes GRMZM2G022558. h The effect of peak locus for GRMZM2G022558 in an association panel

Fig. 4

GRMZM2G101515 and GRMZM2G022558 alter the ratio of fatty acids in maize kernel. a Comparison of the relative expression at peak locus alleles A and C for GRMZM2G101515. b Correlation of C22:0/C24:0 with the relative expression of GRMZM2G10151 in kernels at 15 DAP. c Comparison of the relative expression at peak locus allele A and G for GRMZM2G022558. d Correlation of C18:0/C20:0 with the relative expression of GRMZM2G022558 in kernels at 15 DAP