Genetic analysis of maize crude fat content by multi-locus genome-wide association study

1 The genetic architecture of crude fat content in maize kernels were studied by GWAS using six models. 2 A total of 744 significant QTNs, and 64 novel QTNs were found for the crude fat content in maize kernels. 3 Four known genes were identified and eight promising candidate genes were successfully screened. Crude fat is an important nutritional component of maize kernels. However, the genetic mechanisms underlying crude fat content in maize kernels remain elusive. Previous studies used single-model genome-wide association studies (GWAS) with limited population sizes, which can result in false positives of loci and hinder the identification of functional genes. Therefore, this study used a population consisting of 495 maize inbred lines, combined with 1.25 million single nucleotide polymorphisms (SNPs), and implemented GWAS using six models to identify quantitative trait nucleotides (QTNs) controlling crude fat content and to mine key genes. The results revealed a wide variation in crude fat content (0.62–16.03%) and broad-sense heritability (96.23%). In total, 744 significant QTNs were detected, with 147 co-located across different models, environments, and methods. Based on the 147 co-located QTNs, candidate genes were searched at 50 kb up- and downstream intervals of each QTN. We finally screened eight candidate genes ( GRMZM2G169089, GRMZM2G117935, GRMZM2G002075, GRMZM2G368838, GRMZM2G058496, GRMZM2G090669, GRMZM2G001241 , and GRMZM2G333454 ) related to crude fat content that exhibited high expression levels during kernel development in maize inbred line B73. Notably, GRMZM2G169089, GRMZM2G117935, GRMZM2G002075 , and GRMZM2G368838 are involved in the linoleic acid metabolic pathway, oil metabolism, kernel growth, and development in maize. Furthermore, co-expression network analysis revealed that the eight candidate genes exhibited strong correlations with 30 known genes. Proteins encoded by candidate genes interact with various other proteins and play an important role in oil content and oleic acid metabolism in maize kernels. The best haplotypes of candidate genes might increase crude fat content without decreasing maize yield. These results broaden the understanding of the genetic mechanism of crude fat content and facilitate marker-assisted selection for high-crude fat breeding programs for maize.