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Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels.

ABSTRACT: Dissecting the genetic basis and regulatory mechanisms for the biosynthesis and accumulation of nutrients in maize could lead to the improved nutritional quality of this crop. Gene expression is regulated at the genomic, transcriptional, and post-transcriptional levels, all of which can produce diversity among traits. However, the expression of most genes connected with a particular trait usually does not have a direct association with the variation of that trait. In addition, expression profiles of genes involved in a single pathway may vary as the intrinsic cellular state changes. To work around these issues, we utilized a statistical method, liquid association (LA) to investigate the complex pattern of gene regulation in maize kernels.We applied LA to the expression profiles of 28,769 genes to dissect dynamic trait-trait correlation patterns in maize kernels. Among the 1000 LA pairs (LAPs) with the largest LA scores, 686 LAPs were identified conditional correlation. We also identified 830 and 215 LA-scouting leaders based on the positive and negative LA scores, which were significantly enriched for some biological processes and molecular functions. Our analysis of the dynamic co-expression patterns in the carotene biosynthetic pathway clearly indicated the important role of lcyE, CYP97A, ZEP1, and VDE in this pathway, which may change the direction of carotene biosynthesis by controlling the influx and efflux of the substrate. The dynamic trait-trait correlation patterns between gene expression and oil concentration in the fatty acid metabolic pathway and its complex regulatory network were also assessed. 23 of 26 oil-associated genes were correlated with oil concentration conditioning on 580 LA-scoutinggenes, and 5% of these LA-scouting genes were annotated as enzymes in the oil metabolic pathway.By focusing on the carotenoid and oil biosynthetic pathways in maize, we showed that a genome-wide LA analysis provides a novel and effective way to detect transcriptional regulatory relationships. This method will help us understand the biological role of maize kernel genes and will benefit maize breeding programs.

SUBMITTER: Xu X

PROVIDER: S-EPMC5644097 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The husk is a leafy outer tissue that encloses a maize ear. Previously, we identified the optimum husk structure by measuring the husk length, husk layer number, husk thickness and husk width. Husk tightness (HTI) is a combined trait based on the above four husk measurements. Unveiling the genetic basis of HTI will aid in guiding the genetic improvement of maize for mechanical harvesting and for protecting the ear from pest damage and pathogen infection. Here, we used a maize associate population of 508 inbred lines with tropical, subtropical and temperate backgrounds to analyze the genetic architecture of HTI. Evaluating the phenotypic diversity in three different environments showed that HTI exhibited broad natural variations and a moderate heritability level of 0.41. A diversity analysis indicated that the inbred lines having a temperate background were more loosely related than those having a tropical or subtropical background. HTI showed significant negative correlations with husk thickness and width, which indicates that thicker and wider husks wrapped the ear tighter than thinner and slimmer husks. Combining husk traits with ∼1.25 million single nucleotide polymorphisms in a genome-wide association study revealed 27 variants that were significantly associated with HTI above the threshold of P < 7.26 × 10-6. We found 27 candidate genes for HTI that may participate in (1) husk senescence involving lipid peroxidation (GRMZM2G017616) and programmed cell death (GRMZM2G168898 and GRMZM2G035045); (2) husk morphogenesis involving cell division (GRMZM5G869246) and cell wall architecture (GRMZM2G319798); and (3) cell signal transduction involving protein phosphorylation (GRMZM2G149277 and GRMZM2G004207) and the ABSISIC ACID INSENSITIVE3/VIVIPAROUS1 transcription factor (GRMZM2G088427). These results provide useful information for understanding the genetic basis of husk development. Further studies of identified candidate genes will help elucidate the molecular pathways that regulate HTI in maize.

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Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels.

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