Novel strategies for genomic and phenomic investigations of quantitative traits in maize (Zea mays L.)

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Zheng, Zihao
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Schnable, Patrick
Lawrence-Dill, Carolyn
Nettleton, Daniel
Yu, Jianming
Hufford, Matthew
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The genetic improvement of maize (Zea mays L.) over the past century has helped meet the world’s increasing demands for food, feed, fuel and fiber. With a still-growing population, changing dietary preferences, and a fast-changing climate that impacts agricultural production, interdisciplinary innovations including novel strategies for genomic and phenomic research become even more important. By providing a better understanding of genotype-phenotype relationships of agronomically important quantitative traits of maize, they promise to increase the efficiency of plant breeding solutions. Root system architecture (RSA) plays important roles the adaptation of crops to the environments in which they are grown, but the genetic basis of RSA traits is understudied due to the difficulty of phenotyping for RSA under field conditions. To deal with this challenge, a high-throughput RSA phenotyping pipeline CREAMD (Core Root Excavation using Compressed-air) COFE (Core Root Feature Extraction) was developed for field-grown roots and was applied to diversity panels of maize and sorghum. Comparative genome-wide association studies (GWAS) between maize and sorghum revealed a degree of shared genetic control of RSA traits between these two crop species. In addition to RSA, functional traits of the root system such as anchorage are also agronomically relevant, the failure of which (i.e., root lodging), is a major cause of yield loss. However, the genetic control of root lodging remains largely unknown. We phenotyped root lodging of a maize diversity panel after one of the most devastating derechos ever recorded in the U.S corn belt and conducted GWAS and transcriptome-wide association studies (TWAS) using transcriptome data from multiple tissues. Candidate genes from GWAS and TWAS revealed complex regulatory networks of physiological and biochemical pathways underlying root lodging. One of the most important factors that contributes to maize yields increase is heterosis, the phenomenon that hybrid offspring outperform their inbred parents. Despite its wide application in plant breeding, the molecular mechanism of heterosis remains elusive. To identify candidate genes associated with hybrid performance and heterosis, a new statistical approach termed trio-based TWAS was developed for a half-diallel population taking advantages of within-family information and variation in transcriptome data. Regulatory network analyses provide evidence of the involvement of trio-based TWAS candidate genes in the hybrid performance per se and heterosis of maize quantitative traits.
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