Location: Responsive Agricultural Food Systems Research Unit
Project Number: 3093-10700-001-007-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Mar 1, 2026
End Date: Feb 29, 2028
Objective:
The objective of the proposed research is to develop comprehensive genomic toolkits to investigate the genetic mechanisms underlying the Hi-A (high anthocyanin and high antioxidants) traits in corn. The work will establish a high quality reference genome assembly and a genotyping platform that will enable efficient and precise selection in Hi-A corn breeding programs.
Approach:
Hi-A corn was developed using conventional breeding, using introgression of teosinte and Tripsacum into corn cultivars. These introgressed cultivars were used to generate the Hi-A F1 hybrid. Hi-A corn has unique traits not found in other corn varieties which may be the result of introgressed alleles. We will identify whether introgressed alleles have retained some of their ancestral sequences, including structural variations such as copy number variants or rearrangements. The project seeks to annotate gene models for the two parental genomes, integrate them with the maize pangenome, and identify novel genes absent from current elite cultivars and to Leverage existing Hi-A–related transcriptome datasets to construct gene co-expression networks and characterize anthocyanin biosynthetic pathways using the newly annotated genes. Gene annotation and repetitive sequence annotation of Hi-A hybrids and parent lines. Compare Hi-A corn genomes with existing maize pangenome assemblies to discover wild introgressed genomic reginons and genes. Perform short-variant discovery in an F2 and F6 mapping populations, conduct QTL mapping for Hi-A traits, and identify high-confidence candidate genes for targeted breeding. Identify polymorphic SNPs and develop a custom SNP array that captures the genetic diversity of Texas A&M AgriLife’s core breeding germplasm, including high Hi-A, high-yielding, and drought-tolerant lines. Perform co-expression network to find gene network controlling high anthocynanin accumulation using newly annotated genes. Sequence based genotyping of two F2 mapping populations derived from TAMZ101 and F6 mapping populations of TAMZ102 for gene mapping related to Hi-A traits to examine two known different genetic systems that control the synthesis and accumulation of anthocyanin and antioxidants in corn. Integrate QTL results with transcriptomes to identify candidate genes.