Genome-wide association study of haploid female fertility (HFF) and haploid male fertility (HMF) in BS39-derived doubled haploid maize lines

Authors: FAKUDE, MERCY - Iowa State University; MURITHI, ANN - Iowa State University; FREI, URSULA - Iowa State University; Scott, Marvin; LUBBERSTEDT, THOMAS - Iowa State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2024
Publication Date: 12/11/2024
Citation: Fakude, M., Murithi, A., Frei, U.K., Scott, M.P., Lubberstedt, T. 2024. Genome-wide association study of haploid female fertility (HFF) and haploid male fertility (HMF) in BS39-derived doubled haploid maize lines. Theoretical and Applied Genetics. 138. Article 5. https://doi.org/10.1007/s00122-024-04789-5.
DOI: https://doi.org/10.1007/s00122-024-04789-5

Interpretive Summary: Doubled haploid technology is widely used in commercial maize breeding because it reduces the time required to produce new varieties. This method is currently limited by the need for a toxic chemical treatment and a lack of understanding of the genetic control of fertility. A novel genetic system called Spontaneous Haploid Genome Doubling (SHGD) eliminates the need for chemical treatment. In this study, we examine the genetic control of fertility in plants carrying the SHGD system and compare it to plants that lack this system. We learned that fertility in haploid plants is higher when they carry the SHGD system and we identified several genes that may control fertility. This new understanding will enable the doubled haploid method to be used more efficiently and with reduced reliance on toxic chemicals. This work benefits society by increasing the efficiency with which breeders develop improved varieties.

Technical Abstract: Doubled haploid (DH) breeding accelerates the development of elite inbred lines and facilitates the incorporation of exotic germplasm, offering a powerful tool for maize improvement. Traditional DH breeding relies on colchicine to induce haploid genome doubling. Colchicine is toxic and its application labour-intensive, with most genotypes recording low genome doubling rates (10% to 30%). This study investigates spontaneous haploid genome doubling (SHGD) as a safer and more efficient alternative to colchicine. We evaluated the effectiveness of SHGD in restoring haploid female fertility (HFF) and haploid male fertility (HMF) without colchicine. Using genome-wide association studies (GWAS), we identified genomic regions influencing HFF and HMF. The plant materials included the BS39-HILs and BS39-SHGD-HILs. Our results revealed significant SNP associations for both traits, with candidate genes involved in cell cycle regulation, cytoskeletal organization, and hormonal signaling. Analysis of variance (ANOVA) revealed significant variation in HFF across haploids and two environments. Similarly, HMF showed substantial differences across haploids and between two environments. Spearman correlation between HFF and HMF showed no correlation (r = -0.03) between the two traits. HFF showed high heritability (0.8), indicating strong genetic control, whereas HMF displayed moderate heritability (0.5), suggesting additional environmental influences. The findings underscore the potential of SHGD to enhance DH breeding efficiency and support the development of new maize varieties tailored to diverse agricultural needs.