Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.)

Noel Ndlovu; Rajashekar M Kachapur; Yoseph Beyene; Biswanath Das; Veronica Ogugo; Dan Makumbi; Charles Spillane; Peter C McKeown; Boddupalli M Prasanna; Manje Gowda

doi:10.3389/fgene.2024.1353289

Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.)

Front Genet. 2024 Feb 21:15:1353289. doi: 10.3389/fgene.2024.1353289. eCollection 2024.

Authors

Affiliations

¹ Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway, Ireland.
² International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya.
³ University of Agricultural Sciences, Dharwad, Karnataka, India.

^# Contributed equally.

Abstract

The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and G×E variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The co-localization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels.

Keywords: genomic prediction; grain quality traits; quantitative trait loci; sub-Saharan Africa; tropical maize.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The research was supported by the Bill and Melinda Gates Foundation (B&MGF), Foundation for Food and Agriculture Research (FFAR) and the United States Agency for International Development (USAID) through the Stress Tolerant Maize for Africa (STMA, B&MGF Grant # OPP1134248) Project, IMAS Project, AGG (Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods; B&MGF Investment ID INV-003439) Project and the CGIAR Research Program on Maize (MAIZE). NN, PM, and CS acknowledge funding from the European Commission DESIRA funded LEG4DEV Project [FOOD/2020/418-901] and the Science Foundation Ireland Principal Investigator Grant [13/IA/1820].