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bioRxiv · 10.1101/2025.09.10.675198

HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N2 FIXATION IN ZEA MAYS

O'Donnell, D. A.·Yang, J.·Zamora, P.·Lorant, A.·Miao, C.·Van Deynze, A.·Bennett, A. B.·Ross-Ibarra, J.
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Abstract

Zea mays L. spp. mays (hereafter maize) populations from an indigenous community of Mexico have been reported to perform well using traditional cultivation practices that exclude industrial fertilizers despite low soil nitrate levels. The local maize cultivar is characterized by extended maturity, tall stature, and presence of thick aerial roots that secrete an abundance of polysaccharide-rich root exudate, or mucilage, that is implicated in the recruitment of diazotrophic microbes to facilitate biological nitrogen fixation. Here we estimate the broad sense heritability of traits related to nitrogen fixation in a panel of Zea entries spanning pre-domestication, post-domestication and post-improvement, and identify QTL via F2:F3 families for traits including aerial root node counts and various other yield related traits (i.e. germination rate, time to reproductive maturity, total biomass and nitrogen content of shoot and grain). Across two separate field studies, aerial root node count (AR) demonstrates heritability of 64% and 73%, and genetic mapping reveals three distinct QTL distributed on chromosomes 1 and 9. Further, we report novel QTL for germination rate via stand counts after direct sowing (SC), Plant Total Nitrogen (PTN), Plant Dry Mass (PDM), and a joint QTL for Grain Total Nitrogen (GTN) and Grain Dry Mass (GDM). Finally, we identify overlap between QTL for multiple traits (including AR and SC) and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana) into Totontepec maize, with a greater degree of overlap than expected under a uniform genomic distribution suggesting adaptive introgression from mexicana. Given its pronounced aerial root morphology, we propose that mexicana is the ancestral source for prominent aerial roots and corresponding abundant mucilage production in Totontepec maize and other maize traditional varieties. ARTICLE SUMMARYZea mays aerial roots (AR) and mucilage have been implicated in diazotrophic recruitment. This study estimates heritability and identifies QTL for AR and yield components via a diverse panel of Zea entries and F2:F3 mapping populations. Genetic mapping reveals three QTL for AR and several QTL for other yield traits, both novel and previously reported. This study also compares QTL and regions of elevated introgression from wild Zea mays L. spp. mexicana (hereafter mexicana) into a native cultivar. For AR QTL, enrichment for mexicana-derived haplotypes is greater than expected under a uniform genomic distribution, suggesting adaptive introgression from mexicana.

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O'Donnell, D. A., Yang, J., Zamora, P., Lorant, A., Miao, C., Van Deynze, A., Bennett, A. B., Ross-Ibarra, J.. 2025-09-12. HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N2 FIXATION IN ZEA MAYS. https://doi.org/10.1101/2025.09.10.675198

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