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Association analysis of genes involved in maize (Zea mays L.) root development with seedling and agronomic traits under contrasting nitrogen levels

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Abstract

A better understanding of the genetic control of root development might allow one to develop lines with root systems with the potential to adapt to soils with limited nutrient availability. For this purpose, an association study (AS) panel consisting of 74 diverse set of inbred maize lines were screened for seedling root traits and adult plant root traits under two contrasting nitrogen (N) levels (low and high N). Allele re-sequencing of RTCL, RTH3, RUM1, and RUL1 genes related to root development was carried out for AS panel lines. Association analysis was carried out between individual polymorphisms, and both seedling and adult plant traits, while controlling for spurious associations due to population structure and kinship relations. Based on the SNPs identified in RTCL, RTH3, RUM1, and RUL1, lines within the AS panel were grouped into 16, 9, 22, and 7 haplotypes, respectively. Association analysis revealed several polymorphisms within root genes putatively associated with the variability in seedling root and adult plant traits development under contrasting N levels. The highest number of significantly associated SNPs with seedling root traits were found in RTCL (19 SNPs) followed by RUM1 (4 SNPs) and in case of RTH3 and RUL1, two and three SNPs, respectively, were significantly associated with root traits. RTCL and RTH3 were also found to be associated with grain yield. Thus considerable allelic diversity is present within the candidate genes studied and can be utilized to develop functional markers that allow identification of maize lines with improved root architecture and yield under N stress conditions.

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Acknowledgments

This study was carried out while Dr. Adel Abdel-Ghani was a visiting Fulbright Postdoctoral Fellow and during the sabbatical leave granted from Mu’tah University, Jordon during the academic year 2011–2012 at Iowa State University (ISU), Ames, USA. Dr. Jenaro Reyes-Matamoros contributed in this study while he was on a sabbatical leave at ISU. Authors are very thankful to Guan Yi and Leigh Lihs for their technical assistance. Authors would also like to thank USDA’s National Institute of Food and Agriculture (Project Number: IOW05180) and RF Baker Center for Plant Breeding for funding this work. The authors also thank Ryan Pape, Jeff Schussler, Kanwarpal S. Dhugga and Mark Cooper from DuPont Pioneer for their assistance in carrying this study. Financial assistance from RF Baker Center for Plant Breeding is highly appreciated.

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    1. Department of Plant Production, Faculty of Agriculture, Mu’tah University, P.O. Box 7, Karak, Jordan

      Adel H. Abdel-Ghani & Jordon Pace

    2. Department of Agronomy, Iowa State University, Ames, IA, 50011, USA

      Bharath Kumar, Constantin Jansen, Pedro J. Gonzalez-Portilla, Michael Lee & Thomas Lübberstedt

    3. Science Institute, Autonomous University of Puebla (BUAP), Puebla, Mexico

      Jenaro Reyes-Matamoros

    4. DuPont Pioneer, Johnston, IA, USA

      Juan Pablo San Martin

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    Adel H. Abdel-Ghani and Bharath Kumar have contributed equally to this work.

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    Abdel-Ghani, A.H., Kumar, B., Pace, J. et al. Association analysis of genes involved in maize (Zea mays L.) root development with seedling and agronomic traits under contrasting nitrogen levels. Plant Mol Biol 88, 133–147 (2015). https://doi.org/10.1007/s11103-015-0314-1

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