A maize near-isogenic line population designed for gene discovery and characterization of allelic effects

Authors: ZHONG, TAO - North Carolina State University; MULLENS, ALEX - University Of Illinois; MORALES, LAURA - Cornell University; SWARTS, KELLY - Gregor Mendel Institute; STAFSTROM, WILLIAM - Cornell University; HE, YIJIAN - North Carolina State University; Sermons, Shannon; Holland, James; Balint Kurti, Peter; LOPEZ-ZUNIGA, LUIS - North Carolina State University; RUCKER, ELIZABETH - Virginia Tech; THOMASON, WADE - Virginia Tech; NELSON, REBECCA - Cornell University; YANG, QIN - North Carolina State University; JAMANN, TIFFANY - University Of Illinois

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/7/2025
Publication Date: 6/1/2025
Citation: Zhong, T., Mullens, A., Morales, L., Swarts, K., Stafstrom, W., He, Y., Sermons, S.M., Holland, J.B., Balint Kurti, P.J., Lopez-Zuniga, L., Rucker, E., Thomason, W., Nelson, R., Yang, Q., Jamann, T. 2025. A maize near-isogenic line population designed for gene discovery and characterization of allelic effects. The Plant Journal. https://doi.org/10.1111/tpj.70228.
DOI: https://doi.org/10.1111/tpj.70228

Interpretive Summary: Mapping populations are populations of lines in which each different line carries a unique genetic combination. Using these populations it is possible to map the location of genes that control variation in traits of interest. Near-isogenic line populations are mapping populations in which each member derives the large majority of its genome from a single parent (the recurrent parent). Here we describe a large near isogenic line population consisting of 1264 maize lines for which the widely-used maize line B73 serves as the recurrent parent, with the other genetic contributions deriving from a diverse set of 18 lines. We describe the genetic analysis of about 2/3 of this population. We show that we can use it to map genes that confer resistance to maize leaf diseases. We believe this population will be useful for the identification of genes that confer agronomic effects, and for the analysis of the effects conferred by different versions (or alleles) of these genes.

Technical Abstract: In this study we characterized a panel of 1,264 maize near-isogenic lines (NILs), developed from crosses between 18 diverse inbred lines and the recurrent parent B73, referred to as nested NILs (nNILs). 884 of the nNILs were genotyped using genotyping-by-sequencing (GBS). Subsequently, 24 of these nNILs, and all the parental lines, were re-genotyped using a high-density SNP chip. A novel pipeline for calling introgressions, which does not rely on knowing the donor parent of each nNIL, was developed based on a hidden Markov model (HMM) algorithm. By comparing the introgressions detected using GBS data with those identified using chip data, we optimized the HMM parameters for analyzing the entire nNIL population. A total of 2,972 introgressions were identified across the 884 nNILs. Individual introgression blocks ranged from 21 bp to 204 Mbp, with an average size of 17 Mbp. By comparing SNP genotypes within introgressed segments to the known genotypes of the donor lines we determined that in about one third of the lines, the identity of the donors did not match expectation based on their pedigrees. We characterized the entire nNIL population for three foliar diseases. Using these data, we mapped a number of quantitative trait loci (QTL) for disease resistance in the nNIL population and observed extensive variation in effects among the alleles from different donor parents at most QTL identified. This population will be of significant utility for dissecting complex agronomic traits and allelic series in maize.