Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines

Authors: MORALES, LAURA - Cornell University; REPKA, A - Cornell University; SWARTS, KELLY - Austrian Academy Of Sciences; STAFSTROM, WILLIAM - Cornell University; HE, YIJIAN - North Carolina State University; Sermons, Shannon; YANG, QIN - North Carolina State University; LOPEZ-ZUNIGA, LUIS - North Carolina State University; RUCKER, ELIZABETH - Virginia Polytechnic Institution & State University; THOMASON, WADE - Virginia Polytechnic Institution & State University; NELSON, REBECCA - Cornell University; Balint-Kurti, Peter

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2020
Publication Date: 4/29/2020
Citation: Morales, L., Repka, A.C., Swarts, K.L., Stafstrom, W.C., He, Y., Sermons, S.M., Yang, Q., Lopez-Zuniga, L.O., Rucker, E., Thomason, W.E., Nelson, R.J., Balint Kurti, P.J. 2020. Genotypic and phenotypic characterization of a large, diverse population of maize near-isogenic lines. Plant Journal. https://doi.org/10.1111/tpj.14787.
DOI: https://doi.org/10.1111/tpj.14787

Interpretive Summary: We report the characterization of a near iogenic line population of 1270 maize plants. We genotyped 896 lines of this population. The lines are all ~90-99% similar to each other and to the commonly-used maize line B73 but each line differs from B73 in 1-5 places in the genome where they have incorporated segments derived from one of 19 other maize lines. The population is useful for the analysis of quantitatively inherited traits and is more extensive than other populations of this type that are currently available. We assessed the population for 5 traits and identified several genomic regions that affected variation in each trait.

Technical Abstract: Genome wide association studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect, and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1,270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height, and resistance to three foliar diseases and genotyped with genotyping-by-sequencing. Across traits, phenotypic variation (2- to 18-fold) and broad-sense heritability (0.4-0.8) were relatively high. The 896 genotyped nNILs contain 2,638 introgressions, which span the entire genome with substantial overlap within and among allele donors. Genome wide association with the whole panel identified 37 QTL for height and/or disease resistance with allelic variation across donors. To date, this is the largest and most diverse panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize nested association mapping population in a B73 background combined with data on six morphophysiological traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions and could readily be used for future fine mapping studies.