Expanding Maize Genetic Resources with Predomestication Alleles: Maize–Teosinte Introgression Populations

Teosinte (Zea mays subsp. parviglumis H. H. Iltis & Doebley) has greater genetic diversity than maize inbreds and landraces (Z. mays subsp. mays). There are, however, limited genetic resources to efficiently evaluate and tap this diversity. To broaden resources for genetic diversity studies in maize, we developed and evaluated 928 near-isogenic introgression lines (NILs) from 10 teosinte accessions in the B73 background. Joint linkage analysis of the 10 introgression populations identified several large-effect quantitative trait loci (QTL) for days to anthesis (DTA), kernel row number (KRN), and 50-kernel weight (Wt50k). Our results confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects enabling future research into the genetic basis of these traits. Additionally, we used a targeted set of NILs to validate the effects of a KRN QTL located on chromosome 2. These introgression populations offer novel tools for QTL discovery and validation as well as a platform for initiating fine mapping. Maize was domesticated from its wild progenitor teosinte approximately 9000 yr ago in southwestern Mexico (Matsuoka et al., 2002; Piperno et al., 2009; van Heerwaarden et al., 2011). Many studies have demonstrated that there are lower levels of genetic diversity among inbreds than among landrace and teosinte populations for two reasons: demography (bottlenecks) and selection. Domestication and breeding bottlenecks have resulted in genome-wide reductions in genetic variation in maize relative to teosinte (Tenaillon et al., 2004). Additional studies indicated that approximately 2 to 4% of genes were targets of artificial selection during domestication and breeding (Wright et al., 2005; Hufford et al., 2012), which implies that about 500 to 1000 genes were critical during the evolution of modern maize and are prime subjects for evolutionary and agronomic research. Published in The Plant Genome 9 doi: 10.3835/plantgenome2015.07.0053 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. Z. Liu, J. Cook, M.D. McMullen, and S.A. Flint-Garcia, Division of Plant Sciences, Univ. of Missouri, Columbia, MO 65211; S. MeliaHancock, K. Guill, Ar. Garcia, P. Balint-Kurti, N. Lepak, E. Buckler, M.D. McMullen, S.A. Flint-Garcia, and C. Bottoms, USDA–ARS, Informatics Research Core Facility, Univ. of Missouri, Columbia, MO 65211; O. Ott and R. Nelson, School of Integrative Plant Science, Cornell Univ., Ithaca, NY 14853; J. Recker, Dep. of Crop Science, North Carolina State Univ., Raleigh, NC 27695; P. Balint-Kurti, Dep. of Plant Pathology, North Carolina State Univ., Raleigh, NC 27695; S. Larsson and E. Buckler, Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14850; E. Buckler, Institute for Genomic Diversity, Cornell Univ., Ithaca, NY 14853; L. Trimble and W. Tracy, Dep. of Agronomy, Univ. of Wisconsin–Madison, Madison, WI 53706; S. Larsson, current address: DuPont Pioneer, Windfall, IN 46076. Received 1 July 2015. Accepted 16 Sept. 2015. *Corresponding author (Sherry.Flint-Garcia@ars.usda.gov). Abbreviations: DH, doubled-haploid; DTA, days to anthesis; GBS, genotyping-by-sequencing; KRN, kernel row number; LOD, logarithm of odds; NAM, nested association mapping; NIL, near-isogenic introgression line; QTL, quantitative trait loci; RAD, restriction association DNA; RIL, recombinant inbred line; Wt50k, 50-kernel weight. Published March 4, 2016