TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

Abstract

Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping (TeoNAM) population, derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTL for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.

The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication

“…1We detected a major effect QTL on chromosome 3 for flowering time in teosinte near ZmMADS69, which is under balancing selection. Several recent studies using maize-teosinte mapping populations have mapped a flowering time QTL containing this gene [17,50,51]. Another recent study further fine-mapped ZmMADS69, which functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory network and contributes to both long-day and short-day adaptation [52].…”

“…In contrast, a maize plant produces only one or two multiple-ranked ears, each with hundreds of naked grains, remaining intact on the cob at maturity. Finally, maize has a large number of genomic and genetic resources available (https://maizegdb.org/), including high-quality genomes of inbred lines [12][13][14][15], high-density genotypic data [16], and diverse mapping populations [17,18].…”

dlf1 promotes floral transition by directly activating ZmMADS4 and ZmMADS67 in the maize shoot apex

“…The natural alleles at dlf1 appear to exhibit very small effect. Across the maize and teosinte NAM populations, the flowering time QTL at dlf1 only confers 0.25-1.4 d of additive effect (Buckler et al, 2009;Chen et al, 2019). Despite the minor effect, the consistent detection of dlf1 in distinct maize-teosinte and maize populations strongly indicated that dlf1 plays an important role in fine-tuning flowering and adaptation.…”

“…In this study, we demonstrated that dlf1 underlies qLB7-1, a QTL showing significant effects on leaf number and flowering time in the maize-teosinte BC 2 S 3 RIL population. Several previous studies also identified flowering time QTLs around dlf1 (Buckler et al, 2009;Romay et al, 2013;Romero Navarro et al, 2017;Chen et al, 2019). For example, Buckler et al (2009) performed a large-scale flowering time mapping study using the maize nested association mapping (NAM) population and detected a minor joint-linkage QTL at the end of chromosome 7 that contains the dlf1 gene.…”

“…For example, Buckler et al (2009) performed a large-scale flowering time mapping study using the maize nested association mapping (NAM) population and detected a minor joint-linkage QTL at the end of chromosome 7 that contains the dlf1 gene. Recently, Chen et al (2019) conducted QTL mapping for flowering time using a newly developed teosinte NAM population consisting of five maizeteosinte BC 1 S 4 RIL populations. Interestingly, dlf1 was found to be located in the peak of the flowering time QTL DTA7.2, strongly supporting the possibility that dlf1 might be the underlying gene.…”