Linkage mapping of domestication loci in a large maize teosinte backcross resource

Abstract

An ultimate objective of QTL mapping is cloning genes responsible for quantitative traits. However, projects seldom go beyond segments <5 cM without subsequent breeding and genotyping lines to identify additional crossovers in a genomic region of interest. We report on a QTL analysis performed as a preliminary step in the development of a resource for map-based cloning of domestication and improvement genes in corn. A large backcross (BC)1 population derived from a cross between maize (Zea mays ssp. mays) and teosinte (ssp. parviglumis) was grown for the analysis. A total of 1749 progenies were genotyped for 304 markers and measured for 22 morphological traits. The results are in agreement with earlier studies showing a small number of genomic regions having greater impact on the morphological traits distinguishing maize and teosinte. Despite considerable power to detect epistasis, few QTL interactions were identified. To create a permanent resource, seed of BC1 plants was archived and 1000 BC2S6 BC1-derived lines are in development for fine mapping and cloning. The identification of four BC1 progeny with crossovers in a single gene, tb1, indicated that enough derived lines already exist to clone many QTL without the need to generate and identify additional crossovers.

Figure 1.—

Regions on chromosomes 3 (left) and 10 (right) affecting several traits. A segment of the genetic map is depicted, showing molecular marker names and positions on the chromosome in centimorgans. QTL detected in Wisconsin are shown as solid bars above the chromosome. The placement and length of the bar indicate the position and extent of the 1-LOD drop-off interval. The names of the loci, which include the trait, chromosome, and position, are listed to the left of the bars. QTL detected in Florida are depicted in the same fashion below the chromosome.

Figure 2.—

Genomic distribution of the summed significance levels of seven domestication traits (LIBN, PROL, GLUM, RANK, CUPR, STAM, and LIBN). Each chromosome is depicted as a plot with the x-axis representing genetic position. The likelihood ratio (LR) of each position on the chromosome was standardized for each trait by dividing it by the sum of all LR values across the entire genome. The height of the curve (y-axis) is the sum of the standardized values across the seven traits. The solid and shaded curves are from the Wisconsin and Florida data, respectively. QTL for these seven traits detected in two previous studies of maize–teosinte F₂ populations (Doebley and Stec 1993) are depicted with solid and shaded triangles below each plot. Loci with R²-values greater than or <0.1 are shown as solid or open triangles, respectively.