Academic journal article
By Briggs, William H.; McMullen, Michael D.; Gaut, Brandon S.; Doebley, John
Genetics , Vol. 177, No. 3
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)^sub 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 BC^sub 1^ plants was archived and 1000 BC^sub 2^S^sub 6^ BC^sub 1^-derived lines are in development for fine mapping and cloning. The identification of four BC^sub 1^ 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.
CORN and its wild progenitor, teosinte, differ dramatically in their overall plant architecture and the morphology of their female inflorescences. QTL mapping studies in maize-teosinte F2 populations have been utilized to determine the number, effect, and genomic distribution of loci responsible for differences in key traits related to domestication (Doebley and Stec 1991, 1993; Doebley et al. 1994). These earlier studies utilized low-density genetic maps and relatively few progeny, reducing the power to detect QTL and accurately estimate their location and effect (Beavis 1998). Subsequent advancements in the physical mapping of maize ESTs and SSRs have enabled the construction of genetic maps with more uniform genomic distribution and coverage. Furthermore, the development of inexpensive, high-throughput SNP and SSR assays has permitted the genotyping of greater numbers of progeny, improving mapping precision, estimation, and ability to detect smaller-effect QTL.
An additional drawback of experiments with smaller population sizes and sparsemaps is that fewer crossovers can be identified in the vicinity of a locus. Finemapping of QTL and the discovery of tightly linked markers for positional cloning require larger numbers of recombination events not found in typical F2, backcross, or recombinant inbred line mapping populations. Having a larger sample of genotyped lines and a reasonably dense map can shorten the time needed to hone in on a region and find a tightly linked marker, simply because the chance of identifying crossovers close to the underlying gene is greater. Map-based cloning could be accelerated by creating a large number of advanced inbred backcross lines containing overlapping introgressions. A repository of crossovers would then exist for identifying lines containing recombination events near a QTL in any region of the genome. Such a collection of lines would also provide a permanent resource for future mapping studies and allow the researcher to more quickly breed near-isogenic lines containing introgressions of agronomic or biological interest (Butruille et al. 1999; Doganlar et al. 2002).
In this study, we performed QTL analyses on a maize- teosinte backcross population with teosinte as the donor parent and maize as the recurrent parent. This population has a much larger size and a denser molecular marker map than previous maize-teosinte mapping studies. The population has been backcrossed a second time and is now being inbred by single-seed descent to isolate crossovers throughout the genome in a set of -1000 advanced backcross (BC) recombinant inbred lines (BC2S6 RILs). …