Quantitative trait loci (QTL) mapping is a valuable tool for studying the genetic architecture of trait variation. Despite the large number of QTL studies reported in the literature, the identified QTL are rarely mapped to the underlying genes and it is usually unclear whether a QTL corresponds to one or multiple linked genes. Similarly, when QTL for several traits colocalize, it is usually unclear whether this is due to the pleiotropic action of a single gene or multiple linked genes, each affecting one trait. The domestication gene teosinte branched1 (tb1) was previously identified as a major domestication QTL with large effects on the differences in plant and ear architecture between maize and teosinte. Here we present the results of two experiments that were performed to determine whether the single gene tb1 explains all trait variation for its genomic region or whether the domestication QTL at tb1 fractionates into multiple linked QTL. For traits measuring plant architecture, we detected only one QTL per trait and these QTL all mapped to tb1. These results indicate that tb1 is the sole gene for plant architecture traits that segregates in our QTL mapping populations. For most traits related to ear morphology, we detected multiple QTL per trait in the tb1 genomic region, including a large effect QTL at tb1 itself plus one or two additional linked QTL. tb1 is epistatic to two of these additional QTL for ear traits. Overall, these results provide examples for both a major QTL that maps to a single gene, as well as a case in which a QTL fractionates into multiple linked QTL.
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