Heterosis is the phenomenon whereby the progeny of particular inbred lines have enhanced agronomic performance relative to both parents. Although several hypotheses have been proposed to explain this fundamental biological phenomenon, the responsible molecular mechanisms have not been determined. The maize inbred lines B73 and Mo17 produce a heterotic F 1 hybrid. Global patterns of gene expression were compared in seedlings of these three genotypes by using a microarray that contains 13,999 cDNAs. Using an estimated 15% false discovery rate as a cutoff, 1,367 ESTs (9.8%) were identified as being significantly differentially expressed among genotypes. All possible modes of gene action were observed, including additivity, high-and low-parent dominance, underdominance, and overdominance. The largest proportion of the ESTs (78%; 1,062 of 1,367) exhibited expression patterns that are not statistically distinguishable from additivity. Even so, 22% of the differentially regulated ESTs exhibited nonadditive modes of gene expression. Classified on the basis of significant pairwise comparisons of genotype means, 181 of these 305 nonadditive ESTs exhibited high-parent dominance and 23 exhibited lowparent dominance. In addition, 44 ESTs exhibited underdominance or overdominance. These findings are consistent with the hypothesis that multiple molecular mechanisms, including overdominance, contribute to heterosis.global transcript profiling ͉ heterosis ͉ overdominance

Heterosis refers to the superior performance of hybrid progeny relative to their inbred parents, but the mechanisms responsible are unknown. Hybrids between the maize inbred lines B73 and Mo17 exhibit heterosis regardless of cross direction. These reciprocal hybrids differ from each other phenotypically, and 30 to 50% of their genes are differentially expressed. We identified approximately 4000 expression quantitative trait loci (eQTL) that allowed us to identify markers linked to variation in expression. We found that over three-quarters of these eQTL act in trans (78%) and that 86% of these differentially regulate transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. This result suggests that widespread imprinting contributes to the regulation of gene expression in maize hybrids.

The genetic control of gene expression during shoot development in Arabidopsis thaliana was analyzed by combining quantitative trait loci (QTL) and microarray analysis. Using oligonucleotide array data from 30 recombinant inbred lines derived from a cross of Columbia and Landsberg erecta ecotypes, the Arabidopsis genome was scanned for marker-by-gene linkages or so-called expression QTL (eQTL). Singlefeature polymorphisms (SFPs) associated with sequence disparities between ecotypes were purged from the data. SFPs may alter the hybridization efficiency between cDNAs from one ecotype with probes of another ecotype. In genome scans, five eQTL hot spots were found with significant marker-by-gene linkages. Two of the hot spots coincided with classical QTL conditioning shoot regeneration, suggesting that some of the heritable gene expression changes observed in this study are related to differences in shoot regeneration efficiency between ecotypes. Some of the most significant eQTL, particularly those at the shoot regeneration QTL sites, tended to show cis-chromosomal linkages in that the target genes were located at or near markers to which their expression was linked. However, many linkages of lesser significance showed expected ''trans-effects,'' whereby a marker affects the expression of a target gene located elsewhere on the genome. Some of these eQTL were significantly linked to numerous genes throughout the genome, suggesting the occurrence of large groups of coregulated genes controlled by single markers.

Arabidopsis ecotypes, Columbia (Col) and Landsberg erecta (Ler), differ in their capacity to regenerate shoots in culture, as do many other cultivars and varieties of the same plant species. Recombinant inbred (RI) lines derived from a cross of Col ϫ Ler were scored for shoot regeneration, and the Arabidopsis genome was scanned using composite interval mapping for loci associated with shoot regeneration. Three QTL were identified-a major one on chromosome 5 in which the Col parent contributed the superior allele and two minor QTL on chromosomes 1 and 4 in which the Ler parent contributed the superior alleles. The RI lines were binned into genotypic pools to isolate the effects of the major QTL on chromosome 5 while holding the minor QTL constant. To identify genes with expression levels that are associated with the allelic state of the major QTL on chromosome 5, oligonucleotide array expression patterns for genes in the LLC pool (Ler alleles at the minor QTL and a Col allele at the major QTL) were compared to those in the LLL pool (Ler alleles at all QTL). The genes that were significantly differentially expressed between the two pools included several encoding transcription factors and signaling or transposon-related proteins. A DVENTITIOUS shoot formation in tissue cultureArabidopsis that promote adventitious shoot formation is the means by which many plant species are comin culture. The first such gene discovered was CYTOKImercially micropropagated, particularly ornamental NIN INDEPENDENT1 (CKI1), a gene that when overexplants in the families Araceae, Begoniaceae, Gesneriapressed confers cytokinin-independent shoot formation ceae, and Liliaceae (Preil 2003). It is also the means from callus in Arabidopsis tissue culture (Kakimoto by which many transgenic plants are produced, i.e., by 1996). CKI1 encodes a histidine kinase related to sensory regenerating shoots from transformed cells or tissues.receptors in two-component signaling pathways (Stock A common problem encountered in micropropagation et al. 2000; West and Stock 2001; Lohrmann and and plant transformation is that within a plant species, Harter 2002). At the time of its discovery, CKI1 was different varieties and cultivars vary widely in their caproposed to be a cytokinin receptor (Kakimoto 1996). pacity to regenerate. The unpredictable responses of However, CKI1 has not been shown to bind cytokinins at different varieties to standard shoot induction condiphysiological cytokinin levels, and so its role in cytokinin tions provoked Koornneef et al. (1993) assumption that the activation and not merely the pres-1992), Solanum chacoense (Birhman et al. 1994), Triticum ence of the response regulator is required for signaling. aestivum (Fennell et al. 1996), Hordeum vulgare (KomatIn a protoplast system, transfections with ARR2 consuda et al. 1993), Cucumis sativus (Naldoska-Orezyk and structs basally activated the promoter of a target gene Malepszy 1989), Helianthus annuus (Sarrafi et al. 1996), in the absence of cytokinin; however, cytokinin add...

Due to the multisensory input into the balance system, the loss of one input, such as an ear, can generally be compensated for. However, when a mismatch or incomplete loss of inputs occurs, the ability to compensate for the stimulus misrepresentation may be compromised. The inner ear and cerebellum are important input and processing centers for balance but no genetic models have been generated to assess balance or compensation in the abnormal development of both these organs/brain areas. Important to their formation is regulation of proliferation mediated by the proto-oncogene N-Myc. Conditional knockouts (CKOs) of N-Myc using Tg(Pax2-Cre) have a misshapen and smaller ear with a fused utricle, saccule, and cochlea and absent horizontal canal, aberrant cochlear and vestibular innervations, and a size reduction in the cerebellum. CKOs are viable with obvious behavioral deficits, including circling behavior and unstable gait. To test the degree of ataxia and possible compensation of vestibular defects in these mutant mice, we use the Noldus Catwalk System to assess the gait of Tg(Pax2-Cre) N-Myc CKOs over five months. N-Myc CKOs perform worse than control littermates, in particular, in step regularity. We show that disrupting one member of the Myc family during embryonic development coincides with a differential loss of function in the cochlea compared to the vestibular apparatus. In addition, we show that the distortion in the ear morphology combined with a reduction of the cerebellum, rather than a complete loss of the vestibular-cerebellar pathway, leads to partial behavioral compensation that remains unchanged over time.