Ancestral RET haplotype associated with Hirschsprung's disease shows linkage disequilibrium breakpoint at -1249.

BACKGROUND: Hirschsprung disease (HSCR) is a complex disorder with traditional germline mutations in RET in up to 30% of familial cases and in 3% of sporadic cases in a population-based series. We have previously demonstrated that an ancestral haplotype at the 5' end of RET (haplotype 0) was strongly associated with a large subset of isolated HSCR cases and that a putative low penetrance susceptibility locus was encompassed within this ancestral haplotype, anchored by exon 2 SNP A45A. OBJECTIVE: To determine the 5' extent of the HSCR-associated ancestral haplotype by defining the linkage disequilibrium breakpoint in search for the low penetrance susceptibility locus. METHODS: Systematic screening of the region upstream of the anchoring A45A SNP, comprising RET intron 1, exon 1, and promoter in 117 population-based HSCR cases and 100 controls. Dual luciferase assay to determine differential activities between SNP combinations near a transcription start site. RESULTS: New SNP's were found which formed upstream haplotypes, anchored by A45A, in linkage disequilibrium with HSCR (2 = 76.96, p<0.00000001). Linkage disequilibrium appeared to break at the -1249C/T SNP. Further, the HSCR-associated genotype (00) was found in >60% of HSCR but only 2% of controls. Because only 2 variants, -200A>G and -196C>A, lie within the promoter region and are in proximity to the transcriptional start site (at -195), we modelled these combinations into constructs for luciferase reporter assay. The HSCR-associated SNP combination showed the lowest activity and the control-associated combination, the highest. CONCLUSIONS: Our observations seem to discard the existence of a HSCR-causing mutation as it is conceived in the traditional sense, but strengthen the idea of a specific combination of variants conferring susceptibility to the disease in a low penetrance fashion. The data derived from our functional "in vitro" studies would suggest that the HSCR-associated haplotype 0 may result in a lower level of expression of the RET gene [corrected]

Responses of soybean to oxygen deficiency and elevated root-zone carbon dioxide concentration.

Root flooding is damaging to the growth of crop plants such as soybean (Glycine max L.). Field flooding for 3 d often results in leaf chlorosis, defoliation, cessation of growth and plant death. These effects have been widely attributed solely to a lack of oxygen in the root-zone. However, an additional damaging factor may be CO(2), which attains levels of 30 % (v/v) of total dissolved gases. Accordingly, the effects of root-zone CO(2) on oxygen-deficient soybean plants were investigated in hydroponic culture. Soybean plants are shown to be very tolerant of excess water and anaerobiosis. No oxygen (100 % N(2) gas) and low oxygen (non-aerated) treatments for 14 d had no effect on soybean survival or leaf greenness, but plants became severely chlorotic and stunted when the roots were exposed to no oxygen together with CO(2) concentrations similar to those in flooded fields (equilibrium concentrations of 30 %). When root-zone CO(2) was increased to 50 %, a quarter of soybean plants died. Those plants that survived showed severe symptoms of chlorosis, necrosis and root death. In contrast, rice (Oryza sativa L.) plants were not affected by the combination of no oxygen and elevated root-zone CO(2.) A concentration of 50 % CO(2) did not affect rice plant survival or leaf colour. These results suggest that the high susceptibility of soybean to soil flooding, compared with that of rice, is an outcome of its greater sensitivity to CO(2).