Molecular dissection of the QTL DTY 12.1 for rice yield-under-drought stress: transcription factor, no apical meristem-mediated lateral root profusion as a functional explanation

Drought is a major constraint in rice production. A quantitative trait loci (QTL) DTY 12.1, with a large effect on grain yield under drought stress, mapped on chromosome 12 was analyzed for putative candidate genes. Through an innovative in silico approach, genes within the QTL region were analyzed for their relation to drought tolerance. This approach integrated literature search with pertinent modifications to promoter cis-regulatory element mining and expression pattern searches utilizing various existing databases. Multiple strong candidate genes were postulated. However, the role of transcription factor no apical meristem (NAM) was chosen to be validated first. Cloning of NAM promoter from the two parental lines revealed a 224 bp sequence present only in the donor parent. This stretch contained cis-regulatory elements such as the ethylene response elements (ERE), functional in drought and known to influence processes such as adventitious root formation among others. The coding sequence was also different between the parents and suggested changes in the protein 3D structure. RT-PCR-mediated expression analysis for NAM in normal leaf, flag leaf, panicle and root under mild and severe drought stress during the reproductive stage revealed up-regulation of NAM in certain tissues under stress. Transformed rice plants over-expressing NAM resulted in denser and longer root hairs and profuse lateral roots. A cellulose synthase A (CesA10) gene was also present in the QTL region which influences root hair formation. The Ces A10 promoter contained the NAM-TF binding site. This suggested that transgenic rice plants constitutively over-expressing NAM would over-express Ces A10. This was confirmed through western blot hybridization. These results supported the earlier morpho-physiological studies that revealed increased lateral roots, root hair and water uptake as the reason for DTY12.1 function. Phenotyping of NAM transgenic plants for drought tolerance is underway to assess the overall contribution of NAM in the performance of DTY12.1.