Identification of candidate genes in DTY12.1 region through date mining

A quantitative trait locus, DTY12.1, with a large effect on grain yield under stress was previously mapped on chromosome 12 of Vandana (japonica/aus)/Wayrarem (indica) population in a region flanked by SSR markers RM20848 and RM511. Increased water uptake and relative water content in QTL and NILs implicated a role for DTY12.1 in root development/function. This was further confirmed by better proliferation of root hairs and longer root length under drought and re-watered conditions. Since the source of QTL was from an indica variety, a comparison of genomic sequence of DTY12.1 region between model rice Nipponbare (japonica) and 93-11 (indica) was undertaken. The DTY12.1 region 93-11 spans a total of 2.4 Mb, smaller that the 3.2 Mb in the Nipponbare sequences, which is mainly due to a large insertion/deletion. Alignment of the genes from Nipponbare DTY12.1 region to the 93-11 region using BLAT showed 88 out of 140 genes had more than 80% match. The 93-11 has 68 more genes than the Nipponbare sequence of which 48 encoded novel proteins. Majority of the annotated genes were involved in stress response with major functions in hydrolase activity and in nucleotide/protein binding. To identify candidate genes involved. The authors used existing databases for in silico analysis of a smaller region of the QTL spanning LOD peak. Sequence analysis confirmed presence of a gene named cellulose synthase (CesA10). Cellulose synthase was earlier shown to be responsible for root hair proliferation and elongation. CesA10 gene locates close to the position of SSR marker RM511 which segregates with the drought tolerant phenotype. Further analysis of this gene reported elsewhere implicated a major role of this gene in DTY12.1 function. The CesA10 was absent in the recipient parent Vandana. This results highlighted the need for detailed sequence information of the QTL region in the variety involved as the donor.