Identification of molecular markers for cooking quality traits of rice

The process of determining major cooking and taste qualities are biochemical and, unraveling the quality is possible only after grain maturity which is time consuming and laborious. Thus, there is a need for identification of molecular markers linked to major quality traits which can help rice breeders in selecting progeny with desirable quality traits at early stages of development. Till date, most of the work done related to identification of markers linked to grain quality traits has been done in the japonica germplasm. Hence the present study was carried out with the objectives of (i) validation of markers reported to be linked to grain quality traits in indica germplasm, (ii) identification of more efficient functional markers for the cloned genes associated with grain quality, and (iii) identification of major QTL's controlling cooking and eating quality traits in rice. Association study carried out with 13 reported markers in a set of 360 indica genotypes showed varied levels of association for each trait. Most of these markers were not useful in indica germplam. A functional marker named BADEX7–5 targeting the 8-bp deletion in the exon-7 of BAD-2 (candidate gene for aroma), which can clearly differentiate the aromatic and non-aromatic genotypes efficiently on a simple agarose gel has been identified in this study. In addition, a functional marker named DRR GL-1 targeting an SNP in the major QTL GS3, which is associated with kernel length (KL) and kernel elongation (KE) was identified and validated through QTL-marker linkage analysis involving large populations. Major QTLs for gelatinization temperature, grain breadth, grain length, length to breadth ratio and kernel elongation were identified. The identification of candidate genes in the QTL s may give some vital clues in understanding the genetic control of key grain quality traits of indica genotypes and provide additional markers for immediate use in marker-assisted breeding.