Rice is the fundamental food for about half of the world’s population, supplying 20% of the calories consumed worldwide. In Pakistan, rice is second staple food after wheat and contributes more than two million tones to our food requirements. It shares 5.7 percent of the total value added in agriculture and 1.6 percent to GDP. QTL mapping is a marker facilitated genetic dissection of variation of complex phenotypes through proper experimental strategy and statistical analysis of segregating material. The detection of genes or QTLs for yield and quality traits is based on the principal of genetic recombination during meiosis. This allows the construction of linkage maps consisted of genetic markers for a specific population. In rice, association mapping is a viable alternative to QTL mapping. Based on linkage disequilibrium (LD), association mapping is powerful and high resolution mapping tool for complex traits. It has the potential to utilize the genetic diversity of the worldwide crop germplasm resources. Linkage disequilibrium (LD) refers to a reduced (non random) level of recombination of specific alleles at different loci controlling specific genetic variations in a population. Single nucleotide polymorphisms (SNPs) are most abundant source of genetic polymorphism between two individuals. SNPs have been extensively used to detect population structure and association mapping for yield and quality traits in rice. One of the major concerns in rice breeding is grain quality improvement. Grain quality in rice is second only to yield as a major breeding objective. The amylose content in rice is regarded as one of the most important determinant of cooking and eating quality. In breeding programme, new lines are selected based on amylose content as this indicator is associated with grain quality. To identify the quantitative trait loci (QTLs) or genes for protein content, amylose content and pasting properties of rice, a segregating population was developed by crossing two parents IR-64 and IR-132. A QTL analysis was conducted using 125 SNPs markers distributed on all 12 rice chromosomes on a progeny of 213 plants. Many different genomic regions have been identified to influence the starch pasting properties on different linkage groups. A total of 24 main effect QTLs (M-QTLs) for different grain quality traits were identified and mapped on 7 different chromosomes (1, 4, 7, 8,9,10 &11). 12The potential of genome wide association scans (GWAS) was explored to estimate the genetic structure and to map the genomic regions associated with starch chain length distribution. We used 754 genome wide single nucleotide polymorphisms (SNPs) based markers to study the patterns of linkage disequilibrium (LD) and structure of population among seventy-five diverse rice genotypes (indica, temperate japonica & tropical japonica). All the seventy-five accessions were divided into three major groups based on structure analysis (model based). The three groups represented three different geographic regions. For the 75 genotypes, the complex traits like amylose content, gelatinization temperature, amylose long chains, amylose short chains, amylopectin long chains, and amylopectin short chains were studied. The associations of SNPs markers with a phenotypic trait were disclosed by using the approach of GLM (general linear model). We examined variation both within and among three subgroups revealing significant heterogeneity. A total of 59 association signals were detected. From the results, we found that waxy locus not only affects amylose content and GC but also regulates starch branching patterns in rice. The study will help to provide a way to find out valuable genes and alleles associated with starch structure for grain quality improvement in rice. Our mapping results have clear practical implications for the improvement of rice grain quality. The SNPs markers closely associated with the variation of all the studied phenotypic traits could greatly be used to replace the alleles linked with poor grain quality traits using marker-assisted selection. The possible applications of mapped QTLs include their utilization in screening of parents for introgression or pyramiding purpose.