Sorghum (Sorghum bicolor (L). Moench) is used for human consumption in parts of Africa and Asia and as an animal feed mainly in the U.S. Though sorghum grain contains higher amounts of protein than other cereal grains such as wheat and corn, it is not as readily available for enzyme degradation in humans and animals. Protein body matrices called kafirins surround the starch granules in sorghum. Because the protein is less digestible, the starch is also less digestible for biofuel production. However variation for this trait exists and the line P850029 has a higher protein digestibility compared to other normal grain sorghum lines. This increase in digestibility of protein is due to the rearrangement of the kafirins in the prolamin protein bodies where, the γ-kafirins are rearranged in the seed endosperm and the amount of γ-kafirin in the grain is also reduced. The assay to phenotype the HD trait is time consuming and unpredictable. So identifying a quantitative trait loci (QTL) controlling the protein digestibility trait in sorghum would be beneficial in breeding. A recombinant inbred lines (RILs) population derived from P850029 x ‘Sureno’, were developed and used to map QTL regulating the protein digestibility trait. A single QTL was identified on chromosome 1 between Xtxp43 and Xtxp329. Validation of the identified QTL was done on heterogenous inbred families (HIFs). The results validate the same QTL identified on the RIL population on chromosome 1. Later the high digestibility trait (HD) was integrated with the Waxy trait in sorghum. The Waxy (WX) sorghums have starch completely in the form of amylopectin. The effect of endosperm type on ethanol yield and fermentation efficiencies was studied among HD, WX and HD-WX lines. The HD-WX lines fermented in a shorter time i.e. completed fermentation in 48 h and their fermentation efficiencies were also higher around 90%. The DDGS of the HD-WX lines also had lower residual starch content and 50% higher amino acid lysine content when compared to wildtype sorghum. Moreover, the relation between endosperm traits and grain yield in sorghum has not been fully explored. In this study, we compared the yield and yield components of four unique endosperm phenotypes, HD, WX, HD-WX and wildtype lines. A total of 100 F2:4 derived recombinant inbred lines population from a cross between Tx2907/P850029 were selected with 25 lines from each HD, WX, HD-WX and wild-type line were included in the study. These lines were grown in three replications in College Station and Halfway, Texas in a randomized complete block design. The results show that there are no significant differences in the grain yield.