A THESIS SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHYLOSOPHY OF SOKOINE UNIVERSITY OF AGRICULTURE, MOROGORO, TANZANIA. 2017This work was undertaken in order to improve the performance of some selected rice varieties that are susceptible to phosphorus (P) deficiency through the introgression of P deficiency tolerant genes. This involved screening for tolerance to P deficiency of a diverse set of varieties grown in East and Southern African (ESA) countries and their molecular marker survey, in order to assess the presence or absence of the phosphorus starvation tolerance (PSTOL1) gene. This information served as a basis for selecting varieties for improvement and for use as donors. In this study, it was established that about 41 percent of the 96 germplasm tested lack PSTOL1 while 59 percent of the varieties have the tolerance gene. In addition, the study revealed that among the varieties with PSTOL1, some were not tolerant to P deficiency as expected possibly due to the existence of inhibitors or non-functional-PSTOL1 alleles due to mutations. On the other hand, some varieties without PSTOL1 performed well under P deficiency. Genetic introgression of Pup1 QTL that contains PSTOL1 was successfully conducted into three selected varieties but susceptible to P deficiency namely; Pishori, TXD 88 and Tule na Bwana by markers assisted selection (MAS). The introgression lines presented yield increase between 11 to 70 percent compared to susceptible recipient parents. At the same time, four new candidate QTLs with significant effect on phenotypic expression of grain yield, tiller number, and shoot biomass under P deficiency were detected on chromosomes 4, 5 and 9 among tolerant varieties that did not have Pup1. The results show that, some local genotypes contain vital genes useful for genetic improvement; hence they need to be conserved. Although long term usage of varieties with high P uptake due to the presence of Pup1 may deplete the soil P in low input systems, genetic variability for low grain P concentration as well as good P utilization efficiency (PUE) were observed and should be utilized in the genetic improvement. Also the effect of new P deficiency tolerance QTLs detected should be further validated in different environments due to possibilities of QTL x environment interaction so as to come up with stable and reliable QTLs.