Msc. Dissertation 2019The screen house and field experiments were conducted during the 2017 /2018 rainy season in order to characterize grain yield and root architecture of fifteen(15) selected Faya rice genotypes namely; Faya 14 M 69, Faya Zambia, Faya Mafuta 1, Faya Mafuta 2, Faya Makanjira, Acc 5934, Mw 1685, Acc 9290, Acc 9293, Acc 18037, Acc 18028, Acc 17323, Acc 17344, Acc 5933, and Faya Kalonga, at both molecular and morphological levels for further utilization in crop breeding programmes. The fifteen (15) selected Faya rice genotypes were obtained from Lifuwu Agricultural Research Station (LARS). The molecular work was conducted at the Molecular Biology Laboratory of Sokoine University of Agriculture (Tanzania) using ten (10) Simple Sequence Repeat (SSR) markers. The morphological study was done at Lifuwu Research Station (Malawi) on twelve (12) qualitative and twelve (12) quantitative morphological traits, five (5) root architectural traits and seven (7)grain quality traits in screen house (using PVC pipes) and field conditions. The present study illustrated rich genetic divergence for different quantitative and qualitative traits among the Faya rice genotypes. The quantitative traits such as grain yield, 1000 grain weight, spikelet fertility, number of panicles per plant, number of tillers per plant, panicle length, leaf length, leaf width, flag leaf length, flag leaf width and number of spikelets per panicle illustrated most variation. The studied root architectural traits such as fresh root mass, root number, maximum root length, fresh shoot mass, dry root mass and dry shoot mass showed great variation among the studied genotypes. All the grain quality traits in the present study showed no variation except translucency, chalkiness, gelatinization temperature and gel consistency. The eleven qualitative traits studied depicted great variation. Grain yield trait correlated positively with root number, root thickness (root volume), 1000 grain weight, number of spikelets per panicle, spikelet fertility and plant height and negatively with the other associated traits that were analyzed. The agglomerative hierarchical clustering using twenty five (25) quantitative morphological, grain quality, and root architectural traits grouped the fifteen (15) Faya rice genotypes into four (4) clusters and five Principal Components while the same genotypes were categorized into three clusters when ten (10) SSR markers were used for clustering. All the ten (10) SSR (Microsatellite) markers that were used in studying the 15 Faya rice genotypes turned out to be polymorphic for the target traits and amplified 142 bands and 63 alleles. The least genetic similarity index magnitude detected for and among the genotypes implies that some of the genotypes studied have closely similar genetic constitution while others are distantly similar. The highest Polymerase Information Content (PIC) value was recorded for primer RM215 and all the markers used in this study were neutral, convenient and co-dominant in nature. The screening of the genotypes using both morphological and molecular (SSR) markers for the fifteen (15) rice genotypes has revealed that the genotypes are diverse and would produce significant transgressive segregants if used in general and hybridization breeding work. All the SSR markers used in this study have proven to be a success in studying the land races of rice as evidenced in the current work where all markers turned out to be polymorphic.