Steven RonoSylvester Elikan AnamiNdunge, Munyao Mary2022-08-182022-08-182021http://ir-library.ku.ac.ke/handle/123456789/23976A Thesis Submitted in Partial Fulfillment for the Requirements for the Award of the Degree of Master of Science (Biotechnology) of the School of Pure and Applied Science Kenyatta University, November, 2021Maize is the main human food crop in Kenya. Most farmers in Kenya rely on rainfall to grow maize and other crops. However, the amount of the rainfall in many parts is not reliable resulting to irrigation. Crop production in the coastal areas of Kenya suffers greater constraints because of salinity. In coastal areas salinity is caused by accumulation of salt in soil as a result of salty borehole water. The goal of this research was to identify salt tolerant Quantitative Trait Locus (QTL) using Simple Sequence Repeats (SSR) markers in maize leverag-ing on the similar QTL in rice. In this study, five tropical maize inbred lines – CML 216, CML 395, CML 144, EO4, AO4 and four coastal open pollinated varieties (OPVs)– PH4, DHO4, SC DUMA 43 and DK 8031 were used for analysis of saltol QTL by evaluating their agronomic traits under various levels of Sodium Chloride (NaCl) treatment (0.0mM, 0.02mM, 0.06mM, 0.18mM and 0.54mM). Five replicate seeds of each maize variety were planted one inch in soil in pots and watered daily with one litre of each concentration. A 100% germination performance was observed on soil treated with 0.0, 0.02 and 0.06mM NaCl. At 0.18mM NaCl, DK 8031 and PH4 seeds were the most tol-erant registering germination percentage of 80% whereas AO4, EO4 CML 144, PH4, DHO4 and CML 395 had 20% germination at the same concentra-tion. The most susceptible lines were CML 216 and SC DUMA 43 with 0% germination at 0.18mM NaCl. In bred lines CML 216, CML144, CML 395, DK 8031 and DHO4 exhibited hormesis in 0.02mM NaCl. It was observed that at 0.02mMNaCl DK8031 shoots had a ratio of Na+/K+ as 180/250ppm and therefore DK8031 did not leak K+ ions maintaining a normal Na+/K+ ratio for the cell homeostasis associated to saltol QTL. Among the OPVs, SC DUMA 43 had highest number of seeds 317.43± (11.7030) in 0.02mM NaCl. DK 8031 and SC DUMA 43 were superior with shorter anthesis-silking interval (80 and 78 days after planting) among the OPVs, whereas in 0.02mM NaCl CML 216 and PH4 had poor grain yield with the least number of seeds (2.23± (1.7436) and 8.62± (7.3865) respectively with long anthesis-silking interval (107 and 110 days). Using simple sequence repeats (SSR) markers, this research identi-fied a saltol QTL that confers salt tolerance in maize. Fourteen SSR markers were utilized to predict similar salinity tolerance QTL on maize, which were previously used for saltol-QTL mapping on chromosome 1 in rice. PCR was used to find QTLs. All SSR markers detected saltol QTL on chromosome 1 of rice, while five SSR markers (RM10694, RM490, RM10772, RM10764, and AP3206) detected saltol QTL in maize. The PCR amplified DNA fragments ranged from size 100 to200bp. From this study QTL of salinity tolerance was identified in DK8031 maize at the seedling stage using rice synteny regions. In conclusion SSR markers identified the saltol QTL in maize.enEvaluationAgronomic TraitsTropical MaizeSalt StressIdentificationResponsible SaltolQuantitative Trait LocusThesis