African Journal of Biotechnology Vol. 10(18), pp. 3521-3527, 2 May, 2011 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB10.1389 ISSN 1684–5315 © 2011 Academic Journals Full Length Research Paper Maize breeding for marginal lands: Physiological and molecular approach to decipher response and selection of maize recombinant inbred lines (RILs) under water deficit at early growth stage Malik Nawaz Shuja 1 , Wajid Ali 1 , Aqib Iqbal 1 *, Ijaz Ali 1 , Iqbal Munir 1 , Dawood Ahmad 1 , Inamullah 2 , Shaheenshah 2 , Gulzar Ahmad 3 , M. Arif Khan 2 and Zahoor Ahmad Swati 1 1 Laboratory of Molecular Genetics, Institute of Biotechnology and Genetic Engineering, Agricultural University, Peshawar, Khyber Pakhtoonkhwa, Pakistan. 2 Department of Agronomy, Agricultural University, Peshawar, Khyber Pakhtoonkhwa, Pakistan. 3 Cereals Crops Research Institute, Pirsabak, Nowshera, Pakistan. Accepted 3 January, 2011 Drought is the major abiotic stress constraining the production of maize (Zea mays L.) in the arid and semi-arid areas. Recombinant inbred lines (RILs) with improved performance from the 6th selection cycles were evaluated against drought stress at early growth stages and genetic distance was determined through random amplified polymorphic DNA (RAPD) primers. Significant variation was observed in the rate of water loss (RWL) at 30, 90 and 150 min after excision, relative water content (RWC) and membrane stability among the RILs. In comparison with check variety Azam, 7 RILs maintained a low RWL, 2 had higher RWC and 6 RILs had higher membrane stability, thus showing a higher degree of adaptation to drought stress. The preliminary results showed polymorphism among the drought sensitive and tolerant RILs. The RILs were clustered into three groups on the basis of amplification pattern obtained with 60 RAPD markers. Variation in the genetic makeup of the tolerant RILs was evident from their clustering in different groups, though most were clustered in group III. Furthermore, one RAPD marker could identify maize genotypes, maintaining low RWL from the excised leaves. We are in the process of sequencing the amplified product of this primer and transforming it into sequence characterized amplified region (SCAR) markers for a more reliable marker assisted selection. Key words: Maize recombinant inbred lines (RILs), drought, physiological markers, random amplified polymorphic DNA (RAPD). INTRODUCTION Global climate change is now generally considered to be underway and is expected to result in a long-term trend towards higher temperatures, greater evapotranspiration and an increased incidence of drought in specific regions ( Hillel and Rosenzweig, 2002). Under these conditions, research into plant breeding for developing improved crop varieties and management practices to enhance *Corresponding author. E-mail: aqib72@aup.edu.pk. Tel: +92- 336-9086080. Fax: +92-91-9218102. plant water use efficiency and growth, when water is limi- ting has become increasingly important. As one of the major abiotic stress, drought causes differences between the mean and potential yield, as well as variation from year to year. It has been estimated that crops attain only 25% of their potential yield because of the detrimental effects of environmental stresses (Boyer, 1982). Maize is cultivated worldwide under very diverse climatic condi- tions and has the largest total annual grain production in the world (590.5 million metric tons, mmt) among the major grain crops. Though maize is essential for global food security, in several key production environments, the