International Research Journal of Applied and Basic Sciences © 2013 Available online at www.irjabs.com ISSN 2251-838X / Vol, 4 (8): 2209-2215 Science Explorer Publications Development of an allele-specific functional marker for studying Hd1 effect on flowering time of rice Leila Nayyeripasand 1 , GhorbanAli Nematzadeh 2 , Nadali Babaeian Jelodar 2 , Asadollah Ahmadikhah *3 , Mohammadreza Azimi 3 1. M.Sc. Student of Agricultural Biotechnology, Department of Agronomy and Plant Breeding. Sari Agricultural Sciences and Natural Resources University, Sari, Iran 2. Department of Agronomy and Plant Breeding. Sari Agricultural Sciences and Natural Resources University, Sari, Iran 3. Department of Agronomy and Plant Breeding. University of Zanjan, Zanjan, Iran. *Corresponding Author email:ahmadikhaha@gmail.com ABSTRACT: Photoperiodic control of flowering is one of the most significant components of the interaction between plants and their environment. Hd1 promotes floral transition from vegetative to reproductive growth under short-day (SD) conditions. An indel-specific functional marker in Hd1 first exon was developed and tested in a collection of 44 rice indica cultivars with different flowering times to evaluate its association with the trait. Results showed that the Hd1 indel-specific marker produced three allelic forms A, B and C as expected, with frequencies of 43.2, 47.7 and 9.1 percent, respectively. A high negative correlation (r=-0.556) was detected between flowering time and functional Hd1 indel. Interval mapping (IM) analysis showed that Hd1 had a negative additive effect (~4.5 days) on flowering time and the gene explained 27.4 percent of phenotypic variation of the trait. Our results indicated the role of Hd1 in determining the time of flowering in rice and suggest applicability of Hd1 indel-specific marker in molecular breeding of early flowering. Key Words: Allele; Association; Heading; Mapping. Abbreviations: AMOVA- analysis of molecular variance, ASA- allele specific amplification, HD- heading date, HWE- Hardy-Weinberg equilibrium, IM- interval mapping, LD- long day, LR- likelihood ratio, MAB- marker-assisted backcrossing, MAS- marker-assisted selection, NILs- near isogenic lines, QTL- quantitative trait loci, SD- short day, VM- virtual marker INTRODUCTION The time of flowering or heading date (HD) is considered a crucial factor not only for quantity, but also the quality of rice grain production (Fan et al., 2005). The timing of the transition from vegetative to reproductive phase is important to ensure successful sexual reproduction of plants and is regulated by both endogenous and environmental factors (Kojima et al., 2002). Photoperiodic control of flowering is one of the most significant components of the interaction between plants and their environment (Thomas and Vince-Prue, 1997). Previous studies revealed that several genes are involved in the response to photoperiod in rice (Li et al., 1995; Lu et al., 1997; Lin et al., 1998; Maheswaran et al., 2000; Zhou et al., 2001; Brondani et al., 2002; Yu et al., 2002; Hittalmani et al., 2002; Yokoo et al., 1980, Yamagata et al., 1986, Sano, 1992, Tsai, 1995; Rabiei, 2007). By analyzing natural variation in flowering time, several quantitative trait loci (QTLs) with large effects have been successfully isolated, and this knowledge has improved our understanding of the genetic control of rice flowering (Yano et al., 2000; Takahashi et al., 2001; Kojima et al., 2002; Doi et al., 2004; Xue et al., 2008; Itoh et al., 2010; Ogiso et al., 2010; Wei et al., 2010; Yan et al., 2011). Lin et al (2000), using near isogenic lines (NILs) showed that Hd1, Hd2 and Hd3 are involved in photoperiod sensitivity. Certain QTLs were recently shown to be directly involved in complex interactions for heading date and/or photoperiodic responses (Ordonez et al., 2010). For example, a major QTL at the top of chromosome 6 designated Hd1 was shown to promote flowering under short-day conditions and inhibit