Rice Science, 2014, 21(1): 20−28 Copyright © 2014, China National Rice Research Institute Published by Elsevier BV. All rights reserved DOI: 10.1016/S1672-6308(13)60165-1 Seed Length Controlled by Same Locus in Four Different AA Genome Species of Genus Oryza ZHANG Yu 1, # , LI Jing 1, # , ZHOU Jia-wu 1 , XU Peng 1 , DENG Xian-neng 1 , Y ANG Fei 1, 2 , DENG Wei 1 , HU Feng-yi 1 , T AO Da-yun 1 ( 1 Institute of Food and Crops Research, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; 2 Life-Sciences School, Yunnan University, Kunming 650091, China; # These authors contributed equally to this study) Abstract: To broaden the genetic basis and overcome the yield plateau in Asian cultivated rice, the exploitation and utilization of favorable alleles from rice species with the AA genome has become important and urgent in modern breeding programs. Four different interspecific populations were used to detect quantitative trait locus (QTL) for seed length, including a BC 4 F 2 population derived from Oryza glumaepatula crossed with Dianjingyou 1 (a japonica cultivar), a BC 4 F 2 population derived from O. nivara crossed with Dianjingyou 1, a BC 7 F 1 population derived from a cross between O. longistaminata and RD23 (an indica cultivar), and a BC 8 F 1 population derived from a cross between O. glaberrima and Dianjingyou 1. The QTLs for seed length in four different populations were termed as SL-3a, SL-3b, SL-3c and SL-3d, respectively. They had good collinearity and accounted for 49% to 60% of the phenotypic variations. Sequencing data indicated that four QTLs were different alleles of GS3 which were responsible for the seed length variation between O. sativa and its four AA genome relatives. These results will be valuable for confirming the evolution of GS3 and also be helpful for rice breeding. Key words: seed length; O. glumaepatula; O. nivara; O. longistaminata; O. glaberrima; quantitative trait locus Rice is one of the most important food crops for half of the world’s population. In the past half century, two major breakthroughs in rice breeding were made through the use of semidwarf gene and heterosis (Patnaik et al, 1990; Spielmeyer et al, 2002). But in recent years, rice yields have not significantly increased, mainly due to the narrow genetic basis of parental materials (Tanksley and McCouch, 1997). The genus, Oryza, is comprised of two cultivated rice species and 22 wild rice species, and all species of the genus Oryza are classified into six diploid genome types (AA, BB, CC, EE, FF and GG) and four tetraploid genome types (BBCC, CCDD, HHJJ and HHKK) (Vaughan, 1994; Khush, 1997). The species with AA genome are classified into two cultivated species (O. sativa and O. glaberrima), and six wild rice species (O. nivara, O. rufipogon, O. barthii, O. glumaepatula, O. longistaminata and O. meridionalis). Since they share the same AA genome, O. glaberrima and the six wild rice species are the most accessible genetic resources for the improvement of cultivated rice (Ren et al, 2003). Previous reports indicates that 40% of alleles of wild rice is lost during the domestication from wild rice to cultivated rice (Sun et al, 2002), and only 10% to 20% of genetic diversities in wild species are retained in two subspecies of cultivated rice (Zhu et al, 2007). Thus, the exploitation and utilization of favorable alleles of wild rice and related species may overcome yield bottleneck of the Asian cultivated rice (Xiao et al, 1998). Seed length is one of the major determination factors of rice yield (Xing and Zhang, 2010). Seed length not only determines seed appearance, but also affects milling, cooking and eating qualities of rice (Fan et al, 2006), moreover, seed length is also important in the evolution of cereal crops because long grains tend to be selected during the early domestication process, as evidenced by the fact that most cultivated species have longer grains than their wild relatives (Li et al, 2004). Elucidating the molecular and genetic basis of seed length will lay the foundation for improving rice yield and quality, and contribute to the dissection of evolution mechanism underlying grain size in the genus Oryza. Quantitative trait locus (QTL) mapping has been proven to be an effective approach to reveal the genetic basis of phenotypic evolution and domestication (Tanksley and McCouch, 1997; Barton and Keightley, 2002). Seed size is not only a typical quantitative trait, Received: 17 May 2013; Accepted: 13 October 2013 Corresponding author: TAO Da-yun (taody12@aliyun.com)