水稻binmap遗传图谱10.1111@pbr.12248.pdf

Construction of high-throughput genotyped chromosome segment substitution lines in rice (Oryza sativa L.) and QTL mapping for heading dateJI N Y A NZH U1,2,†, YO N G C H A ONI U3,†, YA J U NTA O2, JU NWA N G1, JI A N B OJI A N3, SH U A I S H U A ITA I3, JU NLI3,JI EYA N G1, WE I G O N GZH O N G1, YO N GZH O U2,4and GU O H U ALI A N G2,41Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement,Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China;2Jiangsu Key Laboratory of CropGenetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China;3BGI-shenzhen, Main Building,Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China;4Corresponding author, E-mails: G. Liang: ricegb@;Y. Zhou: zhouyong@With 4 figures and 4 tablesReceived March 17, 2014 / Accepted December 7, 2014 Communicated by S. N. AhnAbstractChromosome segment substitution lines (CSSLs) provide ideal materials for quantitative trait loci (QTLs) mapping and genetic dissection of com- plex traits. In this study, we developed a set of CSSL population consist- ing of 175 lines, which were derived between the recipient ‘Guangluai 4’ and the donor ‘Nipponbare’. Based on 260 molecular markers, we firstly constructed a physical map of core 97 lines. Then, these 97 lines were further genotyped based on resequencing data, and a resequencing-based physical map was constructed. Compared with the molecular marker- based physical map, the resequencing-based physical map of 97 lines contained 367 substituted segments with 252 newly discovered segments. The total size of the 367 substituted segments was 1,074 Mb, which was 2.81 times the size of rice genome. Using the 97 CSSLs as materials, we identified nine QTLs for heading date and three of them were firstly reported. All the QTLs had positive additive effects, ranging from 9.50 to 16.50 days. These CSSLs may greatly help forge a new resource for functional genomics studies and molecular breeding in rice.Keywords:OryzasativaL.—chromosomesegment substitution lines — molecular marker-assisted selection — high-throughput resequencingRice plays a significant role in people’s lives, feeding over half the global population. Many important traits of rice, such as yield, grain shape, eating quality and heading date, show contin- uous phenotypic variation. The genetic basis for these traits is explained by quantitative trait loci (QTLs), and the phenotypic effects of QTLs are relatively small. Furthermore, the phenotypic manifestations of these quantitative traits are always influenced by environmental factors and genetic backgrounds. Thus, it is difficult to identify QTLs in rice. Over the past few decades, many studies have been performed to analyze the genetic basis of QTLs in rice. In early studies, tra- ditional primary mapping populations, such as F2and BC1popu- lations, were used for QTL analysis (Araki and Kato 1995, Li et al. 1995). However, these populations are not suitable for QTL fine mapping or cloning due to their genetic background noise (Yamamoto et al. 2000). As a result, only a few QTLs with relatively large effects have been characterized. To facilitate more comprehensive analysis of complex traits, some secondary mapping populations, such as chromosome segment substitution lines (CSSLs), were developed (Xi et al. 2006, Zhu et al. 2009,Xu et al. 2010, Zhang et al. 2011). CSSLs have the same genetic background as recurrent parent except for the substituted segments from donor parent. These populations make it possible to dissect quantitative trait genes into single Mendelian factors, as they can eliminate most background noise. Therefore, QTL analysis has become more accurater and far easier, and most of the cloned and fine-mapped QTLs regulating quantitative traits in rice were characterized using CSSLs or their derived popula- tions (Takahashi et al. 2001, Mei et al. 2006, Song et al. 2007, Takai et al. 2007 Yu et al. 2007, Zhou et al. 2009a,b). So, more and more CSSLs have been constructed due to the sig- nificant contribution for QTLs characterization and breeding, although the development of such lines requires a large amount of time and labour (Ebitani et al. 2005, Xi et al. 2006, Ando et al. 2008, Shim et al. 2010, Yoshimura et al. 2010, Tomoyuki et al. 2014). Among them, two sets of CSSLs have been further geno- typed based on high-throughput resequencing technology (Xu et al. 2010, Zhang et al. 2011). These achievements would undoubtedly enhance and broaden our understanding of complex traits. In this study, we produced a population of 175 CSSLs using a genome-sequenced japonica cultivar, ‘Nipponbare’, as the donor parent, and a typical indica cultivar, ‘Guangluai 4’, as the recipi- ent parent. After a series of backcros。