Quantitative Trait Locus Mapping and Candidate Gene Analysis for Plant Architecture Traits Using Whole Genome Re-Sequencing in Rice

Abstract

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line ‘SNUSG1’ and indica rice line ‘Milyang23’. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

QTLs for Early Tiller Production and Relationships with Rapid Seedling Growth and Increased Panicle Number in Rice

“…uniculme 4 (cul4), Rossini et al, 2006; tiller inhibition 3 (tin3), Kuraparthy et al, 2008 qTN2 RM106-RM263-RM3730 2 25.2-26.2 Yan et al, 1998;Yan et al, 1999;Miyamoto et al, 2004;Marri et al, 2005;Lim et al (2014).…”

Mapping and Validation of Quantitative Trait Loci Associated with Tiller Production in Rice

“…More than 250 QTLs for various agronomically important traits have been identified in the LT-RILs, but loci affecting TN were not yet determined. Mapping the TN QTLs in TeQing will be very useful in comparing location, trait effect, and parental origin with the reported QTLs associated with panicle and kernel size, a key aspect not fully explored in previous TN QTL studies (Wang et al, 1994;Wu et al, 1995;Lu et al, 1997;Yan et al, 1998;Price et al, 2000;Temnykh et al, 2001;Brondani et al, 2002;Nagata et al, 2002;Xing et al, 2002;Hu et al, 2003;Miyamoto et al, 2004;Ramalingam et al, 2003;Zhang et al, 2005;Li et al, 2006;Huang et al, 2010;Jiang et al, 2013;Lim et al, 2014). Mapping the TN QTLs in TeQing will be very useful in comparing location, trait effect, and parental origin with the reported QTLs associated with panicle and kernel size, a key aspect not fully explored in previous TN QTL studies (Wang et al, 1994;Wu et al, 1995;Lu et al, 1997;Yan et al, 1998;Price et al, 2000;Temnykh et al, 2001;Brondani et al, 2002;Nagata et al, 2002;Xing et al, 2002;Hu et al, 2003;Miyamoto et al, 2004;Ramalingam et al, 2003;Zhang et al, 2005;Li et al, 2006;Huang et al, 2010;Jiang et al, 2013;Lim et al, 2014).…”

“…per panicle (Li et al, 1997); panicle weight (Li et al, 1998); disease resistance (Pinson et al, 2005) Mutations: high tillering dwarf 1 (htd1), Zou et al, 2005; Aberrant panicle organization 2 (APO2), Ikeda-Kawakatsu et al, 2012. QTLs: Wang et al, 1994Lu et al, 1997;nagata et al, 2002;Ramalingam et al, 2003;Gao et al, 2013;Lim et al, 2014. (Li et al, 1997); grain weight per panicle (Li et al, 1997); disease resistance (Pinson et al, 2005) Mutations: ideal plant architecture 1 (ipa1) Miura et al, 2010. QTLs: Wang et al, 1994Temnykh et al, 2001;Brondani et al, 2002;Ramalingam et al, 2003;Miyamoto et al, 2004;Jiang et al, 2013. (Paterson et al, 1995;…”

“…The TN QTLs in TeQing are of particular interest since this trait was pinpointed as critical in enhancing yield in US rice , Samonte et al, 1998. Mapping the TN QTLs in TeQing will be very useful in comparing location, trait effect, and parental origin with the reported QTLs associated with panicle and kernel size, a key aspect not fully explored in previous TN QTL studies (Wang et al, 1994;Wu et al, 1995;Lu et al, 1997;Yan et al, 1998;Price et al, 2000;Temnykh et al, 2001;Brondani et al, 2002;Nagata et al, 2002;Xing et al, 2002;Hu et al, 2003;Miyamoto et al, 2004;Ramalingam et al, 2003;Zhang et al, 2005;Li et al, 2006;Huang et al, 2010;Jiang et al, 2013;Lim et al, 2014).…”

QTL Analysis of Concerned on Ideal Plant Form in Rice

“…개체당 이삭수와 같은 식물 생육특성과 더불어 수량에 대한보 고가 이루어졌다 (Cho et al, 2007;Lim et al, 2014). DNA 마 커와 양적형질유전자좌를 이용하여 DNA 마커의 체계적인 관리 로 양적형질유전자좌를 이용한 도복저항성 벼와 수량의 관계를 보고한 새로운 접근법이 연구되었으며 도복저항성의 개량을 목 적으로 하는 QTL 분석 연구가 이루어졌다 (Ookawa et al, 2010).…”