Identification and Characterization of Quantitative Trait Loci for Shattering in Japonica Rice Landrace Jiucaiqing from Taihu Lake Valley, China

Easy shattering reduces yield from grain loss during rice (Oryza sativa L.) harvest. We characterized a nonshattering japonica rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH). The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of indica IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ~100 gf. Then the chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) of Jiucaiqing in IR26 background were developed for quantitative trait loci (QTL) mapping. Four putative QTL (qSH1JCQ, qSH3JCQ, qSH6JCQ, and qSH11JCQ) for shattering were detected, and the qSH1JCQ was confirmed on chromosome 1. We further mapped qSH1JCQ to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for qSH1JCQ, which colocated with qSH1. Further quantitative realtime polymerase chain reaction (PCR) analyses confirmed that the QTL qSH1JCQ can significantly decrease the expression of shattering related genes (qSH1, OsCPL1, Sh4, SH5, and SHAT1) especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease. The elite allele and the NIL with desirable agronomic traits identified in this study could be useful for rice breeding. Rice is the most important food crop in China. In rice breeding, seed shattering remains an important target trait for improvement (Konishi et al., 2006). Seed shattering habit causes yield loss during crops harvest (Zhou et al., 2012), while nonshattering also confounds those yields by hampering the harvest process (Ji et al., 2006). It is important to cultivate rice with an appropriate level of shattering in rice breeding programs (Subudhi et al., 2014). The identification of shattering genes and loci will positively impact rice breeding programs by transgenic and marker-assisted selection (MAS) approaches. Several shattering genes have been cloned in rice such as sh4 (Li et al., 2006; Lin et al., 2007), qSH1 (Konishi et al., 2006), OsCPL1 (Ji et al., 2010), SHAT1 (Zhou et al., 2012), and SH5 (Yoon et al., 2014). The sh4 encodes a transcription factor with a Myb3 DNA binding domain and promotes hydrolyzing of abscission zone cells during the abscission process (Li et al., 2006; Lin et al., 2007). The OsCPL1 encodes a carboxy-terminal domain phosphataselike protein, which represses development of the abscission zone (Ji et al., 2010). The SHAT1 gene encodes a transcription factor with an APETALA2 domain containing the gene and affects the abscission zone development (Zhou et al., 2012). These results indicated that seed shattering depends on development of an abscission zone. Published in Plant Genome Volume 9. doi: 10.3835/plantgenome2016.03.0034 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, PR China. † J. Cheng and Y. He contributed equally to this work. Received 30 Mar. 2016. Accepted 28 Aug. 2016. *Corresponding authors ([email protected]; [email protected]). Abbreviations: BTS, breaking tensile strength; cDNA, complementary DNA; CSSL, chromosome segment substitution line; DAH, days after heading; gf, grams force; MAS, marker-assisted selection; NIL, near isogenic line; ORF, open reading frame; PCR, polymerase chain reaction; QTL, quantitative trait loci; SSR, simple-sequence repeat. Published September 29, 2016