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

Abstract

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 (qSH1 JCQ , qSH3 JCQ , qSH6 JCQ , and qSH11 JCQ ) for shattering were detected, and the qSH1 JCQ was confirmed on chromosome 1. We further mapped qSH1 JCQ to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for qSH1 JCQ , which colocated with qSH1. Further quantitative realtime polymerase chain reaction (PCR) analyses confirmed that the QTL qSH1 JCQ 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.

Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq

“…The traditional QTL fine mapping and map-based cloning are limited by high-density genetic map and a series of near-isogenic lines. For example, based on conventional mapping methods, 8 years were required for a predecessor to isolate the major salt-tolerant gene, qSE3 (He et al 2019 ; Cheng et al 2016 ). QTL-seq uses a combination of BSA and next-generation sequencing technologies to rapidly identify the chromosome region harboring the genes/QTLs of interest.…”

A quantitative trait locus,qSE3, promotes seed germination and seedling establishment under salinity stress in rice

“…Japonica Jiucaiqing, indica IR26 and 62 CSSLs, developed by introgressing chromosome segments of Jiucaiqing into IR26 (Cheng et al ., ), were used for QTL mapping. A residual heterozygous line (CSSL19) that contained the QTL was used to produce BC 4 F 3 and BC 4 F 4 populations with one or two generations of selfing for fine mapping.…”

“…The mean values of GI and SP in the individual CSSLs were compared with those of the recurrent parent IR26 for QTL mapping. QTLs were assigned to the introgressed region when significant differences in GI and SP were observed in CSSLs (Cheng et al, 2016). Genomic DNA of seedlings from the BC 4 F 3 and BC 4 F 4 populations was extracted using the cetyltrimethylammonium bromide (CTAB) method to screen recombinants for fine mapping (Murray and Thompson, 1980).…”

OsHIPL1, a hedgehog‐interacting protein‐like 1 protein, increases seed vigour in rice

“…Japonica Jiucaiqing and indica IR26, and 62 CSSLs developed by introgressing chromosome segments of Jiucaiqing into IR26 (Cheng et al ., 2016, Tables S1 and S2), were used for QTL mapping. A residual heterozygous line CSSL10 (BC 6 F 2 ) and its selfing population were used for the confirmation of the major qSV3 .…”