Identification and Pyramid of QTLs Based on Rice Short-wide Grain CSSL-Z414, SSSL, DSSL and Candidate Gene Analysis of qGL11 and qGW5

BackgroundMost of rice agronomic traits as grain length etc. are complex traits controlled by multiple genes. Chromosome segment substitution lines (CSSLs) are ideal materials for dissecting and studying of these complex traits. ResultsA rice short-wide grain CSSL Z414 was identified among progeny of the recipient parent Xihui 18 (an indica restorer line) and the donor parent Huhan 3 (a japonica cultivar). Z414 carried 4 substitution segments (average length was 3.04 Mb), and displayed shorter panicle length and less number of primary branches, shorter, wider and larger grain, higher brown rice rate and chalkiness degree when compared with Xihui 18. Then, 9 quantitative trait loci (QTLs) for associated traits were identified using the secondary F2 population from Xihui 18 / Z414. Among them, 6 QTLs (qPL3, qGW5, qGL11, qRLW5, qRLW11, qGWT5) could be verified by corresponding single segment substitution lines (SSSLs, S1-S6). In addition, 4 QTLs (qGL3, qGL5, qCD3 and qCD5) were detected by S1 and S5, which was not detected by the F2 population. Thus, the grain length of Z414 was controlled by qGL11, qGL3 and qGL5, and the grain width of Z414 was answered by qGW5. Then by substitution mapping, qGL11 and qGW5 were delimited within the estimated substitution length of 1.42 and 1.14 Mb on chromosomes 11 and 5, and 4 and 2 candidate genes were found respectively for qGL11 and qGW5 by sequencing. However, only two had expression differences by qRT-PCR analysis. Finally, Analysis of QTL epistatic effects revealed that pyramid of qGL3 (a= 0.22) and qGL11 (a=-0.19) caused grain length of double segment substitution line (DSSL, D2) shorter than that of S5 (qGL11).ConclusionsWe developed a rice short –wide grain CSSL with 4 substitution segments from Huhan 3 based on the genetic backgrounds of Xihui 18. The grain width of Z414 was controlled by qGW5, and GS5 should be the candidate gene for qGW5 by sequencing and qRT-PCR analysis. The grain length of Z414 was controlled by qGL11, qGL3, and qGL5, and CycT1;3 should be the best candidate gene of qGL11, whose specific function of regulating grain length was still unknown, and qGL11 is epistatic to qGL3.