Development of Secondary SSSLs and Analysis of QTL for Grain Size as well as Fine-mapping of qGL3.4 Based on a Rice CSSL-Z668

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Abstract Background Grain size is an important factor affecting yield, appearance and processing quality of rice. Therefore, it is of great significance to explore genes controlling grain size in rice. However, its genetic mechanisms are complex and belong to quantitative inheritance controlled by polygenes with minor effects. Chromosome segment substitution lines are ideal materials for natural variation creation, QTL dissection, functional analysis and pyramid breeding of favorable alleles. Results Z668 was identified containing 8 substitution segments from indica restorer line R225 in the genetic background of Nipponbare. Its average substitution length was 3.63 Mb. Compared with Nipponbare, Z668 plants exhibited significant dwarf, and the grain length, ratio of length to width and 1000-grain weight of Z668 was increased by 39.9%, 31% and 25.9%, respectively, and grain width of Z668 was decreased by 3.3%. Then, a total of 7 QTLs for grain size were identified from F2 populations derived from Nipponbare/Z668, including 3 for grain length (qGL3.4, qGL12-1, qGL12-2), 3 for ratio of length to width (qRLW3.4, qRLW12-1, qRLW12-2), and 1 for 1000-grain weight (qGWT7), which were found distributing on chromosomes 3, 7 and 12. Finally, 5 single segment substitution lines were developed and 13 QTLs (qGL1, qGL6, qGL7, qGL12-2, qGW7-1, qGW7-2, qRLW1, qRLW6, qRLW7-1, qRLW7-2, qRLW12-2, qGWT6 and qGWT7) were detected by them. Among them qGL1, qGL3.4, qGL12-1 and qGL12-2 might be new QTLs identified in the study, In addition, qGL3.4 controlling long grain displayed dominant inheritance by analysis of frequency distribution in F3 population developed by recombinant plants of single qGL3.4 locus and Chi-square test. And qGL3.4 was then fine mapped into the 300 kb region between SSR3 and SSR4 on chromosome 3 by 142 recessive plants with short-grains and 5 polymorphic SSR markers designed in the substitution interval RM5864 and RM5626 where qGL3.4 was located. By gene prediction, 7 genes were found to be associated with grain size. And through DNA amplification and sequencing as well as qRT-PCR analysis, the candidate1 and 3 were considered as preferred candidate genes for qGL3.4.