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Background  Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits.    Results  A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F 2  population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL  qPL7  might be an allele of  OsFAD8  and the remaining 14 QTLs (e.g.,  qSSD5  and  qSSD10  etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL ( qSSD10 ) and two minor QTLs ( qSSD5  and  qSSD8 ). The QTLs  qSSD10 ,  qSSD5 , and  qSSD8  were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that  qSSD5 ,  qSSD8 , and  qSSD10  from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of  qSSD5  and  qSSD8 ,  qSSD5  and  qSSD10 ,  qSSD8  and  qSSD10 , and  qSSD5 ,  qSSD8  and  qSSD10  produced novel genotypes with increased seed-set density.    Conclusions  Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL ( qSSD10 ) and two minor QTLs ( qSSD5  and  qSSD8 ). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes ( OsMPK9  and  OsMPK17 ) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for  qSSD5 , and  OsSAUR32  might be the candidate gene for  qSSD8.  Pyramiding of  qSSD5 ,  qSSD8 , and  qSSD10  enhanced seed-set density.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12284-021-00496-7.

rice

Identification, pyramid and candidate genes of QTLs for associated traits based on a dense erect panicle rice CSSL-Z749 and five SSSLs, three DSSLs and one TSSL