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Background  With an increasing world population and a gradual decline in the amount of arable land, food security remains a global challenge. Continued increases in rice yield will be required to break through the barriers to grain output. In order to transition from hybrid rice to super-hybrid rice, breeding demands cannot be addressed through traditional heterosis. Therefore, it is necessary to incorporate high yield loci from other rice genetic groups and to scientifically utilize intersubspecific heterosis in breeding lines. In this study, 781 lines from a segregating F 2  population constructed by crossing the  indica  variety, “Giant Spike Rice” R1128 as trait donor with the  japonica  cultivar ‘Nipponbare’, were re-sequenced using high-throughout multiplexed shotgun genotyping (MSG) technology. In combination with high-density single nucleotide polymorphisms, quantitative trait locus (QTL) mapping and genetic effect analysis were performed for five yield factors (spikelet number per panicle, primary branches per panicle, secondary branches per panicle, plant height, and panicle length) to explore the genetic mechanisms underlying the formation of the giant panicle of R1128. Also, they were preformed to locate new high-yielding rice genetic intervals, providing data for super-high-yielding rice breeding.    Results  QTL mapping and genetic effect analysis for five yield factors in the population gave the following results: 49 QTLs for the five yield factors were distributed on 11 of 12 chromosomes. The super-hybrid line R1128 carries multiple major genes for good traits, including  Sd1  for plant height,  Hd1  and  Ehd1  for heading date,  Gn1a  for spikelet number and  IPA1  for ideal plant shape. These genes accounted for 44.3%, 21.9%, 6.2%, 12.9% and 10.6% of the phenotypic variation in the individual traits. Six novel QTLs,  qph1-2, qph9-1, qpl12-1, qgn3-1, qgn11-1  and  qsbn11-1  are reported here for the first time.    Conclusions  High-throughout sequencing technology makes it convenient to study rice genomics and makes the QTL/gene mapping direct, efficient, and more reliable. The genetic regions discovered in this study will be valuable for breeding in rice varieties because of the diverse genetic backgrounds of the rice.    Electronic supplementary material  The online version of this article (doi:10.1186/1939-8433-6-21) contains supplementary material, which is available to authorized users.

Genetic analysis of an elite super-hybrid rice parent using high-density SNP markers