Epistasis plays an important role in manipulating rice tiller number, but epistatic mechanism still remains a challenge. Here we showed the process of epistatic analysis between tillering QTLs. A half diallel mating scheme was conducted based on 6 single segment substitution lines and 9 dual segment pyramiding lines to allow the analysis of 4 epistatic components. Additive-additive, additive-dominance, dominance-additive, and dominance-dominance epistatic effects were estimated at 9 stages of development via unconditional QTL analysis simultaneously. Unconditional QTL effect (QTL cumulative effect before a certain stage) was then divided into several conditional QTL components (QTL net effect in a certain time interval). The results indicated that epistatic interaction was prevalent, all QTL pairs harboring epistasis and one QTL always interacting with other QTLs in various component ways. Epistatic effects were dynamic, occurring mostly within 14d and 21–35d after transplant and exhibited mainly negative effects. The genetic and developmental mechanism on several tillering QTLs was further realized and perhaps was useful for molecular pyramiding breeding and heterosis utilization for improving plant architecture.

Background Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. Results We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. Conclusions Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.