how can one do the research with non-model plants,especially those without transgenesis, in an era of omics? It will be appreciated if you can list some famous labs or their papers.
The list of 'famous labs and their papers' can be very long.
You can do research even without using a model plant, transgenesis or OMICS. For example, using conventional breeding methods to increase the yield of carrots for example. In this case, you grow them out, doing 'selection' and inter-cross again between the better lines without really using OMICS or transgenesis. So, it all depends on the goals/topics of your researches and your plant species of interest.
See the pollination behavior of the crop you interested and follow breeding methods accordingly. Even you can genotype the genome of your crop using GBS to generate thousands of SNP for genomic study (attached literature).