The seeds are planted. You have watered the plant, given it enough access to sun, made sure the soil is aerated enough for roots to healthily develop, kept the pH perfect throughout the whole growth, and carefully managed the perfect amount of N/P/K/Ca/Fe/Mg. You have kept the nibbling critters away, made sure no pests have made a feast of its leaves, and grown it fungi and disease free. It's time for harvest! ...And it is a really disappointing harvest.

But What Went Wrong?

In Gardener, the plants are simulated as part of a complete ecosystem. There are many factors that can cause stress, stunting, or slowing your plant's growth. But even a perfect specimen grown in perfect conditions can result in a vastly different plant, depending on a technique known as plant training. Plant training is a crucial process that can turn your mediocre species into a blooming bush full of fruits, or elevate the rare and best plants to even higher levels. And it's really simple once you understand a plant's structure.
Let's look at our simple example tree. With just one branch, our apple tree produces only one apple per season. And it took us a season to get to this point. But don't worry, with proper training, we can improve the yield. We just need to cause the plant to branch out more; grow sideways - instead of up.
To do it, clip the very top of the plant branch, the part of it that is currently growing. Make sure you are cutting a growing branch - cutting it below current growth will just trim the branch, and avoid cutting it too close to its original node, always leaving at least single node in branch intact. If you succeed, the node will branch out into two new nodes, instead of growing up. You can then repeat the process for new nodes, creating four more, etc. This way you can not only shape the plant but also increase its produce. Be aware though - the largest fruits are always growing on the highest branches, and trained branches will produce smaller fruit by volume. Training a plant also causes temporary stress that slows down the growth for a couple of days.

I Missed The Training Window, Now What?

If you accidentally trim the wrong branch or simply forgot about training - don't worry. For annuals - you can always try again, and with perennials, just wait until the plant is between seasons. Once all leaves have fallen, you can trim any branch you want, and once the growth starts again, you will see little branches spurring out from cut nodes. It's also the best moment to train the plant if you want to avoid training stress. In Gardener Plant Creator, all plants are simulated in artificially perfect conditions - an unlikely situation in normal gameplay, but you can experiment with training by clicking on the node you want to cut and simulating the growth by enabling timelapse mode. Remember that training the plant in Plant Creator doesn't affect the plant template in any way, and the created plant design is otherwise always simulated as completely untrained. https://store.steampowered.com/app/2813710/Gardener_Plant_Creator/