What do the seeds that Isabel hides in the hem of her dress mean?

The seeds are very personal to Isabel, because they come from her mother's jar. Hiding them in her dress is a way of protecting them from the harsh conditions of the outside world. Isabel feels a profound sense of duty toward looking after the seeds—making sure that one day, like her, they will grow to their fullest extent.
That's why she's so mad at herself for letting the plants grown from the seeds die of cold. In failing to look after them properly, Isabel believes that she's let her mother down. She already blames herself for the way Ruth was taken and sold. If only she hadn't fallen asleep that night, she tells herself, then maybe it wouldn't have happened. As with her little sister, so with the plants; Isabel blames herself for the damage done to something precious bequeathed to her by her mother.

The seeds are a symbol of Isabel's mother. In the story, Isabel and Ruth receive a unfortunate surprise after their owner, Miss Mary Finch, dies. Instead of the freedom the girls envisioned, they are sold to Robert, Miss Finch's nephew (her only surviving relative).
As for Robert, he plans to sell Ruth and Isabel once they get to Newport. Before they leave, Robert takes the girls back to Miss Finch's home to collect their blankets and shoes. Isabel tells us that she is not permitted to take the bowl her father made her, her mother's shells, or Ruth's baby doll. Apparently, nothing in the house belongs to them. At least, this is the way Robert acts.
So, Isabel secretly takes some flower seeds from her mother's jar. Isabel's mother never had the opportunity to plant those seeds before her death. To Isabel, these seeds are the only link to her mother and her past life on the plantation.