Final answer:
The allele for short pea plants is present but masked by the dominant tall allele in the F1 generation, resulting in tall plants. The recessive short trait can reappear in the F2 generation due to genetic segregation and recombination.
Step-by-step explanation:
The phenotype of pea plants in the F1 generation is typically uniform when one parent is homozygous dominant and the other parent is homozygous recessive for a particular trait. In the case of the height trait, tallness is dominant over shortness. When a true-breeding tall pea plant (TT) is crossed with a true-breeding short pea plant (tt), all the F1 offspring will have the genotype Tt (heterozygous) and will display the tall phenotype. This is because the tall allele (T) is dominant over the short allele (t).
The answer to the student's question about what happens to the phenotype of short pea plants in the F1 generation is: b) The allele for short pea plants is masked during the F1 generation, but it is still present in the genotype. This is due to the presence of the dominant tall allele which masks the effect of the recessive short allele. In the subsequent F2 generation, the recessive short trait can reappear in the phenotype due to segregation and recombination of alleles during gamete formation and fertilization.