**4. Pleiotropic gene interactions during smaize domestication and improvement**

Pleiotropy generally describes the effect of an allele of a gene for producing an unrelated phenotype. It affects the path of evolution as it facilitates if a directional selection of a phenotype affects other beneficial phenotypes' fitness or restricts if the allele has the deleterious effect on another phenotype. Generally, the developmental traits reveal pleiotropy by explaining the association among flowering time in male and female flowers [47], ear and tassel developmental traits [48], leaf length and flower length [49]. Apart from these, QTLs responsible for tassel and ear development are also responsible for flowering time [50].

Understanding pleiotropy and the association between phenotypes will help to explain the selection outcome constraints. For example, the maize allele at *zfl2* is responsible for spiral ear phyllotaxy that increases the kernel number and is involved in other traits like early flowering [51]. So in a well-adapted environment stabilizing selection for flowering might limit directional selection for kernel number. Therefore such pleiotropy may limit domestication alleles when selection disallows variation.

Various researchers have reported that domestication alleles were pleiotropic [11, 12, 52, 53]. The *teosinte branched1 (tb1)* is pleiotropic across many traits; apical dominance, growth of leaves on the lateral branches, length of lateral branches, ear and root architecture [54]. *tb1*, as a transcription factor, binds to many locations in the genome. It directly regulates *gt1* by binding to its promoter. Still, it directly affects the cell cycle by suppressing many cell cycle genes (*proliferating cell nuclear antigen2 (pcna2)* and *minichromosome maintenance2/prolifera (mcm2/prl*) [20]. *zga1* is a MADS-box transcription factor associated with ear size and has a pleiotropic effect on flowering time [33]. *tga1*, a glume architecture allele shown to have pleiotropic effect on lateral branch lengthy, ear phyllotaxy and ear disarticulation [55].
