Hi Nivedita. Following up Maxim's answer, if you find negative variance it means the variance is 0 (computational issues might produce a negative value). And if there is no variance all your samples have the same value, so you can't estimate correlations.

Hope it helps

Pablo

Dear Nivedita Shettigar In principle, variance cannot be negative. However, we may observe 'negative' components of phenotypic variance due to uncontrollable experimental error. Under such a situation, the most reasonable value of negative estimates is taken as zero. Because of such an error, you may find the value of genotypic correlation exceeding one in either direction.

Best regards, AKC

when we analyze genotypic variance from ANOVA the value will be negative because the variation of that trait influenced by environmental factor than genetic that mean error mean square is higher than genotypic mean square and we can write zero value rather than negative.