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Will the genetic reasons majorly affect the child born to copule who married in a close relation?If so, how to avoid that?

Yes..you are right!Recurrent miscarriages, children with genetic disorders all happen due to such marriages..I hope ARTs(Assited Reproductive Technology) may help such people. Like getting surrogated moethers, test tube babies etc.

A genetic disorder is a disease that is caused by an abnormality in an individual's DNA. Abnormalities can range from a small mutation in a single gene to the addition or subtraction of an entire chromosome or set of chromosomes. This possibility is more among the individuals marry in close relations.

I've seen genetic counselors say that the possibility of genetic disorders among offspring of cousins is 2-2% higher than the general population.  Marrying your cousin is legal in many states, and is a norm in some cultures.  Albert Einstein's parents were cousins.  It seems that there is some risk involved, but that genetic counseling and modern technology might mitigate that (even though cousin marriage was well underway long before those modern possibilities). 

But your question didn't specify how close the close relation is.  Sibling marriage is one of the only taboos that all cultures hold, though the reason could be as much sociological as biological.  Most agree, however, that producing offspring with your sibling would result in genetic disorders.