the Ca may have induced Mg deficiency, but there are a lot more things to speculate on, better provide more detailed information!

Vertisol was used,>1600 ppm Mg,29 ppm Na and >2500 ppm Ca  in the soil. The irrigation water was made up of sulphate salts ( saturated gypsum solution, 170ppm Mg, >40 ppm Na, 12 ppm Mn, pH  6.5, EC 302mS/m)

Could it be due to K insufficiency  in soil and water? What are the concentrations of K in soil and water?

Annangi's suggestion is a good one. Soil K status would be useful, Good to keep in mind the fact that vertisols  in South Africa often release considerable amounts of K on air drying prior to analysis mat and appreciably more if heat is used.. Leaf analyses might prove useful.

The soil had 115 ppm and the water 15 ppm potassium, I added 13 ppm potassium in the form of KCl

Please confirm whether it is Vertisols or any other soil .Also mention the extratant used to estimate the soil available K status.As I understand your water soluble K includes the added K.

Some of the micro nutrients are available in b/w ph 4-5 moles/litre.

As N,P and K are available with ph 6-7.5 moles/litre.which are mainly used to increase the yield.so when you apply gypsum in soil, the ph of soil will increase ,which cause unavailabe of some micro nutrient and due to high ph primary nutrients also.so better you apply some amount lime and better you will go through fym application.so that you will get a healthy soil and optimum yield

addition of gypsum increases the soil ph which decreases the micronutrients availability and hence the grain yield decreses

Please consider the tripartite relation between Ca, Mg and K , addition of gypsum tilts Ca plus Mg concentration more to cause K-deficiency... 

Due to  gypsum increases the soil ph which decreases the micronutrients availability and  K insufficiency in soil 

These issues are always soil specific to some extent. However, gypsum is a neutral salt and in our experience, application rates as high as 16 t/ha have not significantly increased topsoil pH levels. Theoretically, the salt effect should actually have lowered the pH, but in the soil we worked with this was not the case,

The initial pH of the soil is 6.25-6.5.The soil may not need lime application. I could not understand the reason behind application of gypsum through irrigation water.Is it to create salinity in the soil or study the effect of saline water on crop and soil ?what is the EC of irrigation water applied to maize?

I am aghast to read the question and understand or imagine the need for gypsum application to a near neutral soil that too for maize crop. I am enlightened to the fact that basic principles of soil science developed over a century is yet to spread the worldover. Dear Mr. Lesogo Madiseng, Please provide the details to justify the need or background to apply gypsum to a near neutral soil to grow maize, before expecting the remedy to successfully grow maize. I thank Dr. A. Subba Rao for his valid queries. 

• The addition of gypsum [ CaSO4] to a neutral soil will increase thesoil pH  and continuous use make the pH greater than 8.5 to become saline.This will make uptake of soil P difficult and the maize plants will loose their cell sap to saline soil condition to obey osmosis law and the yields will reduce drastically

Gypsum application to a neutral soil will not increase the soil pH as gypsum is a neutral salt. Salinity and Sodicity are distinct in soils in that salinity reflects increase in concentration of water soluble salts while sodicity results due to the presence of sodium as sodium carbonate usually which reduces the permeability of soils to absorb water freely, thereby creating impeded drainage. 

Endorsing the good comments from Dr Reddy , let us also consider the gypsum solubility which is hardly 0.20-0.25%, thereby , disqualifying any potential possibility of soil pH  getting changed so drastic , unless soil is infested with sodicity ...  

Thank you very much Dr. Srivastava for your apt and timely addition of a very important point which I missed to mention. 

Usually gypsum is used in reclamation of sodic soil conditions. The Calcium competes with sodium reducing its problems. If you are in a situation where Calcium competes with Magnesium maize can form a Magnesium deficient condition which can occur in maize usually under low soil Magnesium conditions found in sandy acid soil.. My recommendation is to do a complete tissue analysis on your maize from at least 25 leaves at a stated stage and then share these results which will be compared to optimized levels this can be powerful for finding both toxicities and deficiencies and would suggest a remediation by inputs that would supplement a deficiency or remove a toxicity. 

In relation to Calcium when soil is acid liming is recommended when soils are neutral to alkaline lime can make a situation worse engendering Carbonate induced Zinc deficiency in maize. Calcium sulfate will not change the soil pH but lime will so there is care to be taken. While not affecting the pH gypsum will enrich with both Calcium and Sulfate and Calcium will compete with cations and Sulfate with anions this could affect crop nutrition availability and the health and yield of the crop. 

endorsing some good points raised by Dr Hepperly , please also look at the chemical analysis of irrigation water , especially cationic composition to ensure any possible imbalance  between Ca, Mg and K . Have you observed any visual symptoms of any nutrient deficiency..?