OK so these suggestions are from my personal experiences of amplifying a 13kb sequence from more than 10 years ago so there maybe better options. If you can afford to change your Taq then in my opinion the HiFi Taq from Takara (now Clontech) or the Expand Long PCR system from Roche work the best. If you want to go oldschool then try different concentrations of DMSO or glycerol in your PCR mix. Higher concentrations of glycerol may inhibit the enzyme so be careful there. If the Tm of your primers are a possible issue then different concentrations of Formamide and Formaldehyde can also help. You may end up with a smear on your gel, don't be disappointed by that because if the amplified smear covers your desired length then you may have your product in there. Just  excise the DNA corresponding to the 4kb area, extract your DNA and use it for the PCR. Ultimately, you can use the nested primer design if nothing else works it will be a little more work but you will definitely get the work done.

1. What are the Tm for both primers, and Ta (annealing temperature) you set up?

2. What is the 'extension time' you used in PCR?

3. Make sure the purity of your plant gDNA is good enough for PCR. Such as no PCR inhibitors in your DNA samples.

Tm Fw- 59.5, Rv-65.7.

Annealing and extension time according to Takara Prime STAR protocol link underneath

http://www.clontech.com/IN/Products/PCR/High_Fidelity_PCR/ibcGetAttachment.jsp?cItemId=47406&fileId=6108558&sitex=10060:22372:US

I would suggest you to design the primers to isolate your gene in four fragments i mean design the primers for the for 1 kb first then next 1kb likewise and then join the fragments to get full 4kb.

check the image for better understanding

Yes, PCR them into fragments and then assemble them together or using Gibson Assemble is one way to go, but with today's powerful PCR kit, under optimum conditions, 4-kb amplicon should be possible to be amplified.

I am still wondering what were the annealing time and extension time you set. You said, "Annealing and extension time according to Takara Prime STAR protocol." I know, you should follow the 'principles' suggested by the protocol to set your 'time'. But, what was the exact time you used in your PCR conditions? So, we can diagnose the problem.

I was also facing the same problem with one of the genes of  size 4 kb, HF pol. generally do not have terminal transferase activity so you have add A overhang with normal Taq after gel elution of the HF product. But splitting the gene into 2-3 fragments and cloning indivisually and subsequent ligation  will make your job easier, I guess

@Nitesh,

Then, you can simply use Gibson assembly method to finish it. You can amplify 2-3 fragments of a gene with overlapped ends, then use Gibson assembly mix to assemble them together, without ligations. See attached figure.

@ Yuan

I used annealing temp 55oC time 1 min, extension temp 72oC time 4 min