What is the source DNA for the body of Jesus?

Your question assumes that Jesus the man was one singular identity in a human body. This seems to be in error according to what I can determine from the Bible.

Jesus was fully human, and by that we must deduce that he had the same DNA as any other human being,that is 50% human female and 50% human male The 50% human female would have come from the egg provided by Mary, and the 50% male contributed through the Holy Spirit which is one third of the trinity which in turn means contributed by God, as is spelled out in the part about the Holy Spirit coming upon Mary in the Scriptures. Otherwise how could he be tempted in every way as every other human is tempted:

All Scripture is quoted from the King James translation, unless otherwise noted.

Matthew 4:1 Then was Jesus led up of the Spirit into the wilderness to be tempted of the devil.

Mark 1:13 And he was there in the wilderness forty days, tempted of Satan; and was with the wild beasts; and the angels ministered unto him.

Luke 4:2 Being forty days tempted of the devil. And in those days he did eat nothing: and when they were ended, he afterward hungered.

Jesus was also fully God, and here is where most misunderstanding about the dual personage of Jesus comes from:

The Deity of Jesus is a Spirit and being a Spirit has no material aspects, and therefore is able to inhabit the human body of Jesus just as these other Spirits inhabited another human being.

Mark 5:2 through 9 And when he was come out of the ship, immediately there met him out of the tombs a man with an unclean spirit, Who had his dwelling among the tombs; and no man could bind him, no, not with chains: Because that he had been often bound with fetters and chains, and the chains had been plucked asunder by him, and the fetters broken in pieces: neither could any man tame him. And always, night and day, he was in the mountains, and in the tombs, crying, and cutting himself with stones. But when he saw Jesus afar off, he ran and worshipped him, And cried with a loud voice, and said, What have I to do with thee, Jesus, thou Son of the most high God? I adjure thee by God, that thou torment me not. For he said unto him, Come out of the man, thou unclean spirit. And he asked him, What is thy name? And he answered, saying, My name is Legion: for we are many.

From this passage we learn that Jesus had the authority to order these many Spirits to vacate the man's body, and that shows that his Spirit was of God.

This was not the man Jesus ordering them to leave it was the Deity Jesus.

Jesus the man was just like any other man as far as physical nature goes, he got hungry just as we do, and felt the heat of day and cool of night. and all the sensations we feel, and yet the Spirit within him prevented him from succumbing to temptation.

That same Spirit can inhabit our bodies today when we accept Christ as our Savior, however our human body has already experienced sin and will always be tempted by the cloak of desirability Satan uses to blind us to the true nature of sin.

Divine Conception

The answer to your question is relatively simple. Mary provided the egg; God provided the sperm. This may sound shocking, and there is no single verse which "proves" my assertion, but there are many scriptures--particularly Romans chapter 5--which clearly lay out for us the reason why Christ was conceived and born with a sinless human nature. (The "God" part of His being is the reason why. Simply put, God cannot sin, nor can He even be tempted to sin. James 1:13)

Why do I link a "sinless nature" with the DNA of both the God-created part and the Mary-donated part? Let's look in detail at Romans 5:

". . . through one man sin entered into the world, and death through sin . . . [D]eath reigned from Adam to Moses, even over those who had not sinned in the likeness of Adam's offense, who is a type of Him who was to come [viz., Jesus]. . .. [If B]y the transgression of the one, death reigned through the one, much more those who receive the abundance of grace and of the gift of righteousness will reign in life through the One, Jesus Christ. So then as through one transgression there resulted justification of life to all men. For as through the one man's disobedience the many were made sinners, even so through the obedience of the One the many will be made righteous" (vv.12-19, excerpts NASB Updated).

The Argument and Proof of Divine Conception

Notice how Paul lays out his "case" for how the justification provided by God through Christ works in a "legal" sense. Through the use of rhetorical techniques and simple logic Paul lays the foundation for his assertions in Romans 5. Notice in the above verses and elsewhere in the chapter Paul repeats the words much more (vv.9, 10, 15, 17). These words indicate his use of the a fortiori argument, which has been defined as follows:

"An a fortiori argument /ˈɑː fɔːrtɪˈoʊriː/1 is an "argument from a yet stronger reason." For example, if it has been established that a person is dead (the stronger reason), then one can with equal or greater certainty argue that the person is not breathing. "Being dead" trumps other arguments that might be made to show that the person is not breathing, such as for instance, not seeing any sign of breathing.

"An a fortiori argument draws upon existing confidence in a proposition to argue in favor of a second proposition that is held to be implicit in the first. The second proposition may be considered "weaker," and therefore the arguer adduces a "stronger" proposition to support it" [my emphasis].

The proposition of which Paul speaks is that of representation. Adam represents one thing; Christ represents another thing. Whereas Adam represents humankind in general, Christ represents God. Now if the weaker proposition is true (viz., death reigned in humanity from Adam, onward, because of his one sin), then the stronger proposition ("the gift of righteousness will reign in life through the One, Jesus Christ," v.17) is even truer.

Paul, then, as a master lawyer arguing his case, wraps up this section of his forensic oratory in vv.18-21 with several "so" statements. In other words (using a little sanctified imagination):

"So we can see, your honor and honorable members of the jury, that I have proved this part of my case beyond a reasonable doubt."

Representational Theology

Representational theology is at the heart of the answer to your DNA question.

Adam represents humanity in his disobedience, sin, and spiritual and physical death.

Jesus Christ represents humanity in His obedience, sinlessness, and spiritual and physical life.

Adam's "contribution," his "gift" (notice the implied sarcasm in Paul's use of the word) to humanity is sin and death. (Thanks a lot, Adam!). Literally, then, Adam's DNA, as it were, is the agency of successive, generational sin up the to present day and beyond. That "Y chromosome" you refer to is tainted, as it were, by sin. Is this literally so? I do not claim to have an answer to that question. Theologically, however, it is so.

Jesus' contribution, His gift to humanity is righteousness, life, and justification. Literally, then, Jesus' DNA, which originated in God, has the power to pass on to all those who believe in and receive Him, those three gifts, and more!

The "sperm" donated by a holy God to the process of fertilization and conception, and the miraculous creation of a sinless embryo, was impeccable--without sin, sinless--in contrast to a mere man's contribution to fertilization and conception, which is peccable. King David put it this way:

"Behold, I was brought forth in iniquity,

And in sin my mother conceived me" (Psalm 51:5)

Then prophetically--and certainly unbeknownst to him, speaking of his Savior to come he said,

"Behold, You desire truth

in the innermost being

And in the hidden part

You will make me know wisdom" (v.6).

Christ, the Believers' Representative

Whereas David was speaking on one level in this verse about God's desire for all of us to be truthful with Him whenever we sin, and not to attempt to cover up our sin or pretend it does not exist (David, you will recall, committed adultery and murder-by-proxy), David was also speaking on another level about the One who was to come, the One who would one day say,

"I am the truth" (John 14:6)

Moreover, in His relation to all believers in Him--

"to those who are the called, both Jews and Greeks, Christ [has become] the power of God and the wisdom of God" (1 Corinthians 1:24 NAS). Many evangelical Protestant churches affirm not only the truth, who is Christ, but they often quote John 1:14, which is source of comfort to all Christians:

"And the Word became flesh and dwelt among us, and we saw His glory, glory as of the only begotten from the Father, full of grace and truth" (my emphasis)

I highlight the word grace because Jesus, in a sense, did not lead with truth, but grace. The truth is, we're all messed up because of sin. The good news is, He is gracious in looking beyond our fault and seeing our need. Ah, the simplicity and power of the gospel!

Conclusion

In conclusion, the theological concept of representation is a powerful argument which really provides a satisfying answer, I believe, to the heart of your question. Christ's DNA was impeccable. Would it look the same under a microscope as the DNA of any other representative of the human race. Yes. Was it the same DNA? No. It was the DNA of the God-Man, whose life, death, and resurrection became the basis for our justification before a holy God.

My first posting as an answer. (Pardon my english mistakes if any)

The short answer is obviously 3 (except the Mary's part).

Let's think about the Wine Miracle where water turns into wine to get some idea of characteristics of an miracle. The wine is obviously really wine although we don't know whether it is zinfandel or cabernet souvignon nor the age of it (3 years maybe?). Although the wine wasn't fermented from real grape juice that came from real grape trees with history of sunshine and raining, it was real wine in every physical aspect.

Jesus was fully humane and fully divine. So, from physical observance, Jesus must be a real human though the conception process had a jump between a non-miraculous process and another non-miraculous process during the conception.

The question may be the exact point of miracle whether it was the seed(no bad intention) or a fetus appearing Mary's womb. Then, it may be helpful to understand what they thought about birth process at the time and until about 17th century. Up util 17th century, people believed that the essence of a baby comes only from its father, none from mother's side. Figuratively, the seed and the soil. I am quite sure people reading the bible up until that time could imagine The Holy Spirit overshadowing Mary easily and agreed that Jesus is 100% from the Father. But now in 21st century, we know that half essence comes from its mother's side so that the imagination part becomes difficult (with the idea of 100% from the Father) or we need to image a fetus suddenly appearing in Mary's womb.

I think it is also possible to explain the Trinity even after accepting the half of Jesus came from Mary but this wasn't what the two apostles writing about the birth of Jesus thought about.

Anyway, we now need to imagine a bit different (the fetus) from what they imagined at the time or before 17th century (the seed) if we want to keep the intention of the apostles. Either way is miraculous.

Jesus is fully humane and fully divine. So, I am sure that it is the choice 3. But we don't know whether half of it is Mary's or what the other half looks like because of the same reason that we don't know whether the wine is of zinfandel or of cabernet souvignon. Its miraculous jump is impossible to figure out precisely. Just taking the whole as a miracle may be reasonably good enough as in the case of the Wine.

An article about Davinci's drawing surprisingly explains very well about people's thought on conception. An article (pdf)