Where does the spelling as the short e sound (such as bread) come from?
This goes back to Middle English, which seems to have had a vowel system something like this in the standard (London) dialect:
iː i u uː eː e o oː ɛː ɔː a
For the most part, these vowels were spelled pretty much like you'd expect from the IPA, with the "silent E" convention indicating length: bit had a short
/i/, for example, while bite had a long
But the English alphabet had no letters for the open-mid vowels! Since those were always long, in the Later Middle English/Early Modern English period, they started being written with digraphs ea and oa. So e_e or ee meant
/eː/, as in breed (sometimes written brede), and ea meant
/ɛː/, as in bread.
But then the Great Vowel Shift happened, and
/ɛː/ was affected irregularly, due to dialectal differences. While
/eː/ pretty much always became
/i/, for example,
/ɛː/ sometimes became
/ɛ/. There are some general rules for predicting this, but they're full of exceptions: it's usually only
/e/ next to
/r/, for example, as in bear, but not in fear, and it's usually only
/ɛ/ next to alveolar consonants, as in bread, but not in bean. Sometimes former homonyms are only distinguished by this, as in read (present) versus read (past), or lead (verb) versus lead (metal), and sometimes spelling has been intentionally changed to show the pronunciation change, as in red (color)…
All in all, it's a mess. But the short version is, it's spelled with two letters because it used to be a long vowel, once upon a time. The choice of the letters is, presumably, because it was halfway between
/a/, but that's just speculation.
P.S. With other vowels, the GVS was generally more regular: that's why oa is quite consistently
/o/, as in boat, boar, boast, etc.
/ɛː/ just had terrible luck. (And yet, broad…English orthography will always have exceptions somewhere.)