Top Muslim expert on the Qur'an wrote that manifold discriminations against non-Muslims are required by Qur'an 9:29's command to put non-Muslims in a state of subjection

Ibn Kathir's explanation of the Qur'an is likely the most widely used in the world.

Wrote Kathir:
Paying Jizyah [protection money paid by non-Muslims to Muslim overlords] is a Sign of Kufr [unbelief] and Disgrace

Allah said, [in Qur'an 9:29]
(until they pay the Jizyah), if they do not choose to embrace Islam, (with willing submission), in defeat and subservience, (and feel themselves subdued.), disgraced, humiliated and belittled.
Kathir, having thus paraphrased part of Qur'an 9:29, continues:
Therefore, Muslims are not allowed to honor the people of Dhimmah [non-Muslims forced to pay Muslim overlords in exchange for survival as second-class citizens] or elevate them above Muslims, for they [non-Muslims] are miserable, disgraced and humiliated. [Imam] Muslim [in his canonical hadith collection, Book 26, Number 5389] recorded from Abu Hurayrah that the Prophet said,
(Do not initiate the Salam [peace greeting] to the Jews and Christians, and if you meet any of them in a road, force them to its narrowest alley.)
Kathir, having quoted that hadith and Qur'an 9:29, then writes:
This is why the Leader of the faithful Umar bin Al-Khattab [a companion of Muhammad, Umar became the second caliph], may Allah be pleased with him, demanded his well-known conditions be met by the Christians, these conditions that ensured their continued humiliation, degradation and disgrace.
Then Kathir refers to the Pact of Umar, which shows how Umar, the second caliph, institutionalized Qur'an 9:29's demand that non-Muslims be put in a state of subjection. Kathir writes:
The scholars of Hadith narrated from Abdur-Rahman...that he [Abdur-Rahman] said,
I recorded for Umar [the second caliph], may Allah be pleased with him, the terms of the treaty of peace he conducted with the Christians of Ash-Sham [Ash-Sham Syria.  Muhammad died in 632, and Christian Syria was the first Islamic conquest (634-636) outside Arabia]: 
[Christians were compelled to sign this:] "In the Name of Allah, Most Gracious, Most Merciful. This is a document to the servant of Allah, Umar, the Leader of the faithful, from the Christians of such and such city. When you (Muslims) came to us [Christians] we requested safety for ourselves, children, property and followers of our religion. We made a condition on ourselves that we will neither erect in our areas a monastery, church, or a sanctuary for a monk, nor restore any place of worship that needs restoration nor use any of them for the purpose of enmity against Muslims. We will not prevent any Muslim from resting in our churches whether they come by day or night, and we will open the doors [of our houses of worship] for the wayfarer and passerby. Those Muslims who come as guests, will enjoy boarding and food for three days. We will not allow a spy against Muslims into our churches and homes or hide deceit [or betrayal] against Muslims. We will not teach our children the Qur'an, publicize practices of Shirk [Shirk means polytheism and worshiping anyone (including Jesus) that Muslims believe is not God], invite anyone to Shirk, or prevent any of our fellows from embracing Islam, if they choose to do so. We will respect Muslims, move from the places we sit in if they choose to sit in them. We will not imitate their clothing, caps, turbans, sandals, hairstyles, speech, nicknames and title names, or ride on saddles, hang swords on the shoulders, collect weapons of any kind or carry these weapons. We will not encrypt our stamps in Arabic, or sell liquor. We will have the front of our hair cut, wear our customary clothes wherever we are, wear belts around our waist, refrain from erecting crosses on the outside of our churches and demonstrating them and our books in public in Muslim fairways and markets. We will not sound the bells in our churches, except discretely, or raise our voices while reciting our holy books inside our churches in the presence of Muslims, nor raise our voices [with prayer] at our funerals, or light torches in funeral processions in the fairways of Muslims, or their markets. We will not bury our dead next to Muslim dead, or buy servants who were captured by Muslims. We will be guides for Muslims and refrain from breaching their privacy in their homes."
When I [Abdur-Rahman] gave this document to Umar [second caliph], he added to it,
"We will not beat any Muslim. These are the conditions that we [Christians] set against ourselves and followers of our religion in return for safety and protection. If we break any of these promises that we set for your benefit against ourselves, then our Dhimmah (promise of protection) is broken and you are allowed to do with us what you are allowed of people of defiance and rebellion."
Thus Qur'an 9:29, according to Ibn Kathir, who is arguably the most popular Qur'an interpreter of all time (except for Muhammad), requires what we in the United States would consider to be a sacralized form of apartheid or Jim Crow for non-Muslims. And many other Qur'an verses and canonical hadiths point in the same direction.

Islamic law, which treats non-Muslims as inferiors, is enforced to varying degrees in Muslim-majority nations, and sometimes hardly at all. Yet, as a regular stream of news stories shows, there is often what can be called an Islamic-law ethos operating even in nations where Islamic law itself is not formally enforced or present on the nation's lawbooks or constitution. I refer to a cultural sensibility that, nourished by Islamic core texts and traditions, instinctively treats non-Muslims as lesser human beings, takes advantage of them, abuses them, and prevents them from having any legal recourse against Muslim predators, since those in Muslim governments sometimes refuse to prosecute Muslim predation on non-Muslims, and police forces sometimes serve to aid and abet the predation. This happens to varying degrees in a sufficient number of Muslim-majority nations to be a grave concern to the rest of the world. And too many of the Muslims who immigrate to the West bring the Islamic-law ethos along with them.