根癌农杆菌引起植物冠瘿病。通常这种疾病的特征是在受感染的植物上，在根和茎的交界处，有瘤状的增生物或冠瘿瘤。植物冠瘿瘤是由细菌肿瘤诱导质粒（Ti）中的一个DNA片段（T-DNA）的结合转移引起的。与根癌农杆菌相近的物种发根农杆菌也能诱导冠瘿瘤，并携带独特的Ri(根诱导)质粒。尽管农杆菌的分类学目前仍在修订完善，但在该属中大致存在3个生物变种，即根癌农杆菌、发根农杆菌和葡萄农杆菌。已知根癌农杆菌和发根农杆菌中的菌株能够携带Ti质粒或Ri质粒，而葡萄农杆菌菌株(通常限于葡萄树)能够携带Ti质粒。实验室研究表明从环境样品分离得到的非农杆菌菌株也可以含有Ti质粒，并且这些非农杆菌菌株同样含有Ri质粒。一些环境土壤杆菌既没有Ti质粒也没有Ri质粒，这些菌株则是无毒的。[6]
质粒T-DNA被半随机地整合到宿主细胞基因组中，[7] 并且在T-DNA的导致冠瘿瘤形成的基因表达，导致冠瘿瘤的形成。T-DNA携带用于产生非常见氨基酸的生物合成酶的基因，比如说常用的章鱼碱或胭脂碱。它还携带植物激素、生长素和细胞分裂素的生物合成基因，以及冠瘿碱的生物合成基因，为大多数其他微生物不能使用的细菌提供碳源和氮源，使农杆菌具有相对生长优势。[8] 通过改变植物细胞中的激素平衡，这些细胞的分裂不受植物控制，进一步导致冠瘿瘤形成。冠瘿瘤基因产生的生长素和细胞分裂素的比例决定了冠瘿瘤的形态(根状、无特定形状或芽状)。
我们将农杆菌能够将基因转移到植物和真菌的能力应用于生物技术方面，特别是用于植物改良基因工程方面。可以使用改造的Ti或Ri质粒来实现。质粒通过冠瘿瘤诱导基因的缺失能够消除其毒性；T-DNA的必须部分是它的两个小的(25个碱基对)边界重复序列，其中至少有一个是植物转化所必需的。 将导入植物的基因克隆到植物转化载体中，该载体包含去除毒性基因质粒的T-DNA区域，以及筛选标记(如抗生素抗性标记)，从而能够选择转化成功的阳性植物。转化后植物生长在含有抗生素的培养基上，那些T-DNA没有整合到基因组中的的植物将会死亡。另一种方法是农杆菌渗入法。[13][14]
利用农杆菌介导的转化可以通过多种方式实现。原生质体或叶盘可以与农杆菌一起培养实现转化，整个植物的转化可以用植物组织培养技术进而进行转基因植物的构建。农杆菌渗入法则是将农杆菌可以直接注射到植物的叶片组织中。该方法仅转化与农杆菌直接接触的细胞，并导致质粒DNA片段的瞬时表达。[15]
农杆菌渗入法通常用于转化烟草(本氏烟草).。拟南芥的一种常见转化方法是浸花法:[16] 将花序浸在农杆菌悬浮液中，农杆菌可以转化产生雌配子的生殖细胞。然后可以对种子进行抗生素抗性筛选(或另一种需要的标记)，基因组中没有整合质粒DNA的植物在生长在相应抗生素条件下会死亡。[13]
农杆菌不会感染所有的植物物种，但是还可以利用基因枪等几种有效的植物转化技术。
农杆菌介导的遗传转化已经美国GMOs用在一下物种的的遗传转化中:[17]
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