| 2.2比较作图研究
在水稻和玉米中的研究发现，基因序列以及排列顺序在近源物种中是相对保守的，所以富含基因区的BAC探针在近源缘物种中具有较好的通用性[17, 43]。将这些BAC片段在近缘物种中进行杂交，比较杂交信号的分布，即比较作图技术，可以广泛应用于近缘物种染色体的共线性分析，以及结构变异，从而为研究染色体的进化提供了便利[1]。Lysak等人利用拟南芥染色体专一性探针，对近缘的多个芸薹属物种染色体进行杂交，通过比较这些探针在不同物种染色体上的分布，揭示了在这些物种进化历史上发生的一系列基因组加倍和染色体结构变异事件[8, 44]。
在茄属植物中，BAC-FISH首先被应用到了马铃薯6号染色体与其它茄属植物染色体的比较中[35, 45]。通过比较30个来自于马铃薯6号染色体的BAC杂交信号在西红柿6号染色体上的分布, 发现这些BAC片段在两个物种的6号染色体上是完全共线性分布的,但是异染色质的分布模式有很大的不同。同时通过比较杂交信号的排列顺序，还发现在6号染色体短臂的常染色质区存在一个倒位片段。该倒位片段是以前基于遗传图谱比较所没有发现的，这说明相对于传统的遗传学图谱，高密度的细胞遗传学图谱具有极强的检测染色体变异的能力。同样，利用BAC-FISH技术，通过比较比较马铃薯和西红柿的5号，也发现了同臂内的倒位[46]。Lou等人进一步将其中的13个BAC片段杂交到了茄属的其他物种中[47]。利用这些标记，他们对包括马铃薯、西红柿、茄子等在内的7个茄属物种的6号染色体结构进行了分析，研究了6号染色体在茄属植物中的进化。结果显示论文网，6号染色体在这些植物间具有相似的形态，近着丝粒的异染色质区在所有物种中都有发现。这13个克隆在Solanum caripense， S. melongea，马铃薯，以及另外两个野生马铃薯物种中是完全共线性分布的，并且定位在了非常相似的位置。但是在S. etuberosum 中发现了一个包含整个近着丝粒异染色质区在内的巨大倒位片段，分布于该区域的4个BAC片段的排列顺序与其余6个物种是完全颠倒的。通过临近区域其它几个BAC的位置，确定了导致该倒位的断裂点，位于两个BAC片段之间，该长度大约为6号染色体的1%。这是首次在茄属植物中发现染色体臂间倒位事件。该研究通过在不同物种中比较BAC-FISH作图的结果，还首次建立了一个茄属植物6号染色体的祖先核型。
由于棉花减数分裂粗线期染色体较难获得，并且大量的染色体进一步增加了高质量粗线期染色体制片的难度[48]。所以以前对棉属植物染色体的研究主要集中在有丝分裂或减数分裂的中期染色体上[41, 42, 49-52]。通过进一步改进染色体制备技术，利用高浓度长时间的果胶酶和热处理来分散细胞，Wang等人在棉花中制备出高质量的粗线期染色体制片，并成功应用到了棉花BAC-FISH的研究中，进一步提高了BAC-FISH在棉属植物染色体研究中的分辨率和灵敏度[53]。利用该技术，它们对棉属多倍体A和D基因组的12号染色体结构进行了研究[54]。32个被SSR标记定位到遗传图谱上BAC片段，通过原位杂交的方法成功定位到了12号染色体上。综合分析这些BAC片段的遗传距离和物理距离发现，大部分标记在A和D基因组的12号染色体上是共线性分布的，但是这两对染色体在基因组组成、结构和大小上有着明显的差别。这种差异在染色体上是不均匀分布的，在末端区域差异较小，差异最大的区域存在于长臂近着丝粒的区域。这种基因组的差异主要源于染色体在不同区域不均衡的扩张和收缩。这些结果对研究棉属多倍体基因组进化起了很好的指导作用，并为以后的全基因组测序奠定了基础。
BAC-FISH在其他植物比较作图中的研究包括，利用来自高粱9号染色体的32个BAC片段分别对高粱和玉米染色体进行杂交，结果发现几乎所有的标记在两个物种的基因组中都是共线性分布的，但是信号之间的相对位置有些差异，这说明玉米9号染色体的一些区域发生了不均等的扩张[55]。在葫芦科植物染色体比较作图中的研究论文网，首次发现了植物中的着丝粒重排现象[10]。该研究结果显示，葫芦科植物着丝粒的活性与其近着丝粒区域的异染色质紧密相关，着丝粒的激活与休眠都伴随着其附近区域异染色质的大量获得和丢失。比较染色体作图为我们提供了一条研究相关物种中染色体共线性、重排的新方法，该方法不依赖于作图群体，并且能揭示出染色体重排事件的物理特征，如异位、倒位等[35,44-45]。随着越来越多的BAC文库的建立，基于BAC-FISH的比较染色体作图研究将越来越广泛。
2.3功能基因定位
原位杂交技术对探针的长度具有一定的要求。虽然有报道成功检测到1-3kb的单拷贝片段，但是其结果往往很不稳定，甚至难以重复[9, 56-60]。用传统的原位杂交方法，单拷贝的基因片段很难观察到杂交信号。BAC中的插入片段较长，很容易与靶DNA结合，因此可以利用目的基因所在BAC片段，方便地将其定位到染色体上。从1995年，Jiang等人[27]运用BAC-FISH技术首次将Xa-21定位到染色体上以来，一系列的功能基因被成功地定位到了染色体上[42, 46, 61-68]。
在一些没有全基因组序列的物种中，利用BAC-FISH技术定位基因显得尤为重要。例如马铃薯的5号染色体上存在一个遗传上的热点地区，该区域存在一系列对不同病原体具有抗性的基因，通过遗传作图发现这些基因位于两个遗传作图标记间3 cM大小的区域，但是该区域在染色体上的位置及长度始终不清楚。为了精确定位该区域在染色体上的位置，研究人员从马铃薯的BAC库中，选择与该区域相关的5个BAC片段作为探针，对马铃薯和西红柿的5号染色体进行原位杂交。将该区域定位到了5号染色体长臂的中间区域，在两个物种中。同过测量信号间的距离，发现该区域的长度在马铃薯和茄子中分别为0.85和1.2 Mb[46]。利用BAC-FISH的方法，研究人员还将棉花的乙烯反应原件结合因子（ethyleneresponsive element-binding factor）定位到了A基因组的7号染色体上[42]。
将BAC-FISH与其他的细胞遗传学材料结合，例如DNA纤维[56]，机械伸展的染色体[9]论文网，能精确定位相邻的BAC片段在染色体上的排列顺序，从而进一步提高基因定位的精确度[66, 67, 69-74]。例如，Tomita等人利用5个BAC片段作为探针，结合Fiber-FISH技术，将抗烟草花叶病毒基因（tobamovirus resistance gene L3）定位到辣椒的11号染色体大约400kb的区域，同时发现这些BAC间的空白区域大约为30Kb[67]。
3 BAC-FISH技术的发展及展望
DNA测序技术的快速发展，使得植物全基因组测序成为可能。但是几乎所有现行的基因组测序技术都会留下一些未能测通的空白区域，BAC-FISH技术能对这些空白区域的大小及在染色体上的位置准确判断，从而为制定相应的补全策略提供指导[75, 76]。此外，对于一些特殊的基因组区域，FISH技术仍然是确定其序列，并在染色体上精确定位的唯一方法。例如，含有高度重复序列的着丝粒、端粒等区域，这些区域含有大量串联重复序列，很难被测通。以这些含有这些重复序列的BAC片段为探针，结合Fiber-FISH等技术能够帮助我们确定这些重复序列的拷贝和相对位置[9]。
传统的FISH技术只是把DNA序列定位到染色体上，但是许多生物学问题不能由这样的简单的定位信息来解释。将FISH技术与蛋白质免疫杂交相结合所产生的免疫-原位杂交技术，可以将特定的DNA片段与其相互作用的蛋白同时定位到染色体上，为我们提供更多的生物学信息[77-82]。这种技术已经被成功用与研究组蛋白修饰与特定的基因组区域的关系[77-79, 81]，以及着丝粒特异性蛋白与特定重复序列间的关系[80, 82, 83]。将免疫-原位杂交技术与染色体伸展技术相结合，还可以进一`步提高了DNA与蛋白相互作用研究的准确度以及精确性[71, 72, 84]。利用该技术，研究人员将小麦和拟南芥的染色体同时标记上组蛋白CENH3的抗体和着丝粒重复序列探针，从而揭示了着丝粒单元的排列顺序，以及它们与相关蛋白的相互关系[72, 84]。
由于原位杂交中信号的强弱与染色体的状态紧密相关，结构松散的染色体区域能够更好地与探针结合，从而产生强的信号；反之，染色体凝缩的区域与探针很难结合论文网，产生的信号就很弱。因此，杂交信号的强弱可以成为判断染色体状态的一项重要指标。这在研究染色体结构与基因表达、调控的关系中特别重要[85, 86]。最近，研究人员将BAC-FISH与三维空间的原位杂交技术相结合，研究了根表皮发育过程中，染色体结构与基因表达以及细胞分化的关系，结果显示在转录因子GL2附近区域染色体的状态与细胞的分化紧密相关[87]。
利用BAC-FISH技术，以特定染色体专一性的BAC片段为探针，还可以研究染色体的行为。研究人员对玉米B染色体在花粉有丝分裂中的行为进行了研究。利用B染色体专一性探针，对B染色体在不同细胞周期中位置和状态进行研究，结果显示在花粉细胞第一次有丝分裂时，B染色体的大多数能正常分离，但是在第二次有丝分裂时，大多数不能正常分离[88-91]。BAC-FISH技术的进一步发展为我们了解染色体的细微机构，以及染色体行为提供了一个强有力的手段。随着越来越多的基因组被测序，对于染色体结构和行为的研究将有助于我们更好地了解这些植物基因组的功能。
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