Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes.
Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes.
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拟南芥抗病基因重组率异质性
DOI：
10.1371/journal.pgen.1006179
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发表时间：
2016-07
期刊：
影响因子：
4.5
通讯作者：
Henderson IR
中科院分区：
文献类型：
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作者：
Choi K;Reinhard C;Serra H;Ziolkowski PA;Underwood CJ;Zhao X;Hardcastle TJ;Yelina NE;Griffin C;Jackson M;Mézard C;McVean G;Copenhaver GP;Henderson IR
减数分裂交叉频率在染色体上变化很大，通常集中在热点区域。随着重组增加遗传多样性，预计免疫基因将出现热点，其中变异可能是有益的。植物免疫的一个主要组成部分是编码NBS-LRR结构域蛋白的抗性(R)基因对病原无毒(AVR)效应的识别。因此，我们试图利用实验遗传学来测试NBS-LRR基因是否会与减数分裂交叉热点重叠。NBS-LRR基因在植物基因组中倾向于物理聚集；例如，在拟南芥中，大多数基因位于1号和5号染色体南臂上的大簇中。我们在这些簇中实验定位了1,439个交叉，观察到了与NBS-LRR基因相关的热点，通过连锁不平衡分析也发现这些热点也是历史热点。然而，我们也观察到了NBS-LRR基因的冷点，在某些情况下与结构杂合性有关。为了在精细尺度上研究重组，我们使用高通量测序技术分析了近1,000个抗Albugo CANDIDA1(RAC1)R基因热点的交叉。这揭示了编码TIR、NBS和LRR结构域的基因内交叉增加，重叠的核小体占据的外显子。RAC1重组频率最高的是启动子-近端和重叠的CTT-重复DNA序列基序，这些基序以前被认为与植物交叉热点有关。此外，我们利用拟南芥生态型之间的杂交，显示了自然遗传变异对NBS-LRR簇重组率的显著影响。综上所述，我们发现NBS-LRR基因的一个子集是强热点，而其他基因是冷点。这揭示了拟南芥NBS-LRR基因的复杂重组格局，我们认为这是寄主-病原菌关系施加的不同协同进化压力的结果，并受到结构杂合性的影响。
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.