Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode
Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode
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DOI：
10.1104/pp.114.235952
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发表时间：
2014-06-01
期刊：
影响因子：
7.4
通讯作者：
Bent, Andrew F.
中科院分区：
文献类型：
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作者：
Cook, David E.;Bayless, Adam M.;Bent, Andrew F.
除了存在/不存在多态性之外，内切酶规模的基因组DNA片段的拷贝数变异可以是适应性性状的重要驱动力。大豆胞囊线虫病（Heterodera glycines）抗性基因（Rhg 1）是大豆胞囊线虫病（Soybean cyst nematode，SCN）的一个重要数量性状基因。Rhg 1最近被发现是一个复杂的基因座，其中抗性赋予单倍型携带多达10个串联重复拷贝的31-kb的DNA片段，和三个不同的基因存在于每个重复有助于SCN抗性。在这里，我们使用全基因组测序，纤维FISH（荧光原位杂交），和其他方法来发现在Rhg 1的遗传变异在41个不同的大豆品种。基于拷贝数变异，转录丰度，核酸多态性，和差异甲基化的DNA区域，我们发现SCN抗性与多拷贝Rhg 1单倍型，形成两个不同的群体。测试的高拷贝数Rhg 1加入，包括植物引进（PI）88788，包含一个灵活的拷贝数（7至10）的31 kb的Rhg 1重复。已鉴定的低拷贝数Rhg 1组，包括PI 548402（Peking）和PI 437654，含有3个Rhg 1重复拷贝和一个新鉴定的Glyma 18 g 02590等位基因（预测的α-SNAP [α-可溶性N-乙基马来酰亚胺敏感因子附着蛋白]）。有强有力的证据表明，两个耐药赋予多拷贝Rhg 1组和随后的独立进化的共同起源。在Rhg 1中也发现了与SCN抗性相关的差异甲基化DNA区域。这些数据提供了深入了解多基因片段的拷贝数变异，作为一个例子，抗病性状的高经济重要性。
Copy number variation of kilobase-scale genomic DNA segments, beyond presence/absence polymorphisms, can be an important driver of adaptive traits. Resistance to Heterodera glycines (Rhg1) is a widely utilized quantitative trait locus that makes the strongest known contribution to resistance against soybean cyst nematode (SCN), Heterodera glycines, the most damaging pathogen of soybean (Glycine max). Rhg1 was recently discovered to be a complex locus at which resistance-conferring haplotypes carry up to 10 tandem repeat copies of a 31-kb DNA segment, and three disparate genes present on each repeat contribute to SCN resistance. Here, we use whole-genome sequencing, fiber-FISH (fluorescence in situ hybridization), and other methods to discover the genetic variation at Rhg1 across 41 diverse soybean accessions. Based on copy number variation, transcript abundance, nucleic acid polymorphisms, and differentially methylated DNA regions, we find that SCN resistance is associated with multicopy Rhg1 haplotypes that form two distinct groups. The tested high-copy-number Rhg1 accessions, including plant introduction (PI) 88788, contain a flexible number of copies (seven to 10) of the 31-kb Rhg1 repeat. The identified low-copy-number Rhg1 group, including PI 548402 (Peking) and PI 437654, contains three copies of the Rhg1 repeat and a newly identified allele of Glyma18g02590 (a predicted alpha-SNAP [alpha-soluble N-ethylmaleimide-sensitive factor attachment protein]). There is strong evidence for a shared origin of the two resistance-conferring multicopy Rhg1 groups and subsequent independent evolution. Differentially methylated DNA regions also were identified within Rhg1 that correlate with SCN resistance. These data provide insights into copy number variation of multigene segments, using as the example a disease resistance trait of high economic importance.