Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Victoria, Australia.
Plant Biotechnol J. 2012 Feb;10(2):125-38. doi: 10.1111/j.1467-7652.2011.00644.x. Epub 2011 Aug 10.
An understanding of nature and extent of nucleotide sequence variation is required for programmes of discovery and characterization of single nucleotide polymorphisms (SNPs), which provide the most versatile class of molecular genetic marker. A majority of higher plant species are polyploids, and allopolyploidy, because of hybrid formation between closely related taxa, is very common. Mutational variation may arise both between allelic (homologous) sequences within individual subgenomes and between homoeologous sequences among subgenomes, in addition to paralogous variation between duplicated gene copies. Successful SNP validation in allopolyploids depends on differentiation of the sequence variation classes. A number of biological factors influence the feasibility of discrimination, including degree of gene family complexity, inbreeding or outbreeding reproductive habit, and the level of knowledge concerning progenitor diploid species. In addition, developments in high-throughput DNA sequencing and associated computational analysis provide general solutions for the genetic analysis of allopolyploids. These issues are explored in the context of experience from a range of allopolyploid species, representing grain (wheat and canola), forage (pasture legumes and grasses), and horticultural (strawberry) crop. Following SNP discovery, detection in routine genotyping applications also presents challenges for allopolyploids. Strategies based on either design of subgenome-specific SNP assays through homoeolocus-targeted polymerase chain reaction (PCR) amplification, or detection of incremental changes in nucleotide variant dosage, are described.
理解核苷酸序列变异的性质和程度对于发现和描述单核苷酸多态性（SNPs）的计划是必要的，SNP 提供了最通用的分子遗传标记类别。大多数高等植物物种都是多倍体，异源多倍体由于在亲缘关系密切的类群之间形成杂种而非常普遍。除了基因拷贝之间的同源序列之间的旁系同源变异外，突变变异可能在个体亚基因组内的等位基因（同源）序列之间以及亚基因组之间的同源序列之间产生。在异源多倍体中成功验证 SNP 取决于对序列变异类别的区分。许多生物学因素影响可区分性的可行性，包括基因家族复杂程度、近亲繁殖或远缘繁殖的生殖习性以及关于亲本原种的知识水平。此外，高通量 DNA 测序和相关计算分析的发展为异源多倍体的遗传分析提供了通用解决方案。这些问题在一系列异源多倍体物种的经验背景下进行了探讨，这些物种代表了谷物（小麦和油菜）、饲料（牧草豆科植物和草类）和园艺（草莓）作物。在 SNP 发现之后，常规基因分型应用中的检测也为异源多倍体带来了挑战。描述了基于亚基因组特异性 SNP 检测的设计的策略，包括通过同源基因目标聚合酶链反应（PCR）扩增的设计，或检测核苷酸变异剂量的递增变化。
