High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species.
High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species.
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DOI：
10.1186/1471-2229-11-65
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发表时间：
2011-04-14
影响因子：
5.3
通讯作者：
Pappas GJ Jr
中科院分区：
文献类型：
--
作者：
Grattapaglia D;Silva-Junior OB;Kirst M;de Lima BM;Faria DA;Pappas GJ Jr
高通量SNP分型已成为植物分子育种和群体基因组学研究的必要条件。已经报道了几种主流作物的大规模SNP开发。现在，人们越来越关注将遗传分析的速度和分辨率扩展到具有高度杂合基因组的远交物种。当核苷酸多样性高时，需要对目标SNP序列背景进行精细诊断，以使用金门基因分型技术（GGGT）将查询的SNP转换为高质量的基因型。当试图跨物种转移SNP时，这个问题变得更加严重，这是植物中很少探索的主题，并且可能对较少驯化和较少资助的植物属中的群体基因组学和种间育种应用变得重要。我们成功地从混合桑格/454数据库中的1，164，695个EST和E. grandis.对计算机SNP过滤要求的系统评估表明，对SNP周围序列的严格限制对SNP基因分型性能和多态性具有显著影响。SNP检测成功率高，选择了288个SNP，更严格的计算机限制，93%的人提供了高质量的基因型调用，其中71%的多态性在一个不同的面板96个人的五个不同的物种。SNP的可靠性高，在9个桉树种属于三个部分在Symphomyrtus亚属内，仍然令人满意的两个额外的亚属的物种，虽然多态性下降的系统发育距离增加。本研究表明，尽管GGGT的核苷酸多样性≥ 2%，但它在桉树种内和种间都表现良好。在多个桉树物种中开发更大的信息SNP阵列是可行的，尽管强烈依赖于具有来自每个目标物种的许多个体的代表性和足够深的序列集合。一个高密度的SNP平台将有助于进行全基因组系统发育和群体基因组学研究，并实施桉树基因组选择的分子育种。
High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.
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影响因子：
5.3
作者：
Brondani RP;Williams ER;Brondani C;Grattapaglia D
通讯作者：
Grattapaglia D
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
5.4
作者：
BYRNE, M;MURRELL, JC;MORAN, GF
通讯作者：
MORAN, GF
影响因子：
56.9
作者：
Buckler, Edward S.;Holland, James B.;McMullen, Michael D.
通讯作者：
McMullen, Michael D.
影响因子：
4.4
作者：
Chagne, David;Gasic, Ksenija;Korban, Schuyler S.
通讯作者：
Korban, Schuyler S.