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Ad hoc breeding of a genetically depauperate landrace of noble fir ( Abies procera Rehder) using SNP genotyping via high-throughput targeted sequencing
Tree Genetics & Genomes ( IF 2.4 ) Pub Date : 2020-08-11 , DOI: 10.1007/s11295-020-01460-0
Ole K. Hansen , Kurt Lamour , Ross Whetten , Jing Xu , Argelia Cuenca , Md. Shofiqul Islam , Ulrik Braüner Nielsen

Pedigree reconstruction via DNA markers and subsequent quantitative genetic analyses in production stands of trees is an alternative to traditional forest tree breeding. The method requires variable DNA markers; preferably cost-efficient to genotype. We tested the approach in breeding for Christmas tree traits in a Danish landrace of Abies procera. Initial analysis with simple sequence repeats (SSRs) revealed a substantial reduction in genetic diversity of Danish A. procera compared with direct imports from the USA, indicating a genetic bottleneck. Due to the reduced genetic variation, the SSRs were not variable enough for pedigree reconstruction, and 145 single nucleotide polymorphisms (SNPs) were therefore identified and genotyped via high-throughput targeted sequencing. In the field, we phenotypically selected 674 superior trees, based on criteria for good Christmas trees, among 21,000 trees in three Christmas tree plantations originating from an A. procera clonal seed orchard. By SNP-genotyping and parentage analysis, pedigree was reconstructed for the selected individuals, and genetic predictions for the Christmas tree traits were estimated. A final selection of 45 trees out of the 674 genotyped, based on an index of predicted values for different traits, foresees a gain in the Christmas tree score and branch angle score of 16% and 10%, respectively. The study clearly demonstrated the benefits of pedigree reconstruction, even though mass selection seemed to give similar gain. Primarily, the possibilities to control the level of inbreeding, and to check whether the production stands, from where we select trees, actually originate from the declared and desired parent pool.



中文翻译:

通过高通量靶向测序使用SNP基因分型对贵族冷杉(Abies procera Rehder)的无遗传遗传的地方品种进行临时育种

通过DNA标记进行谱系重建以及随后在林木生产林中进行定量遗传分析是传统林木育种的替代方法。该方法需要可变的DNA标记。基因型的成本效益最好。我们在丹麦冷杉(Abies procera)的地方种中测试了圣诞树特性的育种方法。使用简单序列重复(SSR)进行的初步分析显示,丹麦A. procera的遗传多样性大大降低与从美国直接进口相比,表明存在遗传瓶颈。由于减少的遗传变异,SSRs没有足够的可变性用于谱系重建,因此鉴定了145个单核苷酸多态性(SNPs)并通过高通量靶向测序进行了基因分型。在田间,我们根据优质圣诞树的标准在表型上选择了来自A. procera的三个圣诞树种植园中的21,000棵树中的674棵优质树克隆种子园。通过SNP基因分型和亲子关系分析,可以为选定的个体重建谱系,并估算出圣诞树性状的遗传预测。根据不同性状的预测值指标,从674个基因型中最终选择45棵树,预计圣诞树得分和分支角度得分分别增加16%和10%。这项研究清楚地表明了谱系重建的好处,尽管大众选择似乎也带来了类似的收益。首先,可以控制近交水平,并检查生产是否站立(从我们选择树的位置来看),实际上是否源自已声明的所需父池。

更新日期:2020-08-11
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