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首页> 外文期刊>Journal of genetics >Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.
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Microarray-based large scale detection of single feature polymorphism in Gossypium hirsutum L.

机译：基于微阵列的陆地棉单特征多态性的大规模检测。

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摘要

Microarrays offer an opportunity to explore the functional sequence polymorphism among different cultivars of many crop plants. The Affymetrix microarray expression data of five genotypes of Gossypium hirsutum L. at six different fibre developmental stages was used to identify single feature polymorphisms (SFPs). The background corrected and quantile-normalized log(2) intensity values of all probes of triplicate data of each cotton variety were subjected to SFPs call by using SAM procedure in R language software. We detected a total of 37,473 SFPs among six pair genotype combinations of two superior (JKC777 and JKC725) and three inferior (JKC703, JKC737 and JKC783) using the expression data. The 224 SFPs covering 51 genes were randomly selected from the dataset of all six fibre developmental stages of JKC777 and JKC703 for validation by sequencing on a capillary sequencer. Of these 224 SFPs, 132 were found to be polymorphic and 92 monomorphic which indicate that the SFP prediction from the expression data in the present study confirmed a similar to 58.92% of true SFPs. We further identified that most of the SFPs are associated with genes involved in fatty acid, flavonoid, auxin biosynthesis etc. indicating that these pathways significantly involved in fibre development.
机译：微阵列为探索许多农作物不同品种之间的功能序列多态性提供了机会。在六个不同的纤维发育阶段的五个基因型陆地棉的Affymetrix微阵列表达数据用于鉴定单特征多态性（SFP）。使用R语言软件中的SAM程序，对每个棉花品种一式三份数据的所有探针的背景校正和分位数归一化log（2）强度值进行SFP调用。我们使用表达数据在两个上等（JKC777和JKC725）和三个下等（JKC703，JKC737和JKC783）的六对基因型组合中检测到总共37,473个SFP。从JKC777和JKC703的所有六个纤维发育阶段的数据集中随机选择涵盖51个基因的224个SFP，以通过毛细管测序仪进行测序进行验证。在这224个SFP中，发现132个是多态的，而92个是单态的，这表明根据本研究中的表达数据预测的SFP证实了真实SFP的58.92％。我们进一步确定，大多数SFP与与脂肪酸，类黄酮，生长素生物合成等有关的基因有关，表明这些途径显着参与了纤维的发育。

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