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从茶（Camellia sinensis (L.) O. Kuntze）转录因子基因中进行全基因组鉴定和功能相关微卫星标记的特征分析。

Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze).

机构信息

Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.

Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India.

出版信息

Sci Rep. 2022 Jan 7;12(1):201. doi: 10.1038/s41598-021-03848-x.

DOI:10.1038/s41598-021-03848-x
PMID:34996959
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8742041/
Abstract

Tea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory "Transcription factor (TF) genes" can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.

摘要

茶作为最受欢迎的饮料之一，需要大量的分子标记来进行品质、产量和抗逆性的遗传改良。从调控“转录因子（TF）基因”中鉴定出功能相关的微卫星或简单重复序列（SSR）标记资源，可以成为加速分子育种工作的潜在目标。在本研究中，从 20 个流行茶树品种的特定性状转录组资源中，鉴定出了 2776 个编码 TF 的转录本，其中包含 3687 个 SSR 位点，产生了 1843 个侧翼标记。其中，689 个功能相关的 SSR 标记成功验证，并分配到 CSS 基因组的 15 条染色体（Chr）上。有趣的是，589 个多态性标记，包括 403 个核心 TF-SSR 标记，在关键 TF 家族（bHLH、WRKY、MYB 相关、C2H2、ERF、C3H、NAC、FAR1、MYB 和 G2-like）中扩增出 2864 个等位基因。它们与对应香气、品质和抗逆性的关键基因的显著网络相互作用表明，它们在性状解析中具有潜在的意义。此外，CDS 中重复的单个氨基酸揭示了亲水性和疏水性氨基酸的存在。成功地将标记用于 135 个流行茶树品种的遗传多样性特征分析和双亲和群体的分离表明，它们在茶树高通量基因分型研究中具有更广泛的应用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/f129873fd173/41598_2021_3848_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/93f684daa780/41598_2021_3848_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/97c41b3d4f7a/41598_2021_3848_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/c386a39f8336/41598_2021_3848_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/d32166d1ff3f/41598_2021_3848_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/06b366d3ab5d/41598_2021_3848_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/f129873fd173/41598_2021_3848_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/93f684daa780/41598_2021_3848_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/97c41b3d4f7a/41598_2021_3848_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/c386a39f8336/41598_2021_3848_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/d32166d1ff3f/41598_2021_3848_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/06b366d3ab5d/41598_2021_3848_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7966/8742041/f129873fd173/41598_2021_3848_Fig6_HTML.jpg

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