Exploitation of novel drought responsive EST-SSR markers in tetraploid cotton (Gossypium hirsutum L.)

IF 1 Q4 GENETICS & HEREDITY Gene Reports Pub Date : 2024-11-20 DOI:10.1016/j.genrep.2024.102097

Aditi Dwivedi , KiranKumar P. Suthar , Rasmieh Hamid , Komal G. Lakhani , Diwakar Singh , Sushil Kumar , Rajkumar B K , Vijay Vekariya , Praveen Prajapat

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Abstract

Drought is a major environmental challenge that affects the quality and yield of cotton fibres. The aim of the present study was to develop drought-responsive EST-SSRs from cotton transcriptome data. A total of 1946 functionally annotated EST-SSR markers were developed, with tri-nucleotide SSR repeats being the most abundant (40.7 %), followed by di-nucleotides (18.1 %). Gene Ontology (GO) associated with EST-SSR showed the presence of genes related to drought stress, such as PIP, CDK, LEA, etc. A set of 46 EST-SSRs was validated under In-vitro conditions on fourteen cotton genotypes, and 15 EST-SSRs were found to be polymorphic. The polymorphic EST-SSRs markers amplified a total of 44 loci with 32.6 % polymorphism. Genetic analysis revealed that the markers NAU-G-16, NAU-G-39, NAU-G-117 and NAU-G-142 amplified four unique alleles at 121, 163, 224 and 238 bp, respectively, only in drought-tolerant cotton genotypes. The effectiveness of the markers was demonstrated by their high polymorphism information content (PIC), which ranged from 0.35 to 0.89. The large number of markers, 60 %, had a PIC value of >0.6 and were classified as highly informative. The genetic similarity coefficients between cotton genotypes ranged from 0.409 to 0.89, indicating moderate genetic diversity. The Shannon index ranged from 0.21 to 0.65, while the Nei coefficient ranged from 0.12 to 0.46. Clustering and PCo analysis showed the distribution of genotypes into four main clusters, with drought-tolerant genotypes grouped into a single cluster. These drought-responsive markers are promising for the further development of marker-assisted breeding with the aim of increasing the productivity of cotton under drought-prone conditions.

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四倍体棉花（Gossypium hirsutum L.）中新型干旱响应EST-SSR标记的利用

干旱是影响棉纤维质量和产量的主要环境挑战。本研究旨在从棉花转录组数据中开发抗旱EST-SSR。共开发出 1946 个功能注释的 EST-SSR 标记，其中三核苷酸 SSR 重复最多（40.7%），其次是二核苷酸（18.1%）。与EST-SSR相关的基因本体（GO）显示存在与干旱胁迫相关的基因，如PIP、CDK、LEA等。在体外条件下对 14 个棉花基因型的 46 个 EST-SSR 进行了验证，发现其中 15 个 EST-SSR 具有多态性。多态 EST-SSRs 标记共扩增出 44 个位点，多态性为 32.6%。遗传分析表明，标记NAU-G-16、NAU-G-39、NAU-G-117和NAU-G-142仅在耐旱棉花基因型中分别扩增出121、163、224和238 bp的四个独特等位基因。多态性信息含量（PIC）从 0.35 到 0.89 不等，证明了这些标记的有效性。大量标记（60%）的 PIC 值为 0.6，被归类为高信息量标记。棉花基因型之间的遗传相似系数介于 0.409 至 0.89 之间，表明遗传多样性适中。香农指数在 0.21 至 0.65 之间，内系数在 0.12 至 0.46 之间。聚类和 PCo 分析表明，基因型主要分布在四个聚类中，其中耐旱基因型被归入一个聚类。这些干旱响应标记有望进一步发展标记辅助育种，从而提高棉花在干旱条件下的产量。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.