Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation.

التفاصيل البيبلوغرافية
العنوان:	Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation.
المؤلفون:	Patturaj M; Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India., Munusamy A; Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India., Kannan N; Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India., Kandasamy U; Centre for Plant Molecular Biology, Osmania University, Hyderabad 500007, India., Ramasamy Y; Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India.
المصدر:	Genomics & informatics [Genomics Inform] 2021 Sep; Vol. 19 (3), pp. e33. Date of Electronic Publication: 2021 Sep 30.
نوع المنشور:	Journal Article
اللغة:	English
بيانات الدورية:	Publisher: Korea Genome Organization Country of Publication: Korea (South) NLM ID: 101223836 Publication Model: Print-Electronic Cited Medium: Print ISSN: 1598-866X (Print) Linking ISSN: 1598866X NLM ISO Abbreviation: Genomics Inform Subsets: PubMed not MEDLINE
أسماء مطبوعة:	Original Publication: Seoul : Korea Genome Organization
مستخلص:	Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.
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فهرسة مساهمة:	Keywords: E. grandis; E. terticornis; Eucalyptus camaldulensis; simple sequence repeats; whole genome resequencing
تواريخ الأحداث:	Date Created: 20211012 Latest Revision: 20211023
رمز التحديث:	20221213
مُعرف محوري في PubMed:	PMC8510864
DOI:	10.5808/gi.21031
PMID:	34638180
قاعدة البيانات:	MEDLINE

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تدمد:	1598-866X
DOI:	10.5808/gi.21031