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Cross genera transferability of microsatellite markers from other members of family Bignoniaceae to Tecomella undulata (Sm.) Seem

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Abstract

Transferability of SSR markers from related species/genera is a rapid and cost-effective method to enhance genomic database of genetically neglected crops. Monotypic genus Tecomella undulata, a pharmacologically important endangered timber tree, found in hyper arid regions is one such genetic resource limited species, wherein neither SSR identification nor cross transferability studies have been initiated. Transferability of 69 cross-genera SSR primers selected from other members of family bignoniaceae (Incarvillea sinensis, I. mairei, Jacaranda copaia, Tabebuia aurea and Arrabidaea chica) showed 40.58% (28 primers) transferability amplifying 1–10 amplicons ranging in the size from 80to 600 bp in 24 accessions of T. undulata. Per cent marker transferability varied from 66.67% (A. chica) to 38.89% (J. copaia) among the genera tested while no transferable markers could be identified from I. sinensis. Transferability of simple di-/tri-nucleotide repeat (34.2–37.5%) and complex nucleotide sequence (60.0%) based SSR motifs were higher as compared to penta-/hexa-nucleotide based repeat motifs. Within the 28 transferable markers, 26 (92.86%) were polymorphic while 2 (7.14%) were monomorphic. Average number of alleles per primer was 5.39 while average polymorphic alleles per locus were 5.11. The PIC values of SSR markers ranged from 0.23 to 0.85 with an average of 0.59. Efficiency of the identified cross species SSR markers was tested for diversity analysis using a set of 24 trees (8 each of yellow, orange and red flower colour morphotypes). The 24 samples clustered into six groups with similarity coefficient ranging from 0.29 to 0.67, while six accessions formed distinct out groups. Distribution of accessions in the SSR dendrogram showed no correlation with flower colour. More diversity (99%) was observed within populations compared to that existing between populations (1%). The present study can enrich the genomic background of T. undulata by identifying suitable polymorphic markers from confamiliar species that can be applied for genetic diversity studies, mapping of QTLs and cultivar identification as well.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

AMOVA:

Analysis of molecular variance

CTAB:

Cetyltrimethyl ammonium bromide

EST:

Expressed sequence tags

ISSR:

Inter simple sequence repeat

ITS:

Internal transcribed spacer

PCoA:

Principal coordinates analysis

PIC:

Polymorphic information content

RAPD:

Randomly amplified polymorphic DNA

SCoT:

Start codon targeted polymorphism

SSLP:

Simple sequence length polymorphism

SSR:

Simple sequence repeats

STR:

Short tandem repeats

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Acknowledgement

Research work was carried out under DBT, GoI, New Delhi, funded project on Tecomella undulata sanctioned to RKK.

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Authors and Affiliations

  1. Division of Plant Improvement and Pest Management, Central Arid Zone Research Institute (CAZRI), Jodhpur, Rajasthan, 342003, India

    Rajwant K. Kalia, Sidhika Chhajer & Rakesh Pathak

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  1. Rajwant K. Kalia
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  2. Sidhika Chhajer
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Correspondence to Rajwant K. Kalia.

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Kalia, R.K., Chhajer, S. & Pathak, R. Cross genera transferability of microsatellite markers from other members of family Bignoniaceae to Tecomella undulata (Sm.) Seem. Acta Physiol Plant 42, 151 (2020). https://doi.org/10.1007/s11738-020-03138-5

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