EST-SSR marker-based genetic diversity and population structure analysis of Indian Curcuma species: significance for conservation

Sahoo, Ambika; Behura, Sakuntala; Singh, Subhashree; Jena, Sudipta; Ray, Asit; Dash, Biswabhusan; Kar, Basudeba; Panda, Pratap Chandra; Nayak, Sanghamitra

doi:10.1007/s40415-021-00711-1

Cited by 7 publications

(3 citation statements)

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“…Varshney et al (2007) also analyzed the discriminating nature of EST-SSR primers during the evaluation of different species and cultivars of barley (Hordeum vulgare). Sahoo et al (2021) also reported the average MI of 4.84 in Indian Curcuma species using EST-SSR markers which is significantly higher than our study.…”

Section: Joint Analysis Of Agro-phytochemical and Genotypic Datacontrasting

confidence: 73%

“…Poor sampling size of different agroecological populations could be another reason for the low genetic diversity among different populations. Thus, more detailed studies with larger sampling sizes from extended geographical regions could draw a concrete inference ( Sahoo et al., 2021 ). Previously, evaluation of genetic diversity among the geographically isolated germplasm of A.paniculata was carried out using various dominant molecular markers ( Lattoo et al., 2008 ; Minz et al., 2013 ; Tiwari et al., 2016 ; Kumar et al., 2020 ; Hiremath et al., 2020 ) the outcomes of which are in line with our results.…”

Section: Discussionmentioning

confidence: 99%

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Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

et al. 2022

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Andrographis paniculata, commonly known as kalmegh is among the most popular medicinal herbs in Southeast Asia. It is widely cultivated for medicinal purposes. The bioactive molecule, Andrographolide accumulated in herb leaves has immense therapeutic and economic potential. However, comprehensive information regarding genetic diversity is very limited in this species. The present study assessed genetic diversity between and within the six populations (ecotypes) of twenty-four kalmegh accessions using multiple datasets (agro-morphological traits, phytochemical traits, and genic markers). This is the established report where EST-SSR (Expressed sequence tags-Simple Sequence Repeat) markers have been used to unlock genetic variation in kalmegh. Here, we identified and developed ninety-one metabolic pathway-specific EST-SSR markers. Finally, 32 random EST-SSR primer pairs were selected for genetic diversity assessment. Multivariate analysis to unveil the agro-morphological, phytochemical and genotypic variability was helpful in discriminating various germplasms studied in the present study. Among all the morphological discriptors used in present study, days to fifty percent flowering and dry herb yield were found as potential selection index for AP genetic improvement. Hierarchical cluster analysis built with agro-morphological data identified three major groups. However, corresponding analysis with phytochemical and molecular data generated two clear-cut groups among the studied individuals. Moreover, the grouping of individuals into different clusters using multiple datasets was geographically independent, and also showed inconsistency in grouping among agromorphological, phytochemical and molecular dataset based clusters. However, joint analysis using agro-morphological, phytochemical and genotypic information generated two genetic groups, which could be a valuable resource for identifying complementary crossing panels in the kalmegh breeding program. The accessions AP7, AP13, AP5, AP3 belong to cluster I and accessions AP17, AP18 belong to cluster II could be utilized as potential donors for high dry herb yield and andrographolide content, respectively in different selective breeding programs of AP. Thus, our results provided useful information about the overall genetic diversity and variation in economic traits useful for initiating selective breeding programs for contrasting traits of interest and maximizing genetic gain in kalmegh.

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Section: Joint Analysis Of Agro-phytochemical and Genotypic Datacontrasting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

et al. 2022

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“…Unigene-derived SSR markers have been widely used in studies of genetic diversity and population genetics, especially for phylogenetically related species [56][57][58]. In this study, polymorphic SSR markers of U. lagopodioides were developed using NGS technology.…”

Section: Discussionmentioning

confidence: 99%

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

2023

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Background Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. Results Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. Conclusions Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.

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Determination of the genetic diversity and population structure of Vaccinium uliginosum in Northeast China based on the chloroplast matK gene and EST-SSRseq molecular markers

Yang,

Chen,

Wang

et al. 2023

Genet Resour Crop Evol

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EST-SSR marker-based genetic diversity and population structure analysis of Indian Curcuma species: significance for conservation

Cited by 7 publications

References 58 publications

Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

Determination of the genetic diversity and population structure of Vaccinium uliginosum in Northeast China based on the chloroplast matK gene and EST-SSRseq molecular markers

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