Microbiome Fingerprint as Biomarker for Geographical Origin and Heredity in Crocus sativus: A Feasibility Study

Nancy Bhagat,Deepika Trakroo,Rahma Zouagui,Shivali Sharma,Micha Horacek,Sheetal Ambardar,Jyoti Vakhlu,Laila Sbabou,Sushmeeta Raj

doi:10.3389/fsufs.2021.688393

Abstract

Host–microbiome interactions are specific and not random, making them defining entities for the host. The hypothesis proposed by various researchers earlier, that both plants and animals harbor specific inheritable core microbiome, is being augmented in the present study. Additionally, a case for using microbial fingerprint as a biomarker, not only for plant identification but also as a geographical indicator, has been investigated, taking Crocus sativus, saffron, as a study material. Crocus sativus, a monogenetic herb, on account of its male sterility and vegetative propagation, is reported to lack genome based molecular markers. Cormosphere microbiome (microbiome associated with corm) has been compared across three geographical locations, in two continents, to identify the core and unique microbiome, during the vegetative phase of its growth. Microbiome analysis done at phylum and genus level, using next generation sequencing technology, revealed that cormosphere at three locations harbored common phyla. At genus level, 24 genera were found common to all three geographical locations, indicating them to be part of the core microbiome of saffron. However, there were some bacterial genera unique to Kashmir, Kishtwar, and Morocco that can be used to develop microbial markers/geographical indicators for saffron grown in these regions. This is a preliminary study, indicating that the location specific bacterial community can be used to develop microbial barcodes but needs further augmentation with high coverage data from other saffron growing geographical regions.

Highlights

Molecular markers are important tools for plant genome analysis, crop improvement, and development of barcodes for authentic plant identification (Mishra et al, 2016)
The Kishtwar average was compared to the microbiome of saffron cormosphere of Kishtwar-L 17, Kashmir (2013), and Morocco (2016) to discover core and location specific unique microbiome
15 phyla (12 bacterial, 2 fungal, 1 archaeal) were cataloged from the cormosphere of saffron grown in Kishtwar during three consecutive years (2011, 2012, and 2013)

Summary

Introduction

Molecular markers are important tools for plant genome analysis, crop improvement, and development of barcodes for authentic plant identification (Mishra et al, 2016). It does not produce viable seeds and propagates vegetatively, thereby lacking any variations at the genomic level. The stigmas of saffron flowers are plucked and dried, to be used as a seasoning and coloring agent in food (Mzabri et al, 2017; Jafari et al, 2020) It is the world’s highest priced spice with medicinal and aromatic properties, so referred to as ‘golden condiment’ (Monika and Neha, 2014; Pandita, 2021; Su et al, 2021). Saffron is reported to be a monomorphic plant, having no variations at a genomic level across different saffron accessions across the world, as depicted by various molecular markers like RAPD, AFLP, and SSR (Rubio-Moraga et al, 2009; Busconi et al, 2015). There are no authentic molecular markers that can identify these variations till date (Alavi-Kia et al, 2008; Keify and Beiki, 2012; Mir et al, 2021)

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Results

Conclusion