Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment ofgenetic diversity of National Genebank of India and synteny with other related cucurbits.

Bhawna Bonthala,Manjusha Verma,Lalit Arya,Priya Yadav,Chithra D Pandey,Vedprakash Sharma,M Z Abdin

doi:10.1007/s13353-022-00684-1

Bhawna Bonthala, Manjusha Verma + Show 5 more

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https://doi.org/10.1007/s13353-022-00684-1

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Abstract

Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower, and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identification, and phylogenetic studies. Next-generation sequencing has revolutionized the approaches for discovery, assessment, and validation of molecular markers. We conducted a genome-wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data obtained from NCBI. By performing in silico mining of microsatellite repeat motifs, we developed 45,066 perfect SSR markers. Of which 207 markers were successfully validated and 120 (57.97%) polymorphic primer pairs were utilized for an in-depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6%, and 4.3% of di-, penta-, and hexa-nucleotide repeats in the bottle gourd genome, respectively. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%), and 11 of watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery, and for breeding in bottle gourd and other cucurbits species. KEY MESSAGE: Development of 45,066 perfect microsatellite markers as a valuable tool for marker assistedselection (MAS) in plant breeding.

Highlights

IntroductionMicrosatellite markers are considered as an important markers in various research such as population genetics (Innan et al, 1997), linkage mapping (McCouch et al, 2002; Somers et al, 2004), phylogenetics, structural, functional or comparative genomics research (Garza et al, 1995; MacHugh et al, 1997)
Bottle gourd [Lagenaria siceraria (Mol.) Standl.] (2n = 2x = 22), is an edible, medicinal, container and a grafting stock plant cultivated all over the tropics (Heise et al, 1979)
Mapping of genomic simple sequence repeats (SSRs) on linkage groups and, their comparative syntenic relationship was studied with other Cucurbitaceae species. 3.1 Distribution of SSR types in genomic sequences First, a total of 171,019 SSR markers with perfect repeats were detected in the bottle gourd; after removal of the redundant SSR markers, we found 45,066 perfect SSRs

Summary

Introduction

Microsatellite markers are considered as an important markers in various research such as population genetics (Innan et al, 1997), linkage mapping (McCouch et al, 2002; Somers et al, 2004), phylogenetics, structural, functional or comparative genomics research (Garza et al, 1995; MacHugh et al, 1997). Due to their high reproducibility, multi-allelic variation, co-dominant inheritance and abundance in the genome (Tautz et al, 1984), they are widely used for marker-assisted breeding and parentage analysis (Bowers et al, 1997). The work will prove to be useful to study phylogenetic, DNA fingerprinting and in breeding for bottle gourd and other cucurbits crop species, which have very less or no genomic markers

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