Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach

Negi, Ankita; Singh, Kalpana; Jaiswal, Sarika; Kokkat, Johnson George; Angadi, U. B.; Iquebal, Mir Asif; Umadevi, P.; Rai, Anil; Kumar, Dinesh

doi:10.3389/fpls.2022.846937

Cited by 8 publications

(4 citation statements)

References 53 publications

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“…Furthermore, the grouping of polymorphic SSRs based on the five classes of perfect SSRs and compound SSRs showed that the dinucleotides were dominant. The higher tendency of dinucleotide SSRs to be polymorphic is consistent with other studies on genomic SSRs in apples ( Silfverberg-Dilworth et al., 2006 ), peanuts ( Zhao et al., 2012a ), watermelon ( Zhao et al., 2012b ), and black pepper ( Negi et al., 2022 ). However, in a previous study where a repeat-rich genomic library screening method was used to generate SSR markers, the compound SSRs were found to be more polymorphic in cashew ( Croxford et al., 2006 ).…”

Section: Discussionsupporting

confidence: 90%

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

Savadi,

Muralidhara,

Venkataravanappa

et al. 2023

Front. Plant Sci.

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The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12–<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, “Cashew Microsatellite Database (CMDB),” was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.

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Section: Discussionsupporting

confidence: 90%

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

Savadi,

Muralidhara,

Venkataravanappa

et al. 2023

Front. Plant Sci.

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“…Genetic diversity in the sampled accessions of P . nigrum was relatively low compared to the previous genetic analyses carried out using RAPD [ 11 ], AFLP [ 13 ], and SSR [ 15 , 18 ] markers. The accessions used in this study were those in cultivation at present, which have been subjected to different selective pressures, particularly for improved yield and quality characteristics.…”

Section: Discussionmentioning

confidence: 62%

“…Using this reference genome, 50 genome-wide SSR markers were developed that discriminated 30 Indian black pepper landrace accessions in four distinct clusters [ 17 ]. More recently, Negi et al [ 18 ] characterized chromosomal location-specific polymorphic SSRs from 29 Indian black pepper accessions, with potential application in diversity analysis. Although SSR markers have been the most widely used for assessing the genetic diversity of crops, the characterization of large germplasm collections by this method could be time-consuming and expensive.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers

Wimalarathna,

Wickramasuriya,

Metschina

et al. 2024

PLoS ONE

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Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.

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“…The first P. nigrum reference genome data and its assembly were reported recently (Hu et al, 2019), providing an evolutionary perspective and insight into the metabolic processes and molecular basis of species-specific Piperine biosynthesis. Very recently, a comprehensive web-genomic resource of black pepper was developed by (Negi et al, 2022), which catalogues genome-wide deep mining of SSR markers from the genome assembly of black pepper. Studies on the identification of putative biotic and abiotic stress-associated genes by transcriptomics sequencing approaches (Hao et al, 2016) (Negi et al, 2021), have produced important basic information and serve as valuable resources for future breeding programmes.…”

Section: Introductionmentioning

confidence: 99%

‘Priming’ protects Piper nigrum L. from Phytophthora capsici through reinforcement of phenylpropanoid pathway and possible enhancement of Piperine biosynthesis

et al. 2022

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Piper nigrum L. (black pepper), a woody perennial spice crop indigenous to India is positioned at the phylogenetically unique basal lineage of angiosperms. Cultivation of this major spice crop is constrained by rampant fungal and viral infections leading to a lack of disease-free planting material. The major disease that poses severe threat to P. nigrum plantations and nurseries is ‘quick wilt’ caused by the oomycete Phytophthora capsici, which affects the leaf, stem, spike, collar and root. In this paper, we report the consequence of priming in modulating Piper nigrum defense against Phytophthora capsici. Glycol Chitosan (GC) was used to infiltrate detached leaves of mature P. nigrum plants. It was observed that pre-treatment of GC for 24 hours resulted in significant reduction of disease symptoms in infected leaves, as evidenced by the marked decrease in the size of lesions, and also delayed the appearance of symptoms up to 72 hpi. Experiments repeated in P. nigrum seedlings under controlled growth conditions indicate that delayed disease symptoms of GC pre-treated leaves do not spread to healthy uninfiltrated leaves suggesting a priming-associated systemic defense response. An ROS-mediated manifestation of Hypersensitive Response (HR) induced by Chitosan was also evident in pre-treated leaves. A corresponding visual indication of increased lignification was observed, which correlated with an enhanced lignin content of GC-treated leaves. Enhanced callose deposition was also apparent in GC infiltrated leaves, establishing a stimulatory effect of GC in triggering HR through ROS production, enhanced lignification and callose deposition. Key genes of the core phenylpropanoid and isoprenoid pathways along with major defense signalling pathway genes of P. nigrum, including pathogenesis-related genes and hormone signalling genes showed significant transcript enrichment consequential to GC treatment. A significant quantitative enhancement in Piperine content was evident in GC-infiltrated leaves. The systemic nature of priming on disease protection was established through experiments conducted in rooted cuttings monitored for 30 days after disease infection. This is the first report that provides strong molecular evidence endorsing the twofold advantage of defense priming in P. nigrum by improving crop protection with a concomitant enhancement in Piperine biosynthesis.

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Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach

Cited by 8 publications

References 53 publications

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers

‘Priming’ protects Piper nigrum L. from Phytophthora capsici through reinforcement of phenylpropanoid pathway and possible enhancement of Piperine biosynthesis

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