Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm

Yirgu, Mihret; Kebede, Mulugeta; Feyissa, Tileye; Lakew, Berhane; Woldeyohannes, Aemiro Bezabih; Fikere, Mulusew

doi:10.1186/s12863-023-01109-6

Cited by 5 publications

(5 citation statements)

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“…Multi-allelic codominant markers, such as SSRs, can have PIC values ranging from 0 to 1, with highly informative markers typically having values greater than 0.5. In contrast, SNP markers have a maximum PIC value of 0.5 due to their bi-allelic nature [79,[82][83][84][85]. Our results showed an average PIC value of 0.132, indicating that the SNP markers identified in black pepper are moderately informative.…”

Section: Plos Onementioning

confidence: 65%

“…Private alleles (Np), which represent genetic variants unique to a particular population [77], were much more numerous in subpopulation 1 (20,208) compared to subpopulation 2 (40). However, this discrepancy is likely due to the larger number of genotypes clustered in subpopulation 1 (152) compared to subpopulation 2 (23), rather than an indication of greater allelic richness in subpopulation 1. The ability of a molecular marker to detect polymorphism, often quantified by its PIC, is a valuable parameter for assessing the informativeness of markers in genetic studies, particularly in genetic diversity and linkage analysis [78][79][80][81].…”

Section: Plos Onementioning

confidence: 99%

“…In addition, SNPs are amenable to high throughput detection platforms, allowing rapid analysis of large data sets. In recent years, SNP markers have been used to evaluate the genetic diversity of many important crops including rice [ 21 ], oil palm [ 22 ] and barley [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Plos Onementioning

confidence: 65%

Section: Plos Onementioning

confidence: 99%

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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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“…The polymorphic information content (PIC) value is a metric employed to gauge the effectiveness of polymorphic loci in exploring genetic diversity using markers [46]. In this investigation, the mean PIC value was determined to be 0.22.…”

Section: Discussionmentioning

confidence: 99%

Revealing Genetic Diversity and Population Structure in Türkiye’s Wheat Germplasm Using iPBS-Retrotransposon Markers

Demirel,

Yıldırım,

Eren

et al. 2024

Agronomy

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Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Türkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon’s information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei’s genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation.

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“…The use of molecular tools has facilitated the examination of genetic markers, such as microsatellites or single-nucleotide polymorphisms (SNPs), to explore the relatedness among Pst isolates collected from different geographical regions (Yirgu et al, 2023). By analyzing these markers, researchers have been able to discern patterns of gene flow, identify distinct populations, and infer migration events.…”

Section: Advances In Understanding Wheat Stripe Rust Through Molecula...mentioning

confidence: 99%

Unraveling the Genetic and Geographic Diversity of Puccinia striiformis f. sp. Tritici (Pst) Populations for Effective Control of Stripe Rust in Global Wheat Production

Afzal,

Syed,

Nawaz

et al. 2024

PJAR

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| Stripe rust, caused by Puccinia striiformis f.sp. tritici (Pst), results in reduced yield and grain quality substantially, and increases production expenses, leading to billions of dollars in economic damages globally every year. Understanding the lifecycle of pathogens is vital in formulating effective management strategies for plant diseases. Pst has a complex life cycle that entails both sexual and asexual reproduction, facilitating the rapid evolution of new strains. The evolution of new races is primarily driven by the selection pressure imposed by the deployment of resistance genes in wheat cultivars. Work documented by prominent researchers conducted in diverse regions of the planet has been reviewed in this article to understand how disease perpetuates from one year to next year. Recent studies have shown that Pst populations can undergo rapid adaptation to changing environmental conditions such as temperature and humidity, which can influence the timing and severity of stripe rust epidemics. The evolution and diversity of Pst pose significant challenges for the management and control of stripe rust in wheat crops. Effective strategies for disease control require a better understanding of the genetic and geographic diversity of Pst populations and the factors driving their evolution. Effective monitoring of Pst populations is critical for developing strategies to control stripe rust and ensure the long-term sustainability of wheat production. Pathogenicity surveys, which involve testing Pst samples against differential host plants, and molecular techniques such as PCR and DNA sequencing are discussed as effective tools for tracking Pst populations, identifying new introductions and monitoring their evolution over time. A combination of traditional and molecular techniques has generated valuable data for understanding populations virulence of Pst.

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Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm

Cited by 5 publications

References 65 publications

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

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

Revealing Genetic Diversity and Population Structure in Türkiye’s Wheat Germplasm Using iPBS-Retrotransposon Markers

Unraveling the Genetic and Geographic Diversity of Puccinia striiformis f. sp. Tritici (Pst) Populations for Effective Control of Stripe Rust in Global Wheat Production

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