Assessment of genetic diversity and population structure in local alfalfa genotypes using iPBS molecular markers

Eren, Barış; Keski̇n, Bilal; Demirel, Fatih; Demirel, Serap; Türkoğlu, Aras; Yılmaz, Abdurrahim; Haliloğlu, Kamil

doi:10.1007/s10722-022-01450-2

Cited by 10 publications

(9 citation statements)

References 39 publications

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“…Notably, the H value obtained in this study surpasses those reported in earlier wheat research utilizing iPBS markers for characterization [11]. Additionally, Shannon information index (I) value (0.31) and the effective number of alleles (Ne, 1.48) observed in this research exceed the values reported in previous studies of various plant species employing iPBS markers [11,37,50]. The heightened values observed for several diversity indices in this research may be attributed to variations in germplasm and the characteristics of the employed molecular marker [11].…”

Section: Discussioncontrasting

confidence: 73%

“…Using the COPH module, the cophenetic value matrix was initially computed by using the tree matrix that was obtained from the iPBS analysis. The MXCOMP module was used to investigate the goodness-of-fit value (r) representing the relationship between the UPGMA dendrogram and the Dice similarity index matrix [37]. To undertake an analysis of the population structure of wheat varieties, STRUCTURE version 2.3.4 was utilized [38].…”

Section: Ipbs Data Scoring and Analysismentioning

confidence: 99%

“…The appropriate number of subpopulations (delta K value) was determined using the approach described by Evanno et al [39] using the STRUCTURE HARVESTER program [40]. The STRUCTURE program was used to determine the expected heterozygosity (He) and fixation index (F ST ) values that reflect populations [37].…”

Section: Ipbs Data Scoring and Analysismentioning

confidence: 99%

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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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Section: Discussioncontrasting

confidence: 73%

Section: Ipbs Data Scoring and Analysismentioning

confidence: 99%

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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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“…Also, Acharya et al [22] reported a high and stable improvement of dry matter yield in alfalfa genetic materials that may be utilized in order to develop high performing and well-adopted alfalfa cultivars. Eren et al [23] analyzed alfalfa genetic diversity and local population structure by molecular markers. They concluded that the iPBS molecular markers can be a helpful tool in identifying parents with high genetic diversity in alfalfa breeding.…”

Section: Introductionmentioning

confidence: 99%

Modeling Stability of Alfalfa Yield and Main Quality Traits

Greveniotis,

Bouloumpasi,

Skendi

et al. 2024

Agriculture

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Alfalfa (Medicago sativa L.) is used to support livestock. A stability study was carried out over three years. The stability indices for yield and main quality characteristics such as plant height, number of nodes, the yield of green mass and dry matter, crude protein and fiber (%), and ash (%), were examined. Statistical analysis revealed significant differences that indicated the presence of high genotype–year interactions. Heritability was higher in the case of qualitative traits than quantitative traits. The most intriguing correlation was between green mass yield and crude protein content because positive correlations may lead to indirect and simultaneous selection. According to the statistical biplot models AMMI and GGE, the best genotypes for almost all traits to use, regardless of the environment and cultivation type, were the G8 (Population 2) followed by cultivar G3 (Yliki). Despite the high index values shown by the parameter number of nodes, the latter and yield showed low heritability.

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“…As a result of the adaptation of alfalfa subspecies to different geographies and climatic conditions, it has been observed that they differentiate from each other on the basis of population or subpopulation over time (Şakiroğlu et al 2015). Therefore, it is critical to evaluate and compare populations in terms of alfalfa populations grown in different geographies (İlhan, 2018a;Eren et al 2022). Agriculture 2022; 5 (2) 50-56 https://dergipark.org.tr/tr/pub/ja 51 Molecular markers, and especially next-generation sequencing technologies, serve as useful tools to determine population structures and divergences in alfalfa.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Tetraploid Alfalfa (Medicago sativa L.) Populations Collected from Turkey and Former Soviet Countries

İlhan

2022

Journal of Agriculture

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Tetraploid Medicago sativa L. subspecies; M. sativa subsp. sativa, M. sativa subsp. falcata and M. sativa subsp. varia form the primary gene pool of the alfalfa. The center of diversity for this subspecies is seen as the Caucasus, Northwest Iran and Northeast Turkey, and its natural range is the former Soviet Union and the southern border of North Africa as the northern border. Genetic diversity among the primary gene pool and comparisons between regions of diversity provide a good reference for breeders when utilizing genetic resources. The United States Department of Agriculture Genetic Resources Information Network (USDA-GRIN) System provides reference data from its entire natural range, including Turkey and the Former Soviet region. In this study, seven populations collected from Turkey and thirteen alfalfa populations collected from Former Soviet Countries held in the USDA GRIN System were evaluated using 20 SSR markers. Within the scope of the study, the information between the locations of the subspecies was compared to reveal the hierarchical population structure. The results obtained from the STRUCTURE and PCA analyzes show that the populations are clustered in two main groups for both countries, but there is a high similarity in hybrid genome contents in the subspecies belonging to the Former Soviet countries. In addition, it was determined by AMOVA analysis that the variance within the populations was higher than that between the populations according to the subspecies analyzed from both countries. It is thought that the results will be effective in terms of using alfalfa genetic resources of these countries in breeding programs.

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Assessment of genetic diversity and population structure in local alfalfa genotypes using iPBS molecular markers

Cited by 10 publications

References 39 publications

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

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

Modeling Stability of Alfalfa Yield and Main Quality Traits

Comparison of Tetraploid Alfalfa (Medicago sativa L.) Populations Collected from Turkey and Former Soviet Countries

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