Examinando por Materia "Genotyping-by-sequencing"

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Genomic insights into Lolium multiflorum diversity for forage breeding in Andean livestock systems
(Frontiers Media S.A., 2026-06-10) Bobadilla , Leidy G.; Ortiz, Rodomiro; Castillo, Gianmarco; Matías, Felipe; Gutiérrez, Lucía; Valqui, Leandro; Carrasco Chilón, William Leoncio; Díaz Valderrama, Jorge R.; Venancio, Thiago M.; Alava, E.I.; Castillo, Miguel S.; Vásquez, Héctor V.
Understanding the genetic diversity of Lolium multiflorum is essential for developing targeted breeding programs that can effectively support pasture-based livestock systems in the Peruvian Andean. This study assessed genomic variability and population structure in 27 L. multiflorum accessions from the Cajamarca region and the INIA Amazonas germplasm bank (Peru), using the genotyping-by-sequencing (GBS) technique. DNA extracted from young leaves was sequenced on an Illumina NovaSeq 6000 platform. After bioinformatic processing, 2,070 single nucleotide polymorphisms (SNPs) with heterogeneous distribution were obtained across seven chromosomes. A Principal Coordinate and an Unweighted Pair Group Method with Arithmetic Mean analyses revealed two distinct genetic groups were identified, reflecting a complex structure shaped by gene flow and local selection. The analysis of molecular variance showed that 90% of the genetic variation occurs within populations, whereas the remaining 10% corresponds to interregional differences (PhiPT = 0.099, p < 0.006). The negative Inbreeding Coefficient (F_IS) values (Cajamarca = -0.2312; Amazonas = -0.5489) indicate an excess of heterozygotes, a pattern typically associated with predominantly outcrossing species. Additionally, high observed heterozygosity (Ho > 0.57) points to potential hybrid vigor and indicates that these populations may maintain stable genetic equilibrium. Collectively, these findings demonstrate that Peruvian L. multiflorum harbors a broad genetic base, shaped by historical germplasm exchange and local environmental adaptation. This diversity provides critical insights for conservation strategies and can supports breeding programs aimed at enhancing forage resilience and productivity in high-Andean ecosystems.
In-depth genetic diversity and population structure of endangered Peruvian Amazon rosewood germplasm using Genotyping by Sequencing (GBS) technology
(MDPI, 2021-02-08) Azhar Nadeem, Muhammad; Vasquez Guizado, Stalin Juan; Qasim Shahid, Muhammad; Amjad Nawaz, Muhammad; Habyarimana, Ephrem; Ercişli, Sezai; Ali, Fawad; Karaköy, Tolga; Aasim, Muhammad; Hatipoğlu, Rüştü; Castro Gómez, Juan Carlos; Marapara Del Aguila, Jorge Luis; Adrianzén Julca, Pedro Marcelino; Torres Canales, Esperanza; Hwan Yang, Seung; Chung, Gyuhwa; Shehzad Baloch, Faheem
Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e.; STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.