Examinando por Autor "Arbizu Berrocal, Carlos Irvin"

Mostrando 1 - 20 de 50

Agro-morphological characterization and diversity analysis of Coffea arabica germplasm collection from INIA, Peru
(John Wiley & Sons Inc., 2023-06-06) Paredes Espinosa, Richard; Gutiérrez Reynoso, Dina Lida; Atoche Garay, Diego Fernando; Mansilla Córdova, Pedro Javier ; Abad Romaní, Yudi Gertrudis; Girón Aguilar, Rita Carolina; Flores Torres, Itala; Montañez Artica, Ana Gabriela; Arbizu Berrocal, Carlos Irvin; Amasifuen Guerra, Carlos Alberto; Maicelo Quintana, Jorge Luis; Poemape Tuesta, Carlos Augusto; Guerrero Abad, Juan Carlos
Coffee (Coffea arabica L.) plays a major role in the economy of Peru and the world. The present study aims to elucidate the agro-morphological variability of coffee genotypes maintained in the INIA´s germplasm collection. Therefore, 20 vegetative, reproductive, and phytosanitary traits of 162 coffee accessions of INIA’s germplasm collection were evaluated and analyzed. Correlation results indicate that a simultaneous selection of characters, such as number of branches per plant, number of nodes per branch, leaf area and weight of a hundred fruits, can contribute to increase coffee yields. Additionally, coffee yield was negatively correlated with the incidence and severity of coffee leaf rust, and interestingly the occurrence of small and compact coffee plants with high resistance to the disease was also found. The analysis of Tocher and Mahalanobis D2 determined the formation of 10 groups of divergent coffee accessions; where clusters 1 (accession codes 20, 29, 38, 54, 67, 71, 117, 24, 26 and 27), 5 (accession codes 46 and 53), 9 (accession code 159), and 10 (accession code 203) group promising accessions that can be used in breeding programs. Principal component analysis (PCA) showed that at least five of its principal components managed to explain 70.01% of the total variation in the collection. Finally, the high coefficients obtained for the phenotypic, genotypic and heritability variation confirm the existence of additive genes in the evaluated population, that would ensure the success of coffee breeding programs based on the selection of traits of agronomic importance.
Agro-morphological characterization and diversity analysis of Coffea arabica germplasm collection from INIA, Peru
(John Wiley & Sons Inc., 2023-04-04) Paredes Espinosa, Richard; Gutiérrez Reynoso, Dina Lida; Atoche Garay, Diego Fernando; Abad Romaní, Yudi Gertrudis; Girón Aguilar, Rita Carolina; Flores Torres, Itala; Montañez Artica, Ana Gabriela; Arbizu Berrocal, Carlos Irvin; Amasifuen Guerra, Carlos Alberto; Poemape Tuesta, Carlos Augusto; Guerrero Abad, Juan Carlos
Coffee (Coffea arabica L.) plays a major role in the economy of Peru and the world. The present study aims to elucidate the agro-morphological variability of coffee genotypes maintained in the INIA´s germplasm collection. Therefore, 20 vegetative, reproductive, and phytosanitary traits of 162 coffee accessions of INIA’s germplasm collection were evaluated and analyzed. Correlation results indicate that a simultaneous selection of characters, such as number of branches per plant, number of nodes per branch, leaf area and weight of a hundred fruits, can contribute to increase coffee yields. Additionally, coffee yield was negatively correlated with the incidence and severity of coffee leaf rust, and interestingly the occurrence of small and compact coffee plants with high resistance to the disease was also found. The analysis of Tocher and Mahalanobis D2 determined the formation of 10 groups of divergent coffee accessions; where clusters 1 (accession codes 20, 29, 38, 54, 67, 71, 117, 24, 26 and 27), 5 (accession codes 46 and 53), 9 (accession code 159), and 10 (accession code 203) group promising accessions that can be used in breeding programs. Principal component analysis (PCA) showed that at least five of its principal components managed to explain 70.01% of the total variation in the collection. Finally, the high coefficients obtained for the phenotypic, genotypic and heritability variation confirm the existence of additive genes in the evaluated population, that would ensure the success of coffee breeding programs based on the selection of traits of agronomic importance.
Assessment of the genetic diversity and population structure of the peruvian andean legume, tarwi (Lupinus mutabilis), with high quality SNPs
(MDPI, 2023-03-16) Huaringa Joaquin, Amelia Wite; Saldaña Serrano, Carla Lizet; Saravia Navarro, David; García Bendezú, Sady; Rodriguez Grados, Pedro Manuel; Salazar Coronel, Wilian; Camarena Mayta, Felix; Injante Silva, Pedro Hugo; Arbizu Berrocal, Carlos Irvin
Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.
Assessment of the genetic structure and diversity of arracacha (Arracacia xanthorrhiza) using genotyping-by-sequencing
(International Society for Horticultural Science, 2024-04-13) Arbizu Berrocal, Carlos Irvin; Saldaña Serrano, Carla Lizet; Lazo, E.; Suca Damiano, Esther Stefany; Santa Cruz Padilla, Angel Esteban; Chávez Cabrera, Alexander; Cabrera Hoyos, Héctor Antonio; Guerrero Abad, Juan Carlos; Maicelo Quintana, Jorge Luis
Arracacha, also known as “Peruvian carrot”, is a native crop from the Andean region, and is considered an unexplored root. To date, studies on this crop were mainly focused at the morphological and agronomic level. However, its genetics remains unclear. Today it is feasible to study the genetic composition of this Andean root by next-generation sequencing techniques such as genotyping-by-sequencing (GBS). We here for the first time employed 183 accessions of arracacha from six Andean localities of Peru and identified 8976 SNP markers. STRUCTURE analysis revealed this Andean crop is clustered into four populations, and with few accessions intermingled. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups. Genetic diversity estimation was conducted considering the four populations identified, revealing very high expected heterozygosity (0.432). AMOVA revealed the greatest variation within populations (89.66%) and indicated that variability between populations is 10.34%. Population divergence (Fst) ranged from 0.02 (cluster 1 vs. cluster 3) to 0.036 (cluster 1 vs. cluster 4). Negative Fis values were also detected for all populations of arracacha, indicating it depends on cross-pollination. We hope this work stimulates the development of additional molecular tools for this orphan crop in order to establish a modern breeding program and conservation strategies of this important Andean crop.
Assessment of vegetation índices derived from UAV images for predicting biometric variables in bean during ripening stage
(Universidad de Tarapacá, 2022-03-01) Quille Mamani, Javier Alvaro; Porras Jorge, Rossana; Saravia Navarro, David; Herrera, Jordán; Chávez Galarza, Julio César; Arbizu Berrocal, Carlos Irvin; Valqui Valqui, Lamberto
Here, we report the prediction of vegetative stages variables of canary bean crop employing RGB and multispectral images obtained from UAV during the ripening stage, correlating the vegetation indices with biometric variables measured manually in the field. Results indicated a highly significant correlation of plant height with eight vegetation indices derived from UAV images from the canary bean, which were evaluated by multiple regression models, obtaining a maximum correlation of R2 = 0.79. On the other hand, the estimated indices of multispectral images did not show significant correlations.
Change of vegetation cover and land use of the Pómac forest historical sanctuary in northern Peru
(Springer Nature, 2024-04-06) Vera Díaz, Elvis; Camila Leandra, Cruz Grimaldo; Barboza Castillo, Elgar; Salazar Coronel, Wilian; Canta Ventura, Jorge Marino; Salazar Hinostroza, Evelin Judith; Vásquez Pérez, Héctor Vladimir; Arbizu Berrocal, Carlos Irvin
The dry forests of northern Peru, in the regions of Piura, Tumbes, Lambayeque, and La Libertad, have experienced significant changes as a result of deforestation and changes in land use, leading to the loss of biodiversity and resources. This work analyzed for the first time the changes in vegetation cover and land use of the Pómac Forest Historical Sanctuary (PFHS), located in the department of Lambayeque (northern Peru). The employed approach was the random forest algorithm and visually interpreted Landsat satellite images for the periods 2000–2002, 2002–2004, and 2004–2008. Gain and loss rates were computed for each period, and the recovery process was assessed using the normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI). Results indicate an expansion of agricultural land during each period, resulting in the deforestation of 102.6 hectares of dense dry forest and 739.9 hectares of open dry forest between 2000 and 2008. The degree of reforestation in the cleared areas was measured using the NDVI and EVI indices, revealing an improvement from 0.22 in NDVI in 2009 to 0.36 in 2022, and from 0.14 to 0.21 in EVI over the same period. This study is expected to pave the way for executing land management plans, as well as the use and conservation of natural resources in the PFHS in a sustainable manner.
Changes in bulk and rhizosphere soil microbial diversity communities of native quinoa due to the monocropping in the Peruvian Central Andes
(MDPI, 2023-07-28) Estrada Cañari, Richard; Cosme de la Cruz, Roberto Carlos; Porras Valencia, Angie Tatiana; Reynoso Zárate, Auristela Florencia; Calderon, Constatino; Arbizu Berrocal, Carlos Irvin; Arone, Gregorio J.
Quinoa (Chenopodium quinoa) is a highly nutritious crop that is resistant to adverse conditions. Due to the considerable increase in its commercial production in Andean soils, the plant is suffering the negative effects of monocropping, which reduces its yield. We used for the first time a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the bulk and rhizosphere in soils of native C. quinoa affected by monocropping in the central Andes of Peru. The results showed that the bacterial and fungal community structure among the treatments was significantly changed by the monocropping and the types of soil (rhizosphere and bulk). Also, in soils subjected to monocropping, there was an increase in Actinobacteria and a decrease in Proteobacteria, and the reduction in the presence of Ascomycota and the increase in Basidiomycota. By alpha-diversity indices, lower values of bacteria and fungi were observed in the monoculture option compared to the soil not affected by monocropping, and sometimes significant differences were found between both. We detected differentially abundant phytopathogenic fungi and bacteria with growth-stimulating effects on plants. Also, we denoted a decrease in the abundance of the functional predictions in bacteria in the monocropped soils. This research will serve as a starting point to explore the importance and effects of microorganisms in degraded soils and their impact on the growth and quality of quinoa crops.
Characterization of the complete chloroplast genome of a Peruvian landrace of Capsicum chinense Jacq. (Solanaceae), arnaucho chili pepper
(Taylor & Francis Group, 2022-01-05) Arbizu Berrocal, Carlos Irvin; Saldaña Serrano, Carla Lizet; Ferro Mauricio, Rubén Darío; Chávez Galarza, Julio César; Herrera Flores, Jordán Valentín; Contreras Liza, Sergio; Guerrero Abad, Juan Carlos; Maicelo Quintana, Jorge Luis
In this study, we sequenced the first complete chloroplast (cp) genome of a Peruvian chili pepper landrace, “arnacucho” (Capsicum chinense). This cp genome has a 156,931 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (87,325 bp) and a 17,912 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (25,847 bp); and the percentage of GC content was 37.71%. Arnaucho chili pepper chloroplast genome possesses 133 genes that consists of 86 protein-coding genes, 37 tRNA, eight rRNA, and two pseudogenes. Phylogenetic analysis revealed that this Peruvian chili pepper landrace is closely related to the undomesticated species C. galapagoense; all belong to the Capsiceae tribe.
The complete mitochondrial genome of a Peruvian creole cattle (Bos taurus) and its phylogenetic analysis
(Wageningen Academic Publishers, 2023-02-09) Arbizu Berrocal, Carlos Irvin; Ferro Mauricio, Rubén Darío; Chávez Galarza, Julio César; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Poemape Tuesta, Carlos Augusto; Gonzáles, J.; Quilcate Pairazamán, Carlos Enrique; Corredor Arizapana, Flor Anita
The population of Peruvian creole cattle (PCC) is decreasing mainly due to the introduction of more productive breeds in recent years. We report the complete mitochondrial genome sequence of a PCC bull for the first time. This genome was 16,339 bp in length with the base composition 31.43% A, 28.64% T, 26.81% C, and 13.12% G. It contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. Among the 37 genes, 28 were positioned on the H-strand and 9 were positioned on the L-strand. The most frequently used codons were CUA (Leucine), AUA (Isoleucine), AUU (Isoleucine), AUC (Isoleucine) and ACA (Threonine). Maximum likelihood analysis clearly demonstrated that PCC are strongly related to a native African breed, giving insights into the maternal ancestry of PCC. The annotated mitochondrial genome of PCC would serve as an important genetic data set for further breeding work and conservation strategies.
Complete mitogenome of “pumpo” (Bos taurus), a top bull from a Peruvian genetic nucleus, and its phylogenetic analysis
(MDPI, 2024-05-28) Estrada Cañari, Richard; Figueroa Venegas, Deyanira Antonella; Romero Avila, Yolanda; Alvarez García, Wuesley Yusmein; Rojas Cruz, Diorman; Alvarado, Wigoberto; Maicelo, Jorge L.; Quilcate Pairazamán, Carlos Enrique; Arbizu Berrocal, Carlos Irvin
The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices.
Cover and land use changes in the dry forest of Tumbes (Peru) using sentinel-2 and google earth engine data
(MDPI, 2022-10-21) Barboza Castillo, Elgar; Salazar Coronel, Wilian; Gálvez Paucar, David; Valqui Valqui, Lamberto; Saravia Navarro, David; Gonzales, Jhony; Aldana, Wiliam; Vásquez Pérez, Héctor Vladimir; Arbizu Berrocal, Carlos Irvin
Dry forests are home to large amounts of biodiversity, are providers of ecosystem services, and control the advance of deserts. However, globally, these ecosystems are being threatened by various factors such as climate change, deforestation, and land use and land cover (LULC). The objective of this study was to identify the dynamics of LULC changes and the factors associated with the transformations of the dry forest in the Tumbes region (Peru) using Google Earth Engine (GEE). For this, the annual collection of Sentinel 2 (S2) satellite images of 2017 and 2021 was analyzed. Six types of LULC were identified, namely urban area (AU), agricultural land (AL), land without or with little vegetation (LW), water body (WB), dense dry forest (DDF), and open dry forest (ODF). Subsequently, we applied the Random Forest (RF) method for the classification. LULC maps reported accuracies greater than 89%. In turn, the rates of DDF and ODF between 2017 and 2021 remained unchanged at around 82%. Likewise, the largest net change occurred in the areas of WB, AL, and UA, at 51, 22, and 21%, respectively. Meanwhile, forest cover reported a loss of 4% (165.09 km2 ) of the total area in the analyzed period (2017–2021). The application of GEE allowed for an evaluation of the changes in forest cover and land use in the dry forest, and from this, it provided important information for the sustainable management of this ecosystem
Current and future distribution of Shihuahuaco (Dipteryx spp.) under climate change scenarios in the Central-Eastern Amazon of Peru
(MDPI, 2023-05-10) Cárdenas Rengifo, Gloria Patricia; Bravo Morales, Nino Frank; Barboza Castillo, Elgar; Salazar Coronal, Wilian; Ocaña Reyes, Jimmy Alcides; Vásquez Macedo, Miguel; Lobato Gálvez, Roiser Honorio; Injante Silva, Pedro Hugo; Arbizu Berrocal, Carlos Irvin
The consequences of climate change influence the distribution of species, which plays a key role in ecosystems. In this work, the modeling of the current and potential future distribution was carried out under different climate change scenarios of a tree species of high economic and commercial value, Dipteryx spp. This is a hardwood species that plays an important role in carbon sequestration, providing food and nesting for wildlife species, reaching more than 40 m in height with an average diameter of 70 to 150 cm. This species is currently threatened by overexploitation. Thirty-six bioclimatic, topographic and edaphic variables with ~1 km2 spatial resolution obtained from the WorldClim, SoilGrids and SRTM databases where used. Highly correlated variables were identified with the MaxEnt software for forecasting how the species distribution will be affected until the year 2100, according to the climate scenarios SPP1-2.6, SSP2-4.5, SSP3-7.0, SSP5-8.5, representing the periods 2021–2040, 2041–2060, 2061–2080 and 2081–2100, respectively. The AUC accuracy value of 0.88 to 0.89 was found for the distribution models and the highest contributing variables used were Bio 5, precipitation, Bio 2, and Bio 14. In the climate scenario SPP1-2.6 (Bio 5, precipitation and Bio 2) in 2061–2080, suitable and very suitable habitats represented 30.69% of the study area (2616 ha and 586.97 ha, respectively) and those increased by 1.75% under current climate conditions, and the suitable and unsuitable habitats represented 69.31% of the total area. The results of this research provide valuable information on the current and future distribution of the species and identify zones that can be used as the basis for the creation of conservation areas, formulation of restoration projects, reforestation and sustainable management to avoid the extinction of the species in the face of the effects of climate change.
Draft genome sequence and SSR data mining of “pumpo” (Bos taurus), a top bull from a peruvian genetic nucleus
(MDPI, 2024-06-18) Estrada Cañari, Richard; Romero Avila, Yolanda; Figueroa Venegas, Deyanira Antonella; Quilcate Pairazaman, Carlos Enrique; Casanova Nuñez-Melgar, David Pavel; Vásquez Pérez, Hector Vladimir; Alvarado Chuqui, Wigoberto; Maicelo Quintana, Jorge Luis; Arbizu Berrocal, Carlos Irvin
Pumpo is a Simmental breed and an essential livestock resource in the nucleus genetic cattle of Peru. This study provides a draft genome sequence of a top bull using a de novo assembly approach on the Illumina Novaseq X platform, yielding 208 GB of raw sequencing data with 150 bp paired‐end reads. The final genome assembly resulted in a size of 2.06 Gb with an N50 contig length of 108 Mb and a completeness of 95.7% according to BUSCO analysis. A total of 973,925 simple sequence repeats (SSRs) were identified, with a predominance of mononucleotide repeats. The genome showed low heterozygosity (0.568%) and moderate repeatability (11.5%), aligning with other Bos taurus genomes. Reference‐guided scaffolding improved the assembly quality significantly, producing an N50 scaffold value of 108 Mb. The SSR analysis of the Pumpo genome identified 973,925 SSRs with a frequency of 2,808 SSRs per kilobase, predominantly mononucleotide repeats, and 85,453 found in compound formations. Obtaining knowledge of the genome of a breeding Simmental bull is essential to optimize breeding programs and improve productivity.
Draft genome sequence resource of Erwinia sp. Strain INIA01, a phytopathogen isolated from a diseased stalk of peruvian maize
(Microbiology resource announcements, 2023-04-13) Estrada Cañari, Richard; Saldaña Serrano, Carla Lizet; Pérez Porras, Wendy Elizabeth; Arteaga, Linda; Martínez Vidal, Gabriel; Injante Silva, Pedro Hugo; Duran Gomez, Moises Rodrigo; Salazar Coronal, Wilian; Cosme de la Cruz, Roberto Carlos; Poemape Tuesta, Carlos Augusto; Arbizu Berrocal, Carlos Irvin
Here, we report the complete genome sequence of Erwinia sp. strain INIA01, a bacterium isolated from lesions of Zea mays from northern Peru. This genome possesses two circular replicons, a 4.2-Mb chromosome, and a 438-kb plasmid.
Employing a nondestructive method for the estimation of foliar area of quina (Cinchona officinalis)
(MDPI, 2022-10-15) Sueldo, Andrea; Chumbimune Vivanco, Sheyla Yanett; Mendoza, Erik; Salazar Coronel, Wilian; Minaya, Benjamin; Arbizu Berrocal, Carlos Irvin
Leaf area is related to tree growth, water balance, and mechanical resistance to physical and biotic agents. Given its importance, the purpose of the study was to compare two nondestructive methods of leaf area estimation using the free software ImageJ vs. graph paper in seedlings of quina tree. Three young and mature leaves were evaluated on 18 quina seedlings. Descriptive statistics were obtained, and both methods were compared using the Kruskal–Wallis test, and a regression equation was estimated based on leaf width and length.
Extended studies of interspecific relationships in Daucus (Apiaceae) using DNA sequences from ten nuclear orthologues
(Oxford University, 2019-09-24) Martínez Flores, Fernando; Crespo, Manuel B.; Geoffriau, Emmanuel; Allender, Charlotte; Ruess, Holly; Arbizu Berrocal, Carlos Irvin; Simon, Philipp W.; Spooner, David M.
Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius, and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated.
First draft genome assembly of the Peruvian creole cattle breed (Bos taurus) and its comparative genomics among the Bovinae subfamily
(MDPI, 2022-08-18) Estrada Cañari, Richard; Corredor Arizapana, Flor Anita; Figueroa Venegas, Deyanira Antonella; Salazar Coronel, Wilian; Quilcate Pairazamán, Carlos Enrique; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Gonzales, Jhony; Arbizu Berrocal, Carlos Irvin
The Peruvian creole cattle (PCC) is a neglected breed, and is an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. The obtained genome size of the PCC was 2.77 Gb with a contig N50 of 108Mb and 92.59% complete BUSCOs. Also, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. We downloaded proteomes and genomes of the Bovinae subfamily, and conducted a comparative analysis with our draft genome. Phylogenomic analysis showed that PCC is related to Bos indicus. Also, we identified 7,746 family genes shared among the Bovinae subfamily. This first PCC genome is expected to contribute to a better understanding of its genetics to adapt to the tough conditions of the Andean ecosystem, and evolution.
Genetic Diversity and Population Structure Assessed by SSR in a Peruvian Germplasm Collection of Loche Squash (Cucurbita moschata, Cucurbitaceae)
(MDPI, 2022-03-14) Arbizu Berrocal, Carlos Irvin; Blas Sevillano, Raúl Humberto; Ugás, Roberto
Loche is an ancient landrace of squash from Northern Peru, notable for its vegetative re-production and lack of seeds in fruits. To date, very little is known about its genetics. Here, we used 21 simple sequence repeats to assess the genetic diversity and population structure of a collection of 100 samples of loche from three localities in Peru, and 10 samples of related species, C. pepo and C. maxima (110 accessions in total). A total 85 bands were manually scored, obtaining an average of 4.05 alleles per locus. UPGMA clustering method and principal coordinate analysis showed a clear identification between the three species of Cucurbita. Population structure analysis clustered the 110 accessions into five populations: (i) three of loche, (ii) one of C. pepo, and (iii) one of C. maxima. Genetic diversity estimation was conducted considering only the three groups (populations) of loche identified, which was 0.024 as an average. AMOVA revealed the greatest variation between populations (79.66%) and indicated that variability within populations is 20.33%. Vegetative prop-agation by means of stem cuttings and cultivation in a very restricted geographical area would ex-plain the rather low diversity of loche. This in turn would suggest that the apparent variation ob-served in fruit shape may be explained by somatic mutation and/or environmental factors.
Genetic diversity and population structure of a Peruvian cattle herd using SNP data
(Frontiers Media S.A., 2023-03-10) Corredor Arizapana, Flor Anita; Figueroa Venegas, Deyanira Antonella; Estrada Cañari, Richard; Salazar Coronel, Wilian; Quilcate Pairazamán, Carlos Enrique; Vásquez Pérez, Héctor Vladimir; Gonzales Malca, Jhony Alberto; Maicelo Quintana, Jorge Luis; Medina Morales, Percy Edilberto; Arbizu Berrocal, Carlos Irvin
New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and ma les with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold’s distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.
Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers
(MDPI, 2021-08-22) Saldaña Serrano, Carla Lizet; Cancan, Johan D.; Cruz Hilacondo, Wilbert Eddy; Correa, Mirian; Ramos León, Haydeé Miriam; Cuellar Bautista, José Eloy; Arbizu Berrocal, Carlos Irvin
Capirona (Calycophyllum spruceanum Benth.) is a tree species of commercial importance widely distributed in South American forests that is traditionally used for its medicinal properties and wood quality. Studies on this tree species have been focused mainly on wood properties, propagation, and growth. However, genetic studies on capirona have been very limited to date. Currently, it is possible to explore genetic diversity and population structure in a fast and reliable manner by using molecular markers. We here used 10 random amplified polymorphic DNA (RAPD) markers to analyze the genetic diversity and population structure of 59 samples of capirona that were sampled from four provinces located in the eastern region of the Peruvian amazon. A total of 186 bands were manually scored, generating a 59 × 186 presence/absence matrix. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups that correspond to the geographic origin of the capirona samples (LBS, Irazola, Masisea, Iñapari). Similarly, a discriminant analysis of principal components (DAPC) and STRUCTURE analysis confirmed that capirona is grouped into four clusters. However, we also noticed that a few samples were intermingled. Genetic diversity estimation was conducted considering the four groups (populations) identified by STRUCTURE software. AMOVA revealed the greatest variation within populations (71.56%) and indicated that variability among populations is 28.44%. Population divergence (Fst) between clusters 1 and 4 revealed the highest genetic difference (0.269), and the lowest Fst was observed between clusters 3 and 4 (0.123). RAPD markers were successful and effective. However, more studies are needed, employing other molecular tools. To the best of our knowledge, this is the first investigation employing molecular markers in capirona in Peru considering its natural distribution, and as such it is hoped that this helps to pave the way towards its genetic improvement and the urgent sustainable management of forests in Peru.