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...

Plant scientists make inferences and predictions from phylogenetic trees to solve scientific problems. Crop losses due to disease damage is an important problem that many plant breeders would like to solve, so the ability to predict traits like disease resistance from phylogenetic trees derived from diverse germplasm would be a significant approach to facilitate cultivar improvement. Alternaria leaf blight (ALB) is among the most devastating diseases of carrots (Daucus spp., Apiaceae) worldwide. Thus, new approaches to identify resistant germplasm to this disease are needed. In a study of 106 accessions of wild and cultivated Daucus and related genera, we determined plant height is the best explanatory variable to predict ALB resistance using a phylogenetic linear regression model. Using the estimated area under the disease progress curve, the most resistant species to ALB were the non-c...

Here, we report the first complete chloroplast (cp) genome of Cinchona officinalis. This cp genome has a 156,984 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (83,929 bp) and an 18,051 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (27,502 bp). The total GC content was 37.75%. Quina tree chloroplast genome possesses 135 genes that consisted of 89 protein-coding genes, 37 tRNA, eight rRNA, and one pseudogene. Phylogenetic analysis showed that C. officinalis is sister to C. pubescens and sister to them is Isertia laevis; all belong to the Cinchonoideae sub-family.

Cattle spread throughout the American continent during the colonization years, originating creole breeds that adapted to a wide range of climate conditions. The population of creole cattle in Peru is decreasing mainly due to the introduction of more productive breeds in recent years. During the last 15 years, there has been significant progress in cattle genomics. However, little is known about the genetics of the Peruvian creole cattle (PCC) despite its importance to (i) improving productivity in the Andean region, (ii) agricultural labor, and (iii) cultural traditions. In addition, the origin and phylogenetic relationship of the PCC are still unclear. In order to promote the conservation of the PCC, we sequenced the mitochondrial genome of a creole bull, which also possessed exceptional fighting skills and was employed for agricultural tasks, from the highlands of Arequipa for the firs...

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.

Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Pe...

Peru is a place with abundant biological resources that should be employed for the benefit of society in general. However, to date, the use of Peruvian plant genetic resources was not fully exploited for the development of improved crops. This work was mostly conducted by the international private sector. The Climate Change Laboratory at Instituto Nacional de Innovación Agraria, and other laboratories at Universidad Nacional José Faustino Sánchez Carrión and Universidad Nacional Agraria La Molina together with other research programs of other institutions seek to promote the massive and sustainable use of plant genetic resources maintained in germplasm banks. It is planned to make use of modern molecular and morphological techniques. Moreover, infrastructure and human resources are being improved. As a result, we will be able to maintain the growth of the agricultural activity in Per...

•Premise of the study: We explored the utility of multiple nuclear orthologs for the taxonomic resolution of wild and cultivated carrot, Daucus species. •Methods: We studied the phylogeny of 92 accessions of 13 species and two subspecies of Daucus and 15 accessions of related genera (107 accessions total) with DNA sequences of 94 nuclear orthologs. Reiterative analyses examined data of both alleles using ambiguity codes or a single allele with the highest coverage, trimmed vs. untrimmed homopolymers; pure exonic vs. pure intronic data; the use of all 94 markers vs. a reduced subset of markers; and analysis of a concatenated data set vs. a coalescent (species tree) approach. •Key results: Our maximum parsimony and maximum likelihood trees were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades. They resolved multiple accessions of m...

•Premise of study: Molecular phylogenetics of genome‐scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. A companion phylogenomics analysis of Daucus using 94 conserved nuclear orthologs supported many of the traditional species but showed unexpected results that require morphological analyses to help interpret them in a practical taxonomic context. •Methods: We evaluated character state distributions, stepwise discriminant analyses, canonical variate analyses, and hierarchical cluster analyses from 40 morphological characters from 81 accessions of 14 taxa of Daucus and eight species in related genera in an experimental plot. •Key results: Most characters showed tremendous variation with character state overlap across many taxa. Multivariate analyses separated the outgroup taxa easily from the Daucus ingroup. Concordant with molecular ...

In a previous study using 94 nuclear orthologs, we reported the species status of the Daucus guttatus complex to be unresolved, partitioned into three clades. In the present study, a subset of ten of these 94 orthologs was used to infer the phylogeny of the D. guttatus complex and related species. A near parallel set of accessions, planted in a common garden, was used for morphological analyses. The molecular trees are highly resolved for most of the clades, grouping accessions of the D. guttatus complex into four clades. Bayesian concordance analysis and a coalescent approach gave slightly different topologies. Morphological data likewise support four taxa in the complex. Moreover, herbarium research from a companion study informs nomenclature for taxa of the complex. We identify these four clades as D. bicolor, D. conchitae, D. guttatus, and D. setulosus; internested in or among these ...

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 id...

Universidad Nacional Agraria La Molina. Facultad de Agronomía. Departamento Académico de Fitotecnia

Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individu...

•Premise of the Study: osible ies boundaries of wild and cultivated potatoes are controversial, with osible the taxonomic problems in the cultivated potato clade. We here provide the first in‐depth phylogenetic study of the cultivated potato clade to explore osible causes of these problems. •Methods: We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony‐informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness‐of‐fit tests. •Key Results: There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The res...

Background Loche (Cucurbita moschata) is a pre-Columbian squash that is cultivated exclusively in the northern coast of Peru, Lambayeque. This crop is notable for the presence of warts in its skin and for its vegetative reproduction as it commonly lacks of seeds in fruits. Currently, loche may be considered a new product for international markets, recognizing the gastronomy of Lambayeque in the world and dynamizing the Peruvian agro-export area. However, genomic information about this squash is very limited.

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.

Here, we report the prediction of vegetative stages variables of canary bean crop by means of 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 RGB image vegetation indices for the canary bean crop, which were used for predictive models, obtaining a maximum correlation of R2 = 0.79. On the other hand, the estimated indices of multispectral images did not show significant correlations.

Tomato (Solanum lycopersicum) (Solanaceae) is an important vegetable crop worldwide that contains significant amounts of vitamins A and C. It also possesses a powerful antioxidant, lycopene, which can help prevent the development of many forms of cancer. However, this vegetable is highly susceptible to a number of emerging viruses. Since the first report of ToBRFV in Jordan, this emerging virus has been detected in Germany, Israel, Italy, Mexico, Palestine, and the United States, but its incidence was not reported in Peru. We collected 56 samples of fresh leaves of tomato plants with viral symptoms and 13 without symptoms as control from two regions that comprise more than 50% of tomato production in Peru, Lima and Ica. Mosaic, mottling, plant stunting and brown rugose symptoms were observed in collected leaves that were preserved in liquid nitrogen until processing. We extracted RNA usi...

Avocado crop (Persea americana Mill.) is of great commercial importance due to its high profitability. However, it is being affected by various diseases and pests that affect yield and reduce fruit quality. The aim of this research was to develop methodologies for the evaluation of avocado plantations using different non-destructive technologies for rapid phenotyping and early detection of the incidence of diseases or damage due to stress in the stem. A plot of 0.7 ha. was evaluated, with a total of 44 individuals using Field-Map technology (dasometric and morphological characterization), RGB-multispectral images from Remotely Piloted Aircraft System (RPAS) (rapid phenotyping), while 15 individuals were evaluated using tomography (assessment of the internal state of the stem). The results with tomography indicated that there is a tree with wood rot of 14% with a lower acoustic speed with...

Silvopastoral systems (SPS) are presented as an alternative for the protection and recovery of soils; however, the relationship between the tree component and the physical-chemical characteristics of the soil is unknown. Thus, the objective of this study was to evaluate the physical-chemical characteristics of the soil under four silvopastoral systems (SPS), alder (Alnus acuminata), pine (Pinus patula), cypress (Cupressus macrocarpa), and pona (Ceroxylon quindiuense), and a treeless system (TS) in the Amazonas region. A completely randomized design (CRD) with five treatments and three replicates was used. The experimental units were sampled at two depths, 0–15 and 15–30 cm. The parameters evaluated were pH, electrical conductivity (dS/m), organic matter (%), phosphorus (ppm), potassium (ppm), cation exchange capacity (meq/100 g), porosity (%), mechanical resistance (kg/cm2), bulk den...