Diversidad genética del Loche (Cucurbita moschata duchesne ex Lam.) cultivado en Lambayeque, Perú mediante marcadores microsatélites

Universidad Nacional Agraria La Molina. Facultad de Agronomía. Departamento Académico de FitotecniaLa presente investigación contribuye al conocimiento de las relaciones genéticas entre los cultivares de loche (Cucurbita moschata) cultivados en Lambayeque, Perú. Noventa y ocho accesiones de loche cultivadas en Lambayeque y Amazonas, Perú, que representan la distribución geográfica del cultivo fueron tomadas de forma selectiva y aleatoria para estudios de diversidad genética mediante el uso de 21 marcadores microsatélites. Adicionalmente, se incluyeron 10 accesiones de C. pepo y C. maxima en este estudio para determinar su relación con el loche. Se detectaron un total de 85 bandas. La diversidad genética de Nei (0,10) indica que el loche cultivado en Lambayeque y Amazonas tiene una baja diversidad genética. El análisis de los resultados de la varianza molecular demuestra que la diferencia genética entre el loche cultivado en Lambayeque y el Amazonas es pequeño. La propagación vegetativa mediante estacas y el cultivo del loche en una zona geográfica muy restringida explicaría la escasa diversidad del cultivo. Esto a su vez sugiere que la aparente variación observada en la forma del fruto puede explicarse por la mutación somática y / o factores ambientales.The current research contributes to the knowledge of genetic relationships among loche cultivars (Cucurbita moschata) cultivated in Lambayeque, Peru. Ninety eight accessions of loche grown in Lambayeque, and Amazonas, Peru representing the geographical distribution of the crop were selectively and randomly taken for genetic diversity studies by means of 21 Simple Sequence Repeats (SSRs) markers. Additionally 10 accessions of C. pepo and C. maxima were included in this study to determine their relationship with loche. A total of 85 bands were detected. Nei ́s genetic diversity (0.10) indicates that loche grown in Lambayeque and Amazonas has a low genetic diversity. Analysis of molecular variance results demonstrate genetic difference between loche cultivated in Lambayeque and Amazonas is little. Vegetative propagation by means of stem cuttings and cultivation in a very restricted geographical area would explain the rather low diversity of the crop. This in turn would suggest that the apparent variation observed in fruit shape may be explained by somatic mutation and/or environmental factors.Tesi

Diversidad genética del Loche (Cucurbita moschata duchesne ex Lam.) cultivado en Lambayeque, Perú mediante marcadores microsatélites

Universidad Nacional Agraria La Molina. Facultad de Agronomía. Departamento Académico de FitotecniaLa presente investigación contribuye al conocimiento de las relaciones genéticas entre los cultivares de loche (Cucurbita moschata) cultivados en Lambayeque, Perú. Noventa y ocho accesiones de loche cultivadas en Lambayeque y Amazonas, Perú, que representan la distribución geográfica del cultivo fueron tomadas de forma selectiva y aleatoria para estudios de diversidad genética mediante el uso de 21 marcadores microsatélites. Adicionalmente, se incluyeron 10 accesiones de C. pepo y C. maxima en este estudio para determinar su relación con el loche. Se detectaron un total de 85 bandas. La diversidad genética de Nei (0,10) indica que el loche cultivado en Lambayeque y Amazonas tiene una baja diversidad genética. El análisis de los resultados de la varianza molecular demuestra que la diferencia genética entre el loche cultivado en Lambayeque y el Amazonas es pequeño. La propagación vegetativa mediante estacas y el cultivo del loche en una zona geográfica muy restringida explicaría la escasa diversidad del cultivo. Esto a su vez sugiere que la aparente variación observada en la forma del fruto puede explicarse por la mutación somática y / o factores ambientales.The current research contributes to the knowledge of genetic relationships among loche cultivars (Cucurbita moschata) cultivated in Lambayeque, Peru. Ninety eight accessions of loche grown in Lambayeque, and Amazonas, Peru representing the geographical distribution of the crop were selectively and randomly taken for genetic diversity studies by means of 21 Simple Sequence Repeats (SSRs) markers. Additionally 10 accessions of C. pepo and C. maxima were included in this study to determine their relationship with loche. A total of 85 bands were detected. Nei ́s genetic diversity (0.10) indicates that loche grown in Lambayeque and Amazonas has a low genetic diversity. Analysis of molecular variance results demonstrate genetic difference between loche cultivated in Lambayeque and Amazonas is little. Vegetative propagation by means of stem cuttings and cultivation in a very restricted geographical area would explain the rather low diversity of the crop. This in turn would suggest that the apparent variation observed in fruit shape may be explained by somatic mutation and/or environmental factors

Inter-primer binding site (iPBS) retrotransposon markers provide insights into the genetic diversity and population structure of carrots (Daucus, Apiaceae)

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 individual clusters. The other clade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity

Genetic Diversity and Population Structure Assessed by SSR in a Peruvian Germplasm Collection of Loche Squash (Cucurbita moschata, Cucurbitaceae)

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

Nuevas propuestas para fortalecer el boom de la agricultura en el Perú: uso masivo de recursos genéticos y desarrollo de programas modernos de mejoramiento

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 Peru in terms of space and time

Prediction of biometric variables through multispectral images obtained from UAV in beans (Phaseolus vulgaris L.) during ripening stage

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

Assessment of vegetation índices derived from UAV images for predicting biometric variables in bean during ripening stage

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

Genetic structure and diversity of a peruvian collection of a high-quality wood tree species, Ulcumano (Retrophyllum rospigliosii, Podocarpaceae

Ulcumano, which is native to South America, is an important conifer in Peru. Molecular studies are scarce, limiting modern breeding and appropriate conservation activities. Currently, molecular markers are widely employed to explore genetic structure and diversity parameters of plant species in a fast and precise manner. The objective of this study was to analyze the genetic diversity and population structure of ulcumano in Peru by using DNA-based molecular markers. Nine Randomly Amplified Polymorphic DNA (RAPD) markers were used, while 95 individuals of ulcumano were sampled from three departments of Peru. A total of 265 DNA fragments were manually scored, but 247 of them were kept after removing the non-polymorphic markers. Genetic distances were calculated using R software based on Provesti´s coefficient. A dendrogram was obtained using the UPGMA clustering algorithm, showing no clear clustering. The principal coordinate analysis agreed with two population structure analyses, demonstrating that ulcumano is contained within two clusters, (i) Junín + Pasco, and (ii) Cajamarca, while very few individuals are intermixed. Genetic diversity parameters were estimated considering the two groups (populations) identified by STRUCTURE software. Nei’s genetic diversity estimate varied between 0.22 and 0.28, while Shannon index ranged from 3.43 to 4.16. Population divergence (Fst) between the two clusters revealed low genetic differentiation (0.064). AMOVA analysis revealed that 87.31 and 12.69% of the total genetic variation were found within populations and between individuals, respectively. To the best of our knowledge, this is the first molecular study in ulcumano in Peru, and provides valuable information for the genetic improvement and sustainable management of this conifer in the country

Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers

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

Characterization of the complete chloroplast genome of a Peruvian landrace of Capsicum chinense Jacq. (Solanaceae), arnaucho chili pepper

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