Browsing by Author "Carrasco, Basilio"

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    A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (Phaseolus vulgaris L.)
    (2024) Arriagada, Osvin; Arevalo, Barbara; Pacheco, Igor; Schwember, Andres R.; Meisel, Lee A.; Silva, Herman; Marquez, Katherine; Plaza, Andrea; Perez-Diaz, Ricardo; Pico-Mendoza, Jose; Cabeza, Ricardo A.; Tapia, Gerardo; Fuentes, Camila; Rodriguez-Alvarez, Yohaily; Carrasco, Basilio
    The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types 'Tortola', 'Sapito', 'Coscorron', and 'Frutilla'. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (pi = 0.053; uHe = 0.53) and the negative value of Tajima' D (D = -1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean.
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    Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools
    (2022) Carrasco, Basilio; Arevalo, Barbara; Perez-Diaz, Ricardo; Rodriguez-Alvarez, Yohaily; Gebauer, Marlene; Maldonado, Jonathan E.; Garcia-Gonzales, Rolando; Chong-Perez, Borys; Pico-Mendoza, Jose; Meisel, Lee A.; Ming, Ray; Silva, Herman
    A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.
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    Efficient protocols for the extraction of microbial DNA from the rhizosphere of hydrophilic forests in Chile
    (PONTIFICIA UNIV CATOLICA CHILE, FAC AGRONOMIA INGENIERIA FORESTAL, 2012) Caceres, Pablo; Cordero, Cecilia; Gonzalez, Gloria; Quiroz, Karla; Bobadilla, Juan C.; Bravo, Carmen; Caligari, Peter D. S.; Carrasco, Basilio; Garcia Gonzales, Rolando
    P. Caceres, C. Cordero, G. Gonzalez, K. Quiroz, J.C. Bobadilla, C. Bravo, P.D.S. Caligari, B. Carrasco, and R. Garcia-Gonzales. 2012. Efficient protocols for the extraction of microbial DNA from the rhizosphere of hydrophilic forests in Chile. Cien. Inv. Agr. 38(3): 585-592. A lysis buffer-based protocol (Protocol BA), a modified lysis buffer-based protocol (Protocol BA Mod) and a commercial extraction kit (Protocol PS Kit) (Power Soil, Mo bio Laboratories, CA USA) were each evaluated for their ability to produce high-quality DNA with yields sufficient to allow its use in biodiversity studies. Similarly, the effect of liquid nitrogen on the process of cell disruption in all of the protocols that were studied. DNA yields ranged from 12.4 ng g(-1) of processed soil to 9620 ng g(-1) using the modified lysis buffer and commercial extraction kit, respectively. The quality of the DNA was determined by the ability of the DNA to produce efficient and reproducible polymerase chain reaction (PCR) products, using primers for universal 16S and 18S ribosomal RNA regions from bacteria and fungi, respectively. High-quality DNA was obtained to run PCRs in all protocols, but the efficiency of the method depended on the dilution of the DNA prior to performing the PCR. The three extraction methods generated PCR products with 90% efficiency. The DNA produced with the commercial kit was able to produce the highest PCR efficiency (95%) when the 10(-1) dilution was used. The method based on the use of lysis buffer produced the highest efficiency (90%) using a 10(-2) dilution. Meanwhile, the modified lysis buffer-based protocol generated the highest efficiency of PCR products using the 10(-3) dilution factor with 95% of efficiency. For the first time, reliable and efficient DNA isolation from the rhizosphere of hydrolic forest is documented, enabling a wide range of applications for this technique.
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    Genetic characterization of Japanese plum cultivars (Prunus salicina) using SSR and ISSR molecular markers
    (2012) Carrasco, Basilio; Diaz, Carole; Moya, Mario; Gebauer, Marlene; Garcia-Gonzalez, Rolando
    B. Carrasco, C. Diaz, M. Moya, M. Gebauer and R. Garcia-Gonzalez. 2012. Genetic characterization of Japanese plum cultivars (Prunus salicina) using SSR and ISSR molecular markers. Cien. Inv. Agr. 39(3): 533-543. The genetic characterization of 29 elite Japanese plum cultivars (Prunus salicina) and 4 Prunus cultivars was carried out by analyzing 97 Simple Sequence Repeat (SSR) alleles and 232 binary Inter Simple Sequence Repeat (ISSR) loci. A high level of genetic variability was found for these two molecular markers among the Japanese plum cultivars compared to other Prunus species. On average, the variability found by analyzing the SSR alleles were Na = 12.1, Ne = 5.2, Ho = 0.9, He = 0.8 and F = -0.127, whereas ISSR yielded values of h = 0.15 and I = 0.27. The genetic relationship among cultivars was estimated with Principal Coordinate Analysis (PCA) and a Bayesian clustering approach using the software program Structure. This program identified two subgroups (k=2). The first group included cultivars of four Prunus species: P. salicina, P. armeniaca, P. domestica and P. ceracifera, whose memberships ranged between 0.74 and 1.0. The second group included 19 Japanese plum cultivars and one plumcot cultivar, with memberships between 0.57 and 0.99. With some exceptions, similar relationships among cultivars were foundPCA. The level of genetic differentiation between two groups was low (G(st)=0.055 and phi(ST)=0.04), and a low level of linkage disequilibrium (LD) was observed for all allele combinations. These results suggest that the high level of genetic variability, the low level of LD and the scarce degree of differentiation detected by Structure between the two genetic groups can be explained by the self-incompatibility mechanism that favors the exchange between genetically distant Prunus cultivars and by the intra- and interspecific hybridization strategies frequently used in plum breeding programs.
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    Genetic diversity and population structure of Chilean blueberry Gaultheria pumila (L.f.) DJ Middleton (Ericaceae)
    (2020) Pico-Mendoza, Jose; Garcia-Gonzales, Rolando; Quiroz, Karla; Pinoargote, Miryan; Rodriguez-Alvarez, Yohaily; Chong, Borys; Caceres-Ruz, Pablo; Pino, Hugo; Caligari, Peter D. S.; Carrasco, Basilio
    Gaultheria pumila (L.f.) D.J. Middleton is a native shrub of Chile that produces edible berry fruits. This species is related to the cultivated Vaccinium species; for this reason it is currently called Chilean blueberry locally. Although G. pumila has important attributes, it has been largely ignored, and remains an unexplored genetic resource. This study investigates the genetic diversity to support the efforts to domesticate the species. Sampling was carried out in 11 sites collected from four Regions of Chile. In total, 160 individuals were collected and analyzed using a set of 10 simple sequence repeats (SSRs) markers. The average observed heterozygosity was Ho = 0.50, while the expected heterozygosity was He = 0.46. The fixation index (F-IS) showed an average of -0.07, and the proportion of differentiation among populations (F-ST) was 0.11. The average level of polymorphic loci in all populations (PPL) was 96.97%. AMOVA showed that the genetic diversity among populations was very low (Phi PT = 6%). Significant correlations were found between genetic and geographic distance. Multivariate and Bayesian analyses identified two genetic groups. These results will be very useful to support the efforts to domesticate and increase the value of this species.
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    Genetic structure of highland papayas (Vasconcellea pubescens (Lenn, et C. Koch) Badillo) cultivated along a geographic gradient in Chile as revealed by Inter Simple Sequence Repeats (ISSR)
    (SPRINGER, 2009) Carrasco, Basilio; Avila, Patricio; Perez Diaz, Jorge; Munoz, Patricio; Garcia, Rolando; Lavandero, Blas; Zurita Silva, Andres; Retamales, Jorge B.; Caligari, Peter D. S.
    In Chile Vasconcellea pubescens is cropped to produce canned fruit, juice, jam and processed sweets. Additionally this species produces latex with a high level of papain, an important and valuable proteolytic enzyme with industrial applications. In this investigation seven ISSR primers were used to study the level and organization of genetic diversity in 333 samples of V. pubescens. Out of the 114 bands recorded, 63 proved to be polymorphic (P = 55.3%). At the species level, the genetic diversity was rather low (h = 0.01 +/- A 6,80188E-05, Shannon's Index I = 0.16 +/- A 0,000148). The major portion of the genetic diversity was found within groups (65%). The genetic differentiation between the different groups was significant, as the AMOVA analysis suggested (I broken vertical bar(pt) = 0.35). When analysing the Northern area alone, the differentiation increased to I broken vertical bar(pt) = 0.40. When only the Southern area was analysed, I broken vertical bar(pt) decreased to 0.18, indicating greater genetic similarity among the samples. The results generated from Structure and Bayesian Analysis of Population Structure distinguished 8 genetically different groups, five of them located in the north and three in the south. The results are discussed in the light of the growers' practices.
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    Heterogeneous genetic structure in a natural population of Rauli (Nothofagus nervosa)
    (2011) Carrasco, Basilio; Eaton, Lafayette; Letelier, Luis; Diaz, Carole; Garcia-Gonzales, Rolando
    B. Carrasco, L. Eaton, L. Letelier, C. Diaz, and R. Garcia-Gonzales. 2011. Heterogeneous genetic structure in a natural population of Rauli (Nothofagus nervosa). Cien. Inv. Agr. 38(3): 441-452. Heterozygote deficiencies in natural populations of outbreeding tree species are common and thought to be due mainly to biparental inbreeding. Inbreeding is believed to be caused by family structure within populations, a product of limited seed dispersal and probably limited pollen dispersal. Although both theory and simulation studies predict that structure should be apparent where trees are isolated by distance, most studies of structure in natural populations have detected only a weak spatial genetic structuring. In this contribution, we compare the use of spatial autocorrelation methodology and F statistics with the concept of relatedness to examine the spatial genetic structure in the natural population of a native southern beech and to explore the discrepancy between theory and observations. Autocorrelation detected structure in only a few of the nine enzyme loci tested in an estimated patch size of approximately 10 m. By successively eliminating the largest distances in the Gabriel map, the population was separated into groups or patches of neighbors, which were then tested for relatedness. Three groups of relatives were found interspersed with seven groups of unrelated individuals. The F statistics for these groups also showed weak genetic structure. We suggest that heterogeneity of family structure within natural populations may be one reason why more spatial genetic structure has not been detected.
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    In vitro culture of Luma chequen from vegetative buds
    (2013) Mancilla, Hector; Quiroz, Karla; Arencibia, Ariel; Carrasco, Basilio; Garcia-Gonzales, Rolando
    Luma chequen, a small tree or large shrub belonging to the Myrtaceae family, is endemic to South America and has medicinal, nutritional and ornamental potential. However, its native habitat is deteriorating gradually, and it is suffering from the effects of fragmentation that is being caused by the conversion of forest land to agricultural land and the natural expansion of monocultural plantations of exotic species, such as Pinus radiata. The purpose of this work is to develop an effective procedure for establishing in vitro cultures of the native Chilean species L. chequen. Aseptic nodal segments were evaluated after exposure to a disinfecting agent (1% solution of sodium hypochlorite) for different lengths of time. Murashige and Skoog (MS) or Woody Plant (WPM) culture media with 6-Bencilaminopurine (BAP) or 2-isopentenil adenine (2-iP) added to a concentration of 1 mg L-1 were evaluated. Although no significant differences were observed between cultures with and without additives, 40.43% of the explant cultures were successfully established. Furthermore, the choice of basal medium or the addition of plant growth regulators was not found to affect the shoot formation efficiency.
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    IN VITRO PROPAGATION OF CEDAR (Cedrela odorata L.) FROM JUVENILE SHOOTS
    (2011) Garcia-Gonzales, Rolando; Delgado, Miladys; Gonzalez, Yailin; Gonzalez, Anibal; Garriga, Miguel; Caligari, Peter D. S.; Carrasco, Basilio; Quiroz, Karla
    Cedrela odorata L. is one of the most important timber species currently traded in the Caribbean and Central America; however, it has been intensively exploited. In vitro techniques and clonal propagation can help to develop new plantations and assist in establishing improvement programs for this species. The aim of this study was to develop a protocol to establish in vitro conditions and to micropropagate this species from nodal explants from juvenile cuttings taken from field trees. Disinfection of node explants with 5% propiconazole CE 25 during 3 min resulted in 100% explant disinfection and 60% morphogenic response on those established explants. Shoot development was optimized by cultivating in vitro node explants in Murashige and Skoog basal medium supplemented with 2 mg L-1 6-bencilaminopurine and 3 mg L-1 naphthaleneacetic acid. This medium resulted in 100% shoot development from the in vitro node explants with a 3.93 cm mean height. Rooting was also stimulated 6 wk after individualization of the regenerated plants on the same micropropagation medium with a mean of 3.9 roots per plant. In vitro plants did not show morphologic differences when compared to ex vitro seeds.
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    Meta-QTL Analysis for Yield Components in Common Bean (Phaseolus vulgaris L.)
    (2023) Arriagada, Osvin; Arevalo, Barbara; Cabeza, Ricardo A.; Carrasco, Basilio; Schwember, Andres R.
    Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
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    MOLECULAR TOOLS FOR RAPID AND ACCURATE DETECTION OF BLACK TRUFFLE (Tuber melanosporum Vitt.) IN INOCULATED NURSERY PLANTS AND COMMERCIAL PLANTATIONS IN CHILE
    (2011) Cordero, Cecilia; Caceres, Pablo; Gonzalez, Gloria; Quiroz, Karla; Bravo, Carmen; Ramirez, Ricardo; Caligari, Peter D. S.; Carrasco, Basilio; Garcia-Gonzales, Rolando
    Truffle (Tuber melanosporum Vitt.) culture is an agroforestry sector in Chile of increasing interest due to the high prices that truffles fetch in the national market and the recent evidence that its commercial production is possible in Chilean climatic and soil conditions. In this study, the efficiency of three methods of DNA extraction from a mix of 5 g of soil and roots from both nursery and field plants of Quercus ilex L. mycorrhized with T. melanosporum were evaluated, and a simple and reproducible protocol was established. Detection of T. melanosporum was performed by the technique of cleaved amplified polymorphic sequence (CAPS) from amplicons generated with the primers ADL1 (5'-GTAACGATAAAGGCCATCTATAGG-3') and ADL3 (5'-CGTTTTTCCTGAACTCTTCATCAC-3'), where a restriction fragment of 160 bp specific for T. melanosporum was generated, which allows the discrimination of this species from the rest of the species belonging to the Tuber sp. genus. Direct detection of T. melanosporum in one step was also obtained by polymerase chain reaction (PCR) from total DNA isolated from mycorrhized roots and with the primers ITSML (5'-TGGCCATGTGTCAGATTTAGTA-3') and ITSLNG (5'-TGATATGCTTAAGTTCAGCGGG-3'), generating a single amplicon of 440 bp. The molecular detection of T. melanosporum by the methods presented here will allow the rapid and accurate detection of mycorrhization of trees, both under nursery and field conditions. This technology will also provide more security to farmers by controlling the quality of the mycorrhized trees they will plant and also by following the mycorrhization status of established orchards.
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    Morphological and Molecular Characterization of Selected Chilean Runner Bean (Phaseolus coccineus L.) Genotypes Shows Moderate Agronomic and Genetic Variability
    (2021) Arriagada, Osvin; Schwember, Andres R.; Greve, Maria Jesus; Urban, Milan O.; Cabeza, Ricardo A.; Carrasco, Basilio
    The runner bean is the third most economically important Phaseolus species, which is cultivated on small-scale agriculture for the production of immature pods or to obtain dry seeds. However, despite the economic importance and agronomic potential of this species, the runner bean has been little studied from the genetic standpoint. Therefore, the main objective of this study was to characterize ten selected lines of runner bean obtained from Central (Santiago) and Southern (Valdivia and Villarica) Chile based on morphological and agronomic traits. In addition, the genetic variability of these lines was determined using 12 Inter-Simple Sequence Repeat (ISSR) markers to evaluate the potential of this germplasm for breeding and commercial purposes. As a result, the lines from Central Chile were characterized, and had a higher number of pods per plant compared to the Southern lines, although the size and weight of their seeds were lower. Moreover, a low level of genetic diversity (He = 0.251) was encountered in this population. Finally, this is one of the first studies that generate relevant and novel information on the morphological, agronomic and genetic characterization of the P. coccineus germplasm present in Chile.
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    Nutritional Characterization of Chilean Landraces of Common Bean
    (2024) Marquez, Katherine; Arriagada, Osvin; Perez-Diaz, Ricardo; Cabeza, Ricardo A.; Plaza, Andrea; Arevalo, Barbara; Meisel, Lee A.; Ojeda, Daniela; Silva, Herman; Schwember, Andres R.; Fuentes, Camila; Flores, Monica; Carrasco, Basilio
    Common bean (Phaseolus vulgaris L.) is the primary grain legume cultivated worldwide for direct human consumption due to the high nutritional value of its seeds and pods. The high protein content of common beans highlights it as the most promising source of plant-based protein for the food industry. Additionally, landraces of common bean have great variability in nutritional traits, which is necessary to increase the nutritional quality of elite varieties. Therefore, the main objective of this study was to nutritionally characterize 23 Chilean landraces and 5 commercial varieties of common bean to identify genotypes with high nutritional value that are promising for the food industry and for genetic improvement programs. The landrace Phv23 ('Palo') was the most outstanding with high concentrations of minerals such as P (7.53 g/kg), K (19.8 g/kg), Mg (2.43 g/kg), Zn (52.67 mg/kg), and Cu (13.67 mg/kg); essential amino acids (364.8 mg/g protein); and total proteins (30.35 g/100 g seed). Additionally, the landraces Phv9 ('Cimarron'), Phv17 ('Juanita'), Phv3 ('Araucano'), Phv8 ('Cabrita/Senorita'), and Phv4 ('Arroz') had a high protein content. The landrace Phv24 ('Peumo') stood out for its phenolic compounds (TPC = 218.1 mg GA/100 g seed) and antioxidant activity (ORAC = 22,167.9 mu mol eq trolox/100 g extract), but it has moderate to low mineral and protein concentrations. In general, the concentration of nutritional compounds in some Chilean landraces was significantly different from the commercial varieties, highlighting their high nutritional value and their potential use for the food industry and for genetic improvement purposes.
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    Phenotypic and genetic analysis of a peach and a Japanese plum core collection for pre-breeding and distinctness assessment
    (2022) Carrasco, Basilio; Ramirez, Cesar; Gebauer, Marlene; Meisel, Lee A.; Hasbun, Rodrigo; Silva, Herman
    To know the relationships between phenotypic and genetic variables in a germplasm collection of fruit crops is useful a pre-breeding and cultivar distinctness. A core collection of 23 peaches/nectarines (Prunus persica (L.) Batsch), and 16 Japanese plum (Prunus salicina Lindl. var. salicina) cultivars were evaluated for 33 and 29 characteristics (botanical/ productive) respectively during two growing seasons. Also, eight specific simple sequence repeats (SSRs) markers were analyzed in both species. Principal components analyses revealed seven characteristics (related to the size of the fruit and the firmness of the pulp) as the most important for the 23 peach/nectarine cultivars and four characteristics (yield, fruit size, soluble solids, and harvest time) for the 16 Japanese plum cultivars. These analyses revealed three cultivars of peaches (Diamond Princess, Dixon, and Dr. Davis) and three of nectarines (Ruby diamond, Artic sweet, Summer fire) with the highest values for fruit size and pulp firmness. Four Japanese plum cultivars (Angeleno, Flavor Rich, Red Heart, and Pink Delight) showed the highest values of yield, fruit size, soluble solids, and harvest time. Elite germplasms to carry out a breeding program were identified from both the phenotypic and genetic analysis. Additionally, cultivar-specific SSR alleles were identified and are a relevant tool for cultivar distinctness.
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    Proximal causes of genetic variation between and within populations of raulí (Nothogafus nervosa).
    (2009) Carrasco, Basilio; Garnier, Maurice; Eaton, Lafayette; Guevara, Rafael; Carú, Margarita