Browsing by Author "Silva, Herman"

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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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    Association between the concentration of n-alkanes and tolerance to cracking in commercial varieties of sweet cherry fruits
    (2015) Rios, Juan Carlos; Robledo, Francisco; Schreiber, Lukas; Zeisler, Viktoria; Lang, Erika; Carrasco Gálvez, Basilio Alejandro; Silva, Herman
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    De novo transcriptome assembly of 'Angeleno' and 'Lamoon' Japanese plum cultivars (Prunus salicina)
    (2016) González, Máximo; Maldonado, Jonathan; Salazar, Erika; Silva, Herman; Carrasco Gálvez, Basilio Alejandro
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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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    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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    Regeneration of highland papaya (vasconcellea pubescens) from anther culture
    (2018) Chong Pérez, Borys; Carrasco Gálvez, Basilio Alejandro; Silva, Herman; Herrera, Francisca; Quiroz, Karla; Garcia Gonzales, Rolando