Browsing by Author "Pico-Mendoza, Jose"

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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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    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.