José Miguel Cotes

Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree

The availability of genomewide dense markers brings opportunities and challenges to breeding programs. An important question concerns the ways in which dense markers and pedigrees, together with phenotypic records, should be used to arrive at predictions of genetic values for complex traits. If a large number of markers are included in a regression model, marker-specific shrinkage of regression coefficients may be needed. For this reason, the Bayesian least absolute shrinkage and selection operator (LASSO) (BL) appears to be an interesting approach for fitting marker effects in a regression model. This article adapts the BL to arrive at a regression model where markers, pedigrees, and covariates other than markers are considered jointly. Connections between BL and other marker-based regression models are discussed, and the sensitivity of BL with respect to the choice of prior distributions assigned to key parameters is evaluated using simulation. The proposed model was fitted to two data sets from wheat and mouse populations, and evaluated using cross-validation methods. Results indicate that inclusion of markers in the regression further improved the predictive ability of models. An R program that implements the proposed model is freely available.

Analyzing genotype by environment interaction in potato using yield-stability index

The plant breeding program of the National University of Colombia carried out 10 potato regional trials during 1998 and 1999 to evaluate 15 promising potato clones (Solanum tuberosum ssp.andigena). Genotype by environment interaction was analyzed using Kang’s methodology, which links yield performance and phenotypic stability. A MACRO was implemented using the SAS system to obtain yield-stability indices. Shukla’s variance was estimated by restricted maximum likelihood (REML), which allowed handling unbalanced data for both genotypes and replicates. In addition, a multivariate analysis methodology was developed, based on the yield-stability index. This methodology is useful when tuber yield is categorized by size and quality, which is usual in Colombian potato harvests.ResumenEl programa de mejoramiento en papa, liderado por la Universidad National de Colombia, estableció 10 pruebas regionales durante los años 1998 y 1999 para la evaluatión de 15 genotipos promisoriosde Solanum tuberosum ssp.andigena. Para el analisis e interpretation de la interaction genotipo por ambiente se utilizó la metodologia propuesta por Kang, la cual utiliza un estadístico que reúne la selection por rendimiento y estabilidad fenotipica. Una MACRO en el programa SAS fue implementada para la obtention del indice de rendimiento-estabilidad y la varianza de Shukla estimada por REML (Restricted Maximum Likelihood), la cual permite trabajar con datos desbalanceados tanto para repeticiones como genotipos. Además, se desarrolló una metodología que permitió el análisis multivariado, utilizando como base el índice de rendimiento-estabilidad, lo cual facilita el analisis del rendimiento cuando este se divide en varias categorias, como es el caso del cultivo de papa en Colombia.

Detection of a complex of viruses in tamarillo (Solanum betaceum) orchards in the Andean region of Colombia

Tamarillo is one of the main fruit crops in the Andean region of Colombia. However, due to expansion of viral diseases, the cultivated area has undergone a rapid decline during recent years. In this work, we report the taxonomical identity of some of the viruses present in the main tamarillo producing regions in Colombia. The presence of AMV, CMV, PLRV, Potyvirus, ToMV, ToRSV and TSWV was evaluated by ELISA in the provinces of Antioquia, Boyaca, Cundinamarca, Narino and Putumayo. These results were complemented with RT-PCR and cDNA sequencing of the corresponding coat regions. Potyvirus, CMV and PLRV are the most predominant viruses, each virus being detected in at least one sample. Sequencing results revealed high levels of identity of PVY and PLRV from tamarillo with virus strains from potato crops, suggesting the possibility of cross infection. Our findings confirm that a virus complex is responsible for the decline of tamarillo productivity in Colombia.

Uso de esquejes de tallo lateral para evaluar la resistencia de genotipos de Solanum phureja a Spongospora subterranea f. sp. subterranea

In order to evaluate the resistance to Spongospora subterranea f. sp. subterranea on 105 genotypes of Solanum phureja (local name in Colombia papa criolla), bioassays were conducted through propagation by lateral stem cuttings. Inoculation was performed with a 1 x 106 sporeballs mL-1 solution. The level of resistance or susceptibility of each genotype to the pathogen was determined at three different times: 1) At 15 days after inoculation (DAI), the presence of zoosporangia was evaluated in roots under optical microscopy; 2) At flowering, the presence of galls was observed in roots and 3) At harvest, the tubers were screened for the detection of pustules. Asymptomatic plants, (i.e. plants seemingly without pathogen´s structures or disease symptoms) were evaluated by PCR using specific primers. At 15 DAI it was not possible to determine the degree of resistance in the genotypes and later there were no disease symptoms on tubers. Nevertheless, disease was detectable through gall formation on roots at the flowering stage. The most susceptible genotype was Criolla Colombia. Thirty genotypes, including the commercial variety Criolla Paisa, were highly resistant and presented neither pathogen´s structures nor symptoms.

Testes multiambientais na seleção de genótipos de arroz utilizando o modelo de regressão nos sítios ou locais

The analysis of genotype x environment interaction in plant breeding have been enlarged with new methodologies in the last decade, improving its efficiency on the selection of genotypes under different environmental conditions. The objective of this research was to analyze the yield and stability of twelve genotypes of rice, in eight environments, during the years 2005 and 2006 in Colombia. Completely randomized block designs with four replications were used. The phenotypic stability parameters and grouping of environments were estimated by the genotype-environment interaction study according to SREG (Sites Regression) method and its biplot graphic (GGE). The statistical analysis indicated significant differences (with 5% probability error) among genotypes and among environments. Also, it pointed out the significance (with 5% probability error) of the genotype-environment interaction, indicating different responses of genotypes confronted with different environments. In SREG method, the two first principal components of interactions explained 75.29% of the interaction. The genotypes 400094, 350361 and the variety Fedearroz were found as the highest yields. According to the biplot GGE graphic the environments La Libertad and Escobal were the ones with small variations during the years of study.