Gregorio Alvarado

International Maize and Wheat Improvement Center, Tezcoco, México, Mexico

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Publications (18)27.35 Total impact

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    Full-text · Dataset · Oct 2015
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    ABSTRACT: A genomic selection index (GSI) is a linear combination of genomic estimated breeding values using genomic markers to predict the net genetic merit and select parents from a non-phenotyped testing population. Some authors have proposed a GSI; however, they have not used simulated or real data to validate the GSI theory and have not explained how to estimate the GSI selection response and the GSI expected genetic gain per selection cycle for the unobserved traits after the first selection cycle in order to obtain information about the genetic gains in each subsequent selection cycle. In this paper, we develop the theory of a GSI and apply it to two simulated and four real data sets with four traits. Also, we numerically compare its efficiency with that of the phenotypic selection index (PSI) using the ratio of the GSI response over the PSI response, and the PSI and GSI expected genetic gain per selection cycle for observed and unobserved traits, respectively. In addition, we used the Technow inequality to compare GSI vs PSI efficiency. Results from the simulated data were confirmed by the real data, indicating that GSI was more efficient than PSI per unit of time. Copyright © 2015 Author et al.
    Full-text · Article · Aug 2015 · G3-Genes Genomes Genetics
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    ABSTRACT: Understanding the factors that define a given interaction is important in agricultural, agronomic, and plant breeding research, where agronomic treatments or genotypes are evaluated under several environmental conditions and where interactions usually complicate a researcher’s decisions. We give examples of how interactions, in common agricultural experiments, can be examined and studied to make use of the rich information available on the interaction term of the model. Examples with different levels of interaction complexity are used to illustrate how to analyze and interpret interactions and how interaction components can be partitioned into comparisons with sensible biological interpretations. It will offer researchers a greater understanding of how to exploit interaction information beyond the standard statistical tests performed in the usual analysis of variance. Simple SAS codes for performing standard interaction contrasts and defining interaction covariables are provided. © 2015 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved.
    Full-text · Article · Mar 2015 · Agronomy journal
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    ABSTRACT: In marker-assisted recurrent selection (MARS), a subset of molecular markers significantly associated with target traits of interest are used to predict the breeding value of individual plants, followed by rapid recombination and selfing. This study estimated genetic gains in grain yield (GY) using MARS in 10 biparental tropical maize (Zea may L.) populations. In each population, 148 to 184 F2:3 (defined as C0) progenies were derived, crossed with a single-cross tester, and evaluated under water-stressed (WS) and well-watered (WW) environments in sub- Saharan Africa (SSA). The C0 populations were genotyped with 190 to 225 single-nucleotide polymorphism (SNP) markers. A selection index based on marker data and phenotypic data was used for selecting the best C0 families for recombination. Individual plants from selected families were genotyped using 55 to 87 SNPs tagging specific quantitative trait loci (QTL), and the best individuals from each cycle were either intercrossed (to form C1) or selfed (to form C1S1 and C1S2). A genetic gain study was conducted using test crosses of lines from the different cycles F1 and founder parents. Test crosses, along with five commercial hybrid checks were evaluated under four WS and four WW environments. The overall gain for GY using MARS across the 10 populations was 105 kg ha−1 yr−1 under WW and 51 kg ha−1 yr−1 under WS. Across WW environments, GY of C1S2–derived hybrids were 8.7, 5.9, and 16.2% significantly greater than those of C0, founder parents, and commercial checks, respectively. Results demonstrate the potential of MARS for increasing genetic gain under both drought and optimum environments in SSA.
    Full-text · Article · Jan 2015 · Crop Science
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    ABSTRACT: When reporting on well-conducted research, a characteristic of a complete and proper manuscript is one that includes analyses and interpretations of all interactions. Our purpose is to show how to analyze and interpret interactions in agronomy and breeding research by means of three data sets comprising random and fixed effects. Experiment 1 tested wheat (Triticum aestivum L.) at two N and four P fertilizer rates in two soil types. For this data set, we used a fixed-effect linear model with the highest order (three-way) interaction considered first and then worked down through the lower order interactions and main effects to illustrate the importance of interactions in data analysis. Experiment 2 evaluated maize (Zea mays L.) hybrids under four rates of N for 3 yr. For this data set, we used a linear mixed model and partitioned the four N rates into orthogonal polynomials. Experiment 3 evaluated genotypes in six environments where the objective was to show how to study genotype × environment interactions. Researchers must analyze all interactions, determine if they are due to changes in rank (crossover) or only to changes in scale, and then judge whether reporting on significant main effects or interactions would best explain the biological responses in their experiments. In an experiment with more than one factor, complete and correct analysis of interactions is essential for reporting and interpreting the research properly.
    Full-text · Article · Aug 2014 · Agronomy Journal
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    ABSTRACT: Selection indices are estimates of the net genetic merit of the individual candidates for selection and are calculated based on phenotyping and molecular marker information collected on plants under selection in a breeding program. They reflect the breeding value of the plants and help breeders to choose the best ones for next generation. Rindsel is an R package that calculates phenotypic and molecular selection indices.
    Full-text · Article · May 2014 · Methods in molecular biology (Clifton, N.J.)
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    ABSTRACT: The development of an integrated breeding field book (IBFieldbook) for different crops involves the generation, handling and analysis of large amounts of data. Managing the integration of environmental, pedigree, and phenotypic information for plant breeding data analyses requires appropriate and successful software that facilitates breeders, technicians, and researchers management of the vast collected field information in an easy, efficient and interactive way. Users may also need methods to exchange information with different devices used to record information in the field. Additionally, collected information needs to be analyzed inside or outside the application, and then generate reports for germplasm improvement.
    Full-text · Article · Jul 2013 · Revista fitotecnia mexicana publ. por la Sociedad Mexicana de Fitogenética
  • Mateo Vargas · Emily Combs · Gregorio Alvarado · Gary Atlin · Ky Mathews · Jose Crossa
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    ABSTRACT: Multienvironment trials (METs) enable the evaluation of the same genotypes under a variety of environments and management conditions. We present META (Multi Environment Trial Analysis), a suite of 33 SAS programs that analyze METs with complete or incomplete block designs, with or without adjustment by a covariate. The entire program is run through a graphical user interface. The program can produce boxplots or histograms for all traits, as well as univariate statistics. It also calculates best linear unbiased estimators (BLUEs) and best linear unbiased predictors (BLUPs) for the main response variable and BLUEs for all other traits. For all traits, it calculates variance components by restricted maximum likelihood, least significant difference, coefficient of variation, and broad-sense heritability using PROC MIXED. The program can analyze each location separately, combine the analysis by management conditions, or combine all locations. The flexibility and simplicity of use of this program makes it a valuable tool for analyzing METs in breeding and agronomy. The META program can be used by any researcher who knows only a few fundamental principles of SAS.
    No preview · Article · Jan 2013 · Agronomy journal
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    ABSTRACT: Genetic biofortification to improve zinc (Zn) and iron (Fe) concentrations in bread wheat (Triticum aestivum L.) could reduce micronutrient malnutrition-related problems in the developing world. A breeding program on wheat was started to enhance Zn and Fe concentrations and other essential traits needed in a successful commercial variety. The first set of advanced lines derived from crosses of high yielding wheats with genetic resources possessing high Zn and Fe such as Triticum spelta, landraces and synthetic wheat based on Triticum dicoccon were tested at nine locations in South Asia and Mexico for Zn and Fe concentration, grain yield and other traits. Analyses of variance across locations revealed significant genotypic, environmental and genotype × environment (G × E) effects for grain Zn and Fe concentrations and grain yield. Variances associated with environmental effects were larger than the genotypic and G × E effects for all three traits, suggesting that environmental effects have relatively greater influence. Although G × E interaction was significant, high heritabilities were observed for Zn and Fe concentrations at individual sites and across environments, reflecting non-crossover type of interaction. This trend was confirmed by the high genetic correlations between locations that showed similar ranking of entries across locations, indicating that it is possible to select the best adapted entries with high Zn and Fe concentration. Pooled data across locations showed increments of 28% and 25% over the checks for Zn and Fe. A considerable number of entries exceeded intermediate to full breeding target Zn concentrations, indicating that it is possible to develop Zn-biofortified varieties with competitive yields and other farmer preferred agronomic traits. The positive and moderately high correlation between Zn and Fe concentration suggest good prospects of simultaneous improvement for both micronutrients.
    Full-text · Article · Oct 2012 · Field Crops Research
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    ABSTRACT: For in vivo production of doubled haploid (DH) lines in maize, the rate of haploid induction is of crucial importance. Maternal haploid induction depends primarily on the inducer used as a pollinator. However, the source germplasm used as a maternal parent and the environmental conditions for induction may also influence haploid induction and these aspects have not been examined in tropical maize so far. The objectives of our study were to (i) monitor the variation for haploid induction rate (HIR) among diverse source germplasm in tropical maize, (ii) determine the relative importance of general (GCA) and specific (SCA) combining abilities for HIR, and (iii) investigate the influence of summer and winter seasons and genotype×season interactions on this trait. Ten inbreds were mated in a half diallel design. The resulting 45 F1 single crosses were pollinated with the haploid inducer hybrid RWS×UH400 during the summer 2008 and winter 2009 seasons in a lowland tropical environment in Mexico. HIR of the single crosses averaged over seasons ranged from 2.90 to 9.66% with an overall mean of 6.74%. Mean HIR was significantly (P<0.01) higher during the winter (7.37%) than summer season (6.11%). Significant (P<0.01) variation was observed due to GCA effects of parental inbreds of single crosses but not for SCA, GCA×season and SCA×season interactions. Our study underpins that a higher HIR in tropical maize can be obtained by selecting appropriate source germplasm and undertaking pollination under favorable environmental conditions. KeywordsHaploid induction rate–Tropical source germplasm–Diallel crosses–General combining ability–Season–Maize
    Full-text · Article · Jul 2011 · Euphytica
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    Full-text · Article · Feb 2011 · Euphytica
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    ABSTRACT: Great variation for many traits seems to be available in Capsicum genetic resources but yet to be fully used by plant breeders. Adequate characterization of genebank accessions is needed to facilitate the utilization of germplasm by end-users. The aim of this research was to use multivariate techniques with both qualitative and quantitative descriptors in the five domesticated species of Capsicum for grouping them after assessing inter- and intra-specific variation. Key qualitative descriptors (seed color, corolla color and spot, calyx constriction, numbers of flowers per node and filament color) served for assigning most accessions to their respective species, whereas intra-specific multivariate diversity was better assessed by quantitative descriptors such as fruit length/width ratio, numbers of days to flowering, leaf width, and anther, filament and pedicel length. The modified location model an adequate method for classifying Capsicum accessions using quantitative descriptors.
    Full-text · Article · Sep 2010 · Scientia Horticulturae
  • B. S. Vivek · J. Crossa · G. Alvarado
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    ABSTRACT: Maize is an important food crop in sub-Sa- haran Africa. There is an increasing demand for early ma- turing maize cultivars even though long-season maize cul- tivars yield more than early maturing cultivars under favourable conditions. This is because vast areas of maize are routinely affected by drought and low N fertility and early maturing maize cultivars offer more flexibility than full season cultivars for a farmer with respect to cultiva- tion and food security. CIMMYT's early maturing maize program, which aims to supply seed to approximately 3 million hectares of maize area in east and southern Africa lacks adequate information on heterotic relationships of its germplasm. 190 crosses (generated from a diallel of eighteen populations and two within heterotic group sin- gle crosses) and their 20 parentals were evaluated for het- erotic relationships at six locations in Zimbabwe (four op- timal conditions of rainfall and fertilizers (but different agro-ecological regions / mega-environments), one man- aged low nitrogen environment and one managed drought environment). Three heterotic patterns were seen under stress while six heterotic patterns were seen under optimal conditions. P9 (CML312/CML442) expressed a consistent heterotic pattern across stress and non-stress environments thus justifying its continued use as a tester. Moving towards the use of multiple heterotic groups in the CIMMYT-Zimbabwe program may be worthwhile pro- vided that the budgetary scenario still supports its core mandate of germplasm development, germplasm ex- change and strengthening of national research systems.
    No preview · Article · Jan 2009 · Maydica
  • Rodomiro Ortiz · Ricardo Sevilla · Gregorio Alvarado · José Crossa
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    ABSTRACT: Maize (Zea mays L.) landraces are an important source for the genetic improvement of the crop. Classification of genetic resources requires both appropriate descriptors as well as sound numerical and statistical methods. This research was undertaken to assess the use of six internal ear traits for classifying a set of four related Peruvian highland maize races comprising a total of 24 accessions. Several accessions of the four races were included in field trials planted in Peru’s inter-Andean valley. The trials were sown on two planting dates (normal and late) in two consecutive years. Variance components among races and among accessions with races were used to estimate broad-sense heritability and repeatability for each internal ear trait. The Ward-Modified Location model (MLM) and canonical analysis were undertaken for clustering the 24 accessions. For most traits, the variance components among races were more important than the accession within races, and the variance components for race×environment or accession within race×environment were, for the most part, negligible. Results suggest that internal ear traits such as cob and pith diameter, as well as cupule sizes and glume texture, are among the most appropriate for clustering these materials in their respective races. The numerical classification maintained the structure of the more differentiated races but identified two distinct accessions in one race and separated them into a homogeneous group. The Ward-MLM numerical method produced groups with distinct characteristics in terms of internal ear variables.
    No preview · Article · Nov 2008 · Genetic Resources and Crop Evolution
  • R. Ortiz · W. W. Wagoire · O. Stølen · G. Alvarado · J. Crossa
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    ABSTRACT: Wheat breeders rarely apply population improvement schemes or select parental sources according to combining ability and heterotic patterns. They rely on pedigree selection methods for breeding new cultivars. This experiment was undertaken to assess the advantages of using diallel crosses to define combining ability and understand heterosis in a broad-based wheat-breeding population across different environments affected by yellow rust. Sixty-four genotypes derived from a full diallel mating scheme were assessed for grain yield in two contrasting growing seasons at two locations for two consecutive years. Parental genotypes showed significant combining ability for grain yield that was affected by yellow rust and genotype-by-environment (GE) interactions, both of which affected heterosis for grain yield. Significant GE interactions suggested that decentralized selection for specific environments could maximize the use of this wheat germplasm. Cultivar effects and specific heterosis were the most important factors influencing grain yield. Some crosses capitalized on additive genetic variation for grain yield. This research shows the power of available quantitative breeding tools to help breeders choose parental sources in a population improvement programme.
    No preview · Article · Mar 2008 · Plant Breeding
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    ABSTRACT: Spot blotch is an important disease of wheat (Triticum aestivum L.) in South Asia. Division of test sites for this disease into homogenous subregions is expected to contribute to more effi cient evaluation and better differentiation of cultivars. Data from a collaborative regional program of South Asia conducted by CIMMYT were analyzed to group testing sites into rela- tively homogenous subregions for spot blotch area under the disease progress curve (AUDPC). Five-year data of eight locations from Eastern Gangetic Plains Nursery (EGPSN) and fi ve loca- tions of the Eastern Gangetic Plains Yield Trial (EGPYT) conducted in three countries (India, Nepal, and Bangladesh) of South Asia were used. A hierarchical cluster analysis was used to group locations on the basis of genotype × location interaction effects for spot blotch AUDPC. Cluster analysis divided South Asia into two broad regions and four subregions. This classifi cation was not entirely consistent with the geographic distribution of locations, but clusters mostly followed general geographic- climatic locations. The locations Varanasi (India) and Bhairahawa (Nepal) were identifi ed as the most suitable sites for evaluation of spot blotch, followed by Rampur (Nepal). The major determi- nant for the clustering was mean temperature. The results suggest that the major wheat region of South Asia can be divided into subregions, which may reduce the cost of resistance evalua- tion and aid in developing wheat with resistance to this disease.
    Full-text · Article · May 2007 · Crop Science
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    ABSTRACT: Spring sown bread wheat is grown at high latitudes in Europe, Asia and North America. However, it is not clear what the associations are among environments, particularly in Asia and North America, and whether or not cultivars developed in one region may adapt in another. A yield trial comprised of cultivars developed in northern Kazakhstan, western Siberia, the Canadian Prairies, northern USA, northeastern China and broadly adapted genotypes bred by CIMMYT in Mexico was planted in all the above mentioned environments in 2002–2004. In general, cultivars performed best within the regions they were developed. However, cultivars developed in northern Kazakhstan/western Siberia were the most broadly adapted at high latitudes; they were not significantly different for grain yield from the locally developed cultivars in both China and Canada. Stronger photoperiod response, greater plant height and larger seed weight appeared to be key adaptive features of these materials. At lower latitudes, the Kazakh/Siberian cultivars were significantly lower yielding than all other materials. When low latitude Mexican sites were removed from the analysis, the Chinese locations tended to associate, whereas most Canadian and Kazak/Siberian locations were negatively associated with those from China. SSR analysis of the cultivars from each region split the materials into two general groups, one based on North American cultivars and one comprised of Kazakh/Siberian and Chinese cultivars. Lines developed in Mexico were spread across these two groupings. Evidence suggests that considerable scope exists to improve bread wheat adaptation at high latitudes globally through intercrossing materials originating from Asia and North America.
    No preview · Article · Dec 2006 · Euphytica

  • No preview · Article · · Field Crops Research