Patricio R. Munoz del Valle

Patricio R. Munoz del Valle
University of Florida | UF · Department of Horticultural Sciences

Phd Molecular Breeding

About

110
Publications
21,364
Reads
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2,037
Citations
Education
January 2010 - November 2012
University of Florida, Plant Molecular and Cellular Biology
Field of study
  • Breeding and Genomic
August 2007 - December 2009
University of Florida, School of Forest Resources and Conservation
Field of study
  • Breeding and Quantitative Genetics
March 1998 - October 2004
Universidad Católica de Temuco
Field of study
  • Project Evaluation

Publications

Publications (110)
Article
Full-text available
Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing...
Article
Full-text available
Significance Consumers often regard heirloom fruit varieties grown in the garden as more flavorful than commercial varieties purchased at the grocery store. While plant breeders have historically focused on improving producer-orientated traits such as yield, consumer-oriented traits such as flavor have regularly been neglected. This is, in part, du...
Preprint
Full-text available
Among the main features treasured by blueberry consumers, flavor is the most important. Human perception of food flavors can primarily be divided into two main sensory inputs, taste and aroma. Through retronasal olfaction, a group of metabolites called volatile organic compounds (VOCs) emitted from the fruit are able to produce the sensation of aro...
Article
Full-text available
The application of remote sensing in plant breeding is becoming a routine method for fast and non-destructive high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) equipped with sensors. Alfalfa (Medicago sativa L.) is a perennial forage legume grown in more than 30 million hectares worldwide. Breeding alfalfa for herbage accumula...
Article
Blueberry (Vaccinium spp.) is a specialty crop with expanding production and consumption worldwide. Southern Highbush Blueberries (SHB) require few chilling hours and include early-ripening cultivars which can be harvested in an early market window making the crop more profitable for growers in sub-tropical regions. To expand the marketability of t...
Article
Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defense polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial...
Article
Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the...
Article
In diploid species, many multiparental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase the power of QTL detection in comparison with the marker-based association analysis. However, such...
Article
Full-text available
Genomic prediction integrates statistical, genomic and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in mating systems, breeding schemes, propagation methods, and unit of selection, no universal genomic prediction approach can be applied in all crops. In a genome-wide family p...
Article
Full-text available
Blueberry ( Vaccinium corymbosum and hybrids) is a specialty crop with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to expanding production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The...
Article
Full-text available
Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii...
Preprint
Full-text available
Genomic prediction (GP) integrates statistical, genomic and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in biology, breeding scheme, propagation method, and unit of selection, no universal GP approach can be applied in all crops. In a genome-wide family prediction (GWFP) app...
Preprint
Full-text available
Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop, with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to the expansion of production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the glob...
Preprint
Full-text available
Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii...
Preprint
Full-text available
Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by creating computational tools for the analysis of connected F1 populations derived from a set of shared parents. In a companion paper, software to reconstruct F1 progeny in terms o...
Preprint
Full-text available
In diploid species, many multi-parental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase QTL detection power in comparison with the marker-based association analysis. To realize similar b...
Article
In breeding programs, superior parental genotypes are used in crosses to generate novel genetic variability for new selection cycles. Genotypes are usually more adapted to environments where the breeding program is located, since selections are performed under specific agroecosystems. Thus, the objective of this study was to evaluate the performanc...
Article
Full-text available
The demand for blueberry Vaccinium corymbosum L. (and hybrids) plants has significantly increased in the last 30 years due to its market expansion. In vitro propagation of sterile plants are required for commercial purposes but also for research applications such as plant transformation. Thus far, tissue culture characteristics of the tropical-adap...
Article
Full-text available
Blueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry...
Article
Full-text available
The Cynodon spp. collection maintained by United States Department of Agriculture National Plant Germplasm System (USDA-NPGS) has limited information on nutritive value (NV) traits. In this study, crude protein (CP), phosphorous concentration (P), in vitro digestible organic matter (IVDOM), and neutral detergent fiber (NDF) were determined to (i) e...
Article
Full-text available
A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for...
Article
Full-text available
Blueberry (Vaccinium spp.) is an important autopolyploid crop with significant benefits for human health. Apart from its genetic complexity, the feasibility of genomic prediction has been proven for blueberry, enabling a reduction in the breeding cycle time and increasing genetic gain. However, as for other polyploid crops, sequencing costs still h...
Article
Full-text available
Southern highbush blueberry cultivation has expanded into non-traditional growing areas worldwide due to elite cultivars and improved horticultural practices. This article presents a comprehensive review of current production systems—alternatives to traditional open field production—such as production in protected environments, high-density plantin...
Preprint
Although they are staple foods in cuisines globally, commercial fruit varieties have become progressively less flavorful over time. Due to the cost and difficulty associated with flavor phenotyping, many breeding programs have long been challenged in selecting for this complex trait. To address this issue, we leveraged targeted metabolomics of dive...
Article
Full-text available
Mislevy' (Reg. no. CV-46, PI 693070) bermudagrass [Cynodon dactylon (L.) Pers.] was selected at the University of Florida, and a series of research projects was conducted to evaluate the merit of Mislevy to be released as a new bermudagrass cultivar in Florida. A grazing experiment was conducted in South Florida and clipping trials conducted in Sou...
Preprint
Southern highbush blueberry plantations have been expanded into worldwide non-traditional growing areas with elite cultivars and improved horticultural practices. This article presents a comprehensive review of current production systems – alternatives to traditional open field production – such as production in protected environments, high-density...
Article
Estimation of genotype-by-environment interaction (GEI) is important in breeding programs because it provides critical information to guide selection decisions. In general, multi-environment trials exhibit heterogeneity of variances and covariances at several levels. Thus, the objectives of this study were to: (i) find the best genetic covariance m...
Article
Full-text available
Alfalfa is planted in more than 30 million hectares worldwide, but despite its popularity in temperate regions, it is not widely grown in subtropical agroecosystems. It is critical to improve alfalfa for such regions, considering current predictions of global warming and the increasing demands for animal-based products. In this study, we examined t...
Preprint
Full-text available
Blueberry (Vacciunium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last twenty years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueb...
Article
Full-text available
Hybrid breeding programs are driven by the potential to explore the heterosis phenomenon in traits with nonadditive inheritance. Traditionally, progress has been achieved by crossing lines from different heterotic groups and measuring phenotypic performance of hybrids in multiple environment trials. With the reduction in genotyping prices, genomic...
Article
Full-text available
Many commercially important plants are autopolyploid. As a result of the multiple chromosome sets in their genomes, higher orders of allele interactions can occur, implying different degrees of dominance. In contrast with diploids, dominance effects can be heritable in polyploids, potentially having a higher impact on the prediction of genetic valu...
Article
Full-text available
Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, applications to polyploid organisms are still scarce, partly due to limited genome resources and the complexity of this system. Deep learning (DL...
Article
Full-text available
Plants produce a range of volatile organic compounds (VOCs), some of which are perceived by the human olfactory system, contributing for a myriad of flavors. Despite the importance of flavor for consumer preference, most plant breeding programs have neglected it, mainly due to the costs of phenotyping and the complexity of disentangling the role of...
Article
Full-text available
Herbicide resistance is a recurrent evolutionary event that has been reported across many species and for all major herbicide modes of action. The synthetic auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used since the 1940s, however the genetic variation underlying naturally evolving resistance remains largely unknown. In...
Article
Full-text available
Perennial grass hybrids of Urochloa are evaluated for at least two years during the screening stage trials (SS) and advanced trials (AD) in breeding programs, an expensive and time-consuming process. In this study, we aimed to evaluate the potential for early selection of cultivars in this breeding scheme. We used multiple measurements of agronomic...
Article
Full-text available
The genetic merit of individuals can be estimated using models with dense markers and pedigree information. Early genomic models accounted only for additive effects. However, the prediction of non-additive effects is important for different forest breeding systems where the whole genotypic value can be captured through clonal propagation. In this s...
Article
Full-text available
The decreasing costs of next-generation sequencing and the improvements in de novo sequence assemblers have made it possible to obtain reference genomes for most eukaryotes, including minor crops such as the blueberry (Vaccinium corymbosum). Nevertheless, these genomes are at various levels of completeness and few have been anchored to chromosome s...
Article
Full-text available
Many commercially important plants are autopolyploid. As a result of the multiple chromosome sets in their genomes, higher orders of allele interactions can occur, implying different degrees of dominance. In contrast to diploids, dominance effects can be heritable in polyploids, potentially having a higher impact on the prediction of genetic values...
Article
Full-text available
Characterizing phenotypes in germplasm collections and making data publicly available is crucial to ensure their utilization in breeding programs. Variance component estimates are used to calculate genetic parameters needed to make strategic decisions for germplasm conservation and its utilization in plant breeding. This information is lacking for...
Article
Southern highbush blueberries combine the fruit quality and productivity of highbush blueberries with the low chilling requirement necessary to produce a crop in the Florida climate. Written by J. G. Williamson, D. A. Phillips, P. M. Lyrene, and P. R. Munoz and published by the UF/IFAS Horticultural Sciences Department, this 13-page major revision...
Poster
Full-text available
Variation in forage nutritive value (NV) can be due to genotypic and environmental main effects, as well as to genotype by environment interaction (GEI). Limited data is available for NV traits in the Cynodon spp. (bermudagrass thereafter) collection from the USDA. Our objectives were: i) estimate genetic parameters and genotypic performance for NV...
Article
Full-text available
Estimation of allele dosage, using genomic data, in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Some progress has been made when using SNP arrays, but the major challenge is when using next generation sequencing data. Here we compare the use of read depth as continuous parameterization with...
Article
Full-text available
Bermudagrass is the most important warm-season pasture in the Southern USA with exceptional forage production potential and abiotic stress tolerance. However, it requires high nitrogen (N) supply to reach its full biomass and quality potential. Our objectives were to: (1) develop a nitrogen use efficiency (NUE) screening protocol for bermudagrass i...
Article
Full-text available
The Tifton Turfgrass Breeding Program has a long history of releasing high quality turfgrass varieties. Today, the goal of the program is to create turfgrasses that are adapted to a broader range of environments and have improved drought and traffic tolerance. The latest commercial turfgrass release from Tifton is DT-1, an interspecific triploid (2...
Preprint
Full-text available
Estimation of allele dosage in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Here we propose and compare the use of next generation sequencing read depth as continuous parameterization for autotetraploid genomic prediction of breeding values, using blueberry (Vaccinium corybosum spp.) as a mod...
Article
Full-text available
Blueberry (Vaccinium spp.) has been recognized worldwide as a valuable source of health-promoting compounds, becoming a crop with some of the fastest rising consumer demand trends. Fruit firmness is a key target for blueberry breeding as it directly affects fruit quality, consumer preference, transportability, shelf life, and the ability of cultiva...
Article
Full-text available
The successful application of genomic selection (GS) approaches is dependent on genetic makers derived from high-throughput and low-cost genotyping methods. Recent GS studies in trees have predominantly relied on SNP arrays as the source of genotyping, though this technology has a high entry cost. The recent development of alternative genotyping pl...
Preprint
Full-text available
Blueberry (Vaccinium spp.) has been recognized worldwide as a valuable source of health-promoting compounds, becoming a crop with some of the fastest rising consumer demand trends. Fruit firmness is a key target for blueberry breeding as it directly affects fruit quality, consumer preference, transportability, shelf life, and the ability of cultiva...
Article
Full-text available
Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic...
Article
Full-text available
White clover (Trifolium repens L.) is the most important grazing perennial forage legume in temperate climates. However, its limited capacity to survive and restore growth after low temperatures during winter constrains the productivity and wide adoption of the crop. Despite the importance of cold tolerance for white clover cultivar development, th...
Preprint
Full-text available
Hybrid breeding programs are driven by the potential to explore the heterosis phenomenon in traits with non-additive inheritance. Traditionally, progress has been achieved by crossing lines from different heterotic groups and measuring phenotypic performance of hybrids in multiple environment trials. With the reduction in genotyping prices, genomic...
Article
Full-text available
‘Flicker’ is a southern highbush blueberry (SHB, Vaccinium corymbosum) cultivar frequently selected by growers in Central and South Florida. In 2014, several growers in Central Florida experienced issues with anthracnose stem lesions and twig dieback on ‘Flicker’, resulting in a reduction in new plantings and the removal of many existing plantings....
Poster
Full-text available
Bermudagrass (Cynodon spp. L.) is an important warm-season perennial grass grown for forage in subtropical/tropical areas around the world. A world collection of Cynodon species is available at the USDA National Plant Germplasm System (USDA-NPGS). The objective of this study was to calculate genetic parameters in a set of 286 bermudagrass genotypes...
Article
Information contained in this 4-page publication is intended for Florida blueberry growers to use as a guide in the identification of anthracnose, a group of fungal pathogens that affects a wide range of plants, including southern highbush blueberries (SHB). Written by Douglas A. Phillips, Maria C. Velez-Climent, Philip F. Harmon, and Patricio R. M...
Article
Full-text available
The strategy for breeding blueberries has been based on phenotypic selection without accounting for pedigree correlation information. A central premise of classical quantitative genetics is that through knowledge of the relationships among individuals in a population, we can make inferences about breeding values (BVs), estimate genetic parameters,...