Dennis Nicuh Lozada

New Mexico State University | NMSU · Department of Plant and Environmental Sciences

Genome-wide association studies (GWAS) are useful to facilitate crop improvement via enhanced knowledge of marker-trait associations (MTA). A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft red winter wheat (Triticum aestivum) genotypes evaluated across two growing seasons and eight...

Validation of quantitative trait loci (QTLs) is an essential step in marker-assisted breeding. The objectives of this study were to validate grain yield (GY) QTLs previously identified in soft red winter wheat (Triticum aestivum L.) through bipa-rental and association mapping using the spring wheat association mapping initiative (WAMI) panel from C...

Incorporating secondary correlated traits collected from high-throughput phenotyping in genomic selection (GS) models for complex traits has been demonstrated to improve accuracy. The prediction ability of different single and multiple trait partial least square (PLS) regression models for grain yield were assessed for winter wheat lines evaluated...

Snow mold is a yield-limiting disease of wheat in the Pacific Northwest (PNW) region of the US, where there is prolonged snow cover. The objectives of this study were to identify genomic regions associated with snow mold tolerance in a diverse panel of PNW winter wheat lines in a genome-wide association study (GWAS) and to evaluate the usefulness o...

Background: Genomic selection has the potential to increase genetic gains by using molecular markers as predictors of breeding values of individuals. This study evaluated the accuracy of predictions for grain yield, heading date, plant height, and yield components in soft red winter wheat under different prediction scenarios. Response to selection...

Background Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici. This study aimed to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a panel consisting of 157 Capsicum spp. genotypes. Multi-locus genome wide assoc...

Sclerotium rolfsii is a necrotrophic fungus that causes devastating stem rot disease on peanuts under high temperature and humidity conditions. Developing more resistant stem rot varieties is a better disease management strategy from an economic and environmental point of view. In this study, 105 peanut accessions from the USDA mini-core collection...

The nutritional and medicinal significance of jujube ( Ziziphus jujuba ) has led to persistent efforts in genomics to accelerate the utilization of its germplasm resources. However, the absence of accurate genetic identity of existing germplasm limits these studies. In the United States, different names were frequently given to the same jujube cult...

Background Genomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for yield and agronomic traits of 204 chile pepper genotypes evaluated in multi-environment trials in New...

Background Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici. Multi-locus genomewide association study (GWAS) was conducted to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a diversity panel consisting of 157...

Background. Genomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for yield and agronomic traits of 204 chile pepper genotypes evaluated in multi-environment trials in Ne...

Phytophthora capsici is one of the most devastating pathogens facing pepper (Capsicum annuum) producers worldwide. Numerous factors, such as race of the pathogen, the growing environment, and source of resistance, have resulted in an overall lack of widely applicable molecular markers associated with resistance. Our objective was to determine the e...

Univariate genomic selection (UVGS) is an important tool for increasing genetic gain and multivariate GS (MVGS), where correlated traits are included in genomic selection, which can improve genomic prediction accuracy. The objectives for this study were to evaluate MVGS approaches to improve prediction accuracy for four agronomic traits using a tra...

Chile peppers (Capsicum annuum L.) are good sources of vitamins and minerals that can be included in the diet to mitigate nutritional deficiencies. Metabolomics examines the metabolites involved in biological pathways to understand the genes related to complex phenotypes such as the nutritional quality traits. The current study surveys the differen...

In 1922, Phytophthora capsici was described by Leon Hatching Leonian as a new pathogen infecting pepper (Capsicum annuum L.), with disease symptoms of root rot, stem and fruit blight, seed rot, and plant wilting and death. Extensive research has been conducted on P. capsici over the last 100 years. This review succinctly describes the salient mile...

Fruit architecture and morphology-related traits are among the determinants of fruit diversity and are major contributors to yield and yield potential in chile pepper (Capsicum spp.). This study aimed to characterize 105 genotypes of a Capsi-cum diversity panel consisting of cultivars, breeding lines, landrace, and wild species belonging to twelve...

Genome-wide association studies (GWAS) are one of the foundations for modern molecular breeding for plant genetic improvement. Single-locus GWAS methodologies impose constraints in association mapping due to the complex nature of quantitative traits and the often-stringent thresholds used. Multi-locus models, therefore, serve as alternative approac...

Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have “defined” the state of New Mexico, USA. The official state question, “Red or Green?” refers to the preference for either red or the green stage of chile pepper, respectively, reflects the val...

Plant geneticists and breeders have used marker technology since the 1980s in quantitative trait locus (QTL) identification. Marker-assisted selection is effective for large-effect QTL but has been challenging to use with quantitative traits controlled by multiple minor effect alleles. Therefore, genomic selection (GS) was proposed to estimate all...

Most genomic prediction models are linear regression models that assume continuous and normally distributed phenotypes, but responses to diseases such as stripe rust (caused by Puccinia striiformis f. sp. tritici) are commonly recorded in ordinal scales and percentages. Disease severity (SEV) and infection type (IT) data in germplasm screening nurs...

Wheat (Triticum aestivum L.) breeding programs can take over a decade to release a new variety. However, new methods of selection, such as genomic selection (GS), must be integrated to decrease the time it takes to release new varieties to meet the demand of a growing population. The implementation of GS into breeding programs is still being explor...

Plant geneticists and breeders have used marker technology since the 1980s in quantitative trait locus (QTL) identification. Marker-assisted selection is effective for large-effect QTL but has been challenging to use with quantitative traits controlled by multiple minor effect alleles. Therefore, genomic selection (GS) was proposed to estimate all...

Wheat (Triticum aestivum L.) breeding programs can take over a decade to release a new variety. However, new methods of selection such as genomic selection (GS) must be integrated to decrease the time it takes to release new varieties to meet the demand of a growing population. The implementation of GS into breeding programs is still being explored...

Background Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyp...

Most genomic prediction models are linear regression models that assume continuous and normally distributed phenotypes, but responses to diseases such as stripe rust (caused by Puccinia striiformis f. sp. tritici) are commonly recorded in ordinal scales and percentages. Disease severity (SEV) and infection type (IT) data in germplasm screening nurs...

In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS). Meta-QTL analysis for different traits in chile peppers (Capsicum spp.) remains lacking, and therefore it would be necessary to re-evaluate identifie...

Breeding for capsaicinoid content is one of the major objectives for chile pepper breeding programs due to its culinary, agricultural, and medicinal uses. The objectives of the current study were to determine the Scoville Heat Units (SHU) of select New Mexico State University (NMSU) chile pepper varieties and ‘superhot’ genotypes using high-perform...

Background Chile peppers ( Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different...

Background: Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different...

Chile peppers ( Capsicum spp.) are among the most important vegetable crops in the world due to their health-related, economic, and industrial uses. In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS) i...

Genomic selection (GS) is transforming the field of plant breeding and implementing models that improve prediction accuracy for complex traits is needed. Analytical methods for complex datasets traditionally used in other disciplines represent an opportunity for improving prediction accuracy in GS. Deep learning (DL) is a branch of machine learning...

Achieving optimal predictive ability is key to increasing the relevance of implementing genomic selection (GS) approaches in plant breeding programs. The potential of an item-based collaborative filtering (IBCF) recommender system in the context of multi-trait, multi-environment GS has been explored. Different GS scenarios for IBCF were evaluated f...

Increased genetic gain for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selection R values across several selection approaches including phenotypic (PS), ma...

Examining the architecture of traits through genomics is necessary to gain a better understanding of the genetic loci affecting important traits to facilitate improvement. Genomewide association study (GWAS) and genomic selection (GS) were implemented for grain yield, heading date, and plant height to gain insights into the genetic complexity of ph...

Secondary traits from high-throughput phenotyping could be used to select for complex target traits to accelerate plant breeding and increase genetic gains. This study aimed to evaluate the potential of using spectral reflectance indices (SRI) for indirect selection of winter-wheat lines with high yield potential and to assess the effects of includ...

Semi dwarfism in hexaploid wheat (Triticum aestivum L.) is primarily governed by two loci, Rht-B1 and Rht-D1. Cultivars adapted to the soft red winter wheat growing region of southeastern USA are predominantly Rht-D1b genotypes but report no significant grain yield advantage over Rht-B1b semi dwarfing cultivars. The objective of this study was to d...

In order to meet the goal of doubling wheat yield by 2050, breeders must work to improve breeding program efficiency while also implementing new and improved technologies in order to increase genetic gain. Genomic selection (GS) is an expansion of marker assisted selection which uses a statistical model to estimate all marker effects for an individ...

Increased genetic gains for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selection R values across several selection approaches including phenotypic (PS), m...

Background: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "...

The objective of this study was to identify quantitative trait loci (QTL) associated with normalized difference vegetation index (NDVI) measured across different growth stages in a wheat (Triticum aestivum L.) recombinant inbred line (RIL) population and to determine the predictability of NDVI and grain yield (GY) using a genomic selection (GS) app...

The aim of this study was to identify quantitative trait locus (QTL) associated with grain yield (GY) in a recombinant inbred line (RIL) population from a cross between two elite soft red winter wheat (SRWW) cultivars (‘Pioneer 26R61’ and ‘AGS2000’). The RIL population was grown from 2011 to 2014 in 12 site-year combinations throughout the southeas...

Soil waterlogging impacts 25% of the global area planted to wheat and the development of waterlogging tolerant cultivars lags behind progress that has been made for other abiotic stresses. This study was conducted to identify sources of waterlogging tolerance in soft red winter wheat (SRWW) adapted to the southeastern United States, a region prone...

Molecular markers have been useful in developing improved rice breeding lines and have reduced time in releasing new rice varieties. However, conventional marker platforms are still constrained with gel electrophoresis and manual scoring which are laborious and time-consuming. These constraints have been the bottleneck in marker-aided selection and...