Alexander Lipka

Alexander Lipka
University of Illinois, Urbana-Champaign | UIUC · Department of Crop Sciences

Ph.D. in Statistics

About

213
Publications
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Introduction

Publications

Publications (213)
Article
Full-text available
Genomic selection (GS) has been demonstrated to enhance the selection process in breeding programs. The objectives of this study were to experimentally evaluate different GS methods in sugarcane hybrids and to determine the prospect of GS in future breeding approaches. Using sugar and yield-related trait data from 432 sugarcane clones and 10,435 si...
Article
Anthracnose leaf blight (ALB) is an economically important disease of sorghum [Sorghum bicolor (L.) Moench] caused by the fungal pathogen Colletotrichum sublineola Henn. ex Sacc. & Trotter. Although qualitative and quantitative resistance have been identified for ALB, the usefulness of resistance loci differs depending on the pathogen pathotype. Id...
Chapter
With increasing marker density, estimation of recombination rate between a marker and a causal mutation using linkage analysis becomes less important. Instead, linkage disequilibrium (LD) becomes the major indicator for gene mapping through genome-wide association studies (GWAS). In addition to the linkage between the marker and the causal mutation...
Article
Genomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance-controlling loci in association studies will be critical for future breeding efforts. Two statistical approaches that have already b...
Article
Full-text available
Background Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an eff...
Article
The ability to accurately quantify the simultaneous effect of multiple genomic loci on multiple traits is now possible due to current and emerging high‐throughput genotyping and phenotyping technologies. To date, most efforts to quantify these genotype‐to‐phenotype relationships have focused on either multi‐trait models that test a single marker at...
Chapter
Full-text available
Estimation of breeding values through Best Linear Unbiased Prediction (BLUP) using pedigree‐based kinship and Marker‐Assisted Selection (MAS) are the two fundamental breeding methods used before and after the introduction of genetic markers, respectively. The emergence of high‐density genome‐wide markers has led to the development of two parallel s...
Preprint
Full-text available
In quantitative genetics, statistical modeling techniques are used to facilitate advances in the understanding of which genes underlie agronomically important traits and have enabled the use of genome-wide markers to accelerate genetic gain. The logistic regression model is a statistically optimal approach for quantitative genetics analysis of bina...
Article
Full-text available
The total sugarcane (Saccharum L.) production has increased worldwide; however, the rate of growth is lower compared with other major crops, mainly due to a plateauing of genetic gain. Genomic selection (GS) has proven to substantially increase the rate of genetic gain in many crops. To investigate the utility of GS in future sugarcane breeding, a...
Article
Full-text available
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary om...
Article
Full-text available
Stomata are adjustable pores on leaf surfaces that regulate the trade-off of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited discoveries about the genetic basis of stomatal patterning. A high...
Article
Full-text available
The effects of climate change create formidable challenges for breeders striving to produce sufficient food quantities in rapidly changing environments. It is therefore critical to investigate the ability of multi-environment genomic prediction (GP) models to predict genomic estimated breeding values (GEBVs) in extreme environments. Exploration of...
Preprint
Genomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance quantitative trait loci (vQTL) in association studies will be critical for future breeding efforts. Two statistical approaches that...
Article
Full-text available
Hybrid rice varieties can outyield the best inbred varieties by 15 – 30% with appropriate management. However, hybrid rice requires more inputs and management than inbred rice to realize a yield advantage in high-yielding environments. The development of stress-tolerant hybrid rice with lowered input requirements could increase hybrid rice yield re...
Article
Full-text available
Genomic selection (GS) is one of the most powerful tools available for maize breeding. Its use of genome-wide marker data to estimate breeding values translates to increased genetic gains with fewer breeding cycles. In this review, we cover the history of GS and highlight particular milestones during its adaptation to maize breeding. We discuss how...
Article
Full-text available
Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping pa...
Article
Full-text available
Quantification of the simultaneous contributions of loci to multiple traits, a phenomenon called pleiotropy, is facilitated by the increased availability of high-throughput genotypic and phenotypic data. To understand the prevalence and nature of pleiotropy, the ability of multivariate and univariate genome-wide association study (GWAS) models to d...
Article
Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding of development requires insight into the full diversity of cell types and developmental domains and the gene networks required to specify them. Until now, these were identified primarily by mo...
Preprint
Full-text available
Estimation of breeding values through Best Linear Unbiased Prediction (BLUP) using pedigree-based kinship and Marker-Assisted Selection (MAS) are the two fundamental breeding methods used before and after the introduction of genetic markers, respectively. The emergence of high-density genome-wide markers has led to the development of two parallel s...
Article
Full-text available
Background Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy). As the demand for multivariate analyses increases,...
Preprint
Full-text available
Estimation of breeding values through Best Linear Unbiased Prediction (BLUP) using pedigree-based kinship and Marker-Assisted Selection (MAS) are the two fundamental breeding methods used before and after the introduction of genetic markers, respectively. The emergence of high-density genome-wide markers has led to the development of two parallel s...
Article
Full-text available
Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum...
Article
Full-text available
Plant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biol...
Preprint
Full-text available
Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize is a food staple. Extensive natural variation exists for carotenoids in maize grain; to understand its genetic basis, we conducted a joint linkage and genome-wide association study in the U.S. maize nested association mapping panel. Eleven of...
Article
Full-text available
Background: The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specifi...
Article
Significance Honey bee colony defense is an emergent trait composed of individual aggressive responses. Here, we investigated the relationship between individual genotype, colony allele frequency, and aggression in individual bees. Our findings show that the colony-level defense response strongly correlates with colony-level allele frequency in a w...
Article
Motivation: Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipe...
Article
Full-text available
Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus × giganteus (M×g) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Ms...
Preprint
Full-text available
Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)-inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum...
Article
Full-text available
Glutamine (Gln) is a key player in plant metabolism. It is one of the major free amino acids that is transported into the developing seed and is central for nitrogen metabolism. However, Gln natural variation and its regulation and interaction with other metabolic processes in seeds remain poorly understood. To investigate the latter, we performed...
Article
Full-text available
Maize inflorescence is a complex phenotype that involves the physical and developmental interplay of multiple traits. Given the evidence that genes could pleiotropically contribute to several of these traits, we used publicly available maize data to assess the ability of multivariate genome-wide association study (GWAS) approaches to identify pleio...
Preprint
Full-text available
Motivation Advances in genotyping and phenotyping techniques have enabled the acquisition of a great amount of data. Consequently, there is an interest in multivariate statistical analyses that identify genomic regions likely to contain causal mutations affecting multiple traits (i.e., pleiotropy). As the demand for multivariate analyses increases,...
Preprint
Full-text available
Background Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. Methods such as comparing observed and expected heterozygo...
Article
Full-text available
The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specif...
Preprint
Full-text available
Background The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific...
Article
Full-text available
Although energycane (Saccharum spp. hybrids) is widely used as a source of lignocellulosic biomass for bioethanol, breeding this crop for disease resistance is challenging due to its narrow genetic base. Therefore, efforts are underway to introgress novel sources of genetic resistance from Miscanthus into energycane. Given that disease resistance i...
Preprint
Full-text available
The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specif...
Article
Full-text available
To breed improved biomass cultivars of Miscanthus ×giganteus, it will be necessary to select the highest‐yielding and best‐adapted genotypes of its parental species, M. sinensis and M. sacchariflorus. We phenotyped a diverse clonally‐propagated panel of 569 M. sinensis and nine natural diploid M. ×giganteus at one subtropical (Zhuji, China) and fiv...
Article
Full-text available
Emerging evidence suggests a link between young people’s interest in alternative food production practices and dietary quality. The primary purpose of this study was to examine the impact of a student-driven sustainable food systems education and promotion intervention on adolescent school lunch selection, consumption, and waste behaviors. Sixth gr...
Article
Full-text available
Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993‐1780’, in regions where average annual minimum temperatures are ‐26.1 °C (USDA hardiness zone 5) or lower poses a pressing need to...
Article
Full-text available
To improve the efficiency of breeding of Miscanthus for biomass yield, there is a need to develop genomics‐assisted selection for this long‐lived perennial crop by relating genotype to phenotype and breeding value across a broad range of environments. We present the first genome‐wide association (GWA) and genomic prediction study of Miscanthus that...
Article
Full-text available
Genetic testing is becoming more prevalent in detecting risk and guiding cancer treatment in our increasingly personalized medicine model. However, few studies have examined underserved populations’ perceptions of genetic testing, especially those of rural dwelling populations. We asked residents of three rural communities to complete a self-admini...
Article
Full-text available
Goss’s bacterial wilt and leaf blight is one of the most important foliar diseases of maize ( L.). To date, neither large-effect resistance genes, nor practical chemical controls exist to manage the disease. Thus, the importance of discovering durable host resistance necessitates additional genetic mapping for this disease. Unfortunately, because o...
Article
Full-text available
Miscanthus × giganteus (M×g) is the primary species of Miscanthus for bioenergy feedstock production. The current leading biomass cultivar, M×g ‘1993‐1780’, is insufficiently adapted in temperate regions with cold winters such as USDA hardiness zone 5 (average annual minimum temperature of −28.9 to −23.3°C) or lower. Three interconnected Miscanthus...
Article
Full-text available
Certain agronomic crop traits are complex and thus governed by many small-effect loci. Statistical models typically used in a genome-wide association study (GWAS) and genomic selection (GS) quantify these signals by assessing genomic marker contributions in linkage disequilibrium (LD) with these loci to trait variation. These models have been used...
Article
We have previously hypothesized that relatively small and isolated rural communities may experience founder effects, defined as the genetic ramifications of small population sizes at the time of a community's establishment. To explore this, we used an Illumina Infinium Omni2.5Exome-8 chip to collect data from 157 individuals from four Illinois comm...
Article
Full-text available
Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Bayesian genotype calling can mitigate these issues, but previousl...
Poster
Full-text available
Genotype calling from sequencing data can be problematic in polyploid organisms due to uncertainty in allele dosage in heterozygotes, in addition to erroneous calling of heterozygotes as homozygotes due to undersampling of alleles. Bayesian methods have been used to ameliorate this uncertainty by setting prior probabilities for genotypes based on e...
Article
Full-text available
Dependable flow rate measurements are necessary to calculate flow volumes and resulting nutrient loads from subsurface drainage systems and associated conservation practices. The objectives of this study were (1) to develop appropriate weir equations for a new stainless steel-edged 45° V-notch weir developed for AgriDrain inline water level control...
Article
Full-text available
The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach now makes it practical to use the LMM to search for...
Data
Scree plot from a principal component analysis of genome-wide markers in the Goodman maize diversity panel. The X-axis is the principal component number and the Y-axis is the amount of variance explained. This plot suggests that the first three principal components adequately explain the variation among the genome-wide markers. (TIFF)
Data
Comparison of -log10(P-values) from the logistic mixed model and the unified mixed linear model. Plot of -log10(P-values) of SNPs from the logistic mixed model (Y-axis) against those from the unified mixed linear model (X-axis) for the genome-wide association study conducted for α-tocopherol levels in maize grain in the Goodman diversity panel dich...
Data
An assessment of computational time for performing a genome-wide association study for marker sets of various sizes using the unified mixed linear model and the logistic mixed model. All analyses were performed on a MacBook Pro laptop. (DOCX)
Data
Scree plot from a principal component analysis of genome-wide markers in the US sorghum association panel. The X-axis is the principal component number and the Y-axis is the amount of variance explained. This plot suggests that the first three principal components adequately explain the variation among the genome-wide markers. (TIFF)
Data
Manhattan plots summarizing the genome-wide association study (GWAS) results for all analyzed quantitative traits dichotomized at the 50th percentile. The specific trait and species of each plot is indicated in the row labels. The X-axis of each graph is physical position of either the B73_RefGen v2 position of the maize genome (for first three row...
Data
Comparison of -log10(P-values) from the logistic mixed model and the unified mixed linear model. Plot of -log10(P-values) of SNPs from the logistic mixed model (Y-axis) against those from the unified mixed linear model (X-axis) for the genome-wide association study conducted for sorghum branch length in the US sorghum association panel dichotomized...
Data
Comparison of -log10(P-values) from the logistic mixed model and the unified mixed linear model. Plot of -log10(P-values) of SNPs from the logistic mixed model (Y-axis) against those from the unified mixed linear model (X-axis) for the genome-wide association study conducted for maize ear height in the Goodman diversity panel dichotomized at the 50...
Data
Comparison of -log10(P-values) from the logistic mixed model and the unified mixed linear model. Plot of -log10(P-values) of SNPs from the logistic mixed model (Y-axis) against those from the unified mixed linear model (X-axis) for the genome-wide association study conducted for sorghum plant height in the US sorghum association panel dichotomized...
Data
Comparison of -log10(P-values) from the logistic mixed model and the unified mixed linear model. Plot of -log10(P-values) of SNPs from the logistic mixed model (Y-axis) against those from the unified mixed linear model (X-axis) for the genome-wide association study conducted for zeaxanthin levels in maize grain in the Goodman diversity panel dichot...