Zhiwu Zhang

• PhD
• Professor (Full) at Washington State University

Crop pests significantly reduce crop yield and threaten global food security. Conventional pest control relies heavily on insecticides, leading to pesticide resistance and ecological concerns. However, crops and their wild relatives exhibit varied levels of pest resistance, suggesting the potential for breeding pest-resistant varieties. This study...

Crop pests significantly reduce crop yield and threaten global food security. Conventional pest control relies heavily on insecticides, leading to pesticide resistance and ecological concerns. However, crops and their wild relatives exhibit varied levels of pest resistance, suggesting the potential for breeding pest-resistant varieties. This study...

Background The genome-wide association study (GWAS) is a powerful method for mapping quantitative trait loci (QTL). However, standard GWAS can detect only QTL that segregate in the mapping population. Crossing populations with different characteristics increases genetic variability but F2 or back-crosses lack mapping resolution due to the limited n...

Background: Root system architecture (RSA) is of growing interest in implementing plant improvements with belowground root traits. Modern computing technology applied to images offers new pathways forward to plant trait improvements and selection through RSA analysis (using images to discern/classify root types and traits). However, a major stumbli...

Genome‐wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Alternatively, GWAS can use counts of substrings of length k from longer sequencing reads, k ‐mers, as genotyping data. Using maize cob and kernel color traits, we demonstrated that k ‐mer GWAS can...

Large fruit size is one of the most important breeding objectives for sweet cherry. In the Washington State University (WSU) breeding program, large-fruited germplasm exists, and heritability is reasonably high. An important genetic locus for cherry fruit size has been identified but appears to primarily distinguish between wild and improved phenot...

Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high‐protein pea lines, exploring genetic architecture across environments,...

Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology/topology/distribution and root system architecture (RSA) have been recog...

Background Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene e...

Modern agriculture is a complex system that demands real‐time and large‐scale quantification of trait values for evidence‐based decisions. However, high‐profile traits determining market values often lack high‐throughput phenotyping technologies to achieve this objective; therefore, risks of undermining crop values through arbitrary decisions are h...

The increase in the global human population and the accompanying challenges in meeting nutritional needs amidst climate change are a worldwide concern. Widespread protein and micronutrient deficiencies contribute to a significant number of individuals experiencing malnutrition, leading to severe health repercussions. This issue can be addressed thr...

The introduction of quinoa into new growing regions and environments is of interest to farmers, consumers, and stakeholders around the world. Many plant breeding programs have already started to adapt quinoa to the environmental and agronomic conditions of their local fields. Formal quinoa breeding efforts in Washington State started in 2010, led b...

Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation empower the breeding of climate-resilience crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages with remarkable...

Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology and root system architecture (RSA) have been recognized as increasingly...

Crop pests have profoundly deleterious effects on crop yield and food security. However, conventional pest control depends heavily on the utilization of insecticides, which develops strong pesticide resistance and concerns of food safety. Crop and their wild relatives display diverse levels of pest resistance, indicating the feasibility for breedin...

Genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional nonadditive effects such as dominance. Here, we describe a pipeline developed for joint analysis of phenotypes, effects, and generations (JPEG). As a demonstration, we analyze 12 grain quality traits of 113 inbred lines (male parents), five...

Object Detection (OD) is a computer vision technology that can locate and classify objects in images and videos, which has the potential to significantly improve efficiency in precision agriculture. To simplify OD application process, we developed Ladder - a software that provides users with a friendly graphic user interface (GUI) that allows for e...

The Hagberg–Perten falling number (HFN) method is the international standard used to evaluate the damage to wheat (Triticum aestivum) grain quality due to preharvest sprouting (PHS) and late maturity alpha‐amylase (LMA). However, the HFN test requires specialized laboratory facilities and is time consuming. Spectrometers were known as a potential t...

Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to environmen...

Background Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene e...

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most devastating diseases of wheat and causes large-scale epidemics and severe yield loss. Applying fungicides during early epidemic development is crucial to controlling the disease but is often challenged by resource-limited human visual scouting. Deep learning has the pote...

Identification and visualization of large insertion and deletion (indel) polymorphisms, which contribute significantly to natural phenotypic variation, are challenge from a pan-genome. Here, through streamlining two unsupervised machine learning algorithms, we developed a BRIDGEcereal webapp for surveying and graphing indel-based haplotypes for gen...

A large amount of training data is usually lacking at the beginning of system development and labeling such a large number of RGB (red, green, blue) images is laborious. Interactive recurrent annotation is beneficial to incrementally gain training images in the stream of the system development and provides an opportunity to reduce human workload. W...

Plant breeding primarily focuses on improving agronomy traits, e.g. yield, quality, host plant resistance to pathogens and pests, and abiotic stress tolerance; however, the methods for their genetic improvement are being rapidly enhanced through genomics and phenomics. In the Genomics–Phenomics–Agronomy (G‐P‐A) paradigm, diverse research approaches...

Fall dormancy (FD) is an essential trait to overcome winter damage and for alfalfa (Medicago sativa) cultivar selection. The plant regrowth height (PRH) after autumn clipping is an indirect way to evaluate FD. Transcriptomics, proteomics, and QTL mapping have revealed crucial genes correlated with FD, however, these genes can’t predict alfalfa FD v...

One application of DNA-informed breeding, which has potential to increase the effectiveness of traditional breeding methods, is the use of DNA-based diagnostic tests to estimate genetic potential of breeding individuals. In sweet cherry (Prunus avium L.), cracked or soft fruit are major industry challenges. Recent research detected two quantitative...

Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits1,2. The solution to this problem is to identify all causal genetic variants and to measure their individual contributions3,4. Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 mi...

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...

Genome-wide association study (GWAS) is based on the linkage disequilibrium (LD) between phenotypes and genetic markers covering the whole genome. Besides the genetic linkage between the genetic markers and the causal mutations, many other factors contribute to the LD, including selection and nonrandom mating formatting population structure. Many m...

Precision livestock farming has become an important research focus with the rising demand of meat production in the swine industry. Currently, the farming practice is widely conducted by the technology of computer vision (CV), which automates monitoring pig activity solely based on video recordings. Automation is fulfilled by deriving imagery featu...

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most devastating diseases of wheat and causes large-scale epidemics and severe yield loss. Applying fungicides during early epidemic development is crucial to controlling the disease but is often challenged by resource-limited human visual scouting. Deep learning has the pote...

Hybrid rice has an advantage in its heterosis, resulting in high yield and resistance to biotic and abiotic stress. However, genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional complexity, such as the dominant effect. It is critical to identify a path to efficiently develop inbreds and ident...

This review examines the application, limitations, and potential alternatives to the Hagberg–Perten falling number (FN) method used in the global wheat industry for detecting the risk of poor end‐product quality mainly due to starch degradation by the enzyme α‐amylase. By viscometry, the FN test indirectly detects the presence of α‐amylase, the pri...

Hybrid rice has an advantage in its heterosis, resulting in high yield and resistance to biotic and abiotic stress. However, genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional complexity, such as the dominant effect. It is critical to identify a path to efficiently develop inbreeds and iden...

Unlabelled: Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GW...

Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry creates an attractive alternative to variable results from cultural management practices. DNA-informed breeding increases its efficiency, yet upstream research is needed to identify the genomic regions associated with the trait variation of a breeding-relev...

Background Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to...

Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies such as differential gene expression to respond to environmen...

Unknown genetic architecture makes it difficult to characterize the genetic basis of traits and associated molecular markers because of the complexity of small effect quantitative trait loci (QTLs), environmental effects, and difficulty in phenotyping. Seedling emergence of wheat (Triticum aestivum L.) from deep planting, has a poorly understood ge...

The last decade witnessed an unprecedented increase in the adoption of genomic selection (GS) and phenomics tools in plant breeding programs, especially in major cereal crops. GS has demonstrated the potential for selecting superior genotypes with high precision and accelerating the breeding cycle. Phenomics is a rapidly advancing domain to allevia...

Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein report the de novo assembly of the chromosome-...

Long-term variety testing trials offer unique opportunities to evaluate the profound impact of climate change to agriculture. Here, we systematically dissected the performance trends from a16-year elite spring wheat variety trial into explicit quantifiable climatic patterns. A cool early21 season and warm late-season increased yield. Reduced temper...

Background Gene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions. Therefore, we sought to explore both the genomic and condition-specific characteristics of gene expression heritability within t...

Tissue extracellular matrix (ECM) is a structurally and compositionally unique microenvironment within which native cells can perform their natural biological activities. Cells grown on artificial substrata differ biologically and phenotypically from those grown within their native tissue microenvironment. Studies examining human tissue ECM structu...

Genome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Here we employed an GWAS approach using k-mers, short substrings from sequencing reads. Using maize cob and kernel color traits, we demonstrated that k-mer GWAS can effectively identify associated k...

Fall dormancy (FD) is one of the most important traits of alfalfa ( Medicago sativa ) for cultivar selection to overcome winter damage. Regrowth plant height following autumn clipping is an indirect way to evaluate FD. Although transcriptomics, proteomics analysis, and QTL mapping have revealed some important genes correlated with FD, the genetic a...

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...

Genome-wide association study (GWAS) and genomic prediction/selection (GP/GS) are the two essential enterprises in genomic research. Due to the great magnitude and complexity of genomic and phenotypic data, analytical methods and their associated software packages are frequently advanced. GAPIT is a widely-used genomic association and prediction in...

Traits with an unknown genetic architecture make it difficult to create a useful bi-parental mapping population to characterize the genetic basis of the trait due to a combination of complex and pleiotropic effects. Seedling emergence of wheat (Triticum aestivum L.) from deep planting is a vital factor affecting stand establishment and grain yield,...

Alfalfa (Medicago sativa L.) is a perennial and outcrossing legume crop predominantly grown for hay, silage, or pasture. Intensive selection has made a dramatic improvement on fitness traits, including winter survival and disease resistance. However, there is a minimal improvement on other economically important traits, such as hay yield, which is...

Flavonoids give plants their rich colors and play roles in a number of physiological processes. In this study, we identified a novel colorless maize mutant showing reduced pigmentation throughout the whole life cycle by EMS mutagenesis. E183K mutation in maize chalcone synthase C2 (ZmC2) was mapped using MutMap strategy as the causal for colorless,...

Genome-wide association studies (GWAS) are a powerful tool to detect genes controlling a trait of interest. This is accomplished by identifying loci throughout the genome where variations in genotype are associated with variations in phenotype. From genetic engineering to genomic prediction, GWAS are useful in applications critical to modern plant...

Grain characteristics, including kernel length, kernel width, and thousand kernel weight, are critical component traits for grain yield. Manual measurements and counting are expensive, forming the bottleneck for dissecting these traits' genetic architectures toward ultimate yield improvement. High-throughput phenotyping methods have been developed...

Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a training population to develop prediction models for grain yield selection. An imbalanced set of yield data collected from 102 environments...

Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a trai...

Fall dormancy (FD) is one of the most important traits of alfalfa (Medicago sativa) for cultivar selection to overcome winter stress. Although transcriptomics, proteomics analysis, and QTL mapping have revealed some important genes correlated with FD, the genetic architecture of this trait is still unclear. There are no applicable genes or markers...

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from...

Fall dormancy (FD) is one of the most important traits of alfalfa (Medicago sativa) for cultivar selection to overcome winter stress. Although transcriptomics, proteomics analysis, and QTL mapping have revealed some important genes correlated with FD, the genetic architecture of this trait is still unclear. There are no applicable genes or markers...

Plant breeding primarily focuses on improving conventional agronomic traits, e.g. yield, quality, and resistance to biotic and abiotic stress; however, genetic improvement methods are being rapidly enhanced through genomics and phenomics. In the Genomics-Phenomics-Agronomics (GPA) paradigm, diverse research approaches have been conducted to bridge...

Along with the development of high-throughput sequencing technologies, both sample size and SNP number are increasing rapidly in Genome-Wide Association Studies (GWAS), and the associated computation is more challenging than ever. Here, we present a Memory-efficient, Visualization-enhanced, and Parallel-accelerated R package called "rMVP" to addres...

Alfalfa (Medicago sativa L.), the most valuable perennial legume crop, referred to as "Queen of the Forages" for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are...

Alfalfa is the most widely cultivated forage legume, with approximately 30 million hectares planted worldwide. Genetic improvements in alfalfa have been highly successful in developing cultivars with exceptional winter hardiness and disease resistance traits. However, genetic improvements have been limited for complex economically important traits...

Genome‐wide association studies (GWAS) have developed into a powerful and ubiquitous tool for the investigation of complex traits. In large part, this was fueled by advances in genomic technology, enabling us to examine genome‐wide genetic variants across diverse genetic materials. The development of the mixed model framework for GWAS dramatically...

Background Gene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions. Increasing quantities of high-throughput DNA and RNA sequencing and standardization of research populations has resulted in the...

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...

Genome-Wide Association Study (GWAS) and Genomic Prediction/Selection (GP/GS) are the two essential enterprises in genomic research. Due to the great magnitude and complexity of genomic data, analytical methods and their associated software packages are frequently advanced. GAPIT is a widely used Genomic Association and Prediction Integrated Tool....

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...

Alfalfa (Medicago sativa L.) is a perennial, outcrossing legume crop predominantly grown for hay, silage, or pasture. Intensive selection has resulted in dramatic improvement in fitness traits, including winter survival and disease resistance. However, there has been minimal improvement in other economically important traits, such as hay yield, whi...

Simple Summary Understanding the genetic architecture underlying milk production traits in cattle is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we performed a genome-wide association study for milk production and quality traits in Holstein cattle. In the total of ten significant single-nucleot...

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...

Accurately predicting phenotypes from genotypes holds great promise to improve health management in humans and animals, and breeding efficiency in animals and plants. Although many prediction methods have been developed, the optimal method differs across datasets due to multiple factors, including species, environments, populations, and traits of i...

Along with the development of high-throughout sequencing technologies, both sample size and number of SNPs are increasing rapidly in Genome-Wide Association Studies (GWAS) and the associated computation is more challenging than ever. Here we present a Memory-efficient, Visualization-enhanced, and Parallel-accelerated R package called "rMVP" to addr...

Husk has multiple functions such as protecting ears from diseases, infection, and dehydration during development. Additionally, husks comprised of fewer, shorter, thinner, and narrower layers allow faster moisture evaporation of kernels prior to harvest. Intensive studies have been conducted to identify appropriate husk architecture by understandin...

Grain characteristics, including kernel length, kernel width, and thousand kernel weight, are critical component traits for grain yield. Manual measurements and counting are expensive, forming the bottleneck for dissecting the genetic architecture of these traits toward ultimate yield improvement. High-throughput phenotyping methods have been devel...

The production of high-yield and high-quality milk is the direct economic goals of dairy industry breeding. Understanding the genetic architecture underlying milk-related traits is beneficial so that genetic variants can be targeted toward the overall improvement. In this study, we measured five traits related to milk production and components in H...

Aerial imagery has the potential to advance high-throughput phenotyping for agricultural field experiments. This potential is currently limited by the difficulties of identifying pixels of interest (POI) and performing plot segmentation due to the required intensive manual operations. We developed a Python package, GRID (GReenfield Image Decoder),...

The husk—the leaf-like outer covering of maize ear—has multiple functions, including protecting the ear from diseases infection and dehydration. In previous studies, we genotyped an association panel of 508 inbred lines genotyped with a total of ~550,000 SNPs (Illumina 50 K SNP Chip and RNA-seq). Genome-Wide Association Studies (GWAS) were conducte...

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a major threat to wheat production worldwide, especially in the United States. To identify loci for effective stripe rust resistance in U.S. wheat, a genome-wide association study (GWAS) was conducted using a panel of 616 spring wheat cultivars and breeding lines. The accession...

Apple industries suffer from major apple diseases because of widely planted susceptible cultivars. Developed disease-resistant cultivars that often carry only a single source of resistance are not expected to be durable over time. Cultivars with multiple sources of resistance are often commercially unacceptable due to unsatisfactory fruit quality a...

Background Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapte...