The sucrose concentration in soybean seed significantly affects the flavor of soybean‐derived products. In this study, an association panel of 178 elite accessions and 33,149 single‐nucleotide polymorphisms (SNPs) was utilized to identify quantitative trait nucleotides (QTNs) of sucrose concentration in soybean seeds by genome‐wide association study (GWAS). Five QTNs (rs2688589, rs29026218, rs5926884

The extraordinarily long stigmatic silks of corn (Zea mays L.) are critical for grain production but the biology of their growth and emergence from husk leaves has remained underexplored. Accordingly, gene expression was assayed for inbreds ‘B73’ and ‘Mo17’ across five contiguous silk sections. Half of the maize genes (∼20,000) are expressed in silks, mostly in spatiotemporally dynamic patterns. In

Polyploidy has been a prevalent process during plant evolution and it has made a major impact on the structure and evolution of plant genomes. Many important crop plants are polyploid. There is considerable interest in expression patterns of duplicated genes in polyploids. Alternative splicing (AS) is a fundamental aspect of gene expression that produces multiple final transcript types from a single

Bread wheat, Triticum aestivum L., is one of the most important crops in the world. Understanding its genome organization (allohexaploid; AABBDD; 2n = 6x = 42) is essential for geneticists and plant breeders. Particularly, the knowledge of how homologous chromosomes (equivalent chromosomes from the same genome) specifically recognize each other to pair at the beginning of meiosis, the cellular process

Using genomic information to predict phenotypes can improve the accuracy of estimated breeding values and can potentially increase genetic gain over conventional breeding. In this study, we investigated the prediction accuracies achieved by best linear unbiased prediction (BLUP) for nine potato phenotypic traits using three types of relationship matrices pedigree ABLUP, genomic GBLUP, and a hybrid

Tocochromanols (tocols for short), commonly called Vitamin E, are lipid‐soluble plant antioxidants vital for regulating lipid peroxidation in chloroplasts and seeds. Barley (Hordeum vulgare L.) seeds contain all eight different isoforms of tocols; however, the extent of natural variation in their composition and their underlying genetic basis is not known. Tocol levels in barley seeds were quantified

Flowering time is an important agronomic trait of alfalfa (Medicago sativa L.). Managing flowering time can produce economic benefits for farmers. To understand the genetic basis of this trait, quantitative trait loci (QTL) mapping was conducted in a full‐sib population that consisted of 392 individuals segregating based on flowering time. High density linkage maps were constructed using single nucleotide

Verticillium wilt, a soil‐borne disease caused by the fungal pathogen Verticillium dahliae, threatens strawberry (Fragaria × ananassa) production worldwide. The development of resistant cultivars has been a persistent challenge, in part because the genetics of resistance is complex. The heritability of resistance and genetic gains in breeding for resistance to this pathogen have not been well documented

The identification and characterization of resistance genes should outpace the rapid emergence of new P. graminis f. sp. tritici races, such as TTRTF and TTKTT, to mitigate stem rust damage to wheat. The objective of the current study was to identify and characterize P. graminis f. sp. tritici race resistance association signals. A total of 250 North American spring wheat lines were evaluated at the

Understanding population genetic structure and diversity of a crop is essential in designing selection strategies in plant breeding. About 2010 Ethiopian sorghum accessions were phenotyped for different traits at multiple locations. A subset of the collection, 1628 accessions, predominantly landraces, some improved varieties, and inbred lines were genotyped by sequencing. Phenotypic data revealed association

Salvia miltiorrhiza Bunge, also known as red sage or Danshen, is an important traditional Chinese medicine (TCM) that has been used for thousands of years to treat cardiovascular and other diseases. It is also considered an important model TCM plant. Here, a high‐quality reference genome of S. miltiorrhiza was generated by combining PacBio long‐read sequencing and chromatin interaction mapping (Hi‐C)

MADS‐box genes that are homologous to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been shown to play key roles in the regulation of bud dormancy in perennial species, particularly in the deciduous fruit trees of Rosaceae. However, their evolutionary profiles in Rosaceae have not yet been analyzed systematically. Here, The SVP genes were found to be significantly expanded in Rosaceae when compared

Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a geno

Classical plant breeding has been instrumental in changing the genetic makeup of crop plants for better ecological adaptation and improved quality. This paper provides insights of the genomic changes effected in hard winter wheat (Triticum aestivum L.) through decades of breeding and selection in the Great Plains of the United States. Population structure and differentiation analyses were conducted

Brown stem rot (BSR) reduces soybean [Glycine max (L.) Merr.] yield by up to 38%. The BSR causal agent is Phialophora gregata f. sp. sojae, a slow‐growing, necrotrophic fungus whose life cycle includes latent and pathogenic phases, each lasting several weeks. Brown stem rot foliar symptoms are often misdiagnosed as other soybean diseases or nutrient stress, making BSR resistance especially difficult

Plant genomes contain both protein‐coding and noncoding sequences including transposable elements (TEs) and noncoding RNAs (ncRNAs). The ncRNAs are recognized as important elements that play fundamental roles in the structural organization and function of plant genomes. Despite various hypotheses, TEs are believed to be a major precursor of ncRNAs. Transposable elements are also prime factors that

Most of the bioinformatics tools for enzyme annotation focus on enzymatic function assignments. Sequence similarity to well‐characterized enzymes is often used for functional annotation and to assign metabolic pathways. However, these approaches are not feasible for all sequences leading to inaccurate annotations or lack of metabolic pathway information. Here we present the mApLe (metabolic pathway

Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome‐wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA‐ARS wheat (Triticum aestivum L.) core collection by developing

Breeding forest species can be a costly and slow process because of the extensive areas needed for field trials and the long periods (e.g., five years) that are required to measure economically and environmentally relevant phenotypes (e.g., adult plant biomass or plant height). Genomic selection (GS) and indirect selection using early phenotypes (e.g., phenotypes collected in greenhouse conditions)

The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co‐regulatory genes, are quite unknown. Therefore, to identify the genome‐wide binding sites of PmTCP4 transcription factors and their co‐regulatory

Apple fruit cover color is an important appearance trait determining fruit quality, high degree of fruit cover color or completely red fruit skin is also the ultimate breeding goal. MdMYB1 has repeatedly been reported as a major gene controlling apple fruit cover color. There are also multiple minor‐effect genes affecting degree of fruit cover color (DFC). This study was to identify genome‐wide quantitative

Chinese jujube (Ziziphus jujuba Mill.) is an important fruit crop and harbors many highly diverse traits of potential economic importance. Fruit size, stone size, and fruit cracking have an important influence on the commercial value of jujube. This study is the first to conduct a genome‐wide association study (GWAS) on 180 accessions of jujube and focuses on locating single‐nucleotide polymorphisms

Modifying plant architecture is often necessary for yield improvement and climate adaptation, but we lack understanding of the genotype‐phenotype map for plant morphology in sorghum. Here, we use a nested association mapping (NAM) population that captures global allelic diversity of sorghum to characterize the genetics of leaf erectness, leaf width (at two stages), and stem diameter. Recombinant inbred

Wheat quality improvement is an important objective in all wheat breeding programs. However, due to the cost, time and quantity of seed required, wheat quality is typically analyzed only in the last stages of the breeding cycle on a limited number of samples. The use of genomic prediction could greatly help to select for wheat quality more efficiently by reducing the cost and time required for this

Rapid cycle genomic selection (RC‐GS) helps to shorten the breeding cycle and reduce the costs of phenotyping, thereby increasing genetic gains in terms of both cost and time. We implemented RC‐GS on two multi‐parent yellow synthetic (MYS) populations constituted by intermating ten elite lines involved in each population, including four each of drought and waterlogging tolerant donors and two commercial

When including genotype × environment interactions (G × E) in genomic prediction models, Hadamard or Kronecker products have been used to model the covariance structure of interactions. The relation between these two types of modeling has not been made clear in genomic prediction literature. Here, we demonstrate that a certain model based on a Hadamard formulation and another using the Kronecker product

1 WHEN NEMATODES ATTACK Plant parasitic nematodes are the bane of potato growers around the world because there are so few effective ways to fight them. However, some wild plants, such as Solanum sisymbriifolium (SSI), are able to halt the life‐cycle of invading cyst nematodes long before the animals become sexually mature. Wixom et al. (https://doi.org/10.1002/tpg2.20016) have identified 277 genes

Comprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome‐wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits

Cadmium (Cd) toxicity is a serious threat to future food security and health safety. To identify genetic factors contributing to Cd uptake in wheat, we conducted a genome‐wide association study with genotyping from 90K SNP array. A spring wheat diversity panel was planted under normal conditions and Cd stress (50 mg Cd/kg soil). The impact of Cd stress on agronomic traits ranged from a reduction of

Pigeonpea [Cajanus cajan (L.) Millsp.] is a pulse crop cultivated in the semi‐arid regions of Asia and Africa. It is a rich source of protein and capable of alleviating malnutrition, improving soil health and the livelihoods of small‐holder farmers. Hybrid breeding has provided remarkable improvements for pigeonpea productivity, but owing to a tedious and costly seed production system, an alternative

Fusarium langsethiae is a symptomless pathogen of oat panicles that produces T‐2 and HT‐2 mycotoxins, two of the most potent trichothecenes produced by Fusarium fungi in cereals. In the last few years, the levels of these mycotoxin in oat grain has increased and the European commission have already recommended a maximum level for of 1000 μg kg−1 for unprocessed oat for human consumption. The optimal

Long non‐coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. The spectacular progress made in next‐generation sequencing technologies has enabled a genome‐wide identification of lncRNAs in multiple plant species. In this study, a genome‐wide lncRNA sequencing technology was used to identify cold‐responsive lncRNAs at the booting stage in rice by comparing

DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest

The maize C system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rf4 have been widely used for maize hybrid production; however, the underlying mechanism is still uncertain. The sterility factor functions in mitochondria, where it interacts directly or indirectly with the restorer. Mitoproteomics can capture all participants involved in CMS and restoration at the organelle

Linear and non‐linear models used in applications of genomic selection (GS) can fit different types of responses (e.g., continuous, ordinal, binary). In recent years, several genomic‐enabled prediction models have been developed for predicting complex traits in genomic‐assisted animal and plant breeding. These models include linear, non‐linear and non‐parametric models, mostly for continuous responses

On the cover: Genomic selection can be implemented in lentil to make within‐population and across‐environment predictions. See Haile et al (https://doi.org/10.1002/tpg2.20002).

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one

Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome‐wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging

Mangroves is an umbrella term for plants located across the tropics and sub‐tropics that live in the coastal region, between the sea and the land. All mangroves evolved from terrestrial plants, providing the opportunity to assess convergence, as well as the lineage‐specific features, at the genetic level. In this study, we compared chloroplast genomes from 21 mangrove species, covering main phylogenetic

Callus induction is a dedifferentiation process that accompanies a cell fate transition, and epigenetic regulation plays a crucial role in the process. N6‐methyladenosine (m6A) methylation is an important mechanism in post‐transcriptional epigenetic regulation and functions in cell reprogramming. However, the function of m6A methylation during callus induction is still unknown. Here, we performed transcriptome‐wide

Many researchers today are looking for mechanisms underlying plant defenses against nematodes by identifying differentially expressed genes in domesticated hosts. In order to provide a different perspective, we analyzed the root transcriptome of an undomesticated non‐host species, Solanum sisymbriifolium Lamark (SSI) before and after Globodera pallida infection. Utilizing RNAseq analyses, we identified

Genome‐wide association mapping identifies quantitative trait loci (QTL) that influence the mean differences between the marker genotypes for a given trait. While most loci influence the mean value of a trait, certain loci, known as variance heterogeneity QTL (vQTL) determine the variability of the trait instead of the mean trait value (mQTL). In the present study, we performed a variance heterogeneity

Tomato is an attractive fruiting vegetable crop that can be used as an ornamental plant. Agronomical traits have been subjected to extensive genetic dissection to enhance vegetable breeding programs. By contrast, there are few genetic studies of ornamental traits for the development of ornamental tomato varieties. To investigate genetic loci linked to desired ornamental traits, we performed genetic

Soybean breeding relies on the use of wild (Glycine soja Sieb. and Zucc.) and domesticated [Glycine max (L.) Merr.] germplasm for trait improvement. Soybeans are self‐pollinating and accessions can be maintained as pure lines, however within‐accession genetic variation has been observed in previous studies of some landraces and elite cultivars. The objective of this study was to characterize within‐line

Crown rust, caused by Puccinia coronata f. sp. avenae Erikss., is the most important disease impacting cultivated oat (Avena sativa L.). Genetic resistance is the most desirable management strategy. The genetic architecture of crown rust resistance is not fully understood, and previous mapping investigations have mostly ignored temporal variation. A collection of elite oat lines sourced from oat breeding

Genomic selection (GS) is a marker‐based selection initially suggested for livestock breeding and is being encouraged for crop breeding. Several statistical models are used to implement GS; however, none have been tested for use in lentil (Lens culinaris Medik.) breeding. This study was conducted to compare the accuracy of different GS models and prediction scenarios based on empirical data and to

The primary domestication of olive (Olea europaea L.) in the Levant dates back to the Neolithic period, around 6,000–5,500 BC, as some archeological remains attest. Cultivated olive trees are reproduced clonally, with sexual crosses being the sporadic events that drive the development of new varieties. In order to determine the genomic changes which have occurred in a modern olive cultivar, the genome

Vitamin A deficiency is one of the most prevalent nutritional deficiencies worldwide. Sorghum [Sorghum bicolor L. (Moench)] is a major cereal crop consumed by millions of people in regions with high vitamin A deficiency. We quantified carotenoid concentrations in a diverse sorghum panel using high‐performance liquid chromatography and conducted a genome‐wide association study (GWAS) of grain carotenoids

Root anatomical phenes have important roles in soil resource capture and plant performance; however, their phenotypic plasticity and genetic architecture is poorly understood. We hypothesized that (a) the responses of root anatomical phenes to water deficit (stress plasticity) and different environmental conditions (environmental plasticity) are genetically controlled and (b) stress and environmental

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome‐wide variants for 24 founders of the

African wild rice Oryza longistaminata, one of the eight AA‐ genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high‐quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating

Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental

A genome‐wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS (e.g. population structure, sample size, and sequence analysis and field testing costs) need to be considered. Mixed populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic

Genomic selection (GS) based recurrent selection methods were developed to accelerate the domestication of intermediate wheatgrass [IWG, Thinopyrum intermedium (Host) Barkworth & D.R. Dewey]. A subset of the breeding population phenotyped at multiple environments is used to train GS models and then predict trait values of the breeding population. In this study, we implemented several GS models that

Genomic prediction (GP) might be an efficient way to improve haploid induction rate (HIR) and to reduce the laborious and time‐consuming task of phenotypic selection for HIR in maize (Zea mays L.). In this study, we evaluated GP accuracies for HIR and other agronomic traits of importance to inducers by independent and cross‐validation. We propose the use of GP for cross prediction and parental selection

A barrier to the adoption of genomic prediction in small breeding programs is the initial cost of genotyping material. Although decreasing, marker costs are usually higher than field trial costs. In this study we demonstrate the utility of stratifying a narrow‐base biparental oat population genotyped with a modest number of markers to employ genomic prediction at early and later generations. We also

Ethylene is one of the most important phytohormone in plants and plays a critical role during growth, development, maturity, and aging. The framework of the ethylene signaling pathway is well reported. Nevertheless, studies on Ethylene Insensitive 3 (EIN3), the downstream regulator of the ethylene signaling pathway, need to be investigated, especially in peach [Prunus persica (L.) Batsch]. In this

Assessing the allelic diversity within a germplasm collection and identifying individuals carrying favorable alleles is challenging. Advances in high‐throughput technologies allow the genotyping of many individuals for thousands of markers but bridging the gap between single nucleotide polymorphisms (SNPs) and relevant alleles remains difficult. We developed a systematic approach that defines haplotypes

Considering the practicality of applying genomic selection (GS) in the line development stage of a hard red winter (HRW) wheat (Triticum aestivum L.) variety development program (VDP), the effectiveness of GS was evaluated by prediction accuracy and by the response to selection across field seasons that demonstrated challenges for crop improvement under significant climate variability. Important breeding