With an aim of enhancing drought tolerance using a marker‐assisted backcrossing (MABC) approach, we introgressed the “QTL‐hotspot” region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought‐tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92‐3. Of eight simple sequence repeat (SSR) markers in the

Good understanding of the genes controlling root development is required to engineer root systems better adapted to different soil types. In wheat (Triticum aestivum L.), the 1RS.1BL wheat–rye (Secale cereale L.) translocation has been associated with improved drought tolerance and a large root system. However, an isogenic line carrying an interstitial segment from wheat chromosome arm 1BS in the distal

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 reduced the number of false positives compared with

Rice (Oryza sativa L.) in rainfed marginal environments is prone to multiple abiotic and biotic stresses, which can occur in combination in a single cropping season and adversely affect rice growth and yield. The present study was undertaken to develop high‐yielding, climate‐resilient rice that can provide tolerance to multiple biotic and abiotic stresses. An assembled first‐crossing scheme was employed

Stripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to bread wheat production worldwide. The breakdown in resistance of certain major genes and newly emerging aggressive races of stripe rusts pose serious concerns in all main wheat growing areas of the world. To identify new sources of resistance and associated QTL for effective utilization in future breeding

Genetic enhancement for resistance against the pod borer, Helicoverpa armigera is crucial for enhancing production and productivity of chickpea. Here we provide some novel insights into the genetic architecture of natural variation in H. armigera resistance in chickpea, an important legume, which plays a major role in food and nutritional security. An interspecific recombinant inbred line (RIL) population

Sorghum is an important food crop in many parts of Africa and Asia. Landraces of sorghum are known to exhibit variation in food quality traits including starch and protein content and composition. In this study, a panel of diverse sorghum breeding lines and 788 sorghum conversion (SC) lines representing the global germplasm diversity of the crop were evaluated for variation in starch quality based

1 ALLELE SHIFTS IN IMPROVED WHEAT Selection is the deliberate act of increasing the frequency of favorable alleles in a genome thereby affecting the phenotypic performance of the organism. Breeding for high yielding and disease resistant wheat cultivars has a long history in the United States. Ayalew et al. (https://doi.org/10.1002/tpg2.20032) identified significant selection signatures caused by several

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

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

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

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)

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

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

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

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

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

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

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

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

Cuticular waxes play important eco‐physiological roles in protecting plants against abiotic and biotic stresses and show high sensitivity to environmental changes. In order to clarify the responses of cuticular waxes on faba bean (Vicia faba L.) leaves to different light wavelengths, the phenotypic plasticity of cuticular waxes was analyzed when plants were subjected to white, red, yellow, blue, and

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

Soft red winter wheat (SRWW) cultivar AGS 2038 has a high level of seedling and adult plant leaf rust (LR) resistance. To map and characterize LR resistance in AGS 2038, a recombinant inbred line (RIL) population consisting of 225 lines was developed from a cross between AGS 2038 and moderately resistant line UGA 111729. The parents and RIL population were phenotyped for LR response in three field

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

Phytophthora sojae causes Phytophthora root and stem rot of soybean and has been primarily managed through deployment of qualitative Resistance to P. sojae genes (Rps genes). The effectiveness of each individual or combination of Rps gene(s) depends on the diversity and pathotypes of the P. sojae populations present. Due to the complex nature of P. sojae populations, identification of more novel Rps

The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome

Southern corn rust (SCR), which is caused by the fungal pathogen Puccinia polysora Underw, is a prevalent foliar disease in maize. Breeding for resistant cultivars is a desirable way for the efficient control of this disease. To identify quantitative trait loci (QTL) for conferring resistance to SCR, a recombinant inbred population including 138 lines (RILs) derived from the SCR‐resistant line CML496

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so‐called triads represent only one

Safflower, a minor oilseed crop, is gaining increased attention for food and industrial uses. Safflower genebank collections are an important genetic resource for crop enhancement and future breeding programs. In this study, we investigated the population structure of a safflower collection sourced from the Australian Grain Genebank and assessed the potential of genomic prediction (GP) to evaluate

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

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

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

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