Spinach (Spinacia oleracea) is a diploid (2n = 2x = 12), wind-pollinated and highly heterozygous crop. The plants are mostly dioecious, although some monoecious plants exist. Spinach is an economically important cool-season leafy vegetable crop. Demand for spinach is increasing worldwide, particularly due to its high nutritional content. Spinach is a versatile crop eaten raw or cooked and used as salads or mixed with other cuisines. This review article provides an overview of origin and domestication, genetic diversity and population structure, genetic and genomic resources, major diseases threatening spinach production, breeding progress, and synthesizing how these resources can help in spinach improvement. The rapid development of genomic and sequence resources of spinach has increased biological and genetics research and laid the foundation for adopting molecular breeding. Downy mildew is the most serious disease affecting spinach and breeding programs focus on developing cultivars resistant to continually emerging new races of downy mildew pathogens. The use of genomic and molecular resources and approaches offers promises in population improvement and hybrid development to address biotic and abiotic stresses production challenges and provide improved breeding materials and strategies against the rapidly changing pathogen races and climatic conditions.

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete Peronospora effusa. In the past two decades, new pathogen races have repeatedly overcome the resistance used in newly released cultivars, urging the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew pathogens and are effective against some pathogen races/isolates. This work aimed to evaluate the worldwide USDA spinach germplasm collections and commercial cultivars for resistance to downy mildew pathogen in the field condition under natural inoculum pressure and conduct genome wide association analysis (GWAS) to identify resistance-associated genomic regions (alleles). Another objective was to evaluate the prediction accuracy (PA) using several genomic prediction (GP) methods to assess the potential implementation of genomic selection (GS) to improve spinach breeding for resistance to downy mildew pathogen. More than four hundred diverse spinach genotypes comprising USDA germplasm accessions and commercial cultivars were evaluated for resistance to downy mildew pathogen between 2017–2019 in Salinas Valley, California and Yuma, Arizona. GWAS was performed using single nucleotide polymorphism (SNP) markers identified via whole genome resequencing (WGR) in GAPIT and TASSEL programs; detected 14, 12, 5, and 10 significantly associated SNP markers with the resistance from four tested environments, respectively; and the QTL alleles were detected at the previously reported region of chromosome 3 in three of the four experiments. In parallel, PA was assessed using six GP models and seven unique marker datasets for field resistance to downy mildew pathogen across four tested environments. The results suggest the suitability of GS to improve field resistance to downy mildew pathogen. The QTL, SNP markers, and PA estimates provide new information in spinach breeding to select resistant plants and breeding lines through marker-assisted selection (MAS) and GS, eventually helping to accumulate beneficial alleles for durable disease resistance.

Cowpea (Vigna unguiculata L. Walp., 2n = 2x = 22) is a protein-rich crop that complements staple cereals for humans and serves as fodder for livestock. It is widely grown in Africa and other developing countries as the primary source of protein in the diet; therefore, it is necessary to identify the protein-related loci to improve cowpea breeding. In the current study, we conducted a genome-wide association study (GWAS) on 161 cowpea accessions (151 USDA germplasm plus 10 Arkansas breeding lines) with a wide range of seed protein contents (21.8~28.9%) with 110,155 high-quality whole-genome single-nucleotide polymorphisms (SNPs) to identify markers associated with protein content, then performed genomic prediction (GP) for future breeding. A total of seven significant SNP markers were identified using five GWAS models (single-marker regression (SMR), the general linear model (GLM), Mixed Linear Model (MLM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), which are located at the same locus on chromosome 8 for seed protein content. This locus was associated with the gene Vigun08g039200, which was annotated as the protein of the thioredoxin superfamily, playing a critical function for protein content increase and nutritional quality improvement. In this study, a genomic prediction (GP) approach was employed to assess the accuracy of predicting seed protein content in cowpea. The GP was conducted using cross-prediction with five models, namely ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL), applied to seven random whole genome marker sets with different densities (10 k, 5 k, 2 k, 1 k, 500, 200, and 7), as well as significant markers identified through GWAS. The accuracies of the GP varied between 42.9% and 52.1% across the seven SNPs considered, depending on the model used. These findings not only have the potential to expedite the breeding cycle through early prediction of individual performance prior to phenotyping, but also offer practical implications for cowpea breeding programs striving to enhance seed protein content and nutritional quality.

Bacterial wilt (BW), caused by Ralstonia solanacearum, is one of the devastating diseases in tomatoes (Solanum lycopersicum L.). The use of resistant cultivars and breeding for genetic resistance is the most effective, economical, and environmentally friendly management strategy for this disease. It is necessary to screen diverse germplasm and cultivated genotypes to identify resistant resources and to develop resistant cultivars in tomatoes to combat the changing pathogen isolates. This study evaluated 40 United States Department of Agriculture (USDA) tomato accessions for their BW resistance to the R. solanacearum isolate P822 under greenhouse conditions. The tomato plants were inoculated and visually assessed to observe their symptoms, and the disease severity was scored on a scale of 0 to 4 (0 = no leaf wilted, 1 = 25% of leaves wilted, 2 = 50% leaves wilted, 3 = 75% of leaves wilted, and 4 = 100% leaves wilted). Five accessions (PI 645370, PI 647306, PI 600993, PI 355110, and PI 270210) were observed as BW resistance, with PI 645370 showing the greatest resistance. The broad-sense heritability for BW resistance was estimated as 59.9% and 42.8% based on a 0–4 scale of disease incidence and the disease severity index, respectively. Two distinct clusters (sub-populations) were detected among 39 of the 40 accessions. The five identified BW-resistant accessions were distributed in both clusters, suggesting a likely difference in the genetic base among the five resistance accessions. The resistant accessions will contribute significantly to the tomato breeding program to develop new cultivars with BW resistance.

Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.

Drought, a crucial abiotic stressor, markedly reduces the growth and yield of tomato crops (Solanum lycopersicum L.). Consequently, adopting drought-resistant cultivars and implementing breeding programs to enhance drought tolerance have emerged as enduring solutions to alleviate the adverse effects of drought in various tomato cultivation regions. In this study, 68 United States Department of Agriculture (USDA) tomato accessions were assessed in a controlled greenhouse experiment, encompassing both water deficit treatment and a control group subjected to standard watering conditions. The experiment was arranged in a randomized complete block design with three replications. The results of this study pinpointed four accessions, PI 365956, PI 584456, PI 390510, and PI 370091, as drought-tolerant accessions. Additionally, high broad-sense heritability was revealed for leaf wilting, leaf rolling, and SPAD chlorophyll content (total leaf chlorophyll). Furthermore, positive correlations were found among parameters associated with leaf wilting, leaf rolling, and SPAD chlorophyll content. The findings offer valuable insights for tomato breeding initiatives, especially those focused on enhancing drought tolerance in elite cultivars. Future studies will expand the evaluation to include a larger pool of tomato accessions and conduct a genome-wide association study to identify single nucleotide polymorphism (SNP) markers for molecular breeding in tomatoes.