Genome-wide association studies in lettuce reveal the interplay of seed age, color, and germination under high temperatures.

Thermoinhibition, the suppression of seed germination by high temperatures, is an adaptive trait that ensures successful seedling establishment in natural environments. While beneficial for wild plants, thermoinhibition can adversely affect crop yields due to uneven and reduced germination rates, particularly in the face of climate change. To understand the genetic basis of thermoinhibition, we conducted a comprehensive genetic analysis of a diverse panel of Lactuca spp.

SpMS1, a Male Sterility Factor, Interacts with SpAP1 to Regulate Unisexual Flower Development in Dioecious Spinach.

The emergence of unisexual flower is an important event during plant evolution. The molecular mechanism underlying the formation of unisexual flowers remains unclear in dioecious spinach. In this study, we identified the spinach MALE STERILITY1 gene, SpMS1, which serves as a masculine factor to regulate male fertility and sex reversion.

Low frequency of the wild-type freezing-tolerance LsCBF7 allele among lettuce population suggests a negative selection during domestication and breeding.

Sustainable winter production in lettuce requires freezing tolerant varieties. This study identified a wild-type allele of LsCBF7 that could contribute to freezing tolerance improvement in lettuce. Lettuce is one of the most consumed vegetables globally.

Ability of Genomic Prediction to Bi-Parent-Derived Breeding Population Using Public Data for Soybean Oil and Protein Content.

Genomic selection (GS) is a marker-based selection method used to improve the genetic gain of quantitative traits in plant breeding. A large number of breeding datasets are available in the soybean database, and the application of these public datasets in GS will improve breeding efficiency and reduce time and cost. However, the most important problem to be solved is how to improve the ability of across-population prediction.

Evaluation of Tomato Germplasm against Tomato Brown Rugose Fruit Virus and Identification of Resistance in .

The tomato is one of the most important vegetable crops grown worldwide. Tomato brown rugose fruit virus (ToBRFV), a seed-borne tobamovirus, poses a serious threat to tomato production due to its ability to break the resistant genes (, , ) in tomatoes. The objective of this work was to identify new resistant source(s) of tomato germplasm against ToBRFV.

Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa).

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members.

Genetic Architecture of Salt Tolerance in Cowpea ( (L.) Walp.) at Seedling Stage Using a Whole Genome Resequencing Approach.

Cowpea ( (L.) Walp.) is a diploid legume crop used for human consumption, feed for livestock, and cover crops.

Genome-Wide Association Study Reveals a QTL Region for Ashy Stem Blight Resistance in PRA154 Andean Common Bean.

Ashy stem blight (ASB) caused by (Tassi) Goidanich affects the common bean ( L.) at all growing stages. Higher levels of resistance were observed in Andean common beans, but specific resistant quantitative trait loci (QTLs) conferring resistance to this pathogen have not been reported in this gene pool.

A Genome-Wide Association Study Reveals Region Associated with Seed Protein Content in Cowpea.

Cowpea ( L. Walp., 2 = 2 = 22) is a protein-rich crop that complements staple cereals for humans and serves as fodder for livestock.

Skim resequencing finely maps the downy mildew resistance loci and in spinach cultivars whale and Lazio.

Commercial production of spinach ( L.) is centered in California and Arizona in the US, where downy mildew caused by is the most destructive disease. Nineteen typical races of have been reported to infect spinach, with 16 identified after 1990.

A genome-wide association study and genomic prediction for resistance in soybean.

Soybean brown rust (SBR), caused by , is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets.

A Genome-Wide Association Study and Genomic Prediction for Fiber and Sucrose Contents in a Mapping Population of LCP 85-384 Sugarcane.

Sugarcane ( spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations.

Identification of a QTL region for ashy stem blight resistance using genome-wide association and linage analysis in common bean recombinant inbred lines derived from BAT 477 and NY6020-4.

Ashy stem blight (ASB), caused by the fungus (Tassi) Goidanich is an important disease of the common bean ( L.). It is important to identify quantitative trait loci (QTL) for ASB resistance and introgress into susceptible cultivars of the common bean.

Resequencing worldwide spinach germplasm for identification of field resistance QTLs to downy mildew and assessment of genomic selection methods.

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete . 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.

Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing.

Spinach () is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete causes the most important disease in spinach, downy mildew. A total of nineteen races of 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.

Growth and Photosynthetic Responses of Cowpea Genotypes under Waterlogging at the Reproductive Stage.

Waterlogging is an important environmental stress limiting the productivity of crops worldwide. Cowpea ( L.) is particularly sensitive to waterlogging stress during the reproductive stage, with a consequent decline in pod formation and yield.

Genetic dissection of nitrogen induced changes in the shoot and root biomass of spinach.

Efficient partitioning of above and below-ground biomass in response to nitrogen (N) is critical to the productivity of plants under sub-optimal conditions. It is particularly essential in vegetable crops like spinach with shallow root systems, a short growth cycle, and poor nitrogen use efficiency. In this study, we conducted a genome-wide association study (GWAS) to explore N-induced changes using spinach accessions with diverse genetic backgrounds.

Identification of Candidate Genes and Genomic Selection for Seed Protein in Soybean Breeding Pipeline.

Soybean is a primary meal protein for human consumption, poultry, and livestock feed. In this study, quantitative trait locus (QTL) controlling protein content was explored genome-wide association studies (GWAS) and linkage mapping approaches based on 284 soybean accessions and 180 recombinant inbred lines (RILs), respectively, which were evaluated for protein content for 4 years. A total of 22 single nucleotide polymorphisms (SNPs) associated with protein content were detected using mixed linear model (MLM) and general linear model (GLM) methods in Tassel and 5 QTLs using Bayesian interval mapping (IM), single-trait multiple interval mapping (SMIM), single-trait composite interval mapping maximum likelihood estimation (SMLE), and single marker regression (SMR) models in Q-Gene and IciMapping.