Explore the vast range of titles available.

Pea (Pisum sativum L.) is a high‐nutrient, cool‐season legume of increasing relevance in plant‐based nutrition and sustainable agriculture. As demand for alternative protein sources increases, improving pea seeds’ nutritional content and quality through genomics‐assisted breeding has become a priority. Despite its importance, limited research has explored the genetic basis of nutritional traits in pea. In this study, 267 accessions from the United States Department of Agriculture (USDA) Pea Single Plant Plus Collection were evaluated across 3 years at two USDA‐certified organic farms in South Carolina to (1) assess phenotypic variation, (2) characterize the population structure and origin, and (3) perform a genome‐wide association study (GWAS) using 54,316 single‐nucleotide polymorphism markers on five nutritional traits: protein concentration, sulfur‐containing amino acids (SAAs), dietary fiber, total starch, and protein digestibility (PDg). Population structure analysis using ADMIXTURE and principal components analyses identified 10 ancestral subpopulations. GWAS identified 17 marker‐trait associations for protein, SAA, and PDg, including a genomic hotspot on the proximal end of chromosome 5 associated with both protein and SAA. This region harbors candidate genes involved in seed development, germination, and protein biosynthesis, suggesting potential roles in protein and SAAs accumulation. These findings provide valuable insights into the genetic architecture underlying key nutritional traits and highlight candidate target genes for breeding high‐quality, biofortified pea cultivars. This research expands the genetic potential of pea as a sustainable and nutritious crop alternative for plant‐based food systems. Plain Language Summary Peas are cool‐season food legumes that are highly nutritious, whole foods rich in protein, dietary fiber, prebiotic carbohydrates, vitamins, and minerals with low fat content. The objective of this study to evaluate the United States Department of Agriculture (USDA) Pea Single Plant Plus Collection across 3 years at two USDA‐certified organic farms in South Carolina to (1) assess phenotypic variation, (2) characterize the population structure and origin, and (3) perform a genome‐wide association study on five nutritional traits. The results found 17 marker‐trait associations for these five traits. These key genetic markers will be used in future organic pea breeding for plant‐based food systems.

Background: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. Results: A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. Conclusions: A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.

Peanut (Arachis hypogaea L.) root‐knot nematode (PRKN) Meloidogyne arenaria is a very destructive pathogen to which most peanut cultivars are highly susceptible. Current peanut cultivars rely on a single locus for PRKN resistance incorporated from the wild relative A. cardenasii Krapov. & W.C. Greg., that could be overcome as a result of the emergence of new nematode populations. Thus, new sources of resistance are continually needed. A new and strong resistance has been found in the wild diploid relative, A. stenosperma Krapov. & W.C. Greg. Arachis stenosperma‐derived quantitative trait loci (QTL) were described on chromosomes A02 and A09 and reduced nematode development by up to 98.2%. In order to validate these resistance segments, this study screened for PRKN resistance in BC2F1 lines and correlated with molecular genotypes. Here, six BC2F1s carrying chromosome introgressions in A02 and/or A09, showed strong resistance while one line was susceptible. Both phenotype and genotype data allowed us to validate and delineate the chromosomal segments in chromosomes A02 and A09 to ∼8.5Mbp and ∼6.5Mbp regions on the bottom of each, respectively. Within the QTL on A02 and top middle of both chromosomes A02 and A09 there are R‐gene clusters, often implicated in pathogen resistance. We have provided validation of these key resistance QTL that can be used to inform breeding via marker selection and insights into the functional basis of resistance provided by the wild peanut relative A. stenosperma. Core Ideas Validation of peanut root‐knot nematode resistance incorporated in second generation of backcross lines. Incorporation of peanut root‐knot nematode resistance QTL from Arachis stenosperma. Towards the development of root‐knot nematode (Meloidogyne arenaria)‐resistant peanut cultivars.

Crop wild species are increasingly important for crop improvement. Peanut ( Arachis hypogaea L.) wild relatives comprise a diverse genetic pool that is being used to broaden its narrow genetic base. Peanut is an allotetraploid species extremely susceptible to peanut root-knot nematode (PRKN) Meloidogyne arenaria . Current resistant cultivars rely on a single introgression for PRKN resistance incorporated from the wild relative Arachis cardenasii , which could be overcome as a result of the emergence of virulent nematode populations. Therefore, new sources of resistance may be needed. Near-immunity has been found in the peanut wild relative Arachis stenosperma . The two loci controlling the resistance, present on chromosomes A02 and A09, have been validated in tetraploid lines and have been shown to reduce nematode reproduction by up to 98%. To incorporate these new resistance QTL into cultivated peanut, we used a marker-assisted backcrossing approach, using PRKN A. stenosperma -derived resistant lines as donor parents. Four cycles of backcrossing were completed, and SNP assays linked to the QTL were used for foreground selection. In each backcross generation seed weight, length, and width were measured, and based on a statistical analysis we observed that only one generation of backcrossing was required to recover the elite peanut’s seed size. A populating of 271 BC 3 F 1 lines was genome-wide genotyped to characterize the introgressions across the genome. Phenotypic information for leaf spot incidence and domestication traits (seed size, fertility, plant architecture, and flower color) were recorded. Correlations between the wild introgressions in different chromosomes and the phenotypic data allowed us to identify candidate regions controlling these domestication traits. Finally, PRKN resistance was validated in BC 3 F 3 lines. We observed that the QTL in A02 and/or large introgression in A09 are needed for resistance. This present work represents an important step toward the development of new high-yielding and nematode-resistant peanut cultivars.

Multiparent advanced eneration inter-cross (MAGIC) populations improve the precision of quantitative trait loci (QTL) mapping over biparental populations by incorporating increased diversity and opportunities to reduce linkage disequilibrium among variants. Here, we describe the development of a MAGIC B-Line (MBL) population from an inter-cross among 4 diverse founders of grain sorghum [Sorghum bicolor (L.) Moench] across different races (kafir, guinea, durra, and caudatum). These founders were selected based on genetic uniqueness and several distinct qualitative features including panicle architecture, plant color, seed color, endosperm texture, and awns. A whole set of MBL (708 F6) recombinant inbred lines along with their founders were genotyped using Diversity Arrays Technology (DArTseq) and 5,683 single-nucleotide polymorphisms (SNPs) were generated. A genetic linkage map was constructed using a set of polymorphic, quality-filtered markers (2,728 SNPs) for QTL interval-mapping. For population validation, 3 traits (seed color, plant color, and awns) were used for QTL mapping and genome-wide association study (GWAS). QTL mapping and GWAS identified 4 major genomic regions located across 3 chromosomes (Chr1, Chr3, and Chr6) that correspond to known genetic loci for the targeted traits. Founders of this population consist of the fertility maintainer (A/B line) gene pool and derived MBL lines could serve as female/seed parents in the cytoplasmic male sterility breeding system. The MBL population will serve as a unique genetic and genomic resource to better characterize the genetics of complex traits and potentially identify superior alleles for crop improvement efforts to enrich the seed parent gene pool.

Rust is a major pathogen of the peanut crop. Development and adoption of rust-resistant cultivars is the most cost efficient and effective way to control the spread of the disease and reduce yield losses. Some cultivated peanut germplasm accessions have a degree of resistance, but the secondary gene pool is a source of much stronger resistance alleles. Wild species, however, have undesirable agronomic traits that are a disincentive to their use in breeding. The identification of genomic regions that harbor disease resistance in wild species is the first step in the implementation of marker-assisted selection that can speed the introgression of wild disease resistances and the elimination of linkage drag. In this work, we identify genome regions that control different components of rust resistance in a recombinant inbred line population developed from a cross between two Arachis species, the susceptible most probable B genome ancestor of cultivated peanut, Arachis ipaënsis, and an accession of its closest relative, Arachis magna, which is resistant to rust. Quantitative trait loci for several components of resistance were placed in the same position on linkage group B08. Single-nucleotide polymorphism Kompetitive allele-specific polymerase chain reaction markers for rust resistance region were designed and validated for marker function in both diploid and tetraploid contexts.

Root-knot nematodes (RKN; Meloidogyne sp.) are a major threat to crops in tropical and subtropical regions worldwide. The use of resistant crop varieties is the preferred method of control because nematicides are expensive, and hazardous to humans and the environment. Peanut (Arachis hypogaea) is infected by four species of RKN, the most damaging being M. arenaria, and commercial cultivars rely on a single source of resistance. In this study, we genetically characterize RKN resistance of the wild Arachis species A. stenosperma using a population of 93 recombinant inbred lines developed from a cross between A. duranensis and A. stenosperma. Four quantitative trait loci (QTL) located on linkage groups 02, 04, and 09 strongly influenced nematode root galling and egg production. Drought-related, domestication and agronomically relevant traits were also evaluated, revealing several QTL. Using the newly available Arachis genome sequence, easy-to-use KASP (kompetitive allele specific PCR) markers linked to the newly identified RKN resistance loci were developed and validated in a tetraploid context. Therefore, we consider that A. stenosperma has high potential as a new source of RKN resistance in peanut breeding programs.

Identifying more traits of importance that can confer tolerance to various stressors, is the primary goal of scientists and breeders (Roychowdhury et al., 2020). [...]our Research Topic “Characterizing and improving traits for resilient crop development” comprises 14 manuscripts that provide new insights into crop genetic resources, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), haplotype analysis, multi-omics approaches, gene discovery, expression and functional characterization using advanced gene editing tools. In another study,Sheela et al.reported that gene stacking or pyramiding of multiple stress-responsive genes allows rice cultivars to be tolerant to multiple limiting conditions such as moisture stress, salinity, aging, temperature, and oxidative stresses. Sugar maple is an economically important tree species for its syrup and hardwood production, and the trees are highly vulnerable to drought conditions.Mulozi et al.characterized physiological and biochemical traits, where chlorophyll biosynthesis, lipid membrane damage, and osmolyte production play a crucial role in responding to drought. Patchouli is an important medicinal plant for patchouli propagation and oil yield.Warsi et al.studied this drought susceptible plant to establish a rapid and efficient in vitro regeneration method followed by agrobacterium-mediated transformation with ACC deaminase gene.

Root-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma . Here, to study the inheritance of these resistance alleles within the genetic background of tetraploid peanut, an F 2 population was developed from a cross between peanut and an induced allotetraploid that incorporated A. stenosperma , [ Arachis batizocoi x A. stenosperma ] 4× . This population was genotyped using a SNP array and phenotyped for nematode resistance. QTL analysis allowed us to verify the major-effect QTL on chromosome A02 and a secondary QTL on A09, each contributing to a percentage reduction in nematode multiplication up to 98.2%. These were validated in selected F 2:3 lines. The genome location of the large-effect QTL on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses. We conclude that the strong resistance to RKN, derived from the diploid A. stenosperma , is transferrable and expressed in tetraploid peanut. Currently it is being used in breeding programs for introgressing a new source of nematode resistance and to widen the genetic basis of agronomically adapted peanut lines.

The study of microRNAs (miRNAs) in plants has gained significant attention in recent years due to their regulatory role during development and in response to biotic and abiotic stresses. Although cassava (Manihot esculenta Crantz) is tolerant to drought and other adverse conditions, most cassava miRNAs have been predicted using bioinformatics alone or through sequencing of plants challenged by biotic stress. Here, we use high-throughput sequencing and different bioinformatics methods to identify potential cassava miRNAs expressed in different tissues subject to heat and drought conditions. We identified 60 miRNAs conserved in other plant species and 821 potential cassava-specific miRNAs. We also predicted 134 and 1002 potential target genes for these two sets of sequences. Using real time PCR, we verified the condition-specific expression of 5 cassava small RNAs relative to a non-stress control. We also found, using publicly available expression data, a significantly lower expression of the predicted target genes of conserved and nonconserved miRNAs under drought stress compared to other cassava genes. Gene Ontology enrichment analysis along with condition specific expression of predicted miRNA targets, allowed us to identify several interesting miRNAs which may play a role in stress-induced posttranscriptional regulation in cassava and other plants.