Euphytica

Bedassa, Sefawdin Berta; Tadesse, Zerihun; Birhan, Techale; Menamo, Temesgen Matiwos; Abebe, Abush Tesfaye

doi: 10.1007/s10681-026-03703-ypmid: N/A

In bread wheat breeding, connecting genetic diversity is considered important for exploiting positive Genotype-by-Environment Interactions (GEI) and developing stable, climate-resilient varieties. This study investigates the genetic diversity, GEI and stability of thirty bread wheat varieties, with the overall objective of this study was to decipher the relationship between allelic diversity and yield stability in bread wheat to identify optimal genotypes for breeding. Field trials were conducted using an alpha lattice design with two replications across six environments. AMMI and GGE biplot analyses revealed significant GEI, which accounted for 29.9% of the total variation in grain yield. Genetic diversity analysis of the 41 varieties revealed moderate variation, with an observed heterozygosity (Ho = 0.33) and an average polymorphic information content (PIC = 0.53), indicating a moderately diverse gene pool. Nucleotide diversity (π = 8.409688 × 10 − 6) suggests extremely low genetic variation within the population, raising concerns about the crop’s long-term adaptability to rapidly changing environmental conditions. High major allele frequencies (MaF = 0.8) and a low average minor allele frequency (MAF = 0.2). This indicates a skewed allelic distribution with very limited rare alleles, raising concerns about the population’s long-term adaptive capacity. This multi-environment evaluation study revealed distinct performance patterns among the wheat genotypes. The varieties (G4, G26, G1, G30, and G21) demonstrated both high yield potential and exceptional stability across diverse growing conditions. Particularly, genotypes G4 and G26, which uniquely combined superior agronomic performance with enrichment of rare alleles, positioning them as premier candidates for direct breeding applications and cultivar development. A central paradox emerged: genotypes with the highest overall allelic diversity G8, G13, G15) exhibited poor yield stability. This contrasts sharply with the stable, high-yielding genotypes, which possessed more targeted, functionally relevant allelic combinations. This stood in direct contrast to the stable genotypes that possessed more targeted, functionally relevant allelic content. This finding challenges the common assumption that broad genetic diversity alone ensures adaptive potential, instead suggesting that specific allelic combinations, rather than overall richness, may play a larger role in governing stability mechanisms.

Kebede, Firezer G.; Bantte, Kassahun; Mendaye, Taye T.; Menamo, Temesgen; Endalamaw, Chalachew; Legesse, Tokuma; Solomon, Hailemariam

doi: 10.1007/s10681-026-03710-zpmid: N/A

As moisture stress intensifies, breeding drought-tolerant sorghum varieties has become increasingly essential. However, root and physiological traits remain understudied in multi-parental sorghum populations derived from Ethiopian landraces and elite materials. In this study, 364 multi-parental sorghum lines were evaluated under greenhouse conditions to assess genetic variation and identify genomic regions associated with leaf morphology (area and angle), stomatal traits (density and diameter), and root characteristics (weight, number, biomass, and angle). Phenotypic variation was highly significant (P < 0.0001) and heritable for all traits, with estimates ranging from 61% for stomatal number to 88% for root length heritability. Using 5,218 high-quality SNPs and six multi-locus GWAS models, we identified 16 robust markers (identified by multiple models) associated with physiological and root traits, of which most (14) represent putative novel loci. Population structure revealed five distinct subpopulations. The root angle marker (S4_61772402) is linked to Sobic.004G274000, a Mitogen-Activated Protein Kinase Kinase Kinase (MAPKKK) which is associated with ABA-mediated drought response. The gene associated with root dry weight (Sobic.001G485200) contributes to maintaining root growth and enhancing root biomass under water-limited conditions. All three markers detected for stomatal density showed negative allelic effects, indicating reduced stomatal number, a trait increasingly recognized as advantageous under drought. Additionally, associated genes for leaf area and angle were linked to improved water-use efficiency and light interception. These findings provide heritable targets for marker-assisted selection in sorghum breeding for drought. However, as controlled phenotyping did not capture G × E, field validation is necessary to confirm marker utility in breeding.

Van, Kyujung; Clevinger, Elizabeth M.; Biyashev, Ruslan M.; Collakova, Eva; Pilot, Guillaume; Graef, George L.; McHale, Leah K.; Saghai Maroof, M. A.

doi: 10.1007/s10681-026-03712-xpmid: N/A

Protein and amino acid profile in soybean seeds are important factors for its market price, quality of the animal feed produced and producer’s income. With a soybean panel of 189 plant introductions, a genome-wide association study (GWAS) was performed for protein and free amino acid (FAA) content (leaf vs. seed). Correlation analysis of FAA and protein contents identified strong relationships between protein and asparagine (Asn), glutamine relative content in seeds, but not with leaf-FAAs. Significant protein-associated linkage disequilibrium (LD) blocks were identified only on Chromosome 20 known for genomic regions controlling protein/FAA contents along with two novel quantitative trait loci (QTL) on the same chromosome and their significance levels were quite different depending on each environment. For FAA contents, six significant LD blocks for aspartate, lysine, and valine among leaf-FAAs were identified, whereas twelve LD blocks related to Asn, γ-aminobutyric acid (GABA), histidine, methionine, phenylalanine, serine, and threonine were detected by GWAS conducted with seed FAA contents. Five and seven novel QTL for leaf- and seed-FAAs, respectively, were identified. GWAS combined with a correlation-based network analysis utilized network-derived FAA traits from leaf and seed. Seven novel QTL for network-derived traits were detected with leaf-FAAs and three novel QTL for absolute seed-FAAs were also identified. Comparing the candidate genes within the significant genomic regions provided insight into how FAAs are involved in seed development and sink-source partitioning. Overall, network analysis can help to identify genes putatively regulating AA content in soybean seeds, contributing to the development of new and improved cultivars.

Gonzalez Paleo, Luciana; Marino, Lucía; Vilela, Alejandra; Ravetta, Damián

doi: 10.1007/s10681-026-03706-9pmid: N/A

Selection for yield-related traits influences the evolutionary trajectory of a new crop through domestication. These changes are frequently accompanied by unintended, non-targeted modifications that might impact resource acquisition and use efficiency, which support critical environmental services. Our goals were to determine whether selection for increased productivity alters the root phenotypic expression and the resource-use strategy of Silphium, a perennial oilseed crop, and to evaluate the effectiveness of functional leaf-traits as selection criteria for the indirect selection of root phenotypes. We grew four accessions of Silphium in mesocosms for three years, and their root functional traits were compared. Three accessions were semi-domesticated, selected for seed yield (Seed) or their leaf resource-use strategy (Acquisitive or Conservative) and one was unselected (Wild). Functional traits were measured focused on the collaboration axis of the Root Economics Space that reflects the resource acquisition strategy. Seed and Acquisitive showed higher productivity and Shoot to Root ratio than Wild. Changes included thicker roots, with lower SRL, and a shift in the resource acquisition strategy, towards outsourcing to mycorrhiza. Conservative maintained most traits of Wild, including thinner roots and fewer mycorrhiza. Seed and Acquisitive had higher yields, while Wild and Conservative had higher yield stability. Given the strong integration of above-and below-ground functional traits, the use of acquisitive leaf-characters for breeding resulted in the development of larger plants with an acquisitive root system, associated with mycorrhizal symbiosis. The lower RTD and TNC storage suggest a potential for shorter root lifespan, a key trait linked to resource turnover.

Buathong, Phatcharee; Sukkasem, Roypim; Pongjaroenkit, Saengtong; Kophimai, Yuppayao; Kumchai, Jutamas; Vuttipongchaikij, Supachai; Sakulsingharoj, Chotipa

doi: 10.1007/s10681-026-03713-wpmid: N/A

Conventional breeding of pure line plants is a lengthy process, often requiring multiple generations of self-fertilization. Doubled haploid (DH) technology offers an accelerated alternative by enabling the production of completely homozygous lines within a single generation. Targeted mutation of the Domain of Unknown Function 679 membrane protein (DMP) gene has recently emerged as an effective tool for in vivo haploid induction. In this study, the CRISPR/Cas9 system was employed to edit the tomato SlDMP gene, achieving transformation and editing efficiencies of 25.86% and 7.33%, respectively. A selected homozygous line, DMPT1-233, carrying a 1-bp cytosine deletion that resulted in a truncated DUF679 domain, was evaluated for its haploid induction ability. While pollen viability in the edited line remained comparable to the wild type (76% vs. 74%), DMPT1-233 successfully induced haploids across four different maternal backgrounds. Haploid induction rates (HIR) ranged from 0.16 to 1.12%, with the highest efficiency (1.12%) observed in the TM-3 maternal line. Haploid plants were confirmed by flow cytometry and displayed characteristic phenotypes, including significantly reduced plant stature, narrower leaves, and complete male sterility. Quantitative analysis showed that haploid stomatal guard cells were significantly smaller than diploids, measuring approximately 74% in length and 80% in width. Genotypic analysis confirmed the maternal origin of all induced haploids. These findings demonstrate that CRISPR/Cas9-mediated DMP mutations in tomato generate functional haploid inducers, providing a promising approach for the rapid development of inbred lines to accelerate tomato breeding.

Shimoide, Moeno; Nakajima, Misaki; Pohan, Nadya Syafira; Kesumawati, Elly; Koeda, Sota

doi: 10.1007/s10681-026-03711-ypmid: N/A

Begomoviruses are among the most destructive pathogens of tomato worldwide, and the introgression of Ty-genes in tomato is a key strategy for disease management. However, a single Ty-gene often provides incomplete protection against highly virulent begomovirus species. Here, commercial tomato cultivars and a series of breeding lines previously developed by the World Vegetable Center (WorldVeg) were inoculated with one of three begomovirus species that differed in virulence. The presence of Ty-1, Ty-2, Ty-3, Ty-3a, ty-5, and Ty-6 was validated using in-gene markers. Tomato plants carrying only Ty-2 were susceptible to all viruses, whereas those with Ty-1 were resistant to a less-virulent begomovirus, but susceptible to more-virulent viruses. Among the seven WorldVeg’s breeding lines, AVTO1919 (Ty-1/Ty-1, Ty-6/Ty-6) and AVTO1920 (Ty-3/Ty-3, Ty-6/Ty-6) were symptomless in most cases and the lowest viral DNA accumulation across all lines tested indicating strong begomovirus resistance. The resistance of AVTO1919 was comparable to or greater than that of AVTO1701, a line homozygous for Ty-2, Ty-3, ty-5, and Ty-6. Furthermore, F₁ plants derived from crosses between AVTO1919 or AVTO1920 and susceptible Moneymaker exhibited reduced disease tolerance, indicating the resistance conferred by Ty-1 or Ty-3 and Ty-6 is incomplete dominance. These results demonstrate that Ty-1/Ty-3 and Ty-6 integration in homozygous states can provide robust and broad-spectrum resistance to begomoviruses and is a valuable strategy for breeding durable resistant tomato cultivars.

Glison, Nicolás; Monteverde, Eliana; Sandro, Pablo; Bassini, Facundo; Gaiero, Paola; Speranza, Pablo

doi: 10.1007/s10681-026-03717-6pmid: N/A

Domestication of warm-season forage grasses has been slow due to breeding challenges from complex ploidy systems and apomixis, as well as for the lack of genetic and genomic tools to assist breeding. Dallisgrass (Paspalum dilatatum Poir.) is a forage grass well-suited for warm-temperate climates. This apomictic pentaploid species belongs to the Dilatata species complex, along with allotetraploid autogamous sexual species. The phenotypic variability resulting from interspecific hybridization between these sexual species is understudied. Here, we examined the phenotypic variability of 17 quantitative traits within a RIL mapping population obtained after selfing progenies from a single cross between two sexual Dilatata species: P. flavescens and P. plurinerve. The variability was broader than that found in natural variation. Transgressive segregation was detected, and a fraction of the RILs showed phenotypic combinations different from parental lines. Additionally, we built a reliable high-density genetic map for the Dilatata species complex using 1,539 robust SNP markers, with similar quality to maps constructed for other warm-season grasses. To test the map usefulness and resolution and to gain initial insights into quantitative trait genetic architecture in these species, we localized robust QTLs using the phenotypic data for the measured traits. Correlations between traits were rare, and distances higher than 50 cM were registered between most QTLs, indicating independent segregation of traits and QTLs. The results demonstrate the potential of interspecific hybridizations between sexual Dilatata species for forage breeding and genetic and heritability analyses.

Chen, Jianhao; Wang, Ruoqiong; Liu, Baocang; Wang, Xiangjie; Luo, Hongmei; Liu, Zhihong; Xie, Qing

doi: 10.1007/s10681-026-03707-8pmid: N/A

Sea buckthorn (Hippophae rhamnoides) is an excellent shrub with both medicinal and food uses and ecological functions. However, the lack of genetic analyses and molecular markers for traits has limited their genetic improvement. In this study, we phenotyped and genetically analysed 120 F1 progeny of crosses between H. rhamnoides subsp. mongolica 'wulanshalin' and H. rhamnoides subsp. sinensis 'wucixiong'. We assessed the growth-related traits and chlorophyll and carotenoid contents of the F1 populations and performed correlation analysis and principal component analysis (PCA). The results revealed that the major traits of the observed hybrid progeny varied widely. In addition, we performed genetic analyses of the hybrid progeny using SSR markers and association analysis with phenotypic traits based on a mixed linear model (MLM). We identified genetic loci associated with various leaf and seedling traits in sea buckthorn. Specifically, we detected two loci for leaf area (LA), one for leaf perimeter (LP), one for leaf length (LL), two for ground diameter (GD), two for crown width (CW) and one for internodal distance (ID). These findings provide valuable insights for the targeted improvement of sea buckthorn through marker-assisted selection in breeding programs.

Shu, Yangpei; Hua, Xintao; Liu, Xinyan; Li, Huiwen; Zhang, Yan; Li, Yiying; Tang, Ziqi; Yang, Yun; Dai, Zhigang; Sun, Jian; Xie, Dongwei

doi: 10.1007/s10681-026-03716-7pmid: N/A

Okra (Abelmoschus esculentus L.) not only is highly nutritious but also exhibits robust resistance to abiotic stresses. The continuous expansion of saline–alkali soils has promoted the breeding of salt-tolerant okra varieties to effectively use saline–alkali land and expand the planting area of okra. A total of 180 okra accessions from diverse origins were subjected to NaCl treatments at concentrations of 0 mmol/L (CK), 120 mmol/L (T1), and 200 mmol/L (T2). Phenotypic traits related to salt tolerance, including superoxide dismutase (SOD) activity, peroxidase (POD) activity, and catalase (CAT) activity in shoots and roots and seedling height (SH), were measured on the 21st day of salt treatment. The mean phenotype value of the three seedlings constitutes one replicate, and the mean value of the three replicates is used as the phenotype data for GWAS. 189 SNPs significantly associated with salt tolerance were identified through genome-wide association study (GWAS) using the mixed linear model (MLM) in EMMAX software with the threshold of − log10 (P) > 4. Three loci—SNP184025 (controlled seedling height), SNP9134721 (controlled shoot and root CAT activity), and SNP9007603 (controlled shoot SOD activity)—were simultaneously detected under both T1 and T2 conditions. Linkage disequilibrium block analysis revealed nonsynonymous mutations of G/A and T/A in Ae60G010730 and Ae33G006070, respectively, resulting in changes in corresponding amino acids. Also, the trait values of okra accessions containing the two mutant alleles significantly increased. qRT-PCR further confirmed significant upregulation of Ae60G010730 and Ae33G006070 in allelic mutant accessions. This further confirmed that Ae60G010730 and Ae33G006070 were prioritized candidate genes supported by LD/allelic and expression evidence for regulating salt tolerance in okra seedlings under salt stress. This study lays the foundation for the cloning and functional verification of salt-tolerant genes in okra and provides valuable genetic resources for developing new salt-tolerant cultivars.

Mandal, Puja; Babu, Chakrapani; Senthil, Natesan; Chandrakumar, Kalichamy; Deepika, Venkatesan; Hossain, Firoz; Ravikesavan, Rajasekaran

doi: 10.1007/s10681-026-03688-8pmid: N/A

Sweet corn (Zea mays var. saccharata) has gained significant popularity in global agriculture due to its unique taste, improved nutritional profile, and consumer preference. Genetic advancements in sweet corn have played a crucial role in enhancing its palatability, nutritional quality and stress resilience. Key genetic improvements that have shaped modern sweet corn varieties elucidate the genetic basis of essential quality traits, including kernel sweetness, odour, pericarp thickness, and nutrient composition, which are influenced by key endosperm mutations. Additionally, the genetic regulation of stress resilience, encompassing both abiotic and biotic stresses is discussed, with an emphasis on genes and markers that facilitate breeding for sustainable productivity. Meanwhile, advancements in omics technologies, genomic selection (GS) and genome-wide association studies (GWAS) have provided a refined genetic roadmap for various essential attributes, their genes and regulatory mechanisms that contribute to consumer appeal. Advances in high-throughput phenotyping and genome-editing, are contributing to the rapid identification and development of cultivars with desirable attributes. By integrating conventional breeding with molecular tools for a targeted approach to quality traits, sweet corn improvement can be accelerated to meet the demands of the food system. This review synthesizes the current landscape of sweet corn genetics and highlights the importance of trait-based strategies and their relevance to quality-driven, climate-resilient, sustainable food production.