Search Results (316)

Upland cotton (Gossypium hirsutum, AD1) is the most important fiber crop for the world’s textile industry. The genetic base of Upland cotton is narrow, and the introgression of germplasm from other species into Upland cotton can broaden its genetic diversity, including the introduction of new qualitative traits. The objectives of this study were to determine the inheritance, allelism, and linkage relationships of the red anther trait introduced into Upland from the red anther donor G. armourianum (D2-1) through crosses involving a synthetic tetraploid A1D2-1. After two generations of backcrossing to Upland cotton, followed by inbreeding, homozygous red-anthered plants (RA) were selected and used for crosses with two Upland lines, the Upland standard TM-1, the multiple recessive marker line T582, and the multiple dominant marker line T586. All Upland cotton parents, except the RA parents and T586 (possessing yellow anthers), had cream anthers. The anther color of the F₁ plants was red, indicating that the red anther trait is dominant. In nine of ten F₂ populations and four of five testcross populations, the segregation of anther color followed a 3:1 and 1:1 ratio, respectively, as expected under a one-gene model. In three F₂ populations with a total of 885 plants between RA with green leaf and T586 with red leaf (R₁ on chromosome D07), no double recessive genotype (yellow/cream anther and green leaf) was observed, indicating the allelic relationship between R₁ and red anther allele, designated R₁^a. The recombination frequency between R₁^a and cluster-1 (cl₁) on D07 was estimated to be 0.112 in 256 F₂ plants of a cross between RA and T582 based on the maximum likelihood estimation. This new red anther trait and its associated new gene allele provide an important genetic source for understanding the biosynthesis of anthocyanins and may have utility for improving resistance to anther-feeding insects in cotton. Full article

Adult plant resistance (APR) is widely used in wheat breeding, but its behaviour across genetic backgrounds remains poorly understood. In this study, we analysed the expression of three APR loci (Lr34, Lr46, Lr67) following their introgression into elite winter wheat cultivars. BC₂F₁ populations derived from crosses between donor lines and commercial cultivars were evaluated under controlled infection with Puccinia triticina (Pt). Gene expression was assessed using RT-qPCR, and miRNA abundance was quantified by ddPCR at five time points (0–48 hours post-inoculation, hpi). Expression patterns differed markedly between genetic backgrounds, affecting both the magnitude and timing of gene activity. Lr34 and Lr67 showed the highest expression prior to inoculation, with no consistent or sustained induction following infection. In contrast, the candidate gene Lr46-Glu2 displayed a clear tendency towards early induction, with peak expression typically observed at 6–12 hours post-inoculation, although the amplitude of this response varied among genotypes. Levels of miRNA varied across genotypes and time points and did not consistently reflect mRNA expression. The results suggest that the expression of APR-associated loci is influenced by genetic background. Lr34 and Lr67 showed predominantly baseline-associated expression, whereas the Lr46-associated candidate gene Lr46-Glu2 displayed a more infection-responsive transcriptional profile following inoculation. These patterns are consistent with different transcriptional behaviours of the analysed genes but do not establish their functional contribution to resistance. Further phenotypic and functional validation will be required to determine the biological significance of these expression patterns. Full article

Satellite DNA is a dynamic component of plant genomes and a valuable source of cytogenetic markers, but its diversity and chromosomal distribution in polyploid Triticeae remain insufficiently studied. Here, low-coverage whole-genome sequencing, graph-based repeat clustering, quantitative PCR, multivariate statistics and fluorescence in situ hybridization (FISH) were used to identify and characterize satellite repeats in Elymus and related Triticeae species. Sixteen repeat clusters (E1–E16), with monomer lengths of 118–667 bp, showed distinct taxonomic distributions and copy-number profiles across 14 species. Correlation analysis, principal component analysis and hierarchical clustering revealed concerted variation among repeats and separated the perennial taxa Elymus and Pseudoroegneria from Triticum, Secale, Hordeum and Dasypyrum. Spearman correlation analysis identified E7 and E9 as putative candidates associated with St/StY genomic backgrounds, whereas E10 was identified as a putative candidate associated with the H genome. These statistical associations require independent cytogenetic validation. Contrasting copy numbers of E6 and E11 in bread wheat cv. Chinese Spring versus Dasypyrum villosum (L.) Candargy identified them as V-genome candidates. FISH localized E6 to the terminal regions of chromosomes 3VL, 4VS and 7VS, and E11 to 4VL. Karyotyping further revealed that two lines previously considered as wheat-D. villosum addition lines were in fact substitution lines: W3 was identified as a 3V(3D) substitution line and W4 as a 4V(4B) substitution line, whereas W7 retained its 7V addition status. These results expand the set of chromosomal markers for comparative genomics and introgression analysis in wheat. Full article

Perennial wild relatives of annual crops possess traits associated with stress tolerance, efficient nutrient uptake, and increased soil carbon sequestration. They therefore represent valuable genetic resources for developing perennial crops that may reduce environmental and climate impacts and enhance food security. We evaluated 151 introgression lines (ILs) derived from crosses between barley and the perennial relative Hordeum bulbosum, each carrying unique H. bulbosum chromosome segments in a barley genetic background. Growth and regrowth after harvest were evaluated in two field trials, established by spring and fall planting in separate years in central Sweden, and under simulated two-year seasonal cycles in a climate chamber. In the climate chamber, 54% of the ILs exhibited strong regrowth, and two-thirds of these ILs showed reproductive growth across two seasonal cycles. In the field, most ILs showed regrowth after harvest but did not survive the cold winter. The parental genetic background had a strong effect from the barley parent on several growth and reproductive traits, but some ILs exhibited phenotypes not expected based on the barley parent. Of the divergent ILs with high regrowth, identified by PCA combining all studied traits, H. bulbosum introgressions at chromosome arms 2HL and 4HL were highly represented among ILs with cultivar Emir as a barley parent, and introgressions at 1HL among ILs with cultivar Morex as a parent. Perennial growth was observed only under mild conditions, indicating that perenniality of these ILs in a cold-temperate climate requires not only regrowth capacity but also adaptation to photoperiod, vernalization, and frost. ILs with high regrowth and reproductive growth may be used in crossing efforts with cold-tolerant germplasm to support the development of perennial barley. Full article

Common gene mapping approaches mainly include QTL-mapping, BSA-seq (QTL-seq) and GWAS. BSA-seq is designed to facilitate the mapping of quantitative trait loci (QTL) in a cost-effective and high-efficiency manner. In order to accommodate the diverse species-specific traits and population genetic architectures, researchers have developed a series of tailored BSA methodologies. In this study, using six wild rices (Oryza rufipogon) as donors and the elite cultivated rice Youzhan 8 (YZ8) as the recipient, we constructed a BC₄F₈ population through hybridization and backcrossing. These six wild rice introgression lines together constitute a nested association mapping (NAM) population. Upon genotyping 1819 lines of the NAM population for the Sd1 gene, we found that among lines harboring the 383 bp deletion, 98.5–99.3% exhibited a low plant height (LP) phenotype, whereas 0.7–1.5% showed a high plant height (HP) phenotype. Based on this phenotypic segregation, we selected a total of 20 HP lines and 20 LP lines from six BC₄F₈ populations to form the H-bulk and L-bulk, respectively. Using BSA-seq, we identified a total of 33 significantly associated candidate intervals. One candidate interval located on chromosome 1 contains D18, a previously reported gene that regulates plant height. Furthermore, we preliminarily identified two major candidate genomic regions on chromosome 8 (4.60–5.76 Mb and 7.29–7.33 Mb). Integrating RNA-seq data, CAFRI-Rice online functional prediction and RT-qPCR validation, two key candidate genes, LOC_Os08g09900 and LOC_Os08g09000, were selected for subsequent functional characterization. The results of this study indicate that the NAM-BSA technology has great potential to detect QTL associated with complex traits, which can provide a novel technical strategy for the genetic dissection of complex traits in rice. Full article

Kazakhstan possesses considerable potential for the development of organic agriculture. In organic production systems, the use of chemical plant protection products is restricted or completely excluded, making the cultivation of genetically resistant wheat lines to major fungal diseases one of the most effective approaches for maintaining stable grain production. The current study aimed to evaluate disease resistance in wheat genotypes by integrating phenotypic screening and marker-assisted selection and their validation under organic farming conditions. A total of 50 facultative and introgressive wheat lines were evaluated under an artificial infection background for resistance to yellow rust, leaf rust, stem rust, and common bunt. Molecular marker analysis was performed to identify resistance-associated alleles. Integrated phenotypic and molecular analyses enabled the identification of three promising genotypes, namely 1675-52, 1723-32, and 1716-24. They combined a high level of resistance to yellow rust and common bunt with the presence of resistance-associated alleles. These selected genotypes were subsequently validated under organic field conditions. The results demonstrated that these lines maintained stable resistance to yellow rust and common bunt and produced seed yield ranging from 5.45 to 5.94 t/ha, exceeding that of the standard cv. Almaly (4.88 t/ha). The obtained results confirm the effectiveness of integrating phenotypic screening with marker-assisted selection for identifying wheat genotypes with complex disease resistance. These genotypes represent promising prebreeding resources for organic agriculture, subject to validation across a wider range of environments. Full article

Soybean seeds have long been regarded as “storehouses of high-quality proteins”. The breakdown of dietary proteins by digestive proteases is essential for achieving adequate protein digestibility in animals and humans. However, plants have evolved a diverse array of protease inhibitors that regulate or restrict protease activity. In soybean, these inhibitors are concentrated primarily within the 2S protein fraction. Trypsin inhibitors (TIs) of Kunitz trypsin inhibitor (KTI) and Bowman–Birk inhibitor (BBI) are the most impactful due to their strong anti-tryptic activity, which interferes with digestive proteases in humans and animals. Elevated TI levels render raw soybeans unsuitable for direct food or feed use unless thermal or processing inactivation treatments are applied. Elimination or reduction in KTI and BBI using classical and biotechnology-based breeding efforts is a promising strategy. Soybean germplasm harboring BBI null alleles has not been reported. Breeding only for low or null KTI content in soybean would not be sufficient for practical applications. Hybridizing IT105782 × PI 547656 and using the reported Kompetitive Allele-Specific PCR (KASP) markers represents an effective classical breeding strategy. Simultaneous CRISPR/Cas9-mediated knockout of key KTI and BBI genes is expected to enable the development of soybean lines with substantially reduced TI levels, an outcome that cannot be readily achieved through classical introgression of null alleles, as naturally occurring null BBI alleles have not yet been identified. Moreover, this approach avoids the linkage drag associated with donor-derived null KTI alleles. However, this approach remains challenging due to functional redundancy and compensatory effects among KTI and BBI family members, extensive sequence homology among KTI and BBI genes that complicates the minimization of off-target effects, and the genotype dependency of Agrobacterium-mediated soybean transformation. Microtiter plate AACCI/AOCS could be one practical option for measuring TIA in breeding programs in terms of precision. Potential trade-offs associated with reduced trypsin inhibitor levels, including possible effects on plant defense and stress resistance, should be investigated in future studies, as these aspects have received little attention in previous research. Full article

The einkorn wheat group, comprising ancient diploid species (2n = 14, AA), including Triticum monococcum, Triticum boeoticum, and Triticum urartu, represents a valuable source of genetic variation for improving disease resistance in wheat. To develop a practical platform for introgressing powdery mildew resistance into bread wheat, we screened 21 einkorn accessions with Blumeria graminis f. sp. tritici (Bgt) race E09 and identified seven resistant donors. Because direct hybridization between diploid einkorn (AA) and hexaploid wheat (AABBDD) is constrained by genomic divergence and poor cross-compatibility, we crossed resistant einkorn accessions with susceptible durum wheat and induced chromosome doubling in the F₁ hybrids to generate synthetic durum–einkorn amphiploids. Nine amphiploids were obtained. Chromosome counts and genomic in situ hybridization confirmed the expected genomic constitution (AABBAA) in most lines, with limited variation in chromosome number in two amphiploids. Phenotyping against Bgt race E09 showed that three amphiploids retained high resistance, four showed moderate resistance, and two were moderately susceptible. Marker analysis identified five einkorn accessions contain known Pm genes such as Pm60, Pm60b, and PmNCA6/Pm37, as well as their derived amphipliods. Two einkorn accessions and their derived amphiploids may harbor novel Pm genes. Field evaluation of the agronomic traits of these amphiploids indicated some improvement in tillering, spike length, and seed weight. Moreover, these amphiploids had better seed-setting rates in crosses and backcrosses with common wheat. These synthetic durum–einkorn amphiploids thus offer a new bridging platform for transferring alien genes from diploid einkorn to hexaploid common wheat, providing valuable genetic resources for wheat-breeding programs. Full article

In the Iberian Peninsula, the rapid expansion of the invasive species Alburnus alburnus (bleak) has intensified its contact with several endemic cyprinid species, raising concerns about hybridization, introgression, and the loss of genetic diversity. Despite increasing evidence of hybridization, data remain limited for many Iberian River basins, where endemic species persist in fragmented and vulnerable habitats. The aim of this study is to assess the extent and spatial distribution of hybridization between the bleak and the following native cyprinid species, Anaecypris hispanica (jarabugo), Iberochondrostoma lemmingii (pardilla), Pseudochondrostoma willkommii (Guadiana nase), and Squalius alburnoides (calandino), across several rivers within the Guadalquivir Basin. To this end, Sanger sequencing will be performed on the mitochondrial cytochrome b gene (maternal lineage; approximately 1000 base pairs (bp)) and the nuclear β-actin gene (paternal lineage; approximately 950 bp) from individuals of all endemic species and the bleak. Parental species and putative hybrids were initially identified in the field using diagnostic morphological and meristic characters, including number of rays in the anal fin morphology, mouth position, and the number of lateral line scales. Molecular analyses will include haplotype network reconstruction and phylogenetic tree inference to evaluate relationships among individuals from different species and to assess lineage divergence. The results will allow us to: (1) detect hybrids between the bleak and endemic cyprinids, (2) identify hybridization events among endemic cyprinid species, and (3) evaluate the correspondence between diagnostic morphological and meristic traits and the molecular identification of hybrid individuals. Overall, these findings will provide key information for the conservation management of endangered Iberian freshwater fishes in the context of invasive species expansion and global change. Full article

Cowpea (Vigna unguiculata (L.) Walp.) is a legume valued in several countries for its nutritional quality, low input requirements, and economic profitability. However, cowpea productivity is significantly constrained by anthracnose disease caused by Colletotrichum species. Enhancing host resistance through the introgression of resistance alleles from landraces and wild relatives offers a promising strategy for durable disease management. This study evaluated 20 cowpea landraces and 18 V. unguiculata ssp. dekindtiana accessions for resistance to anthracnose under natural field infection. The cultivars Ife Brown and V. vexillata line TVNu-428 were included as susceptible and resistant checks, respectively. The experiment was laid in an alpha lattice design (8 × 5) with three replications arranged. Anthracnose symptoms characterized by enlarged light-brown lesions surrounded by reddish-brown halos were produced on all the accessions and the symptoms progressed throughout the assessment period. Five V. unguiculata ssp. dekindtiana accessions (TVNu-113, TVNu-1506, TVNu-1222, TVNu-420, and TVNu-136) and three cowpea landrace accessions (TVu-14076, TVu-17556, and TVu-17567) were identified as promising sources of anthracnose resistance. These accessions represent valuable genetic resources for broadening the cowpea resistance gene pool and support the strategic utilization of wild cowpea germplasm in breeding programs. Full article

Wheat powdery mildew and stripe rust, caused by Blumeria graminis f. sp. tritici (Bgt) and Puccinia striiformis f. sp. tritici (Pst), respectively, are two devastating diseases that threaten global wheat production. Long-term reliance on a limited number of resistance genes can accelerate resistance breakdown. Triticum urartu (2n = 14, A^uA^u), the progenitor of the wheat A subgenome, serves as a valuable gene pool for disease resistance. In this study, we identified three T. urartu accessions exhibiting high resistance to Bgt and Pst. Molecular marker analysis indicated that PI 428215 and PI 428315 carry Pm60b, whereas CITR 17664 carries both Pm60 and YrU1. Durum–T. urartu amphiploids (AABBA^uA^u) displayed resistance responses identical to their T. urartu parent and were used as bridges to transfer these resistance genes into a common wheat (AABBDD) background. Using marker-assisted selection (MAS), recurrent backcrossing, selfing, and phenotypic screening, we developed wheat lines carrying Pm60, Pm60b, YrU1, or Pm60 + YrU1. Segregation analysis in backcross-derived populations supported the functionality of these genes in the common wheat background. The selected introgression lines have high resistance to Bgt and Pst and showed no obvious adverse agronomic effects, providing useful germplasm for wheat disease resistance breeding. This study used a “multi-resistance, multi-combination” pyramiding strategy by MAS to introduce resistance genes from wild wheat into common wheat. Full article

Hybridization between sugarcane (Saccharum spp.) and its wild relative Erianthus rockii offers a promising route to broadening the narrow genetic base of modern cultivars, but the authenticity and chromosome inheritance patterns of such hybrids remain poorly understood. In this study, we combined molecular marker (tetra-primer ARMS-PCR) and cytogenetic (genomic in situ hybridization, GISH) approaches to verify hybridity and track chromosome transmission in 24 F₁ and 12 BC₁ progeny. The F₁ hybrids exhibited a strict n + n transmission pattern, receiving exactly 15 chromosomes from E. rockii. When F₁ plants were used as the male parent in backcrosses, no BC₁ seeds were obtained due to complete pollen sterility. Remarkably, when F₁ plants served as the female parent, all 12 BC₁ clones retained the entire set of 15 E. rockii chromosomes intact, following an unconventional 2n + n pattern. These findings reveal a strong parent-of-origin effect and, for the first time, demonstrate that the whole E. rockii chromosome complement can be stably transmitted into backcross progeny without loss or recombination. This opens a direct route for introgressing complete wild genomes into sugarcane breeding lines, preserving complex polygenic traits and guiding rational crossing strategies. Full article

Early and late leaf spot (ELS and LLS), caused by Passalora arachidicola and Nothopassalora personata, are major constraints to peanut (Arachis hypogaea L.) production. Durable resistance in cultivated germplasm remains limited due to the crop’s narrow genetic base. Wild Arachis species represent an important but underutilized source of resistance. This study aimed to identify and prioritize wild introgressions associated with foliar disease resistance in advanced peanut backcross lines derived from the induced allotetraploid BatSten1 (Arachis batizocoi × A. stenosperma)^4x. A population of advanced backcross lines carrying reduced wild genome content (~5% to ~1% across advancement) was evaluated through four years of field trials for LLS severity and yield, complemented by detached-leaf bioassays to dissect resistance components for both ELS and LLS. Genome-wide SNP genotyping, combined with mixed-model analysis and association mapping, identified introgressed regions influencing disease response. Genome-wide association studies (GWAS) detected loci on chromosomes A06 and A09 associated with LLS resistance, explaining approximately 25% and 11% of phenotypic variation, respectively, with evidence of additive effects between loci. Component-level analyses further revealed both resistance- and susceptibility-associated introgressions. Although tomato spotted wilt virus (TSWV) incidence was evaluated in field trials, exploratory GWAS did not detect significant marker–trait associations, indicating that genetic components associated with this trait were not resolved under the conditions tested. Overall, these results expand the understanding of the genetic architecture of leaf spot resistance beyond traditional donor sources and provide a framework for prioritizing beneficial wild introgressions while minimizing linkage drag in peanut pre-breeding programs. Full article

Upland cotton is an important fiber and oilseed crop. Cottonseed size, measured by seed index, is an important seed quality trait that affects seed germination, seedling vigor, fiber yield, and cottonseed nutrient content. However, genetic variation in cottonseed size is highly limited within upland cotton, limiting the genetic gain in cottonseed size. Introgression breeding can alleviate this bottleneck effect by introducing desirable genes from pima to upland cotton. This study was conducted to analyze the seed size from both fuzzy and acid-delinted seeds and to assess the appropriate cottonseed size. In 2022, a population of 1600 cotton introgression lines (ILs) was grown at Leyendecker Plant Science Center, NMSU, while three field tests were conducted in 2023, including NM with all the ILs and MS and TX each with 1000 ILs. The analysis of variance of seed size showed that genotypic and environmental variation were found in both types of seeds. The acid-delinted and fuzzy cottonseeds had a mean seed index of 9.58 g and 11.26 g, while the broad sense heritability was 0.56 and 0.32, respectively. Furthermore, the seed index was not significantly correlated with cottonseed oil and different fatty acids. Full article

Indigenous pig breeds represent valuable reservoirs of genetic diversity but face increasing risks of genetic erosion due to uncontrolled crossbreeding with commercial lines. The Ashanti Dwarf Pig (ADP) of Ghana is an important local genetic resource well-adapted to tropical environments but poorly characterised at the genomic level. Using high-density SNP data from the ADPs and publicly available datasets from other African, European, and Asian pig populations, we examined genetic diversity, population structure, inbreeding, and selection signatures. After quality control, 59,124 SNPs across 875 individuals were retained. ADPs exhibited high polymorphism (~99%) and moderate heterozygosity but also elevated inbreeding (FIS = 0.15; FROH = 0.40), indicating recent inbreeding under free-range management. Population structure revealed that ADPs cluster closely with other African pigs and European breeds more than Chinese breeds. ADMIXTURE analysis, however, indicated recent introgression from both European and Chinese lines. Selection scans revealed candidate genes linked to metabolism-Zinc Finger Ran-Binding Protein 3 (ZRANB3), growth-Sortilin Related VPS10 Domain Containing Receptor 1 (SORCS1), reproduction–Sus Scrofa Chromosome 9 quantitative trait loci (SSC9 QTLs), and immunity-Tudor Domain-Containing Protein 3 and CKLF-like MARVEL transmembrane Domain Containing 7 (TDRD3, CMTM7), reflecting adaptation to tropical production systems. Our results provide a comprehensive genomic characterisation of the ADP within a global context, revealing both genetic richness and vulnerability to genetic erosion. These findings underscore the importance of structured breeding and conservation strategies in preserving this unique African genetic resource and supporting sustainable pig production under changing climatic conditions. Full article