Search Results (40)

With global warming, high-temperature stress has become a primary abiotic factor limiting maize yield and quality. Exposure to heat stress induces sunscald on maize leaves, which severely impairs photosynthesis and ultimately leads to yield reduction. In this study, we used the heat-tolerant inbred line Zheng58 and the heat-sensitive inbred line HSBN, both of which are cultivated maize (Zea mays L. subsp. mays) inbred lines, as parents to construct F₂ and F_2:3 populations consisting of 257 lines. Phenotyping for sunscald at the flowering stage was performed across three field environments. The F₂ population was genotyped using the Maize 10K SNP array to construct a genetic map containing 1728 single nucleotide polymorphism (SNP) markers. The map spanned 1406.22 cM, with an average marker density of 0.81 cM per marker. Eight quantitative trait loci (QTLs) associated with heat tolerance were identified in the F₂/F_2:3 populations, distributed on chromosomes 1, 4, 5, and 8, collectively explaining 3.43% to 35.44% of the phenotypic variation. Among them, the stable QTL qHT1-2 on chromosome 1 was consistently detected across all three environments, explaining 11.41% to 35.44% of the phenotypic variation. Additionally, a major QTL, qHT1-3, was identified on the same chromosome, accounting for 33.70% of the phenotypic variation. Transcriptome analysis of flowering-stage leaves from both parents revealed 9262 differentially expressed genes (DEGs). Of these, 21 DEGs were co-localized within the eight QTL intervals. The genes Zm00001eb013260, Zm00001eb012720, Zm00001eb013600, and Zm00001eb013100 exhibited highly significant differential expression between the parental lines, these four genes are identified as candidate genes in response to heat stress in maize, and their specific biological functions require further functional validation. Full article

Heading date (HD) is a key adaptive trait determining wheat regional suitability, yield stability, and resilience to environmental stresses. We dissected the genetic architecture of heading date (HD) by phenotyping a doubled haploid (DH) population (178 lines, CASL7AS × ZNL12) across five environments and constructing a high-density genetic map with the wheat 55K SNP array. A total of 38 QTLs associated with HD were identified on 12 chromosomes, among which 10 were consistently detected across multiple environments. Two major stable loci, QHD.ZAFU.2B and QHD.ZAFU.4A, explained substantial phenotypic variation and were considered key regulators of heading time. Candidate gene analysis revealed Ppd-B1 (TraesCSU02G196100) as the causal gene for QHD.ZAFU.2B. Within QHD.ZAFU.4A, a zinc finger RNA-binding protein gene (TraesCS4A02G394400) exhibiting strong flag-leaf expression at the heading stage was identified as the most promising candidate. Notably, most favorable alleles were derived from ZNL12, highlighting its potential for breeding applications aimed at manipulating heading time. These results provide valuable genomic resources and molecular targets for marker-assisted selection aimed at optimizing flowering time and improving wheat adaptation. Full article

Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is a global disease infecting wheat that seriously affects the yield and the quality of grains. Wheat breeding line C855 is immune to the mixed Pst isolates CYR32 + CYR33 + CYR34 under field conditions. To identify the Yr-loci carried by C855, in this study, an F₂ population derived from the crossing of C855 with Yannong 999, a YR-sensitive cultivar, was established, and the infection type (IT) of each F₂ individual was estimated. The correlation analysis results show that YR resistance was significantly positively correlated with grain weight and grain size. Using a 120K single-nucleotide polymorphism (SNP) array, the F₂ population was genotyped, and a high-density genetic map covering 21 wheat chromosomes and consisting of 5362 SNP markers was built. Then, five Yr-QTLs on chromosomes 1B, 2A, 2B, and 2D were identified. Of these, the QTL on chromosome 2A, temporarily named QYr.sxau-2A.1, is a major-effect QTL explaining 15.62% of the phenotypic variance. One PCR-based marker SSR2A-14 for QYr.sxau-2A.1 was developed, and the C855 allele of SSR2A-14 corresponded to the stronger Yr resistance. QYr.sxau-2A.1, located in the 228.02~241.58 Mbp physical interval, is different from all the known Yr loci on chromosomes 2A. Within the interval, there are 30 annotated genes, including a nucleotide-binding site and a leucine-rich repeat (NBS-LRR)-encoding gene with the linkage marker NRM2A-16 of QYr.sxau-2A.1. Our results reveal a novel major-effect QYr.sxau-2A.1, which provided resistance to YR and is a molecular marker for wheat breeding. Full article

Durum wheat, the world’s second most cultivated wheat species, is a staple crop, critical for global food security, including in Ethiopia where it serves as a center of diversity. However, climate change and genetic erosion threaten its genetic resources, necessitating genomic studies to support conservation and breeding efforts. This study characterized genome-wide diversity, population structure (STRUCTURE, principal coordinate analysis (PCoA), neighbor-joining trees, analysis of molecular variance (AMOVA)), and selection signatures (F_ST, Hardy–Weinberg deviations) in Ethiopian durum wheat by analyzing 376 genotypes (148 accessions) using an Illumina Infinium 25K single nucleotide polymorphism (SNP) array. A set of 7842 high-quality SNPs enabled the assessments, comparing landraces with cultivars and breeding populations. Results revealed moderate genetic diversity (mean polymorphism information content (PIC) = 0.17; gene diversity = 0.20) and identified 26 loci under selection, associated with key traits like grain yield, stress tolerance, and disease resistance. AMOVA revealed 80.1% variation among accessions, with no significant differentiation by altitude, region, or spike density. Landraces formed distinct clusters, harboring unique alleles, while admixture suggested gene flow via informal seed exchange. The findings highlight Ethiopia’s rich durum wheat diversity, emphasizing landraces as reservoirs of adaptive alleles for breeding. This study provides genomic insights to guide conservation and the development of climate-resilient cultivars, supporting sustainable wheat production globally. Full article

Aquaculture has become a crucial component of global food production, yet catfish (10.8% of global finfish production) breeding programs often lack sufficient genetic data to fully utilize their production potential. In the last 15 years, there have been improvements in this field as two high-density (HD) single nucleotide polymorphism (SNP) arrays (250K and 690K) and low-density panels have been developed for North American channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). This lack of genomic tools hinders genetic improvement efforts in other commercially relevant catfish species besides them. Therefore, this review investigated the reason behind the lack of SNP chip usage in genetic-based selections in most catfish breeding programs and the cross-species applicability of the already existing high-density SNP arrays for genotyping members of the Clariidae, African catfish (Clarias gariepinu), and Siluridae, European catfish (Silurus glanis), families. This paper systematically reviews the literature of more than 16 SNP arrays, with 66 non-target species, and assesses the possibility of adapting catfish SNP arrays to the catfish families of interest. With lowered filtering (e.g., MAF > 0) thresholds, the Affymetrix Axiom 250K and Axiom Catfish 690K Genotyping Array could potentially be used on important market species like African and European catfishes. In the long term, chip development would be the solution for these species, but, until then, cross-application is a viable alternative. Despite low polymorphic SNPs (~1%) and call rates (~0%), this SNP array could aid researchers and breeders, improving catfish aquaculture and management. Full article

Evaluating the genetic variability of germplasms is essential for enhancing and developing superior cultivars. However, there is limited information on cultivated germplasm diversity for Australian passion fruit breeding programs. The genetic diversity of Australian passion fruit (Passiflora spp.), including 94 rootstocks and 95 scions, was evaluated to support breeding programs aimed at enhancing productivity, fruit quality, and overall crop resilience. Rootstocks were genotyped using high-density 24k Diversity Arrays Technology (DArT)-based single-nucleotide polymorphism (SNP) markers, while genetic characterization of scions was conducted using eight simple sequence repeat (SSR) markers. The resulting genetic relationships revealed significant variation within rootstock populations. Bayesian cluster analysis in STRUCTURE showed that the rootstock population was divided into six distinct genetic groups, whereas only two subpopulations were identified among the scion accessions. SNP-based genotyping further highlighted the allelic diversity of Australian rootstocks, suggesting a rich reservoir of genetic traits for rootstock improvement. These findings underscore the importance of preserving and utilizing genetic diversity in Australian passion fruit germplasm to drive the development of superior cultivars with enhanced adaptability and performance under diverse environmental conditions. Full article

Fusarium head blight (FHB), caused by Fusarium graminearum, is a globally significant disease that severely impacts the yield and quality of wheat. Breeding resistant wheat varieties using resistance genes is the most cost-effective strategy for managing FHB, but few markers are available for marker-assisted selection (MAS) of resistance. In this study, we evaluated the resistance of a recombinant inbred line (RIL) population to FHB through single-floret inoculation in four field environments over two years. Combined with quantitative trait loci (QTL) detection through high-density genetic mapping based on wheat 50 K SNP arrays, we identified a total of 21 QTLs influencing FHB resistance. It is worth noting that QFhba-5D.2-1 was detected in two field environments as well as in the multi-environment trial (MET) analysis, explaining phenotypic variation ranging from 1.98% to 18.55%. We also pinpointed thirteen resistance genes within the QTL intervals on chromosomes 4A, 5D, 6B, and 7A associated with FHB defense mechanisms. Furthermore, we developed two Kompetitive Allele-Specific PCR (KASP) markers for the QFhba-5D.2-1 and QFhba-7A regions to validate their specificity within the RIL population. Subsequently, we validated the polymorphism of these two markers in 305 wheat germplasms and analyzed their effect on thousand kernel weight (TKW) and spike length (SL). These markers will accelerate the development of FHB-resistant wheat varieties through MAS, significantly reducing yield losses and strengthening food security. Full article

The stay-green (SG) trait enhances photosynthetic activity during the late grain-filling period, benefiting grain yield under drought and heat stresses. CH7034 is a wheat breeding line with SG. To clarify the SG loci carried by CH7034 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross between CH7034 and non-SG SY95-71 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2159 SNP markers was constructed. Then, the chlorophyll content of flag leaf from each RIL was estimated for mapping, and one QTL for SG on chromosome 7D was identified, temporarily named QSg.sxau-7D, with the maximum phenotypic variance explained of 8.81~11.46%. A PCR-based diagnostic marker 7D-16 for QSg.sxau-7D was developed, and the CH7034 allele of 7D-16 corresponded to the higher flag leaf chlorophyll content, while the 7D-16 SY95-71 allele corresponded to the lower value, which confirmed the genetic effect on SG of QSg.sxau-7D. QSg.sxau-7D located in the 526.4~556.2 Mbp interval is different from all the known SG loci on chromosome 7D, and 69 high-confidence annotated genes within the interval expressed throughout the entire period of flag leaf senescence. Moreover, results of an association analysis based on the diagnostic marker showed that there is a positive correlation between QSg.sxau-7D and thousand-grain weight. Our results revealed a novel QTL QSg.sxau-7D whose CH7034 allele had a strong effect on SG, which can be applied in further wheat molecular breeding. Full article

Sheep are a vital species in the global agricultural economy, providing essential resources such as meat, milk, and wool. Merino sheep (Junken type) are a key breed of fine wool sheep in China. However, research on fine wool traits has largely overlooked the role of SNPs and their association with phenotypes. Copy number variations (CNVs) have emerged as one of the most important sources of genetic variation, influencing phenotypic traits by altering gene expression and dosage. To generate a comprehensive CNVR map of the ovine genome, we conducted genome-wide CNV detection using genotyping data from 285 fine wool sheep. This analysis revealed 656 CNVRs, including 628 on autosomes and 28 on the X chromosome, covering a total of 43.9 Mbs of the sheep genome. The proportion of CNVRs varied across chromosomes, from 0.45% on chromosome 26 to 3.72% on chromosome 10. Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses highlighted significantly enriched GO terms, including odorant binding, ATP binding, and sulfuric ester hydrolase activity. The KEGG analysis identified involvement in pathways such as neuroactive ligand–receptor interaction, axon guidance, ECM–receptor interaction, the one-carbon pool by folate, and focal adhesion (p < 0.05). To validate these CNVRs, we performed quantitative real-time PCR experiments to verify copy number predictions made by PennCNV software (v1.0.5). Out of 11 selected CNVRs with predicted gain, loss, or gain–loss statuses, 8 (IDs 68, 156, 201, 284, 307, 352, 411, 601) were successfully confirmed. This study marks a significant step forward in mapping CNVs in the ovine genome and offers a valuable resource for future research on genetic variation in sheep. Full article

Sweet corn (Zea mays var. rugosa Bonaf.) is a crop with a high economic benefit in tropical and subtropical regions. Heat tolerance analysis and heat-tolerant gene mining are of great significance for breeding heat-resistant varieties. By combining improved genotyping using targeted sequencing (GBTS) with liquid chip (LC) technology, a high-density marker array containing 40 K multiple single polynucleotide polymorphisms (mSNPs) was used to genotype 376 sweet corn inbred lines and their heat-stress tolerance was evaluated in the spring and summer of 2019. In general, plant height, ear height and the number of lateral branches at the first level of the male flowers were reduced by 24.0%, 36.3%, and 19.8%, respectively. High temperatures in the summer accelerated the growth process of the sweet corn, shortening the days to shedding pollen by an average of 21.6% compared to the spring. A genome-wide association study (GWAS) identified 85 significant SNPs distributed on 10 chromosomes. Phenotypes in the spring and summer were associated with the 21 and 15 loci, respectively, and significant phenotypic differences between the two seasons caused by the temperature change were associated with the 49 SNP loci. The seed setting rate (SSR) was more susceptible to heat stress. An annotation analysis identified six candidate genes, which are either heat shock transcription factors (Hsfs) or heat shock proteins (Hsps) in Arabidopsis and rice (Oryza sativa), and these candidate genes were directly and indirectly involved in the heat-resistant response in the sweet corn. The current findings provide genetic resources for improving the heat-stress tolerance of sweet corn by molecular breeding. Full article

Landraces are an important reservoir of genetic variation that can expand the narrow genetic base of cultivated cotton. In this study, quantitative trait loci (QTL) analysis was conducted using an F₂ population developed from crosses between the landrace Hopi and inbred TM-1. A high-density genetic map spanning 2253.11 and 1932.21 cM for the A and D sub-genomes, respectively, with an average marker interval of 1.14 cM, was generated using the CottonSNP63K array. The linkage map showed a strong co-linearity with the physical map of cotton. A total of 21 QTLs were identified, controlling plant height (1), bract type (1), boll number (1), stem color (2), boll pitting (2), fuzz fiber development (2), boll shape (3), boll point (4), and boll glanding (5). In silico analysis of the novel QTLs for boll glanding identified a total of 13 candidate genes. Analysis of tissue-specific expression of the candidate genes suggests roles for the transcription factors bHLH1, MYB2, and ZF1 in gland formation. Comparative sequencing of open reading frames identified early stop codons in all three transcription factors in Hopi. Functional validation of these genes offers avenues to reduce glanding and, consequently, lower gossypol levels in cottonseeds without compromising the defense mechanisms of the plant against biotic stresses. Full article

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding. Full article

The control of Tropical Theileriosis, a tick-borne disease with a strong impact on cattle breeding, can be facilitated using marker-assisted selection in breeding programs. Genome-wide association studies (GWAS) using high-density arrays are extremely important for the ongoing process of identifying genomic variants associated with resistance to Theileria annulata infection. In this work, single-nucleotide polymorphisms (SNPs) were analyzed in the Portuguese autochthonous cattle breeds Alentejana and Mertolenga. In total, 24 SNPs suggestive of significance (p ≤ 10⁻⁴) were identified for Alentejana cattle and 20 SNPs were identified for Mertolenga cattle. The genomic regions around these SNPs were further investigated for annotated genes and quantitative trait loci (QTLs) previously described by other authors. Regarding the Alentejana breed, the MAP3K1, CMTM7, SSFA2, and ATG13 genes are located near suggestive SNPs and appear as candidate genes for resistance to Tropical Theileriosis, considering its action in the immune response and resistance to other diseases. On the other hand, in the Mertolenga breed, the UOX gene is also a candidate gene due to its apparent link to the pathogenesis of the disease. These results may represent a first step toward the possibility of including genetic markers for resistance to Tropical Theileriosis in current breed selection programs. Full article

Apple accessions, currently maintained within the two main ex situ collections in Bosnia and Herzegovina (B&H), have previously been genotyped using microsatellite markers. The obtained molecular data provided insight into mislabeled accessions and redundancies, as well as the overall genetic structure of the germplasm. The available dataset enabled the creation of a core collection consisting of 52 accessions. The reliability and usefulness of microsatellites has made this low-density marker system a norm in studies on apple germplasm. However, the increased access to medium- and high-density SNP arrays, developed specifically for apples, has opened new avenues of research into apple genetic resources. In this study, 45 apple genotypes consisting of 33 diploid core collection accessions from B&H and 12 international reference cultivars were genotyped using an Axiom^® Apple 480 K SNP array in order to examine their genetic relationships, population structure and diversity, as well as to compare the obtained results with those calculated on previously reported SSR profiles. The SNPs displayed a better ability to differentiate apple accessions based on their origin, as well as to cluster them according to their pedigree. Calculating identity by descent revealed 16 pairings with first-degree relationships and uncovered the introgression of ‘Delicious’ and ‘Golden Delicious’ into the core collection. Full article

Pigmented cereal grains with high levels of flavonoid compounds have attracted the attention of nutritional science backing the development of functional foods with claimed health benefits. In this study, we report results on the genetic factors controlling grain pigmentation in durum wheat using a segregant population of recombinant inbred lines (RILs) derived from a cross between an Ethiopian purple grain accession and an Italian amber grain cultivar. The RIL population was genotyped by the wheat 25K SNP array and phenotyped for total anthocyanin content (TAC), grain color, and the L*, a*, and b* color index of wholemeal flour, based on four field trials. The mapping population showed a wide variation for the five traits in the different environments, a significant genotype x environment interaction, and high heritability. A total of 5942 SNP markers were used for constructing the genetic linkage map, with an SNP density ranging from 1.4 to 2.9 markers/cM. Two quantitative trait loci (QTL) were identified for TAC mapping on chromosome arms 2AL and 7BS in the same genomic regions of two detected QTL for purple grain. The interaction between the two QTL was indicative of an inheritance pattern of two loci having complementary effects. Moreover, two QTL for red grain color were detected on chromosome arms 3AL and 3BL. The projection of the four QTL genomic regions on the durum wheat Svevo reference genome disclosed the occurrence of the candidate genes Pp-A3, Pp-B1, R-A1, and R-B1 involved in flavonoid biosynthetic pathways and encoding of transcription factors bHLH (Myc-1) and MYB (Mpc1, Myb10), previously reported in common wheat. The present study provides a set of molecular markers associated with grain pigments useful for the selection of essential alleles for flavonoid synthesis in durum wheat breeding programs and enhancement of the health-promoting quality of derived foods. Full article