Additional Quantitative Trait Loci Research Articles

QTL mapping for seed vigor-related traits under artificial aging in common wheat in two introgression line (IL) populations

Background Seed vigor recognized as a quantitative trait is of particular importance for agricultural production. However, limited knowledge is available for understanding genetic basis of wheat seed vigor. Methods The aim of this study was to identify quantitative trait loci (QTL) responsible for 10 seed vigor-related traits representing multiple aspects of seed-vigor dynamics during artificial aging with 6 different treatment times (0, 24, 36, 48, 60, and 72 h) under controlled conditions (48 °C, 95% humidity, and dark). The mapping populations were two wheat introgression lines (IL-1 and IL-2) derived from recipient parent (Lumai 14) and donor parent (Shaanhan 8675 or Jing 411). Results A total of 26 additive QTLs and 72 pairs of epistatic QTLs were detected for wheat seed-vigor traits. Importantly, chromosomes 1B and 7B contained several co-located QTLs, and chromosome 2A had a QTL-rich region near the marker Xwmc667, indicating that these QTLs may affect wheat seed vigor with pleiotropic effects. Furthermore, several possible consistent QTLs (hot-spot regions) were examined by comparison analysis of QTLs detected in this study and reported previously. Finally, a set of candidate genes for wheat seed vigor were predicted to be involved in transcription regulation, carbohydrate and lipid metabolism. Conclusion The present findings lay new insights into the mechanism underlying wheat seed vigor, providing valuable information for wheat genetic improvement especially marker-assisted breeding to increase seed vigor and consequently achieve high grain yield despite of further investigation required.

Identification of quantitative trait loci of pod dehiscence in a collection of soybean grown in the southeast of Kazakhstan.

Soybean [Glycine max (L.) Merr.] is one of the important crops that are constantly increasing their cultivation area in Kazakhstan. It is particularly significant in the southeastern regions of the country, which are currently predominant areas for cultivating this crop. One negative trait reducing yield in these dry areas is pod dehiscence (PD). Therefore, it is essential to understand the genetic control of PD to breed new cultivars with high yield potential. In this study, we evaluated 273 soybean accessions from different regions of the world for PD resistance in the conditions of southeastern regions of Kazakhstan in 2019 and 2021. The field data for PD suggested that 12 accessions were susceptible to PD in both studied years, and 32 accessions, in one of the two studied years. The genotyping of the collection using a DNA marker for the Pdh1 gene, a major gene for PD, revealed that 244 accessions had the homozygous R (resistant) allele, 14 had the homozygous S (susceptible) allele, and 15 accessions showed heterozygosity. To identify additional quantitative trait loci (QTLs), we applied an association mapping study using a 6K SNP Illumina iSelect array. The results suggested that in addition to major QTL on chromosome 16, linked to the physical location of Pdh1, two minor QTLs were identified on chromosomes 10 and 13. Both minor QTLs for PD were associated with calmodulin-binding protein, which presumably plays an important role in regulating PD in dry areas. Thus, the current study provided additional insight into PD regulation in soybean. The identified QTLs for PD can be efficiently employed in breeding for high-yield soybean cultivars.

Mapping rust resistance in European winter wheat: many QTLs for yellow rust resistance, but only a few well characterized genes for stem rust resistance

Key messageStem rust resistance was mainly based on a few, already known resistance genes; for yellow rust resistance there was a combination of designated genes and minor QTLs.Yellow rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) and stem rust (SR) caused by Puccinia graminis f. sp. tritici (Pgt) are among the most damaging wheat diseases. Although, yellow rust has occurred regularly in Europe since the advent of the Warrior race in 2011, damaging stem rust epidemics are still unusual. We analyzed the resistance of seven segregating populations at the adult growth stage with the parents being selected for YR and SR resistances across three to six environments (location–year combinations) following inoculation with defined Pst and Pgt races. In total, 600 progenies were phenotyped and 563 were genotyped with a 25k SNP array. For SR resistance, three major resistance genes (Sr24, Sr31, Sr38/Yr17) were detected in different combinations. Additional QTLs provided much smaller effects except for a gene on chromosome 4B that explained much of the genetic variance. For YR resistance, ten loci with highly varying percentages of explained genetic variance (pG, 6–99%) were mapped. Our results imply that introgression of new SR resistances will be necessary for breeding future rust resistant cultivars, whereas YR resistance can be achieved by genomic selection of many of the detected QTLs.

Analysis of hepatic lentiviral vector transduction; implications for preclinical studies and clinical gene therapy protocols.

Lentiviral vector-transduced T-cells were approved by the FDA as gene therapy anti-cancer medications. Little is known about the host genetic variation effects on the safety and efficacy of the lentiviral vector gene delivery system. To narrow this knowledge-gap, we characterized hepatic gene delivery by lentiviral vectors across the Collaborative Cross (CC) mouse genetic reference population. For 24 weeks, we periodically measured hepatic luciferase expression from lentiviral vectors in 41 CC mouse strains. Hepatic and splenic vector copy numbers were determined. We report that CC mouse strains showed highly diverse outcomes following lentiviral gene delivery. For the first time, moderate correlation between mouse strain-specific sleeping patterns and transduction efficiency was observed. We associated two quantitative trait loci (QTLs) with intra-strain variations in transduction phenotypes, which mechanistically relates to the phenomenon of metastable epialleles. An additional QTL was associated with the kinetics of hepatic transgene expression. Genes comprised in the above QTLs are potential targets to personalize gene therapy protocols. Importantly, we identified two mouse strains that open new directions in characterizing continuous viral vector silencing and HIV latency. Our findings suggest that wide-range patient-specific outcomes of viral vector-based gene therapy should be expected. Thus, novel escalating dose-based clinical protocols should be considered.

Genetic mechanisms of axial patterning in Apeltes quadracus

Abstract The genetic mechanisms underlying striking axial patterning changes in wild species are still largely unknown. Previous studies have shown that Apeltes quadracus fish, commonly known as fourspine sticklebacks, have evolved multiple different axial patterns in wild populations. Here, we revisit classic locations in Nova Scotia, Canada, where both high-spined and low-spined morphs are particularly common. Using genetic crosses and quantitative trait locus (QTL) mapping, we examine the genetic architecture of wild differences in several axial patterning traits, including the number and length of prominent dorsal spines, the number of underlying median support bones (pterygiophores), and the number and ratio of abdominal and caudal vertebrae along the anterior–posterior body axis. Our studies identify a highly significant QTL on chromosome 6 that controls a substantial fraction of phenotypic variation in multiple dorsal spine and pterygiophore traits (~15%–30% variance explained). An additional smaller-effect QTL on chromosome 14 contributes to the lengths of both the last dorsal spine and anal spine (~9% variance explained). 1 or no QTL were detected for differences in the numbers of abdominal and caudal vertebrae. The major-effect patterning QTL on chromosome 6 is centered on the HOXDB gene cluster, where sequence changes in a noncoding axial regulatory enhancer have previously been associated with prominent dorsal spine differences in Apeltes. The QTL that have the largest effects on dorsal spine number and length traits map to different chromosomes in Apeltes and Gasterosteus, 2 distantly related stickleback genera. However, in both genera, the major-effect QTL for prominent skeletal changes in wild populations maps to linked clusters of powerful developmental control genes. This study, therefore, bolsters the body of evidence that regulatory changes in developmental gene clusters provide a common genetic mechanism for evolving major morphological changes in natural species.

Refining flowering date enhances sesame yield independently of day-length

BackgroundThe transition from vegetative to reproductive growth is a key factor in yield maximization. Sesame (Sesamum indicum), an indeterminate short-day oilseed crop, is rapidly being introduced into new cultivation areas. Thus, decoding its flowering mechanism is necessary to facilitate adaptation to environmental conditions. In the current study, we uncover the effect of day-length on flowering and yield components using F2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$_2$$\\end{document} populations segregating for previously identified quantitative trait loci (Si_DTF QTL) confirming these traits.ResultsGenerally, day-length affected all phenotypic traits, with short-day preceding days to flowering and reducing yield components. Interestingly, the average days to flowering required for yield maximization was 50 to 55 days, regardless of day-length. In addition, we found that Si_DTF QTL is more associated with seed-yield and yield components than with days to flowering. A bulk-segregation analysis was applied to identify additional QTL differing in allele frequencies between early and late flowering under both day-length conditions. Candidate genes mining within the identified major QTL intervals revealed two flowering-related genes with different expression levels between the parental lines, indicating their contribution to sesame flowering regulation.ConclusionsOur findings demonstrate the essential role of flowering date on yield components and will serve as a basis for future sesame breeding.

Mining for QTL controlling maize low-phosphorus response genes combined with deep resequencing of RIL parental genomes and in silico GWAS analysis.

Extensive and comprehensive phenotypic data from a maize RIL population under both low- and normal-Pi treatments were used to conduct QTL mapping. Additionally, we integrated parental resequencing data from the RIL population, GWAS results, and transcriptome data to identify candidate genes associated with low-Pi stress in maize. Phosphorus (Pi) is one of the essential nutrients that greatly affect the maize yield. However, the genes underlying the QTL controlling maize low-Pi response remain largely unknown. In this study, a total of 38 traits at both seedling and maturity stages were evaluated under low- and normal-Pi conditions using a RIL population constructed from X178 (tolerant) and 9782 (sensitive), and most traits varied significantly between low- and normal-Pi treatments. Twenty-nine QTLs specific to low-Pi conditions were identified after excluding those with common intervals under both low- and normal-Pi conditions. Furthermore, 45 additional QTLs were identified based on the index value ((Trait_under_LowPi-Trait_under_NormalPi)/Trait_under_NormalPi) of each trait. These 74 QTLs collectively were classified as Pi-dependent QTLs. Additionally, 39 Pi-dependent QTLs were clustered in nine HotspotQTLs. The Pi-dependent QTL interval contained 19,613 unique genes, 6,999 of which exhibited sequence differences with non-synonymous mutation sites between X178 and 9782. Combined with in silico GWAS results, 277 consistent candidate genes were identified, with 124 genes located within the HotspotQTL intervals. The transcriptome analysis revealed that 21 genes, including the Pi transporter ZmPT7 and the strigolactones pathway-related gene ZmPDR1, exhibited consistent low-Pi stress response patterns across various maize inbred lines or tissues. It is noteworthy that ZmPDR1 in maize roots can be sharply up-regulated by low-Pi stress, suggesting its potential importance as a candidate gene for responding to low-Pi stress through the strigolactones pathway.

Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.

Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations. Identifying changes in allele frequency generated by selection provides an alternative genetic mapping approach that can increase the power and precision of QTL detection. This study aimed to map quantitative trait loci (QTL) for SRA by genotyping durum lines created through divergent selection using a combination of marker-assisted selection (MAS) for the major SRA QTL (qSRA-6A) and phenotypic selection for SRA over multiple generations. The created 11 lines (BC1F2:5) were genotyped with genome-wide single-nucleotide polymorphism (SNP) markers to map QTL by identifying markers that displayed segregation distortion significantly different from the Mendelian expectation. QTL regions were further assessed in an independent validation population to confirm their associations with SRA. The experiment revealed 14 genomic regions under selection, 12 of which have not previously been reported for SRA. Five regions, including qSRA-6A, were confirmed in the validation population. The genomic regions identified in this study indicate that the genetic control of SRA is more complex than previously anticipated. Our study demonstrates that selection mapping is a powerful approach to complement genome-wide association studies for QTL detection. Moreover, the verification of qSRA-6A in an elite genetic background highlights the potential for MAS, although it is necessary to combine additional QTL to develop new cultivars with extreme SRA phenotypes.

Pentatricopeptide repeat 153 (PPR153) restores maize C-type cytoplasmic male sterility in conjunction with RF4.

Maize (Zea mays L.) C-type cytoplasmic male sterility (CMS-C) is a highly used CMS system for maize commercial hybrid seed production. Rf4 is the major dominant restorer gene for CMS-C. Inbreds were recently discovered which contain the restoring Rf4 allele yet are unable to restore fertility due to the lack of an additional gene required for Rf4's restoration. To find this additional gene, QTL mapping and positional cloning were performed using an inbred that contained Rf4 but was incapable of restoring CMS-C. The QTL was mapped to a 738-kb interval on chromosome 2, which contains a Pentatricopeptide Repeat (PPR) gene cluster. Allele content comparisons of the inbreds identified three potential candidate genes responsible for fertility restoration in CMS-C. Complementation via transformation of these three candidate genes showed that PPR153 (Zm00001eb114660) is required for Rf4 to restore fertility to tassels. The PPR153 sequence is present in B73 genome, but it is not capable of restoring CMS-C without Rf4. Analysis using NAM lines revealed that Rf4 requires the presence of PPR153 to restore CMS-C in diverse germplasms. This research uncovers a major CMS-C genetic restoration pathway and can be used for identifying inbreds suitable for maize hybrid production with CMS-C cytoplasm.

Multi-model genome-wide association study on key organic naked barley agronomic, phenological, diseases, and grain quality traits

The study objective was to assess the potential benefits of using genomic tools in organic plant breeding programs to enhance selection efficiency. A diversity panel of 247 spring naked barley accessions was characterized under Irish organic conditions over 3 years. Genome-wide association studies (GWAS) were performed on 19 traits related to agronomy, phenology, diseases, and grain quality, using the information on 50 K Single Nucleotide Polymorphisms (SNP). Four models (EMMA, G model, BLINK, 3VMrMLM) were applied to 5 types of Best Linear Unbiased Predictors (BLUP): within-year, mean, aggregated within-year). 1653 Marker-Trait-Associations (MTA) were identified, with 259 discovered in at least two analyses. 3VMrMLM was the best-performing model with significant MTA together explaining the largest proportion of the additive variance for most traits and BLUP types (from 1.4 to 50%). This study proposed a methodology to prioritize main effect MTA from different models’ outputs, using multi-marker regression analyses with markers fitted as fixed or random factors. 36 QTL, considered major, explained more than 5% of the trait variance on each BLUP type. A candidate gene or known QTL was found for 18 of them, with 13 discovered with 3VMrMLM. Multi-model GWAS was useful for validating additional QTL, including 8 only discovered with BLINK or G model, thus allowing a broader understanding of the traits’ genetic architecture. In addition, results highlighted a correlation between the trait value and the number of favorable major QTL exhibited by accessions. We suggest inputting this number in a multi-trait index for a more efficient Marker-Assisted Selection (MAS) of accessions best balancing multiple quantitative traits.

Linkage and association mapping in multi-parental populations reveal the genetic basis of carotenoid variation in maize kernels.

Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.

Identification of QTLs for symbiotic nitrogen fixation and related traits in a soybean recombinant inbred line population.

The genetic architecture of symbiotic N fixation and related traits was investigated in the field. QTLs were identified for percent N derived from the atmosphere, shoot [N] and C to N ratio. Soybean [Glycine max (L.) Merr.] is cultivated worldwide and is the most abundant source of plant-based protein. Symbiotic N2 fixation (SNF) in legumes such as soybean is of great importance; however, yields may still be limited by N in both high yielding and stressful environments. To better understand the genetic architecture of SNF and facilitate the development of high yielding cultivars and sustainable soybean production in stressful environments, a recombinant inbred line population consisting of 190 lines, developed from a cross between PI 442012A and PI 404199, was evaluated for N derived from the atmosphere (Ndfa), N concentration ([N]), and C to N ratio (C/N) in three environments. Significant genotype, environment and genotype × environment effects were observed for all three traits. A linkage map was constructed containing 3309 single nucleotide polymorphism (SNP) markers. QTL analysis was performed for additive effects of QTLs, QTL × environment interactions, and QTL × QTL interactions. Ten unique additive QTLs were identified across all traits and environments. Of these, two QTLs were detected for Ndfa and eight for C/N. Of the eight QTLs for C/N, four were also detected for [N]. Using QTL × environment analysis, six QTLs were detected, of which five were also identified in the additive QTL analysis. The QTL × QTL analysis identified four unique epistatic interactions. The results of this study may be used for genomic selection and introgression of favorable alleles for increased SNF, [N], and C/N via marker-assisted selection.

Quantitative trait loci detection for three tiller-related traits and the effects on wheat (Triticum aestivum L.) yields.

A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for tiller-related traits were reported, and the candidate genes underlying qMtn-KJ-5D, a novel major and stable QTL for maximum tiller number, were characterized. Tiller-related traits play an important role in determining the yield potential of wheat. Therefore, it is important to elucidate the genetic basis for tiller number when attempting to use genetic improvement as a tool for enhancing wheat yields. In this study, a quantitative trait locus (QTL) analysis of three tiller-related traits was performed on the recombinant inbred lines (RILs) of a mapping population, referred to as KJ-RILs, that was derived from a cross between the Kenong 9204 (KN9204) and Jing 411 (J411) lines. A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for spike number per plant (SNPP), maximum tiller number (MTN), and ear-bearing tiller rate (EBTR) were detected in eight different environments. Among these QTLs with additive effects, three major and stable QTLs were first documented herein. Almost all but two pairwise epistatic QTLs showed minor interaction effects accounting for no more than 3.0% of the phenotypic variance. The genetic effects of two colocated major and stable QTLs, i.e., qSnpp-KJ-5D.1 and qMtn-KJ-5D, for yield-related traits were characterized. The breeding selection effect of the beneficial allele for the two QTLs was characterized, and its genetic effects on yield-related traits were evaluated. The candidate genes underlying qMtn-KJ-5D were predicted based on multi-omics data, and TraesKN5D01HG00080 was identified as a likely candidate gene. Overall, our results will help elucidate the genetic architecture of tiller-related traits and can be used to develop novel wheat varieties with high yields.

Identification of additional body weight QTLs in the Berlin Fat Mouse BFMI861 lines using time series data

The Berlin Fat Mouse Inbred line (BFMI) is a model for obesity and metabolic syndrome. The sublines BFMI861-S1 and BFMI861-S2 differ in weight despite high genetic similarity and a shared obesity-related locus. This study focused on identifying additional body weight quantitative trait loci (QTLs) by analyzing weekly weight measurements in a male population of the advanced intercross line BFMI861-S1 x BFMI861-S2. QTL analysis, utilizing 200 selectively genotyped mice (GigaMUGA) and 197 males genotyped for top SNPs, revealed a genome-wide significant QTL on Chr 15 (68.46 to 81.40 Mb) for body weight between weeks 9 to 20. Notably, this QTL disappeared (weeks 21 to 23) and reappeared (weeks 24 and 25) coinciding with a diet change. Additionally, a significant body weight QTL on Chr 16 (3.89 to 22.79 Mb) was identified from weeks 6 to 25. Candidate genes, including Gpt, Cbx6, Apol6, Apol8, Sun2 (Chr 15) and Trap1, Rrn3, Mapk1 (Chr 16), were prioritized. This study unveiled two additional body weight QTLs, one of which is novel and responsive to diet changes. These findings illuminate genomic regions influencing weight in BFMI and emphasize the utility of time series data in uncovering novel genetic factors.

The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'.

Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.

Genetic Analyses of the Shape and Volume of Onion Bulbs and Daylength Effects on Bulbing

The formation of onion (Allium cepa) bulbs is affected by photoperiod length and onion germplasm is commonly classified as short- (SD), intermediate-, or long-day (LD) types. The objectives of this study were to develop a segregating family from a cross between doubled haploids (DHs) of LD and SD onions and complete genetic analyses of bulb shape and volume, as well as daylength effects on bulbing. DH parents and F1 and F2 progenies were grown in a greenhouse under lengthening days. The diameters of the neck constriction and pseudostems were measured weekly and their ratio was used as the determinant of bulbing. Bulbs were harvested when the foliage collapsed and the diameters and heights of individual bulbs were measured and used to calculate a shape index (diameter divided by height) and bulb volume. Single nucleotide polymorphisms (SNPs) were genotyped and a genetic map of 112 SNPs constructed. Genetic analysis revealed two highly significant quantitative trait loci (QTL) affected bulbing under increasing daylengths, and both QTL showed significant additive effects with no dominance. One highly significant QTL was detected for bulb-shape index and explained 30% of phenotypic variation for bulb shape. Three additional QTL were slightly above the significance threshold, and together these four QTL explained over 50% of the phenotypic variation for bulb shape. No significant QTL were detected for bulb volume. These results reveal that bulb-shape and daylength effects on bulbing are relatively simply inherited, and this research should facilitate introgression of traits between onion populations of different daylength sensitivities and efforts to modify bulb shape.

A diallel study to detect genetic background variation for FHB resistance in winter wheat

Breeding for resistance to Fusarium head blight (FHB) relies strongly on a limited number of larger-effect resistance QTL that have been mapped and associated with nearby markers. Smaller-effect (background) resistance QTL may also contribute moderate levels of resistance yet are mostly poorly characterized. Overall resistance of a genotype is determined by the combined action of both types of resistance QTL. This study aimed to identify well-adapted, advanced hard red winter (HRW) wheat breeding lines with useful background resistance QTL. A diallel trial consisting of 11 parents and 55 non-reciprocal F1 hybrids was tested for Type II FHB resistance in a replicated greenhouse experiment. Significant differences were detected among entries for disease severity (DS), general combining ability (GCA) and specific combining ability (SCA) with four parents being identified as the best general combiners with lowest DS. The ratio of GCA:SCA effects suggested that additive QTL effects were of primary importance. Overall, resistance QTL showed incomplete dominance, an excess of dominant alleles, and a greater contribution of positive effect genes. F2 of the six best F1 hybrids with the lowest DS were compared in a second greenhouse FHB trial to select possible transgressive segregates for continued evaluation and line development.

Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel.

Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.

Genetic analysis of late-maturity α-amylase in twelve wheat populations

Main conclusionGenetic loci, particularly those with an effect in the independent panel, could be utilised to further reduce LMA expression when used with favourable combinations of genes known to affect LMA.Late maturity α-amylase (LMA) is a grain quality defect involving elevated α-amylase within the aleurone of wheat (Triticum aestivum L.) grains. The genes known to affect expression are the reduced height genes Rht-B1 (chromosome 4B) and Rht-D1 (chromosome 4D), and an ent-copalyl diphosphate synthase gene (LMA-1) on chromosome 7B. Other minor effect loci have been reported, but these are poorly characterised and further genetic understanding is needed. In this study, twelve F4-derived populations were created through single seed descent, genotyped and evaluated for LMA. LMA-1 haplotype C and the Rht-D1b allele substantially reduced LMA expression. The alternative dwarfing genes Rht13 and Rht18 had no significant effect on LMA expression. Additional quantitative trait loci (QTL) were mapped at 16 positions in the wheat genome. Effects on LMA expression were detected for four of these QTL in a large independent panel of Australian wheat lines. The QTL detected in mapping populations and confirmed in the large independent panel provide further opportunity for selection against LMA, especially if combined with Rht-D1b and/or favourable haplotypes of LMA-1.

Identification of Putative Quantitative Trait Loci for Improved Seed Oil Quality in Peanuts.

Improving seed oil quality in peanut (Arachis hypogaea) has long been an aim of breeding programs worldwide. The genetic resources to achieve this goal are limited. We used an advanced recombinant inbred line (RIL) population derived from JH5 × KX01-6 to explore quantitative trait loci (QTL) affecting peanut oil quality and their additive effects, epistatic effects, and QTL × environment interactions. Gas chromatography (GC) analysis suggested seven fatty acids components were obviously detected in both parents and analyzed in a follow-up QTL analysis. The major components, palmitic acid (C16:0), oleic acid (C18:1), and linoleic acid (C18:2), exhibited considerable phenotypic variation and fit the two major gene and minor gene mixed-inheritance model. Seventeen QTL explained 2.57-38.72% of the phenotypic variation in these major components, with LOD values of 4.12-37.56 in six environments, and thirty-five QTL explained 0.94-32.21% of the phenotypic variation, with LOD values of 5.99-150.38 in multiple environments. Sixteen of these QTL were detected in both individual and multiple environments. Among these, qFA_08_1 was a novel QTL with stable, valuable and major effect. Two other major-effect QTL, qFA_09_2 and qFA_19_3, share the same physical position as FAD2A and FAD2B, respectively. Eleven stable epistatic QTL involving nine loci explained 1.30-34.97% of the phenotypic variation, with epistatic effects ranging from 0.09 to 6.13. These QTL could be valuable for breeding varieties with improved oil quality.