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PubMed1977

Genetic studies of the Fv-1 locus of mice: linkage with Gpd-1 in recombinant inbred lines.

Multiple recombinant inbred lines, derived from crosses between strains permissive to N-tropic murine leukemia viruses (Fv-1n) and strains permissive to B-tropic murine leukemia viruses (Fv-1b), have been characterized as to Fv-1 genotype and other chromosome 4 markers, including the closely linked hexose-6-phosphate dehydrogenase isozyme locus (Gpd-1). Only one recombinant between Fv-1 and Gpd-1 was found among 45 lines tested. On this basis, the distance between Fv-1 and Gpd-1 is estimated to be 0.6 centimorgans. None of the lines was either resistant or susceptible to both N- and B-tropic viruses. Nineteen other inbred strains, previously untested, were characterized as either Fv-1n or Fv-1b.

Animals↗

PubMed2025

Development of recombinant inbred lines and QTL analysis of plant height and fruit shape-related traits in Cucurbita pepo L.

UNLABELLED: Zucchini (Cucurbita pepo subsp. pepo) stands as an economically vital crop in China. In zucchini breeding, plant architectural patterns and fruit morphological characteristics serve as pivotal traits. In this study, we employed quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from two distinct inbred lines, JinGL (subsp. ovifera) and HM-S2 (subsp. pepo), in conjunction with a high-density genetic map. Our investigation focused on ten QTLs associated with six horticulturally significant traits, including hypocotyl length (HL), plant height (PH), and four fruit-related traits: fruit length (FL), fruit diameter (FD), fruit shape index (FSI), and fruit weight (FW). The QTLs governing HL and PH were mapped to Chr03/LG10 and named qhl3.1 and qph3.1, respectively. The candidate gene Cp4.1LG10g05910/CpDw for qph3.1 was successfully identified. Additionally, three novel QTLs related to fruit size and shape were discovered. Among them, qfsi8.1/qfl8.1, demarcated by Marker238258 and Marker240069 on Chromosome 08/Linkage group 17 (Chr08/LG17), is a new major QTL regulating the fruit shape of zucchini. Through genomic insertion-deletion (InDel) and qRT-PCR analyses, we predicted genes within the qfsi8.1/qfl8.1 candidate interval, uncovering Cp4.1LG17g02030/CpIAA12 and Cp4.1LG17g02010/CpCalB as potential candidate genes. We developed molecular markers tightly linked to qph3.1 and qfl8.1 and validated them in 171 and 224 Cucurbita pepo germplasms, achieving accuracy rates of 96% and 100%, respectively. This study deepens our understanding of the genetic basis of key traits and provides valuable references for molecular breeding in Cucurbita pepo. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-025-01592-y.

Cucurbita pepo↗

PubMed1978

Genetic analyses of differences in incidence of mammary tumors and reticulum cell neoplasms with the use of recombinant inbred lines of mice.

The influence of genes, in addition to genes in the H-2 complex, that effect the genesis of mammary tumors was studied. The recombinant inbred (RI) CXB lines were chosen for this investigation, because they are well suited for the study of the genetics of a trait for which the genotype affects probability of phenotype expression and which therefore is measured as incidence. Females of seven RI lines (CXBD, CXBE, CXBG, CXBH, CXBI, CXBJ, and CXBK) and their progenitor strains C57BL/6By (B6) and BALB/cBy (BALB/c) were given ip injections of MuMTV at 3 months of age and were force bred. They were observed for mammary tumors. The B6 strain was least susceptible, and mammary tumors appeared late in life. The BALB/c strain was most susceptible, and the tumors appeared early in life. The course of tumor development in the RI lines fell between these extremes. The RI strain distribution pattern of mammary tumor incidence indicated that at least one and probably several loci in addition to those at H-2 determined the difference between the BALB/c and B6 strains. Effects of the other gene(s) appeared to be even more important than those of H-2. The locations of those loci were not made clear by this study. The spontaneous incidence of reticulum cell neoplasms was also recorded. The most frequently formed neoplasm of the reticular system was a Hodgkin's-like lesion. The data suggested an influence of the H-2 complex.

Animals↗

PubMed1978

X-linked and autosomal genes controlling mouse alpha-galactosidase expression.

Analysis of F2 and backcross animals has confirmed the X-chromosome linkage of Ags, the structural locus for mouse alpha-galactosidase. The position of Ags has been located in the X chromosome, 9 centimorgans from Mo, and the gene order is centromere-Hq-Bn-Ta-Mo-Ags. A variation in the developmental expression of alpha-galactosidase activity, inherited as an autosomal trait, has been characterized using recombinant inbred lines of mice. Among certain recombinant inbred lines, the variation appears to segregate as a single major locus.

Animals↗

PubMed2025

Identifying canopy wilting QTLs and evaluating remote sensing approaches for selecting drought-tolerant soybean.

Drought is the most damaging abiotic stress for soybean yield; cultivars with improved drought tolerance are needed to sustain and increase crop production. PI 603535 previously was identified as an ultra-slow canopy wilting (CW) line in a genome-wide association study but the quantitative trait loci (QTLs) underlying this phenotype have not been determined. In this study, a recombinant inbred line (RIL) population derived from Benning × PI 603535 was evaluated for three years under rain-fed conditions. CW was rated following extended periods of drought when CW variation was present. Aerial multispectral and thermal imagery was also captured in conjunction with visual ratings to explore the feasibility of implementing remote sensing to improve the efficiency and objectivity of drought evaluations. The normalized difference vegetation index (NDVI) and green-based NDVI (GNDVI) exhibited strong, significant correlations (|r|= 0.42-0.44) with CW across years. CW scores and the remote sensing traits were used as phenotypes for QTL mapping. Seven CW QTLs were identified across six chromosomes in the combined analysis, with NDVI and GNDVI QTLs generally colocalizing with the CW QTLs with the highest percentage of variation explained (PVE). The QTLs were not consistently identified among individual years, highlighting the complex genetics and gene expression of drought tolerance. The instability and low additive effect estimates of individual QTLs imply challenges of improving drought tolerance through the selection of a few QTLs. However, the slow CW RILs developed in this study can serve as valuable breeding stocks for future drought improvement breeding efforts and genetic studies.

Quantitative Trait Loci↗

PubMed2026

Quantitative trait loci associated with improved fruit yield under heat-stress conditions in fresh-market tomato.

Rising temperatures and more frequent heat stress events pose a major challenge to global tomato production, particularly in tropical and subtropical regions such as the southern United States. High temperatures during flowering and fruit set lead to poor fruit set and reduced yield. Although several commercial cultivars and breeding lines are described as heat-tolerant, the genetic basis of yield performance under heat stress conditions in fresh-market tomato remains poorly understood. This study aimed to identify genomic regions associated with fruit yield under natural heat stress. A biparental recombinant inbred line (RIL) population developed by the UF/IFAS tomato breeding program was evaluated under natural field heat stress in the fall seasons of 2016, 2017, and 2018, with fruit yield recorded as the primary trait. Genotyping of RILs was performed with the AgriPlex commercial tomato panel. Multi-environment QTL analysis was conducted to identify loci associated with fruit yield under heat stress. A major locus on chromosome 12 was selected for validation. Backcross populations segregating for this region were evaluated in a randomized block design during the fall of 2020 at the Gulf Coast Research and Education Center (GCREC), Balm, Florida. Multi-environment QTL analysis identified several loci on chromosome 4, 5, 6, and 12 associated with fruit yield under natural heat stress conditions. Among these, a locus on chromosome 12 showed consistent effects across multiple harvests and environments and explained a relatively larger proportion of phenotypic variance. Validation using backcross populations confirmed that genotype carrying the chromosome 12 QTL produced significantly higher yield under natural heat stress than susceptible genotypes. Overall, this study identified an agronomically important region on chromosome 12 that can be targeted to improve tomato yield under heat stress. The results also highlight multiple genomic regions contributing to higher yield under heat stress. These findings provide a foundation for developing breeding strategies for developing heat-tolerant fresh-market tomato cultivars.

QTL analysis↗

PubMed1979

Genetic determination of the developmental program for mouse liver beta-galactosidase: involvement of sites proximate to and distant from the structural gene.

The identification and mode of action of genetic loci that program gene expression during development are important for understanding differentiation in higher organisms. Previous work from this laboratory has identified two patterns for the postnatal development of liver beta-galactosidase among inbred mouse strains: type I, where activity levels remain constant after about 30 days of age, is found in strains DBA/2J, CBA/J, and BALB/cJ, among others; type II, where activity levels increase between 25 and 50 days of age to reach a new adult level, is found in strain C57BL/6J and related strains. It has been shown that the type I vs. type II developmental difference between strains C57BL/6J and DBA/2J is due to variation at a locus, Bgl-t, that maps with the beta-galactosidase complex, [Bgl], on chromosome 9. In the present study, we have confirmed the existence of Bgl-t as a temporal locus within [Bgl] by analysis of both a congenic strain carrying the beta-galactosidase complex of strain CBA/J in the C57BL/6J genetic background and a cross of strains CBA/J and C57BL/6J. The existence of additional temporal loci for beta-galactosidase that segregate independently of the structural gene and participate in determination of the type I vs. type II difference was revealed by analysis of: (1) a congenic strain containing the beta-galactosidase complex of strain BALB/cJ in the C57BL/10Sn background; (2) recombinant inbred lines derived from progenitor strains C57BL/6ByJ and BALB/cByJ; and (3) a genetic cross between strains C57BL/6ByJ and BALB/cByJ. Thus, for these pairs of strains, the type I vs. type II developmental difference is due to variation at a temporal locus (or loci) unlinked to the enzyme structural gene, and not at Bgl-t. These facts, together with information gathered from an examination of the distribution of beta-galactosidase phenotypes among over 100 inbred strains (Breen, Lusis and Paigen 1977), have led us to conclude that the postnatal developmental pattern for liver beta-galactosidase is determined by a set of interacting temporal genes. One of these, Bgl-t, is located within [Bgl], and one or more are separable from [Bgl] by recombination. A possible mode of interaction among the temporal and instructural loci is suggested.

Animals↗

PubMed1978

Relationship between Moloney MSV tumor resistance and endogenous virogene expression in AKR mouse strain and its hybrids.

We have examined the induction of Moloney-MSV tumors in AKR and other mouse strains in relation to endogenous virus expression. All virus-free strains so far tested were tumor-susceptible, while AKR was resistant. The selectivity of MSV tumor resistance, characteristic of AKR mice, was associated with AKR virogens segregation in first backcross to MuLV-negative/MSV-susceptible mice, and in a few second backcross families. Stronger evidence that AKR ecotropic virogene expression is the major, but not the sole, determinant of M-MSV tumor resistance in AKR mice was obtained in strains partially congeneic for akv-2 viral gene and in recombinant inbred lines derived from an original cross between AKR and C57L mice. These mice or lines, in which inheritance of endogenous viral genes had occurred, at the same time inherited the ability to show strong resistance to tumor induction by an exogenous oncogenic virus. This finding suggests that ecotropic endogenous viruses can exert a beneficial effect in their hosts providing some protective functions. Although the association between AKR-MuLV and M-MSV resistance is definite, the mechanisms by which MuLV+ mice are refractory to M-MSV tumors have still to be elucidated.

Animals↗

PubMed1977

Sensitization to cocaine stimulation in mice.

Repeated administration of cocaine to B6AF1/J mice increased their running response to 20 mg/kg cocaine as much as four-fold over the response to the first injection. After four daily injections, the extent of the increase was proportional to the dose of cocaine that was used for pretreatment. Sensitization persisted for as long as 2 months after the last injection of cocaine. Cocaine-pretreated mice did not show an increased running response to either morphine or d-amphetamine. The response to cocaine was increased two-fold by treatment with morphine and three-fold by pretreatment with d-amphetamine. Pretreatment with either imipramine or reserpine did not produce sensitization to cocaine. There was no correlation between cocaine sensitization and whole-brain catecholamine levels. There were marked differences in both the running response to cocaine and the extent of cocaine sensitization betwee the parental strains, C57B1/6J and A/J. Experiments with recombinant-inbred lines, derived from C57B1/6By and BALB/cBy mice, suggest that the initial response to cocaine and the development of sensitization are controlled by different genetic determinants.

Animals↗

PubMed2025

Candidate genes at the Rmi1 locus for resistance to Meloidogyne incognita in soybean.

The RKN resistance locus Rmi1 was fine-mapped to two genes on chromosome 10, a glycosyl hydrolase family 9 β-1,4-endoglucanase gene and a type I pectin methylesterase gene. Root-knot nematodes (Meloidogyne spp.) are a serious threat to soybean production in the southeast USA, with yield losses of more than $165 million in 2023. Development and deployment of resistant soybean cultivars is the most effective strategy for managing these nematode pests; however, the identity of the resistance genes and underlying mechanism of resistance remains obscure. An additive resistance gene, Resistance to M. incognita-1 (Rmi1), to the predominant species, was first identified in soybean cultivar Forrest but never mapped to a genomic region. Multiple mapping studies have identified a major quantitative trait locus (QTL) with additive action on chromosome 10. In this study, a population consisting of 170 F2:3 families derived from a cross of Bossier (susceptible) × Forrest (resistant) was initially used to confirm that Rmi1 is in the chromosome 10 QTL. Subsequently, 884 F5:6 recombinant inbred lines (RILs) derived from the same cross were used to fine-map the Rmi1 causal gene(s) to two genes - a β-1,4-endoglucanase (Glyma.10G017000, EG) and a pectin methylesterase/methylesterase inhibitor (Glyma.10G017100, PME1). Both gene candidates have the potential to play a role in the resistance response to M. incognita. Both gene promoters harbor SNPs and indels and the encoded proteins exhibit amino acid polymorphisms, including a premature stop in PME1 of resistant soybeans. Additionally, both genes show a higher expression level in susceptible roots compared to resistant roots in the absence of infection. This suggests that Rmi1 may confer one or more pre-existing differences related to cell wall modification in soybean roots, ultimately leading to a decrease in susceptibility.

Tylenchoidea↗

PubMed2026

A GWAS-derived histone H4 variant linked to ear row number reveals functional insights into the maize ZmHistone gene family.

Ear row number (ERN) is a major yield determinant in maize and a key target for breeding of high-yielding varieties. This study utilized a multi-parent population (MPP) of 780 recombinant inbred lines (RILs) derived from seven inbred lines across three environments. Genotyping-by-sequencing (GBS) of the MPP yielded 638,646 high-quality SNPs. Using genome-wide association study (GWAS), we detected 80 significant SNPs including S2-15316355 and S4-224453431, which were consistently detected in all environments and best linear unbiased prediction (BLUP) analysis. A linkage disequilibrium-defined ±20 kb window around these two lead SNPs contained three positional candidate genes: Zm00001eb072840, Zm00001eb072850 and Zm00001eb202890. Zm00001eb072850 (ZmHistone12), a histone H4 variant, was prioritized for hypothesis-driven follow-up because the lead SNP lies within its coding sequence and the gene is expressed in ear-related tissues. Additionally, we identified 91 ZmHistone genes in the maize genome and described their phylogeny, promoter motif and expression patterns. Public transcriptome and qRT-PCR analysis in seven parental lines provide descriptive evidence of Histone variant genes in maize ear development. These results suggest a potential involvement of chromatin-associated regulation of ERN in maize and provide a foundation for future functional validation.

Ear development↗

PubMed2026

Grain protein and yield stability study in rainfed durum wheat RILs.

Developing durum wheat cultivars with stable grain yield across diverse environments remains a key breeding objective. This study evaluated 118 recombinant inbred lines (RILs) derived from a cross between the drought-adapted cultivar 'Zardak' (Triticum durum) and the landrace 'Iran-249' (T. turanicum) with desirable seed characteristics, across four heterogeneous rainfed environments in Italy and Iran. The assessment focused on grain yield (GY) and grain protein content (GPC) stability. Combined analysis of variance revealed significant (p < 0.01) effects for genotype, environment, and their interaction for both traits. Line ZD-050 showed the highest GY (3.91 t ha⁻¹), while ZD-032 had the highest GPC (14.27%). Stability analysis using parametric and non-parametric methods, along with AMMI and GGE biplot modeling, identified ZD-050 as among the most promising genotypes according to yield-integrating and dynamic-stability approaches. This line showed high grain yield in methods such as the Superiority Index and Kang's rank-sum, although stability rankings differed across the used methods. This line maintained superior yield, demonstrated broad adaptability across environments, and had moderate protein levels, identifying it as an optimal candidate for breeding programs targeting yield stability and wide adaptation under rainfed conditions.

Triticum↗

PubMed1979

Genetic constitution and response to toxic chemicals--an overview.

There is no scientific justification for the use of random-bred or outbred rodents in toxicological and carcinogenesis testing. The frequent desire for heterozygosity in a test population can best be met by using F1 hybrids of inbred progenitor strains. Extrapolation of animal data to humans will ultimately come through an understanding of cellular responses to carcinogenic and toxicological agents. Isogenic animal populations such as inbred strains, F1 hybrids, and the recently developed recombinant inbred lines are currently our best approach to resolving these mechanisms.

Animals↗

PubMed1979

Use of two-dimensional electrophoresis to identify and map new mouse genes.

Cytosol polypeptides from mouse liver have been examined using two-dimensional electrophoresis. About 250 spots were readily discernible. When cytosols from strains BALB/cBy and C57BL/6By were compared eight genetically determined differences were observed. Other strain pairs show comparable numbers of differences. These eight phenotypes were scored in seven recombinant inbred lines derived from the two parental strains, and their strain distribution patterns were compared with previously determined patterns for other genetic markers that differ between the two progenitor strains. Using this information, tentative chromosomes assignments for the genes controlling five of the variant phenotypes have been made, and two of the assignments have been confirmed using congenic resistant strains. These eight genes will be useful reference markers in future crosses designed to map new genes.

Animals↗

PubMed2026

The potential of considering photosynthesis parameters in crop yield breeding by genomic prediction.

To meet the growing demand for agricultural products, optimizing photosynthesis is a promising strategy to improve crop yields. Phenotypic variance in photosynthesis has been observed within or between species. To explore the potential of integrating photosynthetic parameters into crop breeding programs, we explored the genetic variation in photosynthesis by assessing photosynthesis-related parameters across plant development in 631 barley recombinant inbred lines (RILs) from eight HvDRR subpopulations under field conditions. The genetic complexity of these parameters was resolved by analyses of bi-parental and multi-parental quantitative trait loci (QTLs). Finally, we examined the merit of integrating photosynthesis-related parameters in genomic prediction of yield and its components. Significant genotypic variations of the photosynthesis-related parameters were found among the RILs, with their heritability ranging from 0.38 to 0.54. The multiple QTLs and dynamic QTLs for photosynthesis observed across different developmental stages underlined the complexity of the genetics of photosynthesis in barley. The considerably higher percentage of phenotypic variance explained for genomic prediction than multi-parental QTL analysis illustrates that the photosynthesis-related parameters are inherited in a more complex way than classical agronomic traits. Notably, the prediction ability for yield was increased by integrating the photosynthesis-related parameters of some developmental stages into genomic prediction models. Thus, our results suggest a novel perspective on increasing the efficiency of crop breeding programs by integrating photosynthesis-related parameters into prediction models.

Photosynthesis↗

PubMed2026

Comparative Genome-Wide Association Studies of Metabolites and Grain-Related Traits in Common Wheat.

The metabolome is highly diverse and the closest layer to phenotype; therefore, it is commonly regarded as a bridge between the genome and phenome in plants. Here, we performed large-scale metabolome analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 33 grain-related traits in a diverse panel of natural accessions and a recombinant inbred line (RIL) population. We identified a new network of 2286 associations between 947 metabolites and 33 grain-related traits. Systematic integration of metabolic genome-wide association study (mGWAS) and metabolic quantitative trait locus (mQTL) analyses identified 33 566 significant single-nucleotide polymorphisms (SNPs) and 3128 mQTL. Thirteen annotated metabolites co-localized within a physical interval on 7A. Integration of metabolite-based and phenotype-based GWAS and QTL revealed an overlapped region for gibberellin A4 (GA4) content and grain roundness on 4A. Phenotyping of an ethyl methanesulfonate (EMS)-induced mutant confirmed the role of TaSDR in regulating GA4 content and grain morphology. These findings provide novel insights into the metabolic pathways influencing key grain-related traits and advance our understanding of the complex molecular mechanisms regulating grain metabolites and phenotypes in wheat. The identified metabolic markers and candidate genes provide valuable targets for molecular breeding programs aimed at improving wheat yield and quality.

QTL↗

PubMed2025

Combining QTL mapping and RNA-Seq reveals candidate genes controlling flag leaf width in foxtail millet.

BACKGROUND: The flag leaf, a crucial component of plant architecture, significantly influences final grain yield in crops, including foxtail millet (Setaria italica L.). Optimizing flag leaf size is considered an effective strategy for enhancing grain yield potential under higher planting densities. However, the genetic mechanism underlying flag leaf size, particularly flag leaf width (FLW), remains largely unknown under varying planting densities in foxtail millet. RESULTS: An FLW phenotype variation analysis was conducted across multiple planting densities using a recombinant inbred line (RIL) population derived from Heizhigu (narrow leaf) and Changnong 35 (wide leaf). Based on a high-density genetic map with 3795 Bin markers, 11 flag leaf width (FLW) QTLs were identified on chromosomes 3, 5, and 6, explaining 2.35%-36.06%. Among these, qFLW5-2 was a major QTL, detected consistently across 3 environments and explaining a large proportion of FLW variation. The QTL was further validated with 9 InDel markers with its candidate region across different planting densities. Moreover, RNA-seq revealed 2,293 and 2,338 differentially expressed genes (DEGs) between biparents at heading stage and grain filling stage, respectively. There were 11 and 9 DEGs within the location range of qFLW5-2 among 2 comparison groups (HZG-H_vs_CN35-H and HZG-G_vs_CN35-G). Combining QTL mapping and RNA-seq, we speculated that Seita.5g134600 (encoding an auxin responsive protein Aux/IAA) and Seita.5G123900 (encoding a cytochrome P450 family protein) as key candidate genes for qFLW5-2. Furthermore, variation analysis confirmed that the lines or germplasm with Seita.5G1346005UTR277+ allele, both within the RIL population and natural populations, exhibited significantly wider leaves than those with Seita.5G1346005UTR277- allele. These findings advance our understanding of the genetic and molecular regulatory mechanisms governing flag leaf growth. CONCLUSIONS: This study elucidates genetic and molecular mechanism regulating flag leaf growth and development in foxtail millet. The results provide a theoretical foundation for improving plant architecture and facilitating molecular marker-assisted breeding in this crop.

Quantitative Trait Loci↗

PubMed2025

Arabidopsis CNL receptor SUT1 confers immunity in hydathodes against the vascular pathogen Xanthomonas campestris pv. campestris.

Bacterial plant pathogens exploit natural openings, such as pores or wounds, to enter the plant interior and cause disease. Plants guard these openings through defense mechanisms. However, bacteria from the genus Xanthomonas have specialized in that they enter their host via a special entry point, the hydathode-an organ at the leaf margin involved in xylem sap guttation. Hydathodes can mount an immune response against bacteria, including non-adapted and adapted pathogens like X. campestris pv. campestris (Xcc) that cause vascular disease. Previously, it was shown that the RKS1/ZAR1 immune complex confers vascular resistance against Xcc by recognizing XopAC activity, a type III effector (T3E). However, in absence of XopAC recognition, Arabidopsis Col-0 hydathodes still display resistance against Xcc. Here we mapped the causal gene using an inoculation method that promotes Xcc hydathode entry. Using a population of Recombinant Inbred Lines (RILs) of a cross between a susceptible (Oy-0) and resistant accession (Col-0), a major QTL for Xcc resistance was found on the right arm of Chromosome 5 in Col-0. Combining this result with a genome-wide association analysis yielded a single candidate gene encoding a coiled-coil nucleotide-binding leucine-rich repeat (CNL-type) immune receptor protein called SUPPRESSOR OF TOPP4 1 (SUT1). Expression of SUT1 was confirmed in hydathodes. We reveal that RKS1/ZAR1 and SUT1 confer different levels of Xcc resistance in different tissue types. Both RKS1/ZAR1 and SUT1 are alone sufficient for Xcc resistance in Col-0 hydathodes. However, RKS1/ZAR1 resistance is also effective in tissue types that represent late infection stages, i.e., xylem and mesophyll. In contrast, SUT1 resistance is not effective in the xylem, while weakly additive to RKS1/ZAR1 in the mesophyll. We thus identify a novel R gene, SUT1, that confers Xcc resistance primarily early in the infection during hydathode colonization.

Plant Diseases↗