Single Gene Model Research Articles

Genetic Map Construction Using F2 and RIL/DH Mapping Population.

Genetic mapping is the determination of the position and relative genetic distance between genes or molecular markers in the chromosomes of a particular species. The construction of genetic maps uses data from the genotyping of the mapping population. Among the different mapping populations used, two are relatively common: the F2 and recombinant inbred lines (RILs) obtained as a result of the controlled crossing of genetically diverse parental forms (e.g., inbred lines). Also, the dihaploid (DH) population is often used in plants, but obtaining DHs in different crops, including rye, is very difficult or even impossible. Any molecular marker system can be used for genotyping. Polymorphic markers are used for linkage analysis, differentiating parental forms with segregation in the mapping population, consistent with the appropriate single-gene model. A genetic map is a great source of information on a species and can be an exquisite tool for analyzing important quantitative traits (QT).This chapter presents the procedure of genetic map construction with two different algorithms using the JoinMap5.0 program. First, the Materials section briefly informs about the mapping program, showing how to obtain a mapping population and prepare data for mapping. Finally, the Methods section describes the protocol for the mapping procedure itself.

Predicting Molecular Alterations from Blast Morphology of Acute Myeloid Leukemia Bone Marrow Aspirate Smears Using Machine Learning

Introduction Acute Myeloid Leukemia (AML) has enormous molecular and cytogenetic heterogeneity. Evaluation of bone marrow morphology is essential in the diagnosis of AML, however, it requires significant training and there is wide inter-observer variability. Genomic testing has been progressively relied on for AML classification, ultimately helping to dictate prognosis and guide clinical management. However, genomic testing, if performed, can be subject to prolonged turnaround times and lacks clinical penetration in low-resource settings. To overcome these challenges, we aimed to evaluate the feasibility of predicting clinically relevant genomic alterations from bone marrow cell morphology using a machine learning approach. Methods We scanned 799 Wright-stained bone marrow aspirate smear slides, made for routine patient care, for subjects diagnosed with AML. These subjects were linked to clinical data, including pertinent cytogenetic/molecular alterations and subclassified as cases with mutated Nucleophosmin 1 ( NPM1), those with TP53 mutations and those with myelodysplastic-related changes (AML-MRC). Whole slide images were screened for containing spicules and blasts, and were analyzed to detect 180 million cells (blasts and non-blasts) excluding hemodilute and particle regions. We developed a multi-instance model to predict patient molecular subtype by repeatedly sampling 512 cells from each slide and using these to train a classifier that weights cells with morphology relevant to subtype. We also trained a model to predict NPM1 and TP53 mutations independently, as well as other frequent variants reported to impact blast morphology. Results Performance in predicting NPM1/TP53/AML-MRC subtype was moderate (0.80 AUROC). Performance of the single-gene model varied, with NPM1 having the highest performance (0.85 AUROC) followed by IDH (0.80 AUROC), FLT3 (0.79 AUROC) and TP53 (0.62 AUROC). Conclusions This study provides promising preliminary results for prediction of genetic alterations in AML in a large-scale single-institution dataset. Interestingly, this method did not rely on the classification of individual cells, avoiding the need for manually collecting annotations to train a blast cell classifier. Future work will evaluate the morphology of cells attended by the multi-instance model, and explore the value of enriching sampled cells with blasts using cell classification methods.

Traditional Village research based on culture-landscape genes: a Case of Tujia traditional villages in Shizhu, Chongqing, China

ABSTRACT Global urbanization has led to severe damage and even disappearance of traditional villages in large numbers, significantly impacting the diversity of cultural landscapes. To effectively protect and inherit the cultural landscape of traditional villages, this study proposes the “culture-landscape genes” theory and its double-chain model. Taking the traditional Tujia villages in Shizhu County, Chongqing Municipality, China as an example, we identify, extract, correspond, encode, and comprehensively evaluate their culture-landscape genes. Based on the evaluation and analysis results, corresponding protection and development strategies are formulated. The study indicates that: firstly, the identification, extraction, and correlation of genes directly influence the construction of the evaluation system and the assessment of the protection level. Secondly, the comprehensive evaluation system under the double-chain model is more scientific and reasonable compared to the single-gene model of cultural or landscape genes. The culture-landscape genes theory proposed in this study promotes the development of the gene theory of traditional villages, and its double-chain research model effectively supplements the current methods for the protection and sustainable development of traditional villages, demonstrating a wide range of application value.

Inheritance of resistance to S-metolachlor in a waterhemp (Amaranthus tuberculatus) population from central Illinois

AbstractWaterhemp [Amaranthus tuberculatus (Moq.) Sauer] is a dioecious weed that has evolved resistance to very-long-chain fatty-acid elongase (VLCFAE)–inhibiting herbicides via rapid metabolism. Although detoxification enzyme activities are associated with S-metolachlor resistance in two multiple herbicide–resistant (MHR) A. tuberculatus populations from Illinois, the genetic basis of resistance is unknown. Therefore, our goal was to investigate inheritance of S-metolachlor resistance in the Stanford, Illinois–resistant (SIR) population. Specifically, our research objectives were to: (1) generate a uniformly resistant, full-sib near-inbred line (DK3-2) via three generations of recurrent selection for resistance using preemergence S-metolachlor; (2) develop A. tuberculatus populations segregating for S-metolachlor resistance via reciprocal single-plant (one male × one female) full-sib mating of DK3-2 and a VLCFAE-inhibiting herbicide-sensitive population, SEN; (3) quantify S-metolachlor resistance levels in parental lines and their F1 progenies via greenhouse dose–response analysis; and (4) evaluate inheritance of S-metolachlor resistance in F2 progenies. Dose–response analysis using six to eight S-metolachlor concentrations (0.015 to 15.0 μM, varying per population) generated lethal dose (LD) estimates of 50% (LD50) and 90% (LD90) for SIR, SEN, DK3-2, and F1 progenies. LD estimates indicated DK3-2 has a higher magnitude of S-metolachlor resistance than the SIR population, demonstrating single crosses significantly increased S-metolachlor resistance in DK3-2. Levels of S-metolachlor resistance in F1 populations were intermediate compared with DK3-2 and SEN. Segregation of S-metolachlor resistance in F2 families from the paternal-derived lines fit a single-gene model (R:S = 3:1), indicating a single, dominant gene confers S-metolachlor resistance in SIR. However, F2 segregation results from the maternal-derived lines fit a duplicate recessive epistasis model (R:S = 9:7), indicating a second recessive gene may also modify S-metolachlor resistance in SIR. Results and germplasm derived from this research can assist in identifying the gene(s) conferring resistance to S-metolachlor in A. tuberculatus.

Familial aggregation of esophageal cancer.

Familial aggregation of esophageal cancer.

Identification of fertility restoration candidate genes from a restorer line R186 for Gossypium harknessii cytoplasmic male sterile cotton

BackgroundThe utilization of heterosis based on three-line system is an effective strategy in crop breeding. However, cloning and mechanism elucidation of restorer genes for cytoplasmic male sterility (CMS) in upland cotton have yet been realized.ResultsThis research is based on CMS line 2074A with the cytoplasm from Gossypium harknessii (D2-2) and restorer line R186. The offspring of 2074A × R186 were used to conduct genetic analysis. The fertility mechanism of 2074A can be speculated to be governed by multiple genes, since neither the single gene model nor the double genes model could be used. The bulked segregant analysis (BSA) for (2074A × R186) F2 determined the genetic interval of restorer genes on a region of 4.30 Mb on chromosome D05 that contains 77 annotated genes. Four genes were identified as candidates for fertility restoration using the RNA-seq data of 2074A, 2074B, and R186. There are a number of large effect variants in the four genes between 2074A and R186 that could cause amino acid changes. Evolutionary analysis and identity analysis revealed that GH_D05G3183, GH_D05G3384, and GH_D05G3490 have high identity with their homologs in D2-2, respectively. Tissue differential expression analysis revealed that the genes GH_D05G3183, GH_D05G3384, and GH_D05G3490 were highly expressed in the buds of the line R186. The predicted results demonstrated that GH_D05G3183, GH_D05G3384 and GH_D05G3490 might interact with GH_A02G1295 to regulate orf610a in mitochondria.ConclusionOur study uncovered candidate genes for fertility restoration in the restorer line R186 and predicted the possible mechanism for restoring the male fertility in 2074A. This research provided valuable insight into the nucleoplasmic interactions.

STUDIES ON INHERITANCE OF BACTERIAL WILT RESISTANCE IN TOMATO CROP CAUSED BY Ralstonia solanacearum (E.F. SMITH)

The study aimed at the inheritance of bacterial wilt resistance in tomato with six different generations (P1, P2, F1, F2, BC1 and BC2) obtained by 4 crosses (Susceptible X Resistant). Two susceptible cultivars (Arka Meghali and Arka Vikas) and two resistant lines (H-7996 and H-7997) of tomato were crossed during kharif , 2020 in four possible combinations to generate the experimental material. The P1, P2, F1, F2 BC1 and BC2 generations of 4 crosses were screened for bacterial wilt caused by Ralstonia solanacearum (E.F. Smith) in tomato research fields of Monsanto Holdings Private Ltd., Kallinayakana Halli village, Gauribidanuru Taluka, Chikkaballapura District, Karnataka to understand the mode of inheritance. Single dominant gene controlling the resistance to bacterial wilt was observed in two crosses between Arka Meghali x H-7996 and Arka Vikas x H- 7997. Chi-square test for goodness of fit indicated that the F2 is segregating in the ratio 3 resistant to 1 susceptible in the single gene model. Resistant to susceptible ratio in BC2 was 1:1. While, in the crosses between Arka Vikas x H-7996 and Arka Meghali x H-7997 the complimentary gene interaction was observed with the F2 expected ratio of 9:7 indicating duplicate recessive epistasis.

A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker for Improving Soybean Flavor.

The vegetable soybean (Glycine max L. Merr.) plant is commonly consumed in Southeast Asian countries because of its nutritional value and desirable taste. A “pandan-like” aroma is an important value-added quality trait that is rarely found in commercial vegetable soybean varieties. In this study, three novel aromatic soybean cultivars with a fragrant volatile compound were isolated. We confirmed that the aroma of these cultivars is due to the potent volatile compound 2-acetyl-1-pyrroline (2AP) that was previously identified in soybean. A sequence comparison of GmBADH1/2 (encoding an aminoaldehyde dehydrogenase) between aromatic and non-aromatic soybean varieties revealed a mutation with 10 SNPs and an 11-nucleotide deletion in exon 1 of GmBADH2 in Quxian No. 1 and Xiangdou. Additionally, a 2-bp deletion was detected in exon 10 of GmBADH2 in ZK1754. The mutations resulted in a frame shift and the introduction of premature stop codons. Moreover, genetic analyses indicated that the aromatic trait in these three varieties was inherited according to a single recessive gene model. These results suggested that a mutated GmBADH2 may be responsible for the aroma of these three aromatic soybean cultivars. The expression and function of GmBADH2 in aromatic soybean seeds were confirmed by qRT-PCR and CRISPR/Cas9. A functional marker developed on the basis of the mutated GmBADH2 sequence in Quxian No. 1 and Xiangdou was validated in an F2 population. A perfect association between the marker genotypes and aroma phenotypes implied that GmBADH2 is a major aroma-conferring gene. The results of this study are potentially useful for an in-depth analysis of the molecular basis of 2-AP formation in soybean and the marker-assisted breeding of aromatic vegetable soybean cultivars.

Selection of Sub1 Locus for Submergence-Tolerant Introgression in a Backcrossing of South Sumatra Rice based on SSR Markers

The development of a new submergence-tolerant variety is one ideal solution to reduce submergence stress impact caused by the unpredictable occurrence of flooding in the South Sumatra riparian wetland rice cultivation area. The Sub1 gene for submergence tolerance was introgressed into South Sumatra riparian wetland rice from the donor parent FR13A using marker-assisted backcrossing. This study involves a backcrossing between Pelita Rampak and BC1F1 Pelita Rampak, FR13A-derived Sub1 breeding lines. The main objective of this study was to introgress the Sub1 gene in BC2F1 using marker-assisted selection (MAS). The introgression of the Sub1 gene in the backcrossed lines was confirmed by the tightly linked markers RM219 and RM23915. The segregation ratio of RM219 was a good fit to the expected 1:1 Mendelian single-gene model (DF = 1.0, p ≤ 0.05). In the background study, out of 237 SSR markers unlinked to the target loci, 84 were found to be polymorphic between the two parents and were used for background selection among the selected progeny. Recurrent parent genome recovery in the backcrossed lines ranged from 57.1% to 72.6%. Improvements in the tiller number, percentage of filled grain, productive tiller number and percentage of tiller number were found on these backcrossed lines. The five best backcrossed lines were selected based on SSR markers, submergence tolerance, phenotypic study and agronomic performance.

Improvement of the submergence stress tolerance of local South Sumatran rice through the introgression of the Sub1 gene by using marker-assisted selection

Submergence stress due to unpredictable soil flooding is one of the main constraints encountered in rainfed growing areas, especially in Southern Sumatran riparian swamps. The development of submergence-stress-tolerant cultivars through the introgression of Sub1 via marker-assisted backcrossing (MABC) is an ideal solution. This study was carried out during 2020 at Sriwijaya University, Palembang, Indonesia, with the aim to select Sub1-introgressed lines in BC3F1 generations on the basis of MABC and to screen out the SSR markers that were unlinked to the target gene for application in subsequent background selection studies. Results revealed that almost all the backcrossed progenies segregated from the rice parental cultivars ‘FR13A’ and ‘Pegagan’. The backcrossed lines showed significantly improved submergence stress tolerance and recovery rates compared with their parents. Sub1 introgression into the BC3F1 generation was confirmed by the tightly linked Sub1 marker SUB1C173, and marker RM23915 was used for recombinant selection. These markers followed the expected marker segregation ratio in accordance with the Mendelian single gene model. In the parental polymorphism survey, 84 out of 237 SSR markers that were unlinked to the target loci were found to be available for background study. Twenty-seven backcrossed lines were selected on the basis of foreground selection. Seven plants were selected on the basis of the recombinant marker RM23915. Five backcrossed lines were further selected on the basis of submergence stress tolerance and agronomic performance.

Genetic characterization of the brown lint phenotype for desi cotton (Gossypium arboreum) accession PI 408765 (cv. ‘Sanguineum‐1’)

AbstractCotton fibre can show a range in brown colouration, and these coloured lint fibres can be used for textile production reducing the environmental and human health hazards associated with synthetic dyes; however, coloured cotton cultivars have lower yield potential and reduced lint quality. A greater understanding of the genetics of lint colouration would be useful for the development of improved cultivars. Gossypium arboreum L. accession PI 408765 (cv. ‘Sanguineum‐1’) having the brown lint phenotype was identified from the United States Department Agriculture, National Plant Germplasm System cotton collection and crossed with G. arboreum accessions PI 529729 (cv. ‘Garo Hill’) having white lint and with PI 615733 (cv. ‘Zi‐Hua Guang Zi’) having brown lint. Lint colour data from the F2 populations support a single incomplete dominant gene model for the brown lint phenotype. Additionally, the brown lint phenotypes for PI 408765 and PI 615733 are controlled by two independent genes. Plants in these populations showed a range of brown lint colouration, and these data would be useful to further characterize the mechanisms controlling brown lint development.

Use of Simple Sequence Repeat Marker to Assess the Segregating Population of Rice (Oryza sativa) in field for Grain Length Quality Parameter

Rice grain quality is of paramount importance in the consumer preference for rice varieties and therefore the development of rice varieties should match to the consumer preference. Assessment of segregating population of breeding material in rice for quality parameter made it possible by the use of simple sequence repeat(SSR) marker. The F2 mapping population of a cross between a long slender rice genotype VDN 1137-1-1 and a short slender rice landrace Badshabhog was studied for the inheritance of grain length and to identify the marker associated with grain type. The F2 population showed 3:1 ration for long slender to short slender grain type. This segregating population was assessed by 24 SSR markers using bulk segregant analysis. Among these 24 SSR Markers, a marker RM 147 reported polymorphism between the long slender and short slender parents and respective bulks. Genetic analysis indicated goodness of fit for single gene model indicating the association of RM147 with grain length gene in the segregating population. Therefore, SSR marker RM 147 is of immense value in the assessment of grain quality parameter in rice during the development of rice varieties.

Genetic characterization of the red coloured corolla phenotype for Gossypium arboreum accession PI 529731

AbstractFlower corolla colour is an important trait for the attraction of pollinators and for the horticultural industry. Gossypium arboreum (L.) accessions from the United States Department of Agriculture germplasm collection frequently show flowers with a yellow coloured corolla. Accession PI 529731 is unique in that the flowers have a red coloured corolla. Genetic characterization of corolla pigmentation was conducted by crossing PI 529731 with two white flower accessions. Flowers with a red corolla were observed in the F1 generations suggesting a dominant trait. Variation in corolla colour was observed for plants in the F2 populations including dark red, red, light red, white, yellow and white with petals having red coloured margins. These data support a single dominant gene conferring the four red corolla phenotypes. The yellow corolla phenotype also supported a single dominant gene model. Dominant alleles at both loci are required for expression of the PI 529731 phenotype and data support a two gene model with a 9:3:3:1 segregation ratio. These data are useful for the characterization of genetic mechanisms controlling tissue‐specific pigmentation.

A Multi-Gene Model Effectively Predicts the Overall Prognosis of Stomach Adenocarcinomas With Large Genetic Heterogeneity Using Somatic Mutation Features.

BackgroundStomach adenocarcinoma (STAD) is one of the most common malignancies worldwide with poor prognosis. It remains unclear whether the prognosis is associated with somatic gene mutations.MethodsIn this research, we collected two independent STAD cohorts with both genetic profiling and clinical follow-up data, systematically investigated the association between the prognosis and somatic mutations, and analyzed the influence of heterogeneity on the prognosis-genetics association.ResultsTypical association was identified between somatic mutations and overall prognosis for individual cohorts. In The Cancer Genome Atlas (TCGA) cohort, a list of 24 genes was also identified that tended to mutate within cases of the poorest prognosis. The association showed apparent heterogeneity between different cohorts, although common signatures could be identified. A machine-learning model was trained with 20 common genes that showed a similar mutation rate difference between prognostic groups in the two cohorts, and it classified the cases in each cohort into two groups with significantly different prognosis. The model outperformed both single-gene models and TNM-based staging system significantly.ConclusionThe study made a systematic analysis on the association between STAD prognosis and somatic mutations, identified signature genes that showed mutation preference in different prognostic groups, and developed an effective multi-gene model that can effectively predict the overall prognosis of STAD in different cohorts.

The importance of immunity in the development of reliable animal models for psoriasis and atopic dermatitis.

Psoriasis (PS) and atopic dermatitis (AD) are common inflammatory skin diseases characterized by an imbalance in specific T-cell subsets, resulting in a specific cytokine profile in patients. Obtaining models closely resembling both pathologies along with a relevant clinical impact is crucial for the development of new therapies because of the high prevalence of these diseases. Single-gene mouse models developed until now do not fully reflect the complexity of these disorders, in part not only because of inherent differences between mice and humans but also because of the multifactorial nature of these pathologies. The skin-humanized mouse model developed by our group, based on a tissue engineering approach, has been used to test therapeutic strategies, although this methodology is still technically challenging and not widely available. The skin-humanized mouse models for PS and AD reproduce human skin phenotypes, providing valuable tools for drug development and testing in the preclinical setting. The tissue engineering approach allows the development of personalized medicine, covering the broad genotypic spectrum of these pathologies. This review highlights the main differences between available murine models focusing on the tissue-specific immunity of PS and AD. We discuss their contribution to unravel the complex pathophysiology of these diseases and to translate this knowledge into more accurate therapies.

Using multiple reference genomes to identify and resolve annotation inconsistencies

BackgroundAdvances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ. Of particular concern are split-gene misannotations, in which a single gene is incorrectly annotated as two distinct genes or two genes are incorrectly annotated as a single gene. These misannotations can have major impacts on functional prediction, estimates of expression, and many downstream analyses.ResultsWe developed a high-throughput method based on pairwise comparisons of annotations that detect potential split-gene misannotations and quantifies support for whether the genes should be merged into a single gene model. We demonstrated the utility of our method using gene annotations of three reference genomes from maize (B73, PH207, and W22), a difficult system from an annotation perspective due to the size and complexity of the genome. On average, we found several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3–5% of gene models across annotations. To determine which state (i.e. one gene or multiple genes) is biologically supported, we utilized RNAseq data from 10 tissues throughout development along with a novel metric and simulation framework. The methods we have developed require minimal human interaction and can be applied to future assemblies to aid in annotation efforts.ConclusionsSplit-gene misannotations occur at appreciable frequency in maize annotations. We have developed a method to easily identify and correct these misannotations. Importantly, this method is generic in that it can utilize any type of short-read expression data. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.

Genetic characterisation of the petal spot phenotype for Gossypium arboreum accession PI 408798

The occurrence of floral petal spots is common among flowering plants and plays a major role in attracting pollinators. Cotton genotypes having large red petal spots are frequent in the United States Department of Agriculture, National Plant Germplasm System Gossypium arboreum (L.) collection. One accession, PI 408798, showed a unique faint red petal spot phenotype. To genetically characterise this trait, a F<sub>2</sub> population of 226 plants was developed by crossing PI 408798 with G. arboreum accession PI 529714 that lacked pigmented petal spots. From the population, 161 plants showed the presence of faint red petal spots; whereas, 65 plants lacked pigmented petal spots. These data supported the single dominant gene model for the presence of floral petal spots. Accession PI 408798 will provide an important genetic resource to characterise the genes involved in the pathway controlling floral pigmentation.

The relation between crosstalk and gene regulation form revisited.

Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.

Genetic analysis of microsatellites associated with resistance against bacterial leaf blight and blast diseases of rice (Oryza sativa L.)

Bacterial leaf blight (BLB) and blast are among the most destructive diseases of rice. In order to develop new varieties that can resist various races of the pathogens Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae, which cause these two diseases, respectively, it is important to identify suitable markers and a marker-aided selection strategy. Seventeen foreground microsatellites associated with resistance against BLB and blast were screened for polymorphism for possible adoption in a breeding program for resistant cultivar development. A total of 472 background simple sequence repeats (SSRs) were also screened for polymorphism in order to recover the recurrent parent genome. All 72 F1 progenies were also analysed with the 17 foreground and 472 background markers in comparison to the alleles of their parents. The markers were validated using 218 BC2F2 plants. The result revealed six tightly linked polymorphic foreground markers (Xa21FR, pTA248, Xa13prom, MP, RM21 and RM13) associated with resistance against Xoo pathotype P7.7 and two microsatellites (RM6836 and RM8225) associated with resistance against blast pathotype P7.2. A total of 79 polymorphic background markers were identified for recovering the recurrent parent genome. The result also showed that the markers had goodness of fit (blast resistance) to 1:2:1 ratio for single gene model in BC2F2 progenies. These genetically confirmed microsatellite markers were recommended for use in marker-assisted backcross breeding and other marker-assisted selection of BLB and blast resistance genes in order to develop varieties with durable and broad spectrum resistance against the two major rice diseases.

Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

BackgroundConsumers purchase fresh strawberries all year long. Extending the fruiting season for new strawberry cultivars is a common breeding goal. Understanding the inheritance of repeat fruiting is key to improving breeding efficiency. Several independent research groups using multiple genotypes and analytic approaches have all identified a single genomic region in strawberry associated with repeat fruiting. Markers mapped to this region were used to evaluate breeding parents from the United States Department of Agriculture – Agricultural Research Service (USDA-ARS) strawberry breeding program at Beltsville, Maryland.ResultsMarkers mapped to repeat fruiting identified once-fruiting genotypes but not repeat-fruiting genotypes. Eleven of twenty-three breeding parents with repeat-fruiting marker profiles were actually once fruiting, indicating at least one additional locus acting epistatically to suppress repeat fruiting. Family segregation ratios could not be predicted reliably by the combined use of parental phenotypes and marker profiles, when using a single-gene model. Expected segregation ratios were calculated for all phenotypic and marker-profile combinations possible from the mapped locus combined with a hypothetical dominant or recessive suppressor locus. Segregation ratios specific to an epistatic suppressor acting on the mapped locus were observed in four families. The segregation ratios for two families were best explained by a dominant suppressor acting on the mapped locus, and, for the other two, by a recessive suppressor. Not all of the observed ratios could be explained by one model or the other, and when multiple families with a common parent were compared, there was no predicted genotype for the common parent that would lead to all of the observed segregation ratios.ConclusionsConsidering all lines of evidence in this study and others, repeat-fruiting in commercial strawberry is controlled primarily by a dominant allele at a single locus, previously mapped by multiple groups. At least two additional genes, one dominant and one recessive, exist that act epistatically to suppress repeat fruiting. Environmental effects and/or incomplete penetrance likely affect phenotype through the suppressor loci, rather than the primary mapped locus. One of the dominant suppressors acts only in the first year, the year the plant is germinated from seed, and not after the plant has experienced a winter.