Linkage To Markers Research Articles

The calcium-dependent protein kinase CmaCPK4 regulates sex determination in pumpkin (Cucurbita maxima D.).

Pumpkin (Cucurbita maxima D.) is typically monoecious with individual male and female flowers, and its yield is associated with the degree of femaleness, i.e. the ratio of female to male flowers produced by the plant. Subgynoecy represents a sex form with a high degree of femaleness, but the regulatory mechanisms in pumpkin remain poorly understood. In this study, using the F2 population crossed from the subgynoecious line 2013-12 and the monoecious line 9-6, we initially identified a recessive locus to control the subgynoecious trait, and named it sg1. After bulked segregant analysis with whole-genome resequencing (BSA-seq) and molecular marker linkage analysis, the sg1 locus was mapped to pumpkin chromosome 2. Genetic sequence analysis found a pumpkin calcium-dependent protein kinase (CPK) gene, CmaCPK4, in the mapping interval as the candidate gene. A retrotransposon insertion identified within the promoter elevated CmaCPK4 expression in 2013-12. Morphological characterization of near-isogenic lines (NILs) containing the sg1 allele showed increases in the ratio of female flowers and high ethylene contents in terminal buds compared to the receptor parent. Heterologous overexpression of CmaCPK4 significantly increased the ratio of female flowers in cucumber (Cucumis sativus). Furthermore, CmaCPK4 directly interacts with and phosphorylates 1-aminocyclopropane-1-carboxylate synthase 5 (CmaACS5) and 1-aminocyclopropane-1-carboxylate synthase 7 (CmaACS7), resulting in increased ethylene content in 2013-12, which affected pumpkin sex determination. These findings provide insights into the role of the CmaCPK4-CmaACS5/CmaACS7 module in ethylene-induced sex determination in pumpkin.

CsIREH1 phosphorylation regulates DELLA protein affecting plant height in cucumber (Cucumis sativus).

Plant height is a critical agronomic trait that affects crop yield, plant architecture, and environmental adaptability. Gibberellins (GAs) regulate plant height, with DELLA proteins acting as key repressors in the GA signaling pathway by inhibiting GA-induced growth. While DELLA phosphorylation is essential for regulating plant height, the precise mechanisms underlying this process remain incompletely understood. In this study, we identified a cucumber mutant with delayed growth, which exhibited reduced sensitivity to GA treatment. Through bulked segregant analysis (BSA-seq) combined with molecular marker linkage analysis, we successfully identified and cloned the gene responsible for the dwarf phenotype, CsIREH1 (INCOMPLETE ROOT HAIR ELONGATION 1), which encodes an AGC protein kinase. Further research revealed that CsIREH1 interacts with and phosphorylates DELLA proteins, specifically targeting CsGAIP and CsGAI2. We propose that IREH1-dependent phosphorylation of DELLA proteins prevents their excessive accumulation, thereby maintaining normal plant growth. Therefore, investigating the role of IREH1-mediated DELLA phosphorylation provides valuable insights and theoretical foundations for understanding how plants regulate growth mechanisms.

Successful application of preimplantation genetic testing combined with thirdgeneration sequencing for blocking hereditary spastic paraplegia

We report a case of application of third-generation sequencing (TGS) combined with preimplantation genetic testing (PGT) for successful prevention of hereditary spastic paraplegia (HSP) caused by SPAST gene mutations and assess the value of PGT-M and TGS in managing hereditary spastic paraplegia. A family affected by HSP underwent whole exon sequencing (WES), and a c.1699G>T mutation in the SPAST gene was identified. The mutation site in the proband was confirmed through Sanger sequencing. A single nucleotide polymorphism (SNP) site flanking the SPAST gene mutation was selected as the genetic linkage marker, and a SNP haplotype carrying the mutated gene was constructed. Ovarian stimulation using an antagonist regimen was performed for oocyte retrieval, followed by intracytoplasmic sperm injection (ICSI) and embryo culture. Blastocyst trophectoderm cells were biopsied for preimplantation genetic testing for monogenic disorders (PGT-M) to allow the selection of disease-free embryos for transfer. In this cycle, a total of 20 oocytes were retrieved, among which 18 were successfully fertilized to result in 12 blastocysts eligible for biopsy. Genetic testing revealed that all the 12 blastocysts were successfully amplified and confirmed as euploidy. Among them, 8 blastocysts did not carry paternal mutations, and a high-quality euploid embryo was selected for frozen embryo transfer (FET). Subsequent amniotic fluid testing during pregnancy confirmed the absence of paternal mutations in the fetus, resulting in the birth of a healthy baby girl. For cases of genetic diseases with missing pedigree data, the application of third-generation sequencing and PGT-M technique can effectively block vertical transmission of SPAST gene mutation to the offspring, avoid pregnancy with an aneuploid embryo, and help families with autosomal dominant HSP obtain healthy offsprings.

Selective Genotyping and Phenotyping for Optimization of Genomic Prediction Models for Populations with Different Diversity.

To overcome the different challenges to food security caused by a growing population and climate change, soybean (Glycine max (L.) Merr.) breeders are creating novel cultivars that have the potential to improve productivity while maintaining environmental sustainability. Genomic selection (GS) is an advanced approach that may accelerate the rate of genetic gain in breeding using genome-wide molecular markers. The accuracy of genomic selection can be affected by trait architecture and heritability, marker density, linkage disequilibrium, statistical models, and training set. The selection of a minimal and optimal marker set with high prediction accuracy can lower genotyping costs, computational time, and multicollinearity. Selective phenotyping could reduce the number of genotypes tested in the field while preserving the genetic diversity of the initial population. This study aimed to evaluate different methods of selective genotyping and phenotyping on the accuracy of genomic prediction for soybean yield. The evaluation was performed on three populations: recombinant inbred lines, multifamily diverse lines, and germplasm collection. Strategies adopted for marker selection were as follows: SNP (single nucleotide polymorphism) pruning, estimation of marker effects, randomly selected markers, and genome-wide association study. Reduction of the number of genotypes was performed by selecting a core set from the initial population based on marker data, yet maintaining the original population's genetic diversity. Prediction ability using all markers and genotypes was different among examined populations. The subsets obtained by the model-based strategy can be considered the most suitable for marker selection for all populations. The selective phenotyping based on makers in all cases had higher values of prediction ability compared to minimal values of prediction ability of multiple cycles of random selection, with the highest values of prediction obtained using AN approach and 75% population size. The obtained results indicate that selective genotyping and phenotyping hold great potential and can be integrated as tools for improving or retaining selection accuracy by reducing genotyping or phenotyping costs for genomic selection.

The Convergence of Radiology and Genomics: Advancing Breast Cancer Diagnosis with Radiogenomics.

Despite significant progress in the prevention, screening, diagnosis, prognosis, and therapy of breast cancer (BC), it remains a highly prevalent and life-threatening disease affecting millions worldwide. Molecular subtyping of BC is crucial for predictive and prognostic purposes due to the diverse clinical behaviors observed across various types. The molecular heterogeneity of BC poses uncertainties in its impact on diagnosis, prognosis, and treatment. Numerous studies have highlighted genetic and environmental differences between patients from different geographic regions, emphasizing the need for localized research. International studies have revealed that patients with African heritage are often diagnosed at a more advanced stage and exhibit poorer responses to treatment and lower survival rates. Despite these global findings, there is a dearth of in-depth studies focusing on communities in the African region. Early diagnosis and timely treatment are paramount to improving survival rates. In this context, radiogenomics emerges as a promising field within precision medicine. By associating genetic patterns with image attributes or features, radiogenomics has the potential to significantly improve early detection, prognosis, and diagnosis. It can provide valuable insights into potential treatment options and predict the likelihood of survival, progression, and relapse. Radiogenomics allows for visual features and genetic marker linkage that promises to eliminate the need for biopsy and sequencing. The application of radiogenomics not only contributes to advancing precision oncology and individualized patient treatment but also streamlines clinical workflows. This review aims to delve into the theoretical underpinnings of radiogenomics and explore its practical applications in the diagnosis, management, and treatment of BC and to put radiogenomics on a path towards fully integrated diagnostics.

Exploring genetic divergence and marker-trait associations for leaffolder Cnaphalocrocis medinalis (Guenee) resistance in rice landraces.

Rice production faces a significant threat from the rice leaffolder, Cnaphalocrocis medinalis. To address this challenge, growing resistant varieties stands out as a sustainable and eco-friendly pest management strategy. This necessitates identifying resistant sources and understanding their inheritance patterns through employing DNA markers for marker-assisted resistance breeding. Our study involves screening for resistant cultivars following the SES of IRRI, assessing genetic diversity among landraces using molecular markers, and identifying genomic regions associated with resistance. Screening indicated that 33.33%, 27.08%, 19.79%, and 19.80% of genotypes were resistant, moderately resistant, susceptible, and admixture, respectively. Landraces were categorized into three clusters, with clusters I and II predominantly containing moderately resistant and resistant cultivars, and cluster III mainly susceptible types. Molecular variance analysis revealed 12% variation among populations and 88% within the population. Simple linear regression identified significant marker-trait associations, with markers RM 162 and RM 284 on chromosomes 6 and 8, respectively, found highly associated with leaffolder resistance. Phenotypic variation in leaffolder damage correlated highly with the allelic effects of these markers. Further confirmation of marker linkage with resistance loci was established through independent assays on highly resistant and susceptible genotypes. The information derived from genetic diversity and marker-trait associations will be useful for future marker-assisted resistance breeding programs, enhancing the sustainability of rice production.

Структурная и функционально-семантическая классификация корякских полипредикативных конструкций со скрепой тите ‘когда’

The paper presents structural and functional-semantic classifications of Koryak polypredicative constructions with the clause linkage marker tite ‘when’. These are syntactic units prototypically comprising two clauses linked by the word tite and encoding the relation between the events expressed by these predicative units. Given the endangered status of the Koryak language, it seems imperative to document its grammar. Furthermore, the Koryak syntax is particularly intriguing from a typological perspective due to its polysynthetic nature and extensive use of non-finite verb forms with nominal case affixes directly attached to the verb stem. This study employed the methodology developed by the scholars of the Institute of Philology of the SB RAS. The classifications were developed by analyzing the constructions concerned in the texts of the three native speakers. The three main parameters of the analysis were the forms used as predicates of clauses, the morphological nature of the clause linkage markers, and the semantic relation between the events. In terms of the morphology of clause linkage markers, the constructions can be categorized into proper analytic and analyticsynthetic types, while the forms of the predicates determine whether they are bi-finite, monofinite, or bi-nonfinite. The non-finite verb form system exclusively employs negative, locative, dative converbs, and converbs of simultaneity. When considering its functional aspects, the author regards tite as a versatile marker of clause linkage, encompassing temporal-conditional and complement constructions. Posteriority, partial simultaneity, and reality condition are among the most prevalent semantic types. Ultimately, this study emphasizes the correlations between structure and meaning.

Identifying Genetic Linkage Groups and Markers for Leaf Miner Resistance in Chickpea through QTL Analysis and Field Validation

Chickpea is a commonly grown crop, but it is vulnerable to biotic and abiotic stresses. Leaf miner (Liriomyza cicerina) is a pest that can cause severe yield losses of up to 40% if not properly controlled. This study was conducted at ICARDA (Aleppo, Syria) during the 20112012 growing seasons. Two recombinant inbred lines, ILC 5901 (LM resistant) and ILC 3397 (LM susceptible), were crossed to yield 350 F2 plants, which were then screened for pathogen tolerance. The resistance of the plants was screened using a scale of one to nine, with 1 indicating complete resistance and 9 indicating complete susceptibility. A set of 600 simple sequence repeat (SSR) markers were validated on both parents, and 51 of these markers showed variation and were used to construct a genetic linkage map. QTL analysis was performed to determine the linkage groups responsible for line variations. The QTL analysis found that linkage groups TA37, TA34, and H4F03 were responsible for 22% of line variations, while unmapped NCPRG48 and H1C092 revealed 55.3% and 26.8% of the LIS variance, respectively, and displayed a warped dominance toward the susceptible parent. The H1C092 marker, which is significantly associated with LM, is located on Chr3 near a gene encoding the glutathione S-transferase gene family enzyme, which protects cellular macromolecules from attack by reactive electrophiles. The highly associated markers were field tested for three years to confirm their connection with LM resistance in 200 chickpea genotypes. The study showed marker-associated selection, which could accelerate the conventional breeding of LM-resistant chickpea germplasm. The markers linked to LM resistance and the identification of the protective enzyme gene offer promising avenues for further research. This study represents a significant step forward in understanding the genetics of LM resistance in chickpea and provides valuable information for breeding programs aimed at improving chickpea production.

A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line.

A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86-15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the 'Chinese Spring' wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.

Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets.

In modern plant breeding, genomic selection is becoming the gold standard for selection of superior genotypes. The basis for genomic prediction models is a set of phenotyped lines along with their genotypic profile. With high marker density and linkage disequilibrium (LD) between markers, genotype data in breeding populations tends to exhibit considerable redundancy. Therefore, interest is growing in the use of haplotype blocks to overcome redundancy by summarizing co-inherited features. Moreover, haplotype blocks can help to capture local epistasis caused by interacting loci. Here, we compared genomic prediction methods that either used single SNPs or haplotype blocks with regards to their prediction accuracy for important traits in crop datasets. We used four published datasets from canola, maize, wheat and soybean. Different approaches to construct haplotype blocks were compared, including blocks based on LD, physical distance, number of adjacent markers and the algorithms implemented in the software "Haploview" and "HaploBlocker". The tested prediction methods included Genomic Best Linear Unbiased Prediction (GBLUP), Extended GBLUP to account for additive by additive epistasis (EGBLUP), Bayesian LASSO and Reproducing Kernel Hilbert Space (RKHS) regression. We found improved prediction accuracy in some traits when using haplotype blocks compared to SNP-based predictions, however the magnitude of improvement was very trait- and model-specific. Especially in settings with low marker density, haplotype blocks can improve genomic prediction accuracy. In most cases, physically large haplotype blocks yielded a strong decrease in prediction accuracy. Especially when prediction accuracy varies greatly across different prediction models, prediction based on haplotype blocks can improve prediction accuracy of underperforming models. However, there is no "best" method to build haplotype blocks, since prediction accuracy varied considerably across methods and traits. Hence, criteria used to define haplotype blocks should not be viewed as fixed biological parameters, but rather as hyperparameters that need to be adjusted for every dataset.

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

Fine-mapping and candidate gene analysis of the Mcgy1 locus responsible for gynoecy in bitter gourd (Momordica spp.).

The Mcgy1 locus responsible for gynoecy was fine-mapped into a 296.94-kb region, in which four single-nucleotide variations and six genes adjacent to them might be associate with sex differentiation in bitter gourd. Gynoecy plays an important role in high-efficiency hybrid seed production, and gynoecious plants are excellent materials for dissecting sex differentiation in Cucurbitaceae crop species, including bitter gourd. However, the gene responsible for gynoecy in bitter gourd is unknown. Here, we first identified a gynoecy locus designated Mcgy1 using the F2 population (n = 291) crossed from the gynoecious line S156G and the monoecious line K8-201 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and molecular marker linkage analysis. Then, a large S156G × K8-201 F2 population (n = 5,656) was used for fine-mapping to delimit the Mcgy1 locus into a 296.94-kb physical region on pseudochromosome MC01, where included 33 annotated genes different from any homologous gynoecy genes previously reported in Cucurbitaceae species. Within this region, four underlying single-nucleotide variations (SNVs) that might cause gynoecy were identified by multiple genomic sequence variation analysis, and their six neighbouring genes were considered as potential candidate genes for Mcgy1. Of these, only MC01g1681 showed a significant differential expression at two-leaf developmental stage between S156G and its monoecious near-isogenic line S156 based on RNA sequencing (RNA-seq) and qRT-PCR analyses. In addition, transcriptome analysis revealed 21 key differentially expressed genes (DEGs) and possible regulatory pathways of the formation of gynoecy in bitter gourd. Our findings provide a new clue for researching on gynoecious plants in Cucurbitaceae species and a theoretical basis for breeding gynoecious bitter gourd lines by the use of molecular markers-assisted selection.

Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species

Yellow seed is one favorite trait for the breeding of Brassica oilseed crops, but the performance of seed coat color is very complicated due to the involvement of various pigments. The change of seed coat color of Brassica crops is related to the specific synthesis and accumulation of anthocyanin, and the expression level of structural genes in anthocyanin synthesis pathway is specifically regulated by transcription factors. Despite some previous reports on the regulations of seed coat color from linkage marker development, gene fine-mapping and multi-omics association analysis, the trait of Brassica crops is affected by the evolutionary events such as genome triploidization, the regulatory mechanism is still largely unknown. In this study, we identified genes related to anthocyanin synthesis in six Brassica crops in U-triangle at the genome-wide level and performed collinearity analysis. A total of 1119 anthocyanin-related genes were identified, the collinear relationship of anthocyanin-related genes on subgenomic chromosomes was the best in B. napus (AACC) and the worst in B. carinata (BBCC). The comparisons of gene expressions for anthocyanin metabolic pathways in seed coats during seed development revealed differences in its metabolism among these species. Interestingly, the R2R3-MYB transcription factors MYB5 and TT2 were differentially expressed at all eight stages of seed coat development, indicating that they might be the key genes that caused the variation of the seed coat color. The expression curve and trend analyses of the seed coat development period showed that the main reason for the unexpressed copies of MYB5 and TT2 was likely gene silencing caused by gene structural variation. These results were valuable for the genetic improvement of Brassica seed coat color, and also provided new insights into gene multicopy evolution in Brassica polyploids.

Development of Molecular Marker Linked with Cercospora Leaf Spot (CLS) Disease Resistance in Vigna radiata, Cloning, and Expression for Evaluating Antifungal Activity against Cercospora canescens

We developed a molecular marker for MAS of mungbean resistant varieties against CLS from the consensus sequence (MB-CLsRG) of identified RGAs (MB-ClsRCaG1 and MB-ClsRCaG2). The MB-CLsRG sequence-specific primer pair was used to screen Cercospora leaf spot (CLS) resistant varieties of mungbean in genomic analysis that showed congruency with phenotypic screening. Validation of molecular marker linkage with CLS resistance was performed using rtPCR in transcriptomic analysis. The sequenced PCR products showed 100% homology with MB-CLsRG sequence and putative disease resistance proteins that confirmed the linkage of molecular marker with CLS resistance in mungbean. The antifungal potential of MB-CLsRG gene encoding protein was assessed. The MB-CLsRG gene sequence was cloned in the E. coli expression vector for recombinant protein production. The recombinant protein was then investigated for its in vitro antifungal potential against Cercospora canescens. The in vitro investigation showed strong antifungal activity of recombinant protein as it restricted the growth of fungal mycelial mass. The results validated the linkage of developed marker with CLS-resistant mungbean varieties; therefore, it can be used to screen resistant varieties from a large population in MAS. Moreover, the recombinant protein of the MB-CLsRG gene sequence revealed antifungal potential, which proved the gene sequence could be suitable to use in transgenic plants technology to develop fungal-resistant transgenic crops.

A 163-bp insertion in the Capana10g000198 encoding a MYB transcription factor causes male sterility in pepper (Capsicum annuum L.).

Male sterility provides an efficient approach for commercial exploitation of heterosis. Despite more than 20 genic male sterile (GMS) mutants documented in pepper (Capsicum annuum L.), only two causal genes have been successfully identified. Here, a novel spontaneous recessive GMS mutant, designated msc-3, is identified and characterized at both phenotypic and histological levels. Pollen abortion of msc-3 mutant may be due to the delayed tapetum degradation, leading to the non-degeneration of tetrads callosic wall. Then, a modified MutMap method and molecular marker linkage analysis were employed to fine mapping the msc-3 locus, which was delimited to the ~139.91-kb region harboring 10 annotated genes. Gene expression and structure variation analyses indicate the Capana10g000198, encoding a R2R3-MYB transcription factor, is the best candidate gene for the msc-3 locus. Expression profiling analysis shows the Capana10g000198 is an anther-specific gene, and a 163-bp insertion in the Capana10g000198 is highly correlated with the male sterile (MS) phenotype. Additionally, downregulation of Capana10g000198 in male fertile plants through virus-induced gene silencing resulted in male sterility. Finally, possible regulatory relationships of the msc-3 gene with the other two reported pepper GMS genes, msc-1 and msc-2, have been studied, and comparative transcriptome analysis reveals the expression of 16 GMS homologs are significantly downregulated in the MS anthers. Overall, our results reveal that Capana10g000198 is the causal gene underlying the msc-3 locus, providing important theoretical clues and basis for further in-depth study on the regulatory mechanisms of pollen development in pepper.

Preimplantation genetic testing (PGT) for hemophilia A: Experience from one center

ObjectiveHemophilia A (HA) is an X-linked recessive bleeding disease caused by a deficiency or dysfunction of blood coagulation factor VIII (FVIII). Available treatment to replenish the missing factor may not reach a good outcome for all patients because of potential complications that include the development of inhibitor antibodies directed against factor VIII. Therefore, the prevention of transmitting pathogenic mutations to the next generation is the best solution for this disease. Preimplantation genetic testing for a monogenic disorder (PGT-M) has become a standard method to prevent the transmission of monogenic heritable disease. The gold standard of the molecular technique used for PGT-M nowadays is the co-amplification of the polymorphic microsatellite linkage markers that use microsatellite DNA technique that overcomes the limitation of other methods. The important issue of this technique is the definition of markers that are specific for each allele on different loci. Each gene locus needs a characteristic design to allow accurate diagnosis that can be applied on PGT-M due to the limited quantity of DNA available. Here we present our study of four specific self-designed linked polymorphic markers applied on screening the embryos before implantation for hemophilia A families in Vietnam. Material and methodsIn this study, we investigated the feasibility of application and diagnostic value of 4 STR loci (FXS1108, DXS9897, F8int22, DXS9901) in the intragenic or neighbouring regions of the F8 gene. 35 hemophilia A families were recruited for STR analysis to define at least two characteristic heterologous markers for each family and 12 cases of pre-implantation genetic testing (PGT-M) for carrier mothers were performed. ResultAll 4 of these loci (FXS1108, DXS9897, F8int22, DXS9901) were found practical and useful for preimplantation genetic testing (PGT-M). All 12 cases of PGT-M using the method had informative STR results and correct diagnosis was achieved. 9 out of the 12 mothers (75%) were implanted with 1–2 thawed embryos after the biopsy resulting in the birth of 5 healthy babies (55%). ConclusionWe conclude that specific 4 STR markers for rapid pre-implantation genetic testing of hemophilia A can be successfully applied with high confidence and accuracy in clinical settings. The results of the study provide solid evidence confirming that the microsatellite DNA technique is a highly reliable method, suitable for hemophilia A families wishing to determine carrier status or having healthy babies.

Pedigree likelihood formulae based on founder and founder couple symmetry and validation of DNA testing software

Pedigree likelihood ratios are widely used in forensic genetics. Linkage of genetic markers affects the pedigree likelihood ratio. In this study, a series of novel formulae was established based on simplification due to founder and founder couple symmetry of the Lander-Green algorithm for dealing with linkage. These new formulae are based on the inheritance vectors and differ from existing formulae that are based on the number of alleles shared identical-by-descent. In contrast to previous formulae, the formulae of this study expand the calculation to more general relationships, which enables specifying the number of typed individuals in pedigrees, and the new formulae are no longer limited to calculation of pairs of linked markers. Alternatively, pedigree likelihood values incorporating multiple linked markers could be obtained by iterating the vector transition probability between pairs of linkage markers and the probability of genotypes of typed individuals given inheritance vectors; the vector transition probability formulae are provided in a table form. To demonstrate utilization of the proposed formulae system, a series of cases were designed based on the relationships to validate GeneVisa software (www.genevisa.net) with frequency data of three linked markers, SE33-D6S1043-D6S474, on chromosome 6. The calculation results were verified with the FamLink software. The results demonstrated that the proposed formulae can correctly obtain the pedigree likelihood ratio, demonstrating the application potential of these formulae to verify effectiveness of DNA testing software.

Fine mapping of a recessive leaf rust resistance locus on chromosome 2BS in wheat accession CH1539.

The online version contains supplementary material available at 10.1007/s11032-022-01318-4.

Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession.

Modern soybean [Glycine max (L.) Merr] cultivars have low overall genetic variation due to repeated bottleneck events that arose during domestication and from selection strategies typical of many soybean breeding programs. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) alleles is a viable option to increase genetic diversity and identify new sources for traits of value. The objectives of our study were to examine the genetic architecture responsible for seed protein and oil using a recombinant inbred line (RIL) population derived from hybridizing a G. max line (‘Osage’) with a G. soja accession (PI 593983). Linkage mapping identified a total of seven significant quantitative trait loci on chromosomes 14 and 20 for seed protein and on chromosome 8 for seed oil with LOD scores ranging from 5.3 to 31.7 for seed protein content and from 9.8 to 25.9 for seed oil content. We analyzed 3,015 single F4:9 soybean plants to develop two residual heterozygotes derived near isogenic lines (RHD-NIL) populations by targeting nine SNP markers from genotype-by-sequencing, which corresponded to two novel quantitative trait loci (QTL) derived from G. soja: one for a novel seed oil QTL on chromosome 8 and another for a novel protein QTL on chromosome 14. Single marker analysis and linkage analysis using 50 RHD-NILs validated the chromosome 14 protein QTL, and whole genome sequencing of RHD-NILs allowed us to reduce the QTL interval from ∼16.5 to ∼4.6 Mbp. We identified two genomic regions based on recombination events which had significant increases of 0.65 and 0.72% in seed protein content without a significant decrease in seed oil content. A new Kompetitive allele-specific polymerase chain reaction (KASP) assay, which will be useful for introgression of this trait into modern elite G. max cultivars, was developed in one region. Within the significantly associated genomic regions, a total of eight genes are considered as candidate genes, based on the presence of gene annotations associated with the protein or amino acid metabolism/movement. Our results provide better insights into utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement utilizing native traits.

Comparing heritability estimators under alternative structures of linkage disequilibrium.

The single nucleotide polymorphism heritability of a trait is the proportion of its variance explained by the additive effects of the genome-wide single nucleotide polymorphisms. The existing approaches to estimate single nucleotide polymorphism heritability can be broadly classified into 2 categories. One set of approaches models the single nucleotide polymorphism effects as fixed effects and the other treats the single nucleotide polymorphism effects as random effects. These methods make certain assumptions about the dependency among individuals (familial relationship) as well as the dependency among markers (linkage disequilibrium) to provide consistent estimates of single nucleotide polymorphism heritability as the number of individuals increases. While various approaches have been proposed to account for such dependencies, it remains unclear which estimates reported in the literature are more robust against various model misspecifications. Here, we investigate the impact of different structures of linkage disequilibrium and familial relatedness on heritability estimation. We show that the performance of different methods for heritability estimation depends heavily on the structure of the underlying pattern of linkage disequilibrium and the degree of relatedness among sampled individuals. Moreover, we establish the equivalence between the 2 method-of-moments estimators, one using a fixed-single nucleotide polymorphism-effects approach, and another using a random-single nucleotide polymorphism-effects approach.