Marker Loci Research Articles

Field resistance and molecular detection of the orange rust resistance gene linked to G1 marker in Brazilian cultivars of sugarcane

ABSTRACT Sugarcane (Saccharum spp.), an important crop for tropical and subtropical countries, is used in the production of sugar and biofuel. Orange rust, a disease caused by the fungus Puccinia kuehnii, can reduce the yield and harm the sugarcane industry. Molecular markers linked to resistance genes can help breeding programs confirm introgression of favorable alleles, find new resistance sources and release new cultivars that have durable resistance. In the current study, the aims were (i) to evaluate in the field the resistance to orange rust of 24 Brazilian commercial cultivars; (ii) to assess the frequency of the allele at G1 marker locus in the set of cultivars, and (iii) to study the usefulness of G1 marker to predict the resistant phenotype and its potential for marker assisted selection. A diagrammatic scale, which ranged from 1 (plants without symptoms) to 9 (highly susceptible plants), was used to determine the disease severity. Considering resistant cultivars those with mean severity up to 3, G1 marker efficiency in predicting the resistant phenotype was 71.43%. In addition, there was a reduction of 35% in the overall mean severity when G1 marker was present. G1 marker is an important molecular tool that can be used by breeding programs in the search for sugarcane cultivars resistant to orange rust.

VitisGDB: The Multifunctional Database for Grapevine Breeding and Genetics

VitisGDB: The Multifunctional Database for Grapevine Breeding and Genetics

Recessive Z-linked lethals and the retention of haplotype diversity in a captive butterfly population.

Sex chromosomes are predicted to harbour elevated levels of sexually antagonistic variation due to asymmetries in the heritability of recessive traits in the homogametic versus heterogametic sex. This evolutionary dynamic may manifest as high recessive load specifically affecting the homogametic sex, and the retention of haplotype diversity in small populations. We tested the hypothesis that the Z chromosome in the butterfly Bicyclus anynana carries a high inbred load for male fertility and viability. Homozygosity of Z chromosome blocks was produced by daughter-father backcrosses, and inferred from marker loci positioned via a linkage map. Male sterility was, in general, unrelated to homozygosity in any region of the Z, but there was an extreme deficit of homozygous males within a 2 cM interval in all families. In contrast, no corresponding skew in Z genotype was detected in their (hemizygous) sisters. The same pattern was observed in historically inbred lines, indicating a high frequency of recessive lethals in the ancestral population. Allele-frequency changes between 1993 and 2006 (70 generations at Ne ~ 160) show that, despite the loss of many haplotypes, diversity was retained significantly above the neutral expectation. Effective overdominance in the lethal region can account for this effect locally but not in other parts of the chromosome, that are also associated with persistent linkage disequilibrium. These unexpected patterns suggest the operation of other factors, such as epistatic selection, recombination suppression, assortative mating and meiotic drive. Our results highlight the role of balancing selection in maintaining the inbred load and linked genetic diversity.

Genome-Wide Association Study identify the genetic loci conferring resistance to Coffee Berry Disease (Colletotrichum kahawae) in Coffea arabica var. Rume Sudan

Coffee Berry Disease (CBD) caused by the fungal pathogen Colletotrichum kahawae destroys about 80% of the crop on susceptible Coffea arabica cultivars if no control is applied. Resistance to CBD is governed by three genes: T, R that are dominant, and the recessive k in varieties Hibrido de Timor, Rume Sudan (RS), and K7 respectively. The marker for the T-gene had earlier been identified. The study aimed to identify the DNA marker for the R-gene from RS. The mapping population comprised of 106 F2 genotypes from varieties RS (resistant) and SL28 (susceptible). The genotypes were assessed for their reaction to CBD using hypocotyl inoculation test on a scale of 1–12. The Single Nucleotide Polymorphism (SNP) markers were obtained through Genotyping by Sequencing. The population structure was assessed by both principal component analysis and marker-based kinship while pairwise linkage disequilibrium was estimated using squared allele frequency correlations (r2). Genome-Wide Association Study was carried out using a compressed mixed linear model in Genomic Association and Prediction Integrated Tool. Two SNP markers were significantly associated with CBD resistance in coffee Chromosomes (Chr) 1 and 2 accounting for 12.5% and 11% respectively of the total phenotypic variation explained by the model. The sequence search for the markers was associated with proteins for disease resistance within the NCBI database. The two SNP markers 100025973|F|0-59:T > C-59:T > C and 100034991|F|0-44:C > T-44:C > T are identified as DNA markers for the genetic loci conferring resistance to CBD in RS, christened as Ck-2 and Ck-3 and are recommended for marker assisted selection.

Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (Medicago sativa L.).

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

Missing Persons Identification: Genetic profiling of highly charred human remains using sixteen STR loci markers

Law enforcement and Disaster Management Agencies within Governments spend substantial resources to identify human remains and dead bodies after wars, mass disasters and political unrest [1-4]. Under certain legal circumstances such as civil paternity cases and unclaimed human cadavers, biological samples may be collected from living relatives and exhumed human remains, as well as mortal remains for DNA profiling purposes [5,6]

Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.).

The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

Cross-species transferability of Solanum spp. DNA markers and their application in assessing genetic variation in silverleaf nightshade (Solanum elaeagnifolium) populations from Texas, USA

AbstractSilverleaf nightshade (Solanum elaeagnifolium Cav.) is an invasive species that has successfully spread outside its native range to become a noxious weed in 21 states in the United States and 42 countries worldwide. The successful establishment of S. elaeagnifolium outside its native habitat indicates its innate ability to adapt to a multitude of environments. Phenotypic plasticity and/or genetic adaptation have been identified as key mechanisms underlying the adaptive success of invasive species. Whereas phenotypic plasticity allows a species to buffer changes in the environment by altering its phenotypic attributes within the short term, genetic adaptation is responsible for the longer-term adaptability of plants to heterogeneous environments and is dependent on the amount of genetic variation present in the species. In this study, we screened DNA markers that are specific to tomato (Solanum lycopersicum L.) and Solanum lycopersicoides Dunal for their interspecific transferability to S. elaeagnifolium and determined the applicability of the transferable DNA markers in assessing the extent of genetic variation in populations from Lubbock, Littlefield, and Blackwell, TX. Of the 187 markers screened, 78 successfully amplified targets in S. elaeagnifolium, indicating the evolutionary conservation of marker loci across S. lycopersicum, S. lycopersicoides, and S. elaeagnifolium, despite their genetic divergence millions of years ago. Genotyping of S. elaeagnifolium populations using 50 DNA markers that consistently amplified clear bands in more than 60% of the plants identified nine polymorphic markers with 0.014 to 0.621 polymorphism information content. Genetic diversity analysis by DNA marker profiling established genetic variation among populations and within individuals of different populations. Unweighted paired group method with arithmetic mean analysis grouped the plants into six clusters that are generally defined by selection pressures unique to each collection site. Results of the study indicate the capacity of S. elaeagnifolium for genetic differentiation in response to variable selection pressures within the same geographic region.

Relish as a Candidate Marker for Transgenerational Immune Priming in a Dampwood Termite (Blattodae: Archeotermopsidae).

Natural selection should favor the transfer of immune competence from one generation to the next in a context-dependent manner. Transgenerational immune priming (TGIP) is expected to evolve when species exploit pathogen-rich environments and exhibit extended overlap of parent–offspring generations. Dampwood termites are hemimetabolous, eusocial insects (Blattodea: Archeotermopsidae) that possess both of these traits. We predict that offspring of pathogen-exposed queens of Zootermopsis angusticollis will show evidence of a primed immune system relative to the offspring of unexposed controls. We found that Relish transcripts, one of two immune marker loci tested, were enhanced in two-day-old embryos when laid by Serratia-injected queens. These data implicate the immune deficiency (IMD) signaling pathway in TGIP. Although an independent antibacterial assay revealed that embryos do express antibacterial properties, these do not vary as a function of parental treatment. Taken together, Z. angusticollis shows transcriptional but not translational evidence for TGIP. This apparent incongruence between the transcriptional and antimicrobial response from termites suggests that effectors are either absent in two-day-old embryos or their activity is too subtle to detect with our antibacterial assay. In total, we provide the first suggestive evidence of transgenerational immune priming in a termite.

Exaiptasia diaphana from the great barrier reef: a valuable resource for coral symbiosis research

The sea anemone, Exaiptasia diaphana, previously known as Exaiptasia pallida or Aiptasia pallida, has become increasingly popular as a model for cnidarian-microbiome symbiosis studies due to its relatively rapid growth, ability to reproduce sexually and asexually, and symbiosis with diverse prokaryotes and the same microalgal symbionts (family Symbiodiniaceae) as its coral relatives. Clonal E. diaphana strains from Hawaii, the Atlantic Ocean, and Red Sea are now established for use in research. Here, we introduce Great Barrier Reef (GBR)-sourced E. diaphana strains as additions to the model repertoire. Sequencing of the 18S rRNA gene confirmed the anemones to be E. diaphana while genome-wide single nucleotide polymorphism analysis revealed four distinct genotypes. Based on Exaiptasia-specific inter-simple sequence repeat (ISSR)-derived sequence characterized amplified region (SCAR) marker and gene loci data, these four E. diaphana genotypes are distributed across several divergent phylogenetic clades with no clear phylogeographical pattern. The GBR E. diaphana genotypes comprised three females and one male, which all host Breviolum minutum as their homologous Symbiodiniaceae endosymbiont. When acclimating to an increase in light levels from 12 to 28 μmol photons m−2 s−1, the genotypes exhibited significant variation in maximum quantum yield of Symbiodiniaceae photosystem II and Symbiodiniaceae cell density. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes make these animals representative of global E. diaphana diversity and thus excellent model organisms. The addition of these GBR strains to the worldwide E. diaphana collection will contribute to cnidarian symbiosis research, particularly in relation to the climate resilience of coral reefs.

Dynamic Imaging of Moving Cells Based on DNA Nanotechnology

Nanostructures based on DNA self-assembly have made great progress in recent years, and have been widely used. Therefore, the research method of dynamic imaging of moving cells based on DNA nanotechnology is proposed. The dynamic imaging process of moving cells is studied from two kinds of DNA Nanotechnologies: DNA gene locus marker and DNA nano-fluorescence probe. Among them, crispr-cas9 system is used to mark DNA gene sites through in vitro fluorescent labeling of different sgRNAs, which can mark different gene sites in cells in multi-color and track gene sites in living cells dynamically; based on self-assembled CdTe quantum dot @ AnnexinV-DNA nanowire fluorescent probe, based on the DNA fitness of moving cells, the system is designed to be specific to target moving cells. The specific detection of motor cells can be realized by combining the sequences. The key point is to use the structural characteristics of the probe to realize the indication of the physiological changes of the drug receiving cells. The results show that: the polychromatic labeling of different gene sites in the same cell can be realized by using different fluorescent labeled sgRNA. By using fluorescent labeled telomere specific sgRNA to track the movement of telomeres in living cells, it can be seen from the movement track that in living cells, Ma SAT is more flexible than that in living cells. About 84.5% of Ma SAT is not mobile, but only 12.9% for telomere. Ma sat and the direction of telomere movement in the cell nucleus are random and in all directions. CdTe QD @ AnnexinV-DNA nanowire fluorescent probe can not only detect the moving cells, but also indicate the physiological state of normal and apoptotic cells at the same time. A large number of S7 ends of DNA allow the probe to firmly bind to the surface of Ramos cells in the way of "twine ball." The probe can indicate the physiological state of cells, and the corresponding characteristic emission wavelength changes with the change of target cell movement state. It shows that DNA nanotechnology can be used to analyze the dynamic imaging of moving cells in all directions and from multiple angles.

Validation of growth-related quantitative trait loci markers in different Exopalaemon carinicauda families for marker-assisted selection.

We detected growth-related QTL and associated markers from the backcross population of Exopalaemon carinicauda in the previous study. Based on our previous study, the 47 SNP markers associated with candidate growth trait QTL were selected to analyze the association between these markers and body weight (BW), body length and abdominal segment length traits in four different populations including wild population, a full-sib family, a half-sib family and a backcross population for evaluating their potential application of marker-assisted selection in E.carinicauda. The general linear model (GLM) and mixed linear model were applied and the associations between SNP loci and three growth-related traits verified. The results showed that the Marker79268 and Marker100644 were significantly associated with the BW trait in more than three populations by the GLM method. The Marker100644 was significantly associated with BW in the full-sib family, half-sib family and backcross populations by the GLM and mixed linear model methods. Our findings will provide useful SNP markers to go forward to improve growth performance through more refined marker-assisted selection in E.carinicauda.

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

BackgroundWet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population.ResultsThe average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg− 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg− 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg− 1 (RM7309–135 bp on chromosome 9) to 0.45 mg.mg− 1 (RM297–180 bp on chromosome 2). RM297–180 bp showed the largest phenotypic effect value (0.44 mg.mg− 1 in 2016 and 0.45 mg.mg− 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297–175 bp (0.43 mg.mg− 1 in 2016 and 0.44 mg.mg− 1 in 2017).ConclusionNine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

Detection of Adaptive Genetic Diversity in Wild Potato Populations and Its Implications in Conservation of Potato Germplasm

A better understanding on how genetic diversity is structured at natural habitats can be helpful for exploration and acquisition of plant germplasm. Historically, studies have relied on DNA markers to elucidate potato genetic diversity. Current advances in genomics are broadening applications allowing the identification of markers linked to genomic regions under selection. Those markers, known as adaptive markers, unlock additional ways to value and organize germplasm diversity. For example, conservation priorities could be given to germplasm units containing markers associated to unique geographic identity, and/or linked to traits of tolerance to abiotic stresses. This study investigated if adaptive marker loci were possible to be identified in a large AFLP marker dataset of ninety-four populations of the wild potato species S. fendleri. These populations originated from six different mountain ranges in southern Arizona, USA. A total of 2094 polymorphic AFLP markers were used to conduct genetic diversity analyses of populations and mountain ranges. Adaptive markers were detected using Bayesian methods which distinguished marker loci departing significantly from frequencies expected under neutral models of genetic differentiation. This identified 16 AFLP loci that were considered to be adaptive. To contrast diversity parameters generated with each set of markers, analyses that included all the 2094 AFLP markers, and only the 16 adaptive markers were conducted. The results showed that both were efficient for establishing genetic associations among populations and mountain ranges. However, adaptive markers were better on revealing geographic patterns and identity which would suggest these markers were linked to selection at the natural sites. An additional test to determine if adaptive markers associated to climate variables found two loci associated to specific climate variables in populations from different regions but sharing similar environmental structure. The distribution of adaptive markers among populations revealed that only two were needed to build a core subset able to keep all the markers. This preliminary assessment shows that adaptive genetic diversity could offer an additional way to measure diversity in potato germplasm and to set up options for conservation and research.

Grapevine Phenological Quantitative Trait SSR Genotyping Using High-Throughput HRM-PCR Analysis

Discrimination among grapevine varieties based on quantitative traits, such as flowering, veraison and ripening dates is crucial for variety selection in the context of climate change and in breeding programs. These traits are under complex genetic control for which 6 linked SSR loci (VVS2, VVIn16, VMC7G3, VrZAG29, VMC5G7, and VVIB23) have been identified. Using these markers in HRM-PCR analysis, we assessed genetic diversity among a large collection of 192 grapevine varieties. The grapevine germplasm used encompasses the majority of Greek vineyard with 181 varieties, 3 prominent foreign varieties and 11 varieties of Palestinian origin. The SSR markers used were highly polymorphic, displaying unique melting curves for unusually higher number of samples than generally observed in SSR analysis. This prompted us to examine sequence composition for selected samples and found that variation present as SNPs in the flanking sequences of SSR motifs was responsible for the observed polymorphism. Hence, HRM-PCR proved to be a tool of higher analytical power to distinguish genotypes surpassing the discrimination power of conventional gel-based SSR analysis. The study provides a better understanding of genetic variation of SSR marker loci associated to phenological traits in grapevine varieties, signifying an analytical methodology that may be of higher discrimination power in detection of polymorphism for utilization in breeding programs.

Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean.

Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 common bean (Phaseolus vulgaris) landraces and six commercial cultivars collected from 19 provinces of Turkey were evaluated for seed antioxidant activity under four environments and two locations. Antioxidant activity was measured using ABTS radical scavenging capacity and mean antioxidant activity in common bean landraces was 20.03 µmol TE/g. Analysis of variance reflected that genotype by environment interaction was statistically non-significant and heritability analysis showed higher heritability of antioxidant activity. Variations in seed color were observed, and a higher antioxidant activity was present in seeds having colored seed as compared to those having white seeds. A negative correlation was found between white-colored seeds and antioxidant activity. A total of 7900 DArTseq markers were used to explore the population structure that grouped the studied germplasm into two sub-populations on the basis of their geographical origins and trolox equivalent antioxidant capacity contents. Mean linkage disequilibrium (LD) was 54%, and mean LD decay was 1.15 Mb. Mixed linear model i.e., the Q + K model demonstrated that four DArTseq markers had significant association (p < 0.01) for antioxidant activity. Three of these markers were present on chromosome Pv07, while the fourth marker was located on chromosome Pv03. Among the identified markers, DArT-3369938 marker showed maximum (14.61%) variation. A total of four putative candidate genes were predicted from sequences reflecting homology to identified DArTseq markers. This is a pioneering study involving the identification of association for antioxidant activity in common bean seeds. We envisage that this study will be very helpful for global common bean breeding community in order to develop cultivars with higher antioxidant activity.

Genetic diversity of Brazil nut tree (Bertholletia excelsa Bonpl.) in southern Brazilian Amazon

Understanding genetic diversity is the basis of the evolutionary process of any species, as there are mechanisms that increase or reduce genetic variation. Brazil nut (Bertholletia excelsa Bonpl.) occurs in the Amazon region, and is included in the list of endangered species, justifying the importance of this study for the species. This study hypothesized that genetic diversity among individuals collected at different locations in the Amazon (between groups) is greater than genetic diversity between individuals from the same location (within groups). We aimed to study the genetic diversity of four populations of B. excelsa, located in native forests in the Amazon region of the state of Mato Grosso. DNAs were collected from 50 adult trees at each four sites, which were evaluated by seven microsatellite molecular markers (loci Bex06, Bet15, Bet14, Bex09 and Bet16). Genetic diversity of four Brazil nut tree populations collected in the Amazon region were assessed by microsatellite molecular markers. Brazil nut tree revealed to have greater genetic diversity between population than within in individuals in each population, suggesting that seed collection considering a larger number of matrices between a population than within populations is a more effective strategy. The most genetically distant populations were Itaúba and Juína, and Itaúba and Cotriguaçu, showing a relationship with geographical distance and also with differences found in fruit and seed characteristics already reported in other studies evaluating such populations. The findings of this study contribute to the establishment of the species breeding strategies that, in turn, ensure the maintenance and preservation of the genetic diversity of Brazil nut tree in southern Brazilian Amazon.

High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

Carrot (Daucus carota L.) is a versatile vegetable crop and the most economically important member of the Apiaceae family. While there are several important cultivated species in the family such as celery, parsley, cumin, fennel, coriander and parsnip, molecular genetic research in Apiaceae is relatively limited compared to other agriculturally important taxa. In the present work, an in silico approach was employed in order to develop chromosome-anchored simple sequence repeat (SSR) markers from the carrot genome assembly. A total of 55,386 markers were developed and marker loci that correspond to protein coding sequences were determined. In silico mapping analysis predicted that 51,160 of these were single-locus markers and 4,226 amplified more than one locus. Cross-species transferability of the markers was assessed using the fennel (Foeniculum vulgare Mill.) draft genome sequence, resulting in the identification of 578 low-copy transferable markers. These markers can serve for the purposes of interspecific genomic synteny studies and comparative gene identification/cloning. A subset of 50 markers was evaluated on DNA from 17 accessions of carrot. As a result, 46 (92%) produced amplicons from all genotypes, of which 28 (61%) displayed polymorphisms among the 17 carrot accessions, confirming the potential of the newly developed markers to reveal genotypic diversity in cultivated carrot. With the present work, carrot chromosomes were saturated with sequence-specific markers, which constitute a physical map of the carrot genome. The collection of markers will serve as practical molecular tools for germplasm characterization, gene tagging and molecular breeding studies in this important crop species.

Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BackgroundSouthern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs.ResultsWe characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency.ConclusionsOur results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

The utility of NBS-profiling for characterization of yellow rust resistance in an F6 durum wheat population

Seedling and adult plant (field) resistance to yellow rust in the durum wheat (Triticum turgidum ssp. durum) cross Kunduru-1149 x Cham-1 was characterized using a functionally-targeted DNA marker system, NBS-profiling. Chi-squared analysis indicated a four gene model conferring seedling yellow rust resistance against Puccinia striiformis f. sp. tritici isolate WYR85/22 (virulent on Yr2, Yr6, Yr7 and Yr9). Interval mapping located two QTL for yellow rust resistance on the long arm of chromosome 1B, while Kruskal-Wallis single marker regression identified a number of additional marker loci associated with seedling and/or adult plant, field resistance to yellow rust. These results suggested that much of the yellow rust resistance seen in the field may be due to seedling expressed resistance (R) genes. Characterization of the DNA sequence of three NBS marker loci indicated that all showed significant homology to functionally-characterized R-genes and resistance gene analogues (RGAs), with the greatest homology being NBS-LRR-type R-genes and RGAs from cereal species.