Linkage Disequilibrium Mapping Research Articles

Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.).

Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.

Integrating polygenic risk scores into clinical breast cancer models: Influence on prediction in diverse cohorts.

10506 Background: Breast cancer (BC) is the second leading cause of cancer death in women worldwide. Periodic mammography screening has been shown to reduce breast cancer mortality by around 20% in average-risk women and several BC risk models are currently used to identify women at higher risk who can be targeted with increased or earlier screening. However, despite their broad use, these models display only moderate discrimination performance (AUC ranging between 0.51 to 0.68). Here we explore the potential of integrating PRS into a BC risk model using a testing dataset comprising over 175,000 women of diverse ancestry in the UK Biobank and Women Health’s Initiative Cohorts. Methods: We built and validated novel ancestry-specific BC PRSs utilizing novel methodology that leverage multiple Genome Wide Association Studies (GWASs) and linkage disequilibrium maps. We assessed genetic ancestry from 5 continental level ancestry groups across all individuals and applied the PRSs to our testing dataset to assess the clinical implications of integrating genetic information to the Tyrer-Cuzick (TC) breast cancer clinical risk model. Results: The PRSs were well calibrated and displayed high risk stratification (Odds Ratios per Standard Deviation: 1.41 (1.28-1.62) to 1.76 (1.40-2.20; Table) which were comparable or better than benchmarking comparisons with previously published PRS panels. Across genetic ancestries, integrating PRS led to a relative increase of women identified at high lifetime BC risk (20% or higher) from between 1.7 fold (East-Asian ancestry) to around 3 fold (European ancestry). The Net Reclassification Improvement compared to the TC-only model was around 12% for East-Asian (0.001-0.254), European (0.111-0.133), and Admixed American ancestries (0.002-0.228), 17% (0.079-0.266) for South-Asians, and 5% (0.008-0.094) for African ancestry individuals (Table). Conclusions: Our results demonstrate that optimizing PRSs for genetic ancestries and integrating them into BC risk models can lead to a significant improvement in risk stratification. This can enable more targeted use of enhanced screening and prevention strategies improving their cost/benefit ratio.[Table: see text]

The association between vitamin D receptor polymorphism and phases of chronic hepatitis B infection in HBV carriers in Thailand.

Vitamin D receptor (VDR) polymorphism partly regulates the immune system and is associated with hepatic flare in chronic Hepatitis B virus infection (HBV). Our study identified the association between two distinct phases, VDR polymorphisms and HBV inactive carrier (IC) and chronic hepatitis (CH). Chronic HBV patients were enrolled from February to August 2020. An HBV viral load (VL) < 2,000 IU/ml twice for 6 months apart, with no prior history of HBV treatment, defined the IC phase. Six common polymorphisms in the VDR gene, including CdX-2, GATA, FokI, Bsml, ApaI, and TaqI, were studied using real-time PCR. The different outcomes in allele, genotype, and haplotype frequencies in between groups and linkage disequilibrium (LD) mapping were analyzed. Among 324 enrolled patients, there were 163 patients in IC and 161 patients in CH phases. The mean vitamin D levels were not statistically different between groups. The proportion of allele frequencies of CdX-2 in IC and CH was 53.7% and 62.7% for G allele, and 46.3% and 37.3% for A allele (p 0.019). The proportion of GG genotype of CdX-2 was less frequently found in patients with IC compared to that in patients with CH (27% vs 41%, p 0.028). By multivariate analysis, CdX-2 G/A genotypes were independently associated with IC, with adjusted odd ratio (OR) 1.83 (1.10-3.04), p 0.019. The LD mapping of single nucleotide polymorphisms (SNP) revealed high LD scores in Bsml/ApaI/TaqI (BAT) haplotype in both groups while, CdX-2/GATA and GATA/FokI demonstrated high LD score only in CH group. CdX-2 G/A genotypes were independently associated with IC status in Thai patients with chronic HBV infection. The difference in LD of the CdX-2/GATA and GATA/FokI haplotypes in between groups may represent a non-random selection resulting in the variation of immune control.

Pleiotropic Effects of APOB Variants on Lipid Profiles, Metabolic Syndrome, and the Risk of Diabetes Mellitus

Apolipoprotein B (ApoB) plays a crucial role in lipid and lipoprotein metabolism. The effects of APOB locus variants on lipid profiles, metabolic syndrome, and the risk of diabetes mellitus (DM) in Asian populations are unclear. We included 1478 Taiwan Biobank participants with whole-genome sequence (WGS) data and 115,088 TWB participants with Axiom genome-wide CHB array data and subjected them to genotype-phenotype analyses using APOB locus variants. Five APOB nonsynonymous mutations, including Asian-specific rs144467873 and rs13306194 variants, were selected from participants with the WGS data. Using a combination of regional association studies, a linkage disequilibrium map, and multivariate analysis, we revealed that the APOB locus variants rs144467873, rs13306194, and rs1367117 were independently associated with total, low-density lipoprotein (LDL), and non-high-density lipoprotein (non-HDL) cholesterol levels; rs1318006 was associated with HDL cholesterol levels; rs13306194 and rs35131127 were associated with serum triglyceride levels; rs144467873, rs13306194, rs56213756, and rs679899 were associated with remnant cholesterol levels; and rs144467873 and rs4665709 were associated with metabolic syndrome. Mendelian randomization (MR) analyses conducted using weighted genetic risk scores from three or two LDL-cholesterol-level-associated APOB variants revealed significant association with prevalent DM (p = 0.0029 and 8.2 × 10-5, respectively), which became insignificant after adjustment for LDL-C levels. In conclusion, these results indicate that common and rare APOB variants are independently associated with various lipid levels and metabolic syndrome in Taiwanese individuals. MR analyses supported APOB variants associated with the risk of DM through their associations with LDL cholesterol levels.

The Genetic Architecture of Juvenile Growth Traits in the Conifer Torreya grandis as Revealed by Joint Linkage and Linkage Disequilibrium Mapping.

Despite its high economical and ornamental values, Torreya grandis, a dioecious non-timber coniferous species, has long been an underrepresented species. However, the advent and application of advanced genotyping technologies have stimulated its genetic research, making it possible to gain new insight into the genetic architecture of complex traits that may not be detected for model species. We apply an open-pollination (OP) mapping strategy to conduct a QTL mapping experiment of T. grandis, in which nearly 100 unrelated trees randomly chosen from the species’ natural distribution and their half-sib progeny are simultaneously genotyped. This strategy allows us to simultaneously estimate the recombination fractions and linkage disequilibrium (LD) coefficients between each pair of markers. We reconstruct a high-density linkage map of 4,203 SNPs covering a total distance of 8,393.95 cM and plot pairwise normalized LD values against genetic distances to build up a linkage-LD map. We identify 13 QTLs for stem basal diameter growth and 4 QTLs for stem height growth in juvenile seedlings. From the linkage-LD map, we infer the evolutionary history of T. grandis and each of its QTLs. The slow decay of QTL-related LDs indicates that these QTLs and their harboring genomic regions are evolutionarily relatively young, suggesting that they can better utilized by clonal propagation rather than through seed propagation. Genetic results from the OP sampling strategy could provide useful guidance for genetic studies of other dioecious species.

Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits

Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits

Linkage disequilibrium mapping: A journey from traditional breeding to molecular breeding in crop plants

Germplasms are the reservoir of agronomically important traits traditionally maintained by various tribal communities over the year. Maintaining these germplasms generations after generations has little value unless exploited for the desired agronomic traits like biotic and abiotic stress, yield attributes and nutritional enrichment. Association mapping, otherwise called linkage disequilibrium mapping, is a molecular breeding approach for characterizing complex traits with agronomic importance in crop plants. It is a systematic method for identifying novel traits and is treated as an alternative tool to traditional QTL mapping approaches, which involves correlating molecular markers with the phenotypic trait in a diversified population. The map's resolution in association mapping is based on the candidate-gene approach or genome-wide association approach. Therefore, association mapping studies offer a great perspective on crop genetic improvement. Still, considerably large-scale research is required to determine the sensible implementation of association mapping analysis in most crop plants. Currently, there is considerable interest in using association mapping approaches in crop breeding programs, which can be achieved by advanced genomic technology and the development of statistical computer software packages. Here, the linkage disequilibrium approach and its usefulness in association mapping studies, including the steps associated with it are discussed. The current status and future challenges in complex trait dissection by utilizing the linkage disequilibrium mapping in crop plants are also discussed.

Identification of a unique allele in the quantitative trait locus for crown root number in &lt;i&gt;japonica&lt;/i&gt; rice from Japan using genome-wide association studies

To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.

Molecular mapping of QTLs for fiber quality traits in Gossypium hirsutum multi-parent recombinant inbred lines

Cotton is a valuable fiber crop which supplies raw material to more than 50 industries and is produced in more than 70 countries worldwide. The superiority of cotton fiber over other crops is primarily dependent on its quality. However, further improvements in fiber length and strength are required for modern processing technology and for cotton to maintain its position in the global market. Association mapping enables identification of QTLs controlling fiber quality-related traits which can be useful in cotton breeding. In the present study, we performed genetic diversity, linkage disequilibrium and association mapping analyses in 157 G. hirsutum multi-parent recombinant inbred lines using a total of 102 SSR markers. The population had depressed genetic variability (14%), a result of inbreeding of modern cotton genotypes. Despite this, we identified 11 significant and stable marker-trait associations for seed cotton yield, lint percentage, fiber length and fiber strength (p < 0.005). We also detected QTL co-localizations with positive and negative marker additive effects. Our results indicate that selection against negative alleles may be as important as selection for positive alleles. Analysis of the effects of allelic combinations at different QTLs revealed significant and stable marker clusters that can be selected for or against to provide maximum quality gains in cotton fiber quality.

Genetic analysis of QTLs controlling allelopathic characteristics in sorghum.

Mature sorghum herbage is known to contain several water-soluble secondary metabolites (allelochemicals). In this study, we investigated quantitative trait loci (QTLs) associated with allelochemical characteristics in sorghum using linkage mapping and linkage disequilibrium (LD)-based association mapping. A sorghum diversity research set (SDRS) of 107 accessions was used in LD mapping whereas, F2:3 lines derived from a cross between Japanese and African landraces were used in linkage mapping. The QTLs were further confirmed by positional (targeted) association mapping with Q+K model. The inhibitory effect of water-soluble extracts (WSE) was tested on germination and root length of lettuce seedlings in four concentrations (25%, 50%, 75% and 100%). A Significant range of variations was observed among genotypes in both types of mapping populations (P < 0.05). A total of 181 simple sequence repeats (SSRs) derived from antecedently reported map have been used for genotyping of SDRS. A genetic linkage map of 151 sorghum SSR markers was also developed on 134 F2 individuals. The total map length was 1359.3 cM, with an average distance of 8.2 cM between adjacent markers. LD mapping identified three QTLs for inhibition effect on germination and seven QTLs for root length of lettuce seedlings. Whereas, a total of six QTLs for inhibition of germination and ten QTLs for root length were detected in linkage mapping approach. The percent phenotypic variation explained by individual QTL ranged from 6.9% to 27.3% in SDRS and 9.9% to 35.6% in F2:3 lines. Regional association analysis identified four QTLs, three of them are common in other methods too. No QTL was identified in the region where major gene for sorgoleone (SOR1) has been cloned previously on chromosome 5.

Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions.

We utilized 2300 wheat accessions including worldwide landraces, cultivars and primary synthetic-derived germplasm with three Australian cultivars: Annuello, Yitpi and Correll, to investigate field-based resistance to leaf (Lr) rust, stem (Sr) rust and stripe (Yr) rust diseases across a range of Australian wheat agri-production zones. Generally, the resistance in the modern Australian cultivars, synthetic derivatives, South and North American materials outperformed other geographical subpopulations. Different environments for each trait showed significant correlations, with average r values of 0.53, 0.23 and 0.66 for Lr, Sr and Yr, respectively. Single-trait genome-wide association studies (GWAS) revealed several environment-specific and multi-environment quantitative trait loci (QTL). Multi-trait GWAS confirmed a cluster of Yr QTL on chromosome 3B within a 4.4-cM region. Linkage disequilibrium and comparative mapping showed that at least three Yr QTL exist within the 3B cluster including the durable rust resistance gene Yr30. An Sr/Lr QTL on chromosome 3D was found mainly in the synthetic-derived germplasm from Annuello background which is known to carry the Agropyron elongatum 3D translocation involving the Sr24/Lr24 resistance locus. Interestingly, estimating the SNP effects using a BayesR method showed that the correlation among the highest 1% of QTL effects across environments (excluding GWAS QTL) had significant correlations, with average r values of 0.26, 0.16 and 0.55 for Lr, Sr and Yr, respectively. These results indicate the importance of small effect QTL in achieving durable rust resistance which can be captured using genomic selection.

Are scurs in heterozygous polled (Pp) cattle a complex quantitative trait?

BackgroundBreeding genetically hornless, i.e. polled, cattle provides an animal welfare-friendly and non-invasive alternative to the dehorning of calves. However, the molecular regulation of the development of horns in cattle is still poorly understood. Studying genetic characters such as polledness and scurs, can provide valuable insights into this process. Scurs are hornlike formations that occur occasionally in a wide variety of sizes and forms as an unexpected phenotype when breeding polled cattle.MethodsWe present a unique dataset of 885 Holstein–Friesian cattle with polled parentage. The horn phenotype was carefully examined, and the phenotypic heterogeneity of the trait is described. Using a direct gene test for polledness, the polled genotype of the animals was determined. Subsequently, the existence of a putative scurs locus was investigated using high-density genotype data of a selected subset of 232 animals and two mapping approaches: mixed linear model-based association analyses and combined linkage disequilibrium and linkage analysis.ResultsThe results of an exploratory data analysis indicated that the expression of scurs depends on age at phenotyping, sex and polled genotype. Scurs were more prevalent in males than in females. Moreover, homozygous polled animals did not express any pronounced scurs and we found that the Friesian polled allele suppresses the development of scurs more efficiently than the Celtic polled allele. Combined linkage and linkage disequilibrium mapping revealed four genome-wide significant loci that affect the development of scurs, one on BTA5 and three on BTA12. Moreover, suggestive associations were detected on BTA16, 18 and 23. The mixed linear model-based association analysis supports the results of the combined linkage and linkage disequilibrium analysis. None of the mapping approaches provided convincing evidence for a monogenic inheritance of scurs.ConclusionsOur results contradict the initial and still broadly accepted model for the inheritance of horns and scurs. We hypothesise an oligogenetic model to explain the development of scurs and polledness.

Linkage disequilibrium mapping of high-throughput image-derived descriptors of plant architecture traits under field conditions

Plant architectural traits are important factors in determining grain and biomass productivity of sorghum (Sorghum bicolor (L) Moench). However, collecting data on these architectural traits is labor-intensive and time-consuming, especially when using numerous lines in quantitative genetic studies or breeding programs. Therefore, we used the high-throughput field-based robotic platform PhenoBot 1.0 to collect whole canopy stereo images from a large association mapping panel under field conditions. These images were used to create a plot-based 3D reconstruction of the canopy from which phenotypic features were automatically extracted. These features included: plot-based plant height (PPH), plot-based plant width (PPW), plant surface area (PSA), and convex-hull volume (CHV). A small sub-set of sorghum lines were used to obtain ground-truth measurements to validate the image-derived descriptors, and determine their biological significance. PPH was highly correlated with manually measured plant height; PPW correlated with SinAL, defined as leaf length multiplied by the sine of its angle; PSA was associated with manually measured total plant surface area; and CHV was a function of both flag-leaf height and SinAL. Association mapping of PPH identified chromosomal regions containing known plant height genes, confirming the accuracy of the automatic feature extraction process. For the other phenotypic features, significant markers were identified within genomic regions that have been previously reported to control plant architectural characteristics in sorghum such as tiller number, shoot compactness, leaf length, surface area, and angle. The image processing method used in this study contributes new knowledge to the development of high-throughput phenotyping techniques and represents a novel tool for plant breeders.

Gene-dense autosomal chromosomes show evidence for increased selection.

Purifying selection tends to reduce nucleotide and haplotype diversity leading to increased linkage disequilibrium. However, detection of evidence for selection is difficult as the signature is confounded by wide variation in the recombination rate which has a complex relationship with selection. The effective bottleneck time (the ratio of the linkage disequilibrium map to the genetic map in Morgans) controls for variability in the recombination rate. Reduced effective bottleneck times indicate stronger residual linkage disequilibrium, consistent with increased selection. Using whole genome sequence data from one European and three Sub-Saharan African human populations we find, in the African samples, strong correlations between high gene densities and reduced effective bottleneck time for autosomal chromosomes. This suggests that gene-dense autosomes have been subject to increased purifying selection reducing effective bottleneck times compared to gene-poor autosomes. Although previous studies have shown unusually strong linkage disequilibrium for the sex chromosomes variation within the autosomes has not been recognised. The strongest relationship is between effective bottleneck time and the density of essential genes, which are likely targets of greater selective pressure (p = 0.006, for the 22 autosomes). The magnitude of the reduction in chromosome-specific effective bottleneck times from the least to the most gene-dense autosomes is ~17-21% for Sub-Saharan African populations. The effect size is greater in Sub-Saharan African populations, compared to a European sample, consistent with increased efficiency of selection in populations with larger effective population sizes which have not been subject to intense population bottlenecks as experienced by populations of European ancestry. The findings highlight the value of deeper analyses of selection within Sub-Saharan African populations.

Linkage disequilibrium and haplotype block patterns in popcorn populations.

Linkage disequilibrium (LD) analysis provides information on the evolutionary aspects of populations. Recently, haplotype blocks have been used to increase the power of quantitative trait loci detection in genome-wide association studies and the prediction accuracy of genomic selection. Our objectives were as follows: to compare the degree of LD, LD decay, and LD decay extent in popcorn populations; to characterize the number and length of haplotype blocks in the populations; and to determine whether maize chromosomes also have a pattern of interspaced regions of high and low rates of recombination. We used a biparental population, a synthetic, and a breeding population, genotyped for approximately 75,000 single nucleotide polymorphisms (SNPs). The sample size ranged from 190 to 192 plants. For the whole-genome LD and haplotype block analyses, we assumed a window of 500 kb. To characterize the block and step patterns of LD in the populations, we constructed LD maps by chromosome, defining a cold spot as a chromosome segment including SNPs with the same LDU position. The LD and haplotype block analyses were also performed at the intragenic level, selecting 12 genes related to zein, starch, cellulose, and fatty acid biosynthesis. The populations with the higher and lower frequencies of |D'| values greater than 0.75 were the biparental (65–74%) and the breeding population (26–58%), respectively. There were slight differences between the populations regarding the average distance for SNPs with |D'| values greater than 0.75 (in the range of approximately 207 to 229 kb). The level of LD expressed by the r2 values was low in the populations (0.02, 0.04, and 0.04, on average) but comparable to some non-isolated human populations. The frequency of r2 values greater than 0.75 was lower in the biparental population (0.2–0.5%) and higher in the other populations (0.2–1.6%). The average distance for SNPs with r2 values greater than 0.75 was much higher in the biparental population (approximately 80 to 126 kb). In the other populations, the ranges were approximately 6 to 19 and 6 to 35 kb. The heatmaps for the regions covered by the first 100 SNPs in each chromosome, in each population (1 to 3.3 Mb, approximately), provided evidence that the comparatively few high r2 values (close to 1.0) occurred only for SNPs in close proximity, especially in the synthetic and breeding populations. Due to the reduced number of SNPs in the haplotype blocks (2 to 3) in the populations, it is not expected advantage of a haplotype-based association study as well as genomic selection along generations. The results concerning LD decay (rapid decay after 5–10 kb) and LD decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. The LD maps indicate that maize chromosomes had a pattern of regions of extensive LD interspaced with regions of low LD. However, our simulated LD map provides evidence that this pattern can reflect regions with differences in allele frequencies and LD levels (expressed by |D'|) and not regions with high and low rates of recombination.

Heterogeneity in the extent of linkage disequilibrium among exonic, intronic, non-coding RNA and intergenic chromosome regions.

Whole-genome sequence data enable construction of high-resolution linkage disequilibrium (LD) maps revealing the LD structure of functional elements within genic and subgenic sequences. The Malecot-Morton model defines LD map distances in linkage disequilibrium units (LDUs), analogous to the centimorgan scale of linkage maps. For whole-genome sequence-derived LD maps, we introduce the ratio of corresponding map lengths kilobases/LDU to describe the extent of LD within genome components. The extent of LD is highly variable across the genome ranging from ~38 kb for intergenic sequences to ~858 kb for centromeric regions. LD is ~16% more extensive in genic, compared with intergenic sequences, reflecting relatively increased selection and/or reduced recombination in genes. The LD profile across 18,268 autosomal genes reveals reduced extent of LD, consistent with elevated recombination, in exonic regions near the 5' end of genes but more extensive LD, compared with intronic sequences, across more centrally located exons. Genes classified as essential and genes linked to Mendelian phenotypes show more extensive LD compared with genes associated with complex traits, perhaps reflecting differences in selective pressure. Significant differences between exonic, intronic and intergenic components demonstrate that fine-scale LD structure provides important insights into genome function, which cannot be revealed by LD analysis of much lower resolution array-based genotyping and conventional linkage maps.

Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.).

Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.

The Challenge of Genome Sequence Assembly

Background: Although whole genome sequencing is enabling numerous advances in many fields achieving complete chromosome-level sequence assemblies for diverse species presents difficulties. The problems in part reflect the limitations of current sequencing technologies. Chromosome assembly from ‘short read’ sequence data is confounded by the presence of repetitive genome regions with numerous similar sequence tracts which cannot be accurately positioned in the assembled sequence. Longer sequence reads often have higher error rates and may still be too short to span the larger gaps between contigs. Objective: Given the emergence of exciting new applications using sequencing technology, such as the Earth BioGenome Project, it is necessary to further develop and apply a range of strategies to achieve robust chromosome-level sequence assembly. Reviewed here are a range of methods to enhance assembly which include the use of cross-species synteny to understand relationships between sequence contigs, the development of independent genetic and/or physical scaffold maps as frameworks for assembly (for example, radiation hybrid, optical motif and chromatin interaction maps) and the use of patterns of linkage disequilibrium to help position, orient and locate contigs. Results and Conclusion: A range of methods exist which might be further developed to facilitate cost-effective large-scale sequence assembly for diverse species. A combination of strategies is required to best assemble sequence data into chromosome-level assemblies. There are a number of routes towards the development of maps which span chromosomes (including physical, genetic and linkage disequilibrium maps) and construction of these whole chromosome maps greatly facilitates the ordering and orientation of sequence contigs.

SNPSelect: A scalable and flexible targeted sequence-based genotyping solution.

In plant breeding the use of molecular markers has resulted in tremendous improvement of the speed with which new crop varieties are introduced into the market. Single Nucleotide Polymorphism (SNP) genotyping is routinely used for association studies, Linkage Disequilibrium (LD) and Quantitative Trait Locus (QTL) mapping studies, marker-assisted backcrosses and validation of large numbers of novel SNPs. Here we present the KeyGene SNPSelect technology, a scalable and flexible multiplexed, targeted sequence-based, genotyping solution. The multiplex composition of SNPSelect assays can be easily changed between experiments by adding or removing loci, demonstrating their content flexibility. To demonstrate this versatility, we first designed a 1,056-plex maize assay and genotyped a total of 374 samples originating from an F2 and a Recombinant Inbred Line (RIL) population and a maize germplasm collection. Next, subsets of the most informative SNP loci were assembled in 384-plex and 768-plex assays for further genotyping. Indeed, selection of the most informative SNPs allows cost-efficient yet highly informative genotyping in a custom-made fashion, with average call rates between 88.1% (1,056-plex assay) and 99.4% (384-plex assay), and average reproducibility rates between duplicate samples ranging from 98.2% (1056-plex assay) to 99.9% (384-plex assay). The SNPSelect workflow can be completed from a DNA sample to a genotype dataset in less than three days. We propose SNPSelect as an attractive and competitive genotyping solution to meet the targeted genotyping needs in fields such as plant breeding.

Joint linkage and linkage disequilibrium mapping reveals association of BRMS1L with total teat number in a large intercross between Landrace and Korean native pigs

Previously, we reported a quantitative trait locus (QTL) that affects total teat number (TTN) on pig chromosome 7 (SSC7) in a large F2 intercross population between Landrace and Korean native pigs. The aim of this study was to refine the QTL associated with TTN and to identify positional candidate gene(s) within the refined genomic region. TTN was recorded in 1105 F2 progeny. All experimental animals were genotyped using 980 informative single nucleotide polymorphism (SNP) markers located on SSC7. A haplotype-based linkage and association analysis using the PHASEBOOK programme was applied to refine the QTL region. Additionally, linear mixed-effect models were used to assess the effect of a positional candidate gene on TTN and other economically important traits [i.e., thoracic vertebrae number (THO), carcass body length (CBL) and weight (CW), back fat thickness (BFT) and intramuscular fat content (IMF) in loin muscles]. Joint linkage and association analysis refined the critical region to a 4.50 Mb region that included a novel positional candidate gene, BRMS1L that encodes the breast cancer metastasis-suppressor 1-like protein, which could possibly be implicated in normal mammary gland development. Significant association of an SNP marker (g. −1087 G > A) in the 5′-flanking region of BRMS1L with TTN (P = 1.10 × 10−8), THO (P = 5.80 × 10−4), and CBL (P = 0.038) was observed. Based on these data, we propose BRMS1L as a positional candidate gene for TTN in pigs. After validation of the association in other independent populations, these results could be useful in optimizing breeding programmes that improve TTN and other economically important traits in swine.