Genomic prediction of agronomic traits in wheat using different models and cross-validation designs.

KEY MESSAGE: Genomic predictions across environments and within populations resulted in moderate to high accuracies but across-population genomic prediction should not be considered in wheat for small population size. Genomic selection (GS) is a marker-based selection suggested to improve the genetic gain of quantitative traits in plant breeding programs. We evaluated the effects of training population (TP) composition, cross-validation design, and genetic relationship between the training and breeding populations on the accuracy of GS in spring wheat (Triticum aestivum L.). Two populations of 231 and 304 spring hexaploid wheat lines that were phenotyped for six agronomic traits and genotyped with the wheat 90 K array were used to assess the accuracy of seven GS models (RR-BLUP, G-BLUP, BayesB, BL, RKHS, GS + de novo GWAS, and reaction norm) using different cross-validation designs. BayesB outperformed the other models for within-population genomic predictions in the presence of few quantitative trait loci (QTL) with large effects. However, including fixed-effect marker covariates gave better performance for an across-population prediction when the same QTL underlie traits in both populations. The accuracy of prediction was highly variable based on the cross-validation design, which suggests the importance to use a design that resembles the variation within a breeding program. Moderate to high accuracies were obtained when predictions were made within populations. In contrast, across-population genomic prediction accuracies were very low, suggesting that the evaluated models are not suitable for prediction across independent populations. On the other hand, across-environment prediction and forward prediction designs using the reaction norm model resulted in moderate to high accuracies, suggesting that GS can be applied in wheat to predict the performance of newly developed lines and lines in incomplete field trials.

Fusarium Head Blight in Durum Wheat: Recent Status, Breeding Directions, and Future Research Prospects.

Fusarium head blight (FHB) is a major fungal disease affecting wheat production worldwide. Since the early 1990s, FHB, caused primarily by Fusarium graminearum, has become one of the most significant diseases faced by wheat producers in Canada and the United States. The increasing FHB problem is likely due to the increased adoption of conservation tillage practices, expansion of maize production, use of susceptible wheat varieties in rotation, and climate variability. Durum wheat (Triticum turgidum sp. durum) is notorious for its extreme susceptibility to FHB and breeding for resistance is complicated because sources of FHB resistance are rare in the primary gene pool of tetraploid wheat. Losses due to this disease include yield, test weight, seed quality, food and feed quality, and when severe, market access. More importantly, it is the contamination with mycotoxins, such as deoxynivalenol, in Fusarium-infected durum kernels that causes the most serious economic as well as food and feed safety concerns. Several studies and thorough reviews have been published on germplasm development and breeding for FHB resistance and the genetics and genomics of FHB resistance in bread or common wheat (T. aestivum); however, similar reviews have not been conducted in durum wheat. Thus, the aim of this review is to summarize and discuss the recent research efforts to mitigate FHB in durum wheat, including quantitative trait locus mapping, genome-wide association studies, genomic prediction, mutagenesis and characterization of genes and pathways involved in FHB resistance. It also highlights future directions, FHB-resistant germplasm, and the potential role of morphological traits to enhance FHB resistance in durum wheat.

A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping.

BACKGROUND: Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. RESULTS: High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments. CONCLUSIONS: The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

Absorbable Biosynthetic Scaffolds in Place of Silicone for Breast Reconstruction: A 9-Year Experience with 53 Patients.

Background: Few series report on using fat grafting as the primary form of breast reconstruction. A 9-year experience with absorbable biosynthetic scaffolds, used in place of silicone implants, for breast reconstruction is reviewed. Methods: A clinical quality improvement approach was used to evaluate real-world data on a single plastic surgeon's experience treating breast reconstruction patients over a 7-year period. Results: Fifty-three patients had 74 breasts reconstructed, (following 51 therapeutic mastectomies and 23 prophylactic). Five of the 51 breasts (9.80 %) developed a local recurrence (mean follow-up of 4.5-5.5 years). This compared favorably with the practice's previous 6 years of silicone reconstructions. The most common complications were benign fat necrosis and oil cysts. More than 100 radiologic examinations were performed without interference by the absorbable implants. By 12-18 months post implantation, very little immune response was seen on histologic examinations of the biosynthetic scaffold constructs. Mature collagen and robust vascularity characterized the "mesh zone," whereas regenerated adipose tissue was seen in between and on top of the folded sheets of the implants. The average number of fat graft sessions in immediate reconstructions was 2.3, with a mean total fat graft volume of 551 mL, to restore an average mastectomy defect volume of 307 mL. Aesthetic outcomes were much better in the immediate reconstruction of nipple-sparing mastectomy group, which saw 68% achieve an A/B grade; 19%, C grade; and 13%, D/F on subjective grading. Conclusion: This composite strategy, using biosynthetic scaffold and autologous fat grafting, yielded outcomes equivalent to flap reconstructions with the ease of implants.

Identification of novel QTL for resistance to Fusarium head blight in a tetraploid wheat population.

Most tetraploid durum wheat (Triticum turgidum L var. durum) cultivars are susceptible to Fusarium head blight (FHB). This study reports novel quantitative trait loci (QTL) associated with FHB resistance. A backcross recombinant inbred line (BCRIL) population was developed from the cross BGRC3487/2*DT735, and 160 lines were evaluated for resistance to Fusarium graminearum Schwabe (teleomorph Gibberella zeae (Schwein. Petch) in field trials over 3 years (2008-2010) and to a F. graminearum 3-acetyl-deoxynivalenol (3-ADON) chemotype in greenhouse trials. The population was genotyped with 948 polymorphic loci using DArT and microsatellite markers. Eleven QTL were associated with FHB resistance under field conditions on chromosomes 2A, 3B, 5A, 5B, 7A, and 7B. Two of these, QFhb.usw-3B from BGRC3487 and QFhb.usw-7A2, were consistently detected over environments. The QFhb.usw-3B QTL was in a similar position to a resistance QTL in hexaploid wheat. The combination of the two QTL reduced field index by 53.5%-86.2%. Two QTL for resistance to the 3-ADON chemotype were detected on chromosomes 1B and 4B. Both BGRC3487 and DT735 could provide new sources of FHB resistance and the combination of QTL reported here could be valuable tools in breeding FHB-resistant durum wheat.

A new species of Philoria (Anura: Limnodynastidae) from the uplands of the Gondwana Rainforests World Heritage Area of eastern Australia.

The six species of mountain frogs (Philoria: Limnodynastidae: Anura) are endemic to south-eastern Australia. Five species occur in headwater systems in mountainous north-eastern New South Wales (NSW) and south-eastern Queensland (Qld), centred on the Gondwana Rainforests of Australia World Heritage Area. A previous molecular genetic analysis identified divergent genetic lineages in the central and western McPherson Ranges region of Qld and NSW, but sampling was inadequate to test the species status of these lineages. With more comprehensive geographic sampling and examination of the nuclear genome using SNP analysis, we show that an undescribed species, P. knowlesi sp. nov., occurs in the central and western McPherson Ranges (Levers Plateau and Mount Barney complex). The new species is not phylogenetically closely related to P. loveridgei in the nuclear data but is related to one of two divergent lineages within P. loveridgei in the mtDNA data. We postulate that the discordance between the nuclear and mtDNA outcomes is due to ancient introgression of the mtDNA genome from P. loveridgei into the new species. Male advertisement calls and multivariate morphological analyses do not reliably distinguish P. knowlesi sp. nov. from any of the Philoria species in northeast NSW and southeast Qld. The genetic comparisons also enable us to define further the distributions of P. loveridgei and P. kundagungan. Samples from the Lamington Plateau, Springbrook Plateau, Wollumbin (Mt Warning National Park), and the Nightcap Range, are all P. loveridgei, and its distribution is now defined as the eastern McPherson Ranges and Tweed caldera. Philoria kundagungan is distributed from the Mistake Mountains in south-eastern Qld to the Tooloom Scrub on the Koreelah Range, southwest of Woodenbong, in NSW, with two subpopulations identified by SNP analysis. We therefore assessed the IUCN threat category of P. loveridgei and P. kundagungan and undertook new assessments for each of its two subpopulations and for the new taxon P. knowlesi sp. nov., using IUCN Red List criteria. Philoria loveridgei, P. kundagungan (entire range and northern subpopulation separately) and P. knowlesi sp. nov. each meet criteria for Endangered (EN B2(a)(b)[i, iii]). The southern subpopulation of P. kundagungan, in the Koreelah Range, meets criteria for Critically Endangered (CE B2(a)(b)[i, iii]). These taxa are all highly threatened due to the small number of known locations, the restricted nature of their breeding habitat, and direct and indirect threats from climate change, and the potential impact of the amphibian disease chytridiomycosis. Feral pigs are an emerging threat, with significant impacts now observed in Philoria breeding habitat in the Mistake Mountains.

A Systematic Review of Durum Wheat: Enhancing Production Systems by Exploring Genotype, Environment, and Management (G × E × M) Synergies.

According to the UN-FAO, agricultural production must increase by 50% by 2050 to meet global demand for food. This goal can be accomplished, in part, by the development of improved cultivars coupled with modern best management practices. Overall, wheat production on farms will have to increase significantly to meet future demand, and in the face of a changing climate that poses risk to even current rates of production. Durum wheat [Triticum turgidum L. ssp. durum (Desf.)] is used largely for pasta, couscous and bulgur production. Durum producers face a range of factors spanning abiotic (frost damage, drought, and sprouting) and biotic (weed, disease, and insect pests) stresses that impact yields and quality specifications desired by export market end-users. Serious biotic threats include Fusarium head blight (FHB) and weed pest pressures, which have increased as a result of herbicide resistance. While genetic progress for yield and quality is on pace with common wheat (Triticum aestivum L.), development of resistant durum cultivars to FHB is still lagging. Thus, successful biotic and abiotic threat mitigation are ideal case studies in Genotype (G) × Environment (E) × Management (M) interactions where superior cultivars (G) are grown in at-risk regions (E) and require unique approaches to management (M) for sustainable durum production. Transformational approaches to research are needed in order for agronomists, breeders and durum producers to overcome production constraints. Designing robust agronomic systems for durum demands scientific creativity and foresight based on a deep understanding of constitutive components and their innumerable interactions with each other and the environment. This encompasses development of durum production systems that suit specific agro-ecozones and close the yield gap between genetic potential and on-farm achieved yield. Advances in individual technologies (e.g., genetic improvements, new pesticides, seeding technologies) are of little benefit until they are melded into resilient G × E × M systems that will flourish in the field under unpredictable conditions of prairie farmlands. We explore how recent genetic progress and selected management innovations can lead to a resilient and transformative durum production system.

Breast Reconstruction Using a Three-Dimensional Absorbable Mesh Scaffold and Autologous Fat Grafting: A Composite Strategy Based on Tissue-Engineering Principles.

Breast reconstruction remains an important field in plastic surgery, with most procedures using implants and/or autologous tissue. Few series report on experience with fat grafting as the primary form of breast reconstruction. The present article describes a new method of breast reconstruction using a three-dimensional absorbable mesh construct-or Lotus scaffold-and autologous fat grafting. A retrospective review was performed for all patients who underwent breast reconstruction using the Lotus scaffold and autologous fat grafting. Postoperative mammograms and magnetic resonance imaging scans were analyzed. Tissue specimens collected at subsequent procedures were harvested and stained with hematoxylin and eosin for histologic evaluation. Lastly, compression testing of the scaffold was performed using a tensiometer and digital tracking technology. Twenty-two patients underwent reconstruction of 28 breasts using the Lotus scaffold and autologous fat grafting between February of 2015 and February of 2018. Average follow-up was 19 months. All patients were satisfied with final breast shape and size. Mean patient age was 60.5 years and the average body mass index was 28 kg/m. Patients required on average two fat grafting sessions to achieve a successful result (range, zero to four). Postoperative mammography and magnetic resonance imaging showed robust adipose tissue in the breast with a slowly resorbing mesh and no oil cysts or calcifications. Histologic evaluation showed the presence of fat tissue around the scaffold and no evidence of capsule formation. Compression testing revealed the Lotus scaffold to be compliant with a high-resilience profile. The Lotus scaffold with autologous fat grafting is a viable method for breast reconstruction, giving the patient an autologous reconstruction with less morbidity compared to free tissue transfer. CLINICAL QUESTION/LEVEL OF EVIDENCE:: Therapeutic, IV.

Markers to a common bunt resistance gene derived from 'Blizzard' wheat (Triticum aestivum L.) and mapped to chromosome arm 1BS.

Common bunt, caused by Tilletia caries (DC.) Tul. & C. Tul. and T. laevis J.G Kuhn, is an economically important disease of wheat (Triticum aestivum L.) worldwide. The resistance in the winter wheat cultivar 'Blizzard' is effective against known races of common bunt in western Canada. The incorporation of resistance from Blizzard into field-ready cultivars may be accelerated through the use of molecular markers. Using the maize pollen method, a doubled haploid population of 147 lines was developed from the F(1) of the second backcross of Blizzard (resistant) by breeding line '8405-JC3C' (susceptible). Doubled haploid lines were inoculated at seeding with race T19 or T19 and L16 and disease reaction was examined under controlled conditions in 1999 and natural conditions in 2002, and 2003. Resistant:susceptible-doubled haploid lines segregated in a 1:1 ratio for bunt reaction, indicating single major gene segregation. Microsatellite primers polymorphic on the parents were screened on the population. Initial qualitative segregation analysis indicated that the wheat microsatellite markers Xgwm374, Xbarc128 and Xgwm264, located on wheat chromosome 1BS, were significantly linked to the resistance locus. Qualitative results were confirmed with quantitative trait locus analysis. The genetic distance, calculated with JoinMap, between the bunt resistance locus and overlapping markers Xgwm374, Xgwm264 and Xbarc128 was 3.9 cM. The three markers were validated on doubled haploid populations BW337/P9502&DAF1BB and Blizzard/P9514-AR17A3E evaluated for common bunt reaction in the growth chamber in 2007. These markers will be useful in selecting for the common bunt resistance from Blizzard and assist in identifying the resistance among potential new sources of resistance.

Durum wheat genome highlights past domestication signatures and future improvement targets.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

Anatomy of the Superficial Fascia System of the Breast: A Comprehensive Theory of Breast Fascial Anatomy.

BACKGROUND: It has been two centuries since Petrus Camper identified superficial fascia and over 175 years since Sir Astley Cooper wrote his book on the anatomy of the breast. In the 1990s, Ted Lockwood taught us the importance of the superficial fascia layers in body contouring procedures he pioneered. These descriptions, however, fail to explain the three-dimensional fascial system in the breast. The authors set out to discover and describe a theory of superficial fascia structures responsible for breast shape. METHODS: The nature of the superficial fascia system that surrounds the breast and its attachments to the chest were studied in 12 cadaver breast dissections and in clinical cases of both cosmetic and reconstructive breast procedures. RESULTS: The authors found a three-dimensional, closed system of fascia and fat surrounding the corpus mammae, which attaches to the skin by means of specialized vertical cutaneous ligaments, or Cooper ligaments, and which attaches to the chest wall by means of a three-dimensional zone of adherence at the breast's periphery. CONCLUSIONS: The breast is shaped by a three-dimensional, fibrofatty fascial system. Two layers of this system surround the corpus mammae and fuse together around it, and anchor it to the chest wall in a structure we have called the circummammary ligament.

Acute Exposure to Low-to-Moderate Carbon Dioxide Levels and Submariner Decision Making.

BACKGROUND: Submarines routinely operate with higher levels of ambient carbon dioxide (CO2) (i.e., 2000 - 5000 ppm) than what is typically considered normal (i.e., 400 - 600 ppm). Although significant cognitive impairments are rarely reported at these elevated CO2 levels, recent studies using the Strategic Management Simulation (SMS) test have found impairments in decision-making performance during acute CO2 exposure at levels as low as 1000 ppm. This is a potential concern for submarine operations, as personnel regularly make mission-critical decisions that affect the safety and efficiency of the vessel and its crew while exposed to similar levels of CO2. The objective of this study was to determine if submariner decision-making performance is impacted by acute exposure to levels of CO2 routinely present in the submarine atmosphere during sea patrols. METHODS: Using a subject-blinded balanced design, 36 submarine-qualified sailors were randomly assigned to receive 1 of 3 CO2 exposure conditions (600, 2500, or 15,000 ppm). After a 45-min atmospheric acclimation period, participants completed an 80-min computer-administered SMS test as a measure of decision making. RESULTS: There were no significant differences for any of the nine SMS measures of decision making between the CO2 exposure conditions. DISCUSSION: In contrast to recent research demonstrating cognitive deficits on the SMS test in students and professional-grade office workers, we were unable to replicate this effect in a submariner population-even with acute CO2 exposures more than an order of magnitude greater than those used in previous studies that demonstrated such effects.Rodeheffer CD, Chabal S, Clarke JM, Fothergill DM. Acute exposure to low-to-moderate carbon dioxide levels and submariner decision making. Aerosp Med Hum Perform. 2018; 89(6):520-525.

Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height.

Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.

Genetic analysis of resistance to stripe rust in durum wheat (Triticum turgidum L. var. durum).

Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to stripe rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for stripe rust resistance were identified on chromosome 7B (LOD 6.87-11.47) and chromosome 5B (LOD 3.88-9.17). The QTL for stripe rust resistance on chromosome 7B was supported in the breeding panel. Both QTL were anchored to the genome sequence of wild emmer wheat, which identified gene candidates involved in disease resistance. Exome capture sequencing identified variation in the candidate genes between Kofa and W9262-260D3. These genetic insights will be useful in durum breeding to enhance resistance to stripe rust.

High density genetic mapping of Fusarium head blight resistance QTL in tetraploid wheat.

Breeding for Fusarium head blight (FHB) resistance in durum wheat is complicated by the quantitative trait expression and narrow genetic diversity of available resources. High-density mapping of the FHB resistance quantitative trait loci (QTL), evaluation of their co-localization with plant height and maturity QTL and the interaction among the identified QTL are the objectives of this study. Two doubled haploid (DH) populations, one developed from crosses between Triticum turgidum ssp. durum lines DT707 and DT696 and the other between T. turgidum ssp. durum cv. Strongfield and T. turgidum ssp. carthlicum cv. Blackbird were genotyped using the 90K Infinium iSelect chip and evaluated phenotypically at multiple field FHB nurseries over years. A moderate broad-sense heritability indicated a genotype-by-environment interaction for the expression of FHB resistance in both populations. Resistance QTL were identified for the DT707 × DT696 population on chromosomes 1B, 2B, 5A (two loci) and 7A and for the Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B with the QTL on chromosome 1A and those on chromosome 5A being more consistently expressed over environments. FHB resistance co-located with plant height and maturity QTL on chromosome 5A and with a maturity QTL on chromosome 7A for the DT707 × DT696 population. Resistance also co-located with plant height QTL on chromosomes 2A and 3A and with maturity QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Additive × additive interactions were identified, for example between the two FHB resistance QTL on chromosome 5A for the DT707 × DT696 population and the FHB resistance QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Application of the Single Nucleotide Polymorphic (SNP) markers associated with FHB resistance QTL identified in this study will accelerate combining genes from the two populations.

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.

Correction: Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.

[This corrects the article DOI: 10.1371/journal.pone.0170941.].

High density mapping and haplotype analysis of the major stem-solidness locus SSt1 in durum and common wheat.

Breeding for solid-stemmed durum (Triticum turgidum L. var durum) and common wheat (Triticum aestivum L.) cultivars is one strategy to minimize yield losses caused by the wheat stem sawfly (Cephus cinctus Norton). Major stem-solidness QTL have been localized to the long arm of chromosome 3B in both wheat species, but it is unclear if these QTL span a common genetic interval. In this study, we have improved the resolution of the QTL on chromosome 3B in a durum (Kofa/W9262-260D3) and common wheat (Lillian/Vesper) mapping population. Coincident QTL (LOD = 94-127, R2 = 78-92%) were localized near the telomere of chromosome 3BL in both mapping populations, which we designate SSt1. We further examined the SSt1 interval by using available consensus maps for durum and common wheat and compared genetic to physical intervals by anchoring markers to the current version of the wild emmer wheat (WEW) reference sequence. These results suggest that the SSt1 interval spans a physical distance of 1.6 Mb in WEW (positions 833.4-835.0 Mb). In addition, minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that were found to synergistically enhance expression of SSt1 to increase stem-solidness. These results suggest that developing new wheat cultivars with improved stem-solidness is possible by combining SSt1 with favorable alleles at minor loci within both wheat species.

Components separation technique and laparoscopic approach: a review of two evolving strategies for ventral hernia repair.

When faced with large ventral hernias, surgeons frequently must choose between higher incidence of recurrence after primary repair and higher incidence of wound complications after repair with mesh. The aim of this study is to compare early outcomes between laparoscopic repair (LR) and components separation technique (CST), two evolving strategies for the management of large ventral hernias. We reviewed 42 consecutive patients who underwent CST and 45 consecutive patients who underwent LR of ventral hernia defects of at least 12 cm2. Demographics, hernia characteristics, and short-term outcomes were compared between groups. Patients in the LR group were younger (53 +/- 2 vs 68 +/- 2 years, P < 0.0001), had greater body mass index (34 +/- 2 vs 29 +/- 1 kg/m2, P = 0.02), and had larger hernia defects (318 +/- 49 vs 101 +/- 16 cm2, P < 0.0001) than patients in the CST group. The LR resulted in shorter length of hospital stay (4.9 +/- 0.9 vs 9.6 +/- 1.8 days, P < 0.0001), lower incidence of ileus (7% vs 48%, P < 0.0001), and lower incidence of wound complications (2% vs 33%, P < 0.001) than the CST. Both techniques resulted in similar operative times, transfusion requirements, and mortality. Recurrences occurred in 7 per cent of patients at mean follow-up of 16 months in the CST group and 0 per cent at mean follow-up of 9 months after LR. The LR may have a short-term advantage over the CST in terms of incidence of ileus, wound complications, and hospital stay. Because of their unique advantage over traditional hernia repairs, both techniques may play a significant role in the future treatment of large ventral hernias. Adequate training will be essential for the safe and effective implementation of these techniques within the surgical community.