Marker Distance Research Articles

QTL mapping for branch- and leaf-related traits with a high-density SNP genetic map in litchi (Litchi chinensis Sonn.)

Litchi (Litchi chinensis Sonn.), an important fruit tree in tropical and subtropical regions, possesses substantial economic value. The branch- and leaf-related traits of litchi have a significant impact on litchi yield and quality. However, due to limitations such as the density of the genetic linkage map, there have been few studies on mapping QTLs of branch- and leaf-related traits. In this study, a high-density genetic map was constructed by next-generation sequencing (NGS) using an F1 population of 264 progenies, derived from the cross between the cultivars ‘Sanyuehong’ and ‘Ziniangxi’. A total of 2574 high-quality BINs (binomial intervals) were obtained, and a genetic linkage map was constructed with a total length of 1753.3 cM and an average marker distance of 0.68 cM. With the genetic map and the phenotyping of single leaf length (SLL), single leaf width (SLW), leaf shape index (LSI), weight of specific leaf (WSL), petiole length (PL) and compound leaf length (CLL) measured in three seasons, 11, 9, 9, 10, 9 and 12 QTLs were detected for SLL, SLW, WSL, LSI, PL and CLL traits, respectively. Among these QTLs, five QTLs were consistently detected in two seasons and 12 pleiotropic QTLs were identified for at least two traits. These findings will provide new insights for the gene cloning for branch- and leaf-related traits as well as marker-assisted selection (MAS).

New dynamic suture material for tendon transfer surgeries in the upper extremity – a biomechanical comparative analysis

BackgroundEarly mobilization after tendon surgery is crucial to avoid commonly observed postoperative soft tissue adhesions. Recently, a new suture was introduced (DYNACORD; DC) with a salt-infused silicone core designed to minimize laxity and preserve consistent tissue approximation in order to avoid gap formation and allow early mobilization.AimsTo compare the biomechanical competence of DC against a conventional high strength suture (FiberWire; FW) in a human cadaveric tendon transfer model with an early rehabilitation protocol.MethodsSixteen tendon transfers (flexor digitorum superficialis (FDS) IV to flexor pollicis longus (FPL)) were performed in 8 pairs human cadaveric forearms using either DC or FW. Markings were set 0.8 cm proximally and 0.7 cm distally to the level of the interweaving zone of the transfer. All specimens underwent repetitive thumb flexion against resistance in 9 intermittent series of 300 cycles each, simulating an aggressive postoperative rehabilitation protocol. After each series, the distance of the proximal marker to the interweaving zone (proximal), the length of the interweaving zone (intermediate) and the distance of the distal marker to the interweaving zone (distal) were measured.ResultsPooled data over all nine series, normalized to the immediate postoperative status, demonstrated no significant differences between FW and DC (p ≥ 0.355) for the proximal and distal markers. However, at the intermediate zone, DC was associated with significant length shortening (p < 0.001) compared to FW without significant length changes (p = 0.351). Load to catastrophic failure demonstrated significant higher forces in FW (p = 0.011). Nevertheless, due to failure mainly proximal or distal of the transfer zone, these loads are not informative.ConclusionFrom a biomechanical perspective, DC preserved tissue approximation and might be considered as a valid alternative to conventional high-strength sutures in tendon transfer surgery. DC might allow for a shorter interweaving zone and a more aggressive early postoperative rehabilitation program, possibly avoiding commonly observed postoperative soft tissue adhesions and stiffness.

Marker Set Configuration and Rigid Body Attitude Determination.

Image-based motion-analysis systems typically place markers on the bodies of interest. The error in determining segment attitude from these markers is a function the marker position errors, the number of markers, and the spatial distribution of the markers. The spatial distribution includes two factors: the mean square distance of these markers to their geometric center, and the degree of anisotropy in the marker distribution. The purposes of this study were to: (1) present a metric which quantifies the marker spatial distribution (anisotropic to isotropic) and (2) examine the influence of marker distribution on the accuracy of rigid body attitude determination. To test the influence of the marker distribution on body attitude determination 1000 criterion attitudes were determined. These attitudes then had to be estimated for two marker sets for which the marker distribution metric, noise levels, and root-mean-square distance of the markers were systematically varied. Anisotropic marker distributions were shown to negatively affect the accuracy of attitude determination. The influence of anisotropic marker distributions on attitude accuracy could be blunted by increasing the number of markers, increasing the root-mean-square distance of markers from their geometric center, and reducing noise levels. These results have implications for the measurement of the attitudes of body segments. For example, the ability to have a large spatial distribution of markers and a large number of markers to maximize the measurement accuracy of segment attitude is different for a small segment such as the fifth metacarpal compared with the thigh.

Evidence for cryptic sex in parthenogenetic stick insects of the genus Timema.

Obligately parthenogenetic species are expected to be short lived since the lack of sex and recombination should translate into a slower adaptation rate and increased accumulation of deleterious alleles. Some, however, are thought to have been reproducing without males for millions of years. It is not clear how these old parthenogens can escape the predicted long-term costs of parthenogenesis, but an obvious explanation is cryptic sex. In this study, we screen for signatures of cryptic sex in eight populations of four parthenogenetic species of Timema stick insects, some estimated to be older than 1 Myr. Low genotype diversity, homozygosity of individuals and high linkage disequilibrium (LD) unaffected by marker distances support exclusively parthenogenetic reproduction in six populations. However, in two populations (namely, of the species Timema douglasi and T. monikensis) we find strong evidence for cryptic sex, most likely mediated by rare males. These populations had comparatively high genotype diversities, lower LD, and a clear LD decay with genetic distance. Rare sex in species that are otherwise largely parthenogenetic could help explain the unusual success of parthenogenesis in the Timema genus and raises the question whether episodes of rare sex are in fact the simplest explanation for the persistence of many old parthenogens in nature.

1167 Assessing Femoral Cementing Qualities in Total Hip Replacements

Abstract Aim High quality cement mantles are important to the long-term survival of femoral stems in total hip replacements (THRs). There’s variability in the quality of cement mantles and positioning of cement restrictors. The audit aim was to assess current practice of cemented femoral stems in THRs against local standards. Method All patients who underwent THR with a cemented femoral stem between March 2021 and April 2022 were included in the study. TraumaCad software was used to retrospectively collect data on post-operative radiographs for overall cement mantle quality, coronal stem alignment, tip of stem to radio-opaque cement restrictor marker distance, and tip of stem to end of cement mantle distance (Gruen Zone 4). We audited against the following standards:90% of stems have Barrack and Harrison Grade A ratingKhalily angle &amp;lt;5°Tip of stem to radio-opaque marker of 20-40mmGruen zone 4 of 10-30mm Results 126 cemented femoral stems were included. Evaluation of Barrack grading showed 55% (N = 69) compliance with grade A, 45% (N = 57) of stems were grade B, with 0% grade C or D. Mean Khalily angle was 1.67° (98.4% compliance). Mean distance from tip of stem to cement restrictor was 36.5mm (60% compliance). Mean length of cement mantle in Gruen zone 4 was 18.9mm (71% compliance). Conclusions Overall, cement mantle quality and femoral stem coronal alignment were acceptable. There is variability of cement mantle thickness below the tip of the stem and with restrictor placement. We recommend re-auditing following junior surgeon cementing technique education.

The Construction of a High-Density Genetic Map for the Interspecific Cross of Castanea mollissima × C. henryi and the Identification of QTLs for Leaf Traits

Chinese chestnut is an economically and ecologically valuable tree species that is extensively cultivated in China. Leaf traits play a vital role in the photosynthetic capacity, chestnut yield, and quality, making them important breeding objectives. However, there has been limited research on constructing high-density linkage maps of Chinese chestnut and conducting quantitative trait loci (QTL) analyses for these leaf traits. This knowledge gap has hindered the progress of selection in Chinese chestnut breeding. In this study, we selected a well-established interspecific F1 population, consisting of Castanea mollissima ‘Kuili’ × C. henryi ‘YLZ1’, to construct comprehensive genetic maps for chestnut. Through the use of a genotyping-by-sequencing (GBS) technique, we successfully created a high-density linkage map based on single-nucleotide polymorphisms (SNPs) from the F1 cross. The results showed that 4578 SNP markers were identified in the genetic linkage map, and the total length was 1812.46 cM, which was distributed throughout 12 linkage groups (LGs) with an average marker distance of 0.4 cM. Furthermore, we identified a total of 71 QTLs associated with nine chestnut leaf traits: chlorophyll b content (chlb), stomatal conductance (Gs), leaf area (LA), leaf dry weight (LDW), leaf fresh weight (LFW), leaf length (LL), leaf width (LW), petiole length (PL), and specific leaf weight (SLW). These QTLs were identified based on phenotypic data collected from 2017 to 2018. Notably, among the 71 QTLs, 29 major QTLs were found to control leaf area (LA), leaf dry weight (LDW), and leaf width (LW). The high-density genetic mapping and QTL identification related to leaf traits in this study will greatly facilitate marker-assisted selection (MAS) in chestnut breeding programs.

A GBS-based genetic linkage map and quantitative trait loci (QTL) associated with resistance to Xanthomonas campestris pv. campestris race 1 identified in Brassica oleracea.

The production of Brassica oleracea, an important vegetable crop, is severely affected by black rot disease caused by the bacterial pathogen Xanthomonas campestris pv. campestris. Resistance to race 1, the most virulent and widespread race in B. oleracea, is under quantitative control; therefore, identifying the genes and genetic markers associated with resistance is crucial for developing resistant cultivars. Quantitative trait locus (QTL) analysis of resistance in the F2 population developed by crossing the resistant parent BR155 with the susceptible parent SC31 was performed. Sequence GBS approach was used to develop a genetic linkage map. The map contained 7,940 single nucleotide polymorphism markers consisting of nine linkage groups spanning 675.64 cM with an average marker distance of 0.66 cM. The F2:3 population (N = 126) was evaluated for resistance to black rot disease in summer (2020), fall (2020), and spring (2021). QTL analysis, using a genetic map and phenotyping data, identified seven QTLs with LOD values between 2.10 and 4.27. The major QTL, qCaBR1, was an area of overlap between the two QTLs identified in the 2nd and 3rd trials located at C06. Among the genes located in the major QTL interval, 96 genes had annotation results, and eight were found to respond to biotic stimuli. We compared the expression patterns of eight candidate genes in susceptible (SC31) and resistant (BR155) lines using qRT-PCR and observed their early and transient increases or suppression in response to Xanthomonas campestris pv. campestris inoculation. These results support the involvement of the eight candidate genes in black rot resistance. The findings of this study will contribute towards marker-assisted selection, additionally the functional analysis of candidate genes may elucidate the molecular mechanisms underlying black rot resistance in B. oleracea.

QTL detection and candidate gene analysis of grape white rot resistance by interspecific grape (Vitis vinifera L. × Vitis davidii Foex.) crossing.

Grape white rot, a devastating disease of grapevines caused by Coniella diplodiella (Speg.) Sacc., leads to significant yield losses in grape. Breeding grape cultivars resistant to white rot is essential to reduce the regular use of chemical treatments. In recent years, Chinese grape species have gained more attention for grape breeding due to their high tolerance to various biotic and abiotic factors along with changing climatic conditions. In this study, we employed whole-genome resequencing (WGR) to genotype the parents of 'Manicure Finger' (Vitis vinifera, female) and '0940' (Vitis davidii, male), along with 101 F1 mapping population individuals, thereby constructing a linkage genetic map. The linkage map contained 9337 single-nucleotide polymorphism (SNP) markers with an average marker distance of 0.3cM. After 3years of phenotypic evaluation of the progeny for white rot resistance, we confirmed one stable quantitative trait locus (QTL) for white rot resistance on chromosome 3, explaining up to 17.9% of the phenotypic variation. For this locus, we used RNA-seq to detect candidate gene expression and identified PR1 as a candidate gene involved in white rot resistance. Finally, we demonstrated that recombinant PR1 protein could inhibit the growth of C. diplodiella and that overexpression of PR1 in susceptible V. vinifera increased grape resistance to the pathogen.

Revisiting the genetic diversity and population structure of the endangered Green Sea Turtle (Chelonia mydas) breeding populations in the Xisha (Paracel) Islands, South China Sea.

The Green Sea Turtle (Chelonia mydas) is an umbrella species in the South China Sea, a Chinese national first-level protected wild animal, and the only sea turtle that nests in waters around China. The largest C. mydas nesting ground is distributed in the Xisha (Paracel) Islands, which plays a vital role in the survival of sea turtle populations in the region. This study reveals the genetic diversity and population structure of the breeding population of C. mydas in the Xisha (Paracel) Islands using three mitochondrial markers. A total of 15 D-loop, five Cytochrome b (Cyt b), and seven Cytochrome C Oxidase subunit I (COI) haplotypes were identified in the breeding population of C. mydas in the Xisha (Paracel) Islands. D-loop haplotypes are distributed in clades III, IV, and VIII of the C. mydas mitochondrial control region. It is the first time that one haplotype from Clade IV was found in this C. mydas population, and five new D-loop haplotypes were also identified. The haplotype and nucleotide diversity were calculated for each marker: D-loop (0.415 haplotype diversity, 0.00204 nucleotide diversity), Cyt b (0.140, 0.00038) and COI (0.308, 0.00083). The average genetic distance (p) of each molecular marker was less than 0.01. Neutral detection and nucleotide mismatch analysis suggested that the breeding population of C. mydas in the Xisha (Paracel) Islands did not experience a population expansion event in recent history. It is recommended that a sea turtle protection area be established in the Xisha (Paracel) Islands area to strengthen protection and effectively protect the uniqueness and sustainability of the breeding population of C. mydas in the South China Sea.

Construction of a high density genetic linkage map to define the locus conferring seedlessness from Mukaku Kishu mandarin.

Mukaku Kishu ('MK'), a small sized mandarin, is an important source of seedlessness in citrus breeding. Identification and mapping the gene(s) governing 'MK' seedlessness will expedite seedless cultivar development. In this study, two 'MK'-derived mapping populations- LB8-9 Sugar Belle® ('SB') × 'MK' (N=97) and Daisy ('D') × 'MK' (N=68) were genotyped using an Axiom_Citrus56 Array encompassing 58,433 SNP probe sets, and population specific male and female parent linkage maps were constructed. The parental maps of each population were integrated to produce sub-composite maps, which were further merged to develop a consensus linkage map. All the parental maps (except 'MK_D') had nine major linkage groups, and contained 930 ('SB'), 810 ('MK_SB'), 776 ('D') and 707 ('MK_D') SNPs. The linkage maps displayed 96.9 ('MK_D') to 98.5% ('SB') chromosomal synteny with the reference Clementine genome. The consensus map was comprised of 2588 markers including a phenotypic seedless (Fs)-locus and spanned a genetic distance of 1406.84 cM, with an average marker distance of 0.54 cM, which is substantially lower than the reference Clementine map. For the phenotypic Fs-locus, the distribution of seedy and seedless progenies in both 'SB' × 'MK' (55:42, χ2 = 1.74) and 'D' × 'MK' populations (33:35, χ2 = 0.06) followed a test cross pattern. The Fs-locus mapped on chromosome 5 with SNP marker 'AX-160417325' at 7.4 cM in 'MK_SB' map and between two SNP markers 'AX-160536283' and 'AX-160906995' at a distance of 2.4 and 4.9 cM, respectively in 'MK_D' map. The SNPs 'AX-160417325' and 'AX-160536283' correctly predicted seedlessness of 25-91.9% progenies in this study. Based on the alignment of flanking SNP markers to the Clementine reference genome, the candidate gene for seedlessness hovered in a ~ 6.0 Mb region between 3.97 Mb (AX-160906995) to 10.00 Mb (AX-160536283). This region has 131 genes of which 13 genes (belonging to seven gene families) reportedly express in seed coat or developing embryo. The findings of the study will prove helpful in directing future research for fine mapping this region and eventually underpinning the exact causative gene governing seedlessness in 'MK'.

QTL localisation of seed-related traits in Tibetan hulless barley based on a high-density single-nucleotide polymorphism genetic map

The effective use of high-quality and high-yielding germplasm resources is of great importance for the development of hulless barley varieties. Therefore, the search for such resources has long been a goal of the breeding community. In this study, a genotyping-by-sequencing (GBS) analysis was performed on an F2 (Nierumuzha × Kunlun 10) population. A high-density genetic map of hulless barley was constructed, which contained 1 475 efficient single-nucleotide polymorphism markers with 7 052 bin markers. The total length of the seven chromosomes was 1 139.4 cM, with an average marker distance of 0.59 cM. Based on this high-density linkage map, a total of 54 quantitative trait loci (QTLs) related to the seed traits were detected, including seed colour (SC), thousand kernel weight (TKW), seed average area (SAA), seed perimeter (SP), seed length (SL), seed width (SW), seed length/width (SLW), seed diameter (SD), and seed circular degree (SCD). These QTLs explained 3.32–35.73% (mean = 11.45%) of the phenotypic interpretation, including 24 main QTLs and 30 epistatic QTLs. A total of 24 candidate genes were identified within the QTL region, including one SC-associated transcription factor (ANT1), two TSW-related genes, a transcription factor (NAC021), a gene associated with the non-homologous end joining (NHEJ) pathway (ku70), three SAA-associated genes (LOL2, NAC021, TSK), two SL-associated genes (MADS21, MADS4), six SW-associated genes (FIP1, NAC021, DREB 1A, HVA22A, CYP78A6, SAUR71), five LW-related genes (NAM-B2, CRY1, LHY, CYP710A1, WRKY72), two SP-related genes (SKIP11, TCP18), two SD-related genes (NAC021, SKIP8), and three SCD-related genes (MYB1R1, RAX3, NAC100). These genes are involved in the regulation of the cell development, material transport, signal transduction, and plant morphogenesis and play an important role in the regulation of agronomic traits in hulless barley. The high-density genetic mapping and QTL identification of the seed traits in hulless barley provide a valuable genetic resource and the basis for further molecular marker-assisted selection and genomic studies.

The relation between body surface angle and apparel ease distribution under the motion state

PurposeThe purpose of this paper investigates dynamic ease distributions of clothes at bust and waist lines with different body surface angle by using a Qualisys three-dimensional motion capture system (3DMCS).Design/methodology/approachThe current method first obtain the specific markers of participants and their clothes along the bust and waist lines through 3DMCS, then using the least square method and four piecewise polynomial fitting participants and their clothes' bust and waist curves. The coordinates of the markers were tracked by the 3DMCS, while the participants under different body surface angle walked on a treadmill calculated the distances of markers coordinates to the participants' bust and waist curves. Finally, the data of samples were analyzed. It was found that the dynamic ease distributions showed different patterns at different body surface angle.FindingsThe results revealed the bust convex angle is 26.53 degrees (Specification:X3) and back slope angle is 13.96 degrees (Specification: Y1), the fluctuation of participant ease distributions on bust section was most obvious, and the maximum fluctuation value was ±20 mm and ±25 mm. The ease distributions of participant waist section fluctuated most obviously when the bust convex angle is 28.10 degrees (Specification: X5) and the back slope angle is 13.96 degrees (Specification: Y1), and the maximum fluctuation was ±30 mm and ±20 mm. The bust convex angle has the greatest influence on 1# garment, and the back slope angle has the greatest influence on 2# garment.Originality/valueCurrently, there is little information in the literature about dynamic ease distributions of garment on a different body types. This paper takes different body surface angles as the research objects to analyze the ease distributions of different clothes, the conclusion can provide reference data for 3D garment modeling and improve the authenticity of virtual garment fitting.

Correlation between the DNJ content and genetic diversity of SSR markers of 36 mulberry (Morus spp.) germplasm resources

1-deoxynojirimycin (DNJ) has certain medicinal value in lowering blood sugar, lowering blood fat, antiviral and anti-tumor, and Mulberry is one of known species with the highest DNJ content. To take full advantage of medicinal benefits of mulberry, the internal relationships of the genetic diversity of SSR markers and DNJ content was assessed in this study, so as to provide the basis for the exploitation and breeding of mulberry resources with high DNJ content. The results showed that the DNJ content in the leaves of the 36 mulberry germplasm resources varied significantly, with the mean value of 1.2794 mg/g, the amplitude of 1.03–1.61 g/g, and the coefficient of variation of 0.1276. Polymorphism was found in by 5 pairs of SSR primers from 36 mulberry germplasm resources, and a total of 32 genotypes were deteced. The mean allele number was 3.8, the mean heterozygosity was 0.62, the polymorphic information content of 0.61. Cluster analysis based on the genetic distance of SSR markers showed that the tested 36 mulberry germplasm resources could be divided into 3 class, and the analysis based on DNJ content showed that they could be divided into 2 clades. Comparison of the two cluster analyses displayed that the DNJ content in mulberry germplasm resources of the same group was similar. The above results revealed that the genetic diversity of SSR markers was similar to the genetic diversity of DNJ content in mulberry leaf.

High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: Hapalochlaena maculosa)

Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, H. maculosa, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent H. maculosa genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the H. maculosa linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for H. maculosa has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.

Tracking footprints of artificial and natural selection signatures in breeding and non-breeding cats

Stray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for aesthetic traits. Runs of homozygosity (ROH) and demographic measures are useful tools to discover chromosomal regions of recent selection and to characterize genetic diversity in domestic cat populations. To achieve this, we genotyped 150 stray and 26 household non-breeding cats (household) on the Illumina feline 63 K SNP BeadChip and compared them to SIAM and OSH. The 50% decay value of squared correlation coefficients (r2) in stray (0.23), household (0.25), OSH (0.24) and SIAM (0.25) corresponded to a mean marker distance of 1.12 Kb, 4.55 Kb, 62.50 Kb and 175.07 Kb, respectively. The effective population size (Ne) decreased in the current generation to 55 in stray, 11 in household, 9 in OSH and 7 in SIAM. In the recent generation, the increase in inbreeding per generation (ΔF) reached its maximum values of 0.0090, 0.0443, 0.0561 and 0.0710 in stray, household, OSH and SIAM, respectively. The genomic inbreeding coefficient (FROH) based on ROH was calculated for three length categories. The FROH was between 0.014 (FROH60) and 0.020 (FROH5) for stray, between 0.018 (FROH60) and 0.024 (FROH5) for household, between 0.048 (FROH60) and 0.069 (FROH5) for OSH and between 0.053 (FROH60) and 0.073 (FROH5) for SIAM. We identified nine unique selective regions for stray through genome-wide analyses for regions with reduced heterozygosity based on FST statistics. Genes in these regions have previously been associated with reproduction (BUB1B), motor/neurological behavior (GPHN, GABRB3), cold-induced thermogenesis (DIO2, TSHR), immune system development (TSHR), viral carcinogenesis (GTF2A1), host immune response against bacteria, viruses, chemoattractant and cancer cells (PLCB2, BAHD1, TIGAR), and lifespan and aging (BUB1B, FGF23). In addition, we identified twelve unique selective regions for OSH containing candidate genes for a wide range of coat colors and patterns (ADAMTS20, KITLG, TYR, TYRO3—a MITF regulator, GPNMB, FGF7, RAB38) as well as congenital heart defects (PDE4D, PKP2) and gastrointestinal disorders (NLGN1, ALDH1B1). Genes in stray that represent unique selective events indicate, at least in part, natural selection for environmental adaptation and resistance to infectious disease, and should be the subject of future research. Stray cats represent an important genetic resource and have the potential to become a research model for disease resistance and longevity, which is why we recommend preserving semen before neutering.

SNP-based high-density linkage map construction and QTL mapping of black spot disease resistance in Chinese sand pear.

Black spot disease (PBS) caused by Alternaria alternata is an economic disease of pear (Pyrus pyrifolia Nakai). Developing cultivars with durable PBS resistance traits is an important research objective for improving pear germplasm. The Deshengxiang is a popular pear variety in China and resistant to PBS. This study aimed to detect quantitative trait loci (QTL) associated with PBS resistance trait in pear and determine closely linked molecular markers by specific locus amplified fragment sequencing (SLAF-seq). F1 population resulting from a cross between "Deshengxiang" (female) and "Guiguan," a susceptible (male) variety, was developed and evaluated in 2016 and 2017. SLAF technology was used to discover SNPs in the F1 individuals and subsequently a high-density genetic linkage map for PBS resistance was constructed which contained 17,604 SNP markers. Based on the linkage map, the markers were distributed into 17 linkage groups, spanning 1548.48cM, with a mean marker distance of 0.09cM, representing the densest genetic map of the genus Pyrus. QTL analysis of PBS resistance identified a locus strongly related to PBS resistance at 77.68 ~ 112.99cM on linkage group 15, which was further narrowed down to 93.79 ~ 112.99cM. Two markers, Marker94293 and Marker94206, located at 97.47 and 102.93cM, were closely associated with PBS resistance, with a Δ (SNP index) value of 0.46. Co-localization of QTL interval, bioinformatics analysis, and functional annotation revealed PBS putative candidate genes. Overall, the high-density pear linkage map is a suitable reference for mapping PBS resistance trait, QTL, and genes identified in this study contribute information that could be useful for PBS improvement in pear.

An Experimental Study of a 3D Bone Position Estimation System Based on Fluoroscopic Images.

To compare a 3D preoperative planning image and fluoroscopic image, a 3D bone position estimation system that displays 3D images in response to changes in the position of fluoroscopic images was developed. The objective of the present study was to evaluate the accuracy of the estimated position of 3D bone images with reference to fluoroscopic images. Bone positions were estimated from reference points on a fluoroscopic image compared with those on a 3D image. The four reference markers positional relationships on the fluoroscopic image were compared with those on the 3D image to evaluate whether a 3D image may be drawn by tracking positional changes in the radius model. Intra-class correlations coefficients for reference marker distances between the fluoroscopic image and 3D image were 0.98–0.99. Average differences between measured values on the fluoroscopic image and 3D bone image for each marker corresponding to the direction of the bone model were 1.1 ± 0.7 mm, 2.4 ± 1.8 mm, 1.4 ± 0.8 mm, and 2.0 ± 1.6 mm in the anterior-posterior view, ulnar side lateral view, posterior-anterior view, and radial side lateral view, respectively. Marker positions were more accurate in the anterior-posterior and posterior-anterior views than in the radial and ulnar side lateral views. This system helps in real-time comparison of dynamic changes in preoperative 3D and intraoperative fluoroscopy images.

Linkage Disequilibrium, Haplotype Block Structures, Effective Population Size and Genome-Wide Signatures of Selection of Two Conservation Herds of the South African Nguni Cattle.

Simple SummaryKnowledge of linkage disequilibrium (LD), haplotypes blocks, and selective sweeps is important for effective application of genomics in breed characterization, improvement, and conservation, amongst other uses. The South African Nguni cattle breed is a Sanga breed that is well known for its ability to adapt to various environmental conditions such as harsh pedoclimatic and socio-economic conditions which exist in semiarid areas. Nguni cattle are characterized by many eco-types and research populations have been established in an effort to conserve the diversity within the breed by sampling in animals from different ecotypes into the herds. In this study, we calculated autosomal linkage disequilibrium, haplotype block structure, and screened for selection sweeps in two Nguni conservation herds of Bartlow Combine (n = 85) and Kokstad (n = 42), whose animals were genotyped on the Illumina High-Density Bovine SNP BeadChip®. The two herds were generally similar based on a number of genetic parameters. Overall, the study implied reduced genetic diversity in the two herds, calling for corrective measures to maintain the diversity of the South African Nguni cattle.The Nguni cattle of South Africa are a Sanga breed, characterized by many eco-types and research populations that have been established in an effort to conserve the diversity within the breed. The aim of this study was to investigate the overall genetic diversity as well as similarities and differences within and between two conservation herds of the South African Nguni Cattle. Mean LD (r2) estimates were 0.413 ± 0.219 for Bartlow Combine and 0.402 ± 0.209 for Kokstad. Genome-wide average LD (r2) decreased with increasing genetic marker distance for both populations from an average of 0.76 ± 0.28 and 0.77 ± 0.27 at 0–1 kb bin to 0.31 ± 0.13 and 0.32 ± 0.13 at 900–1000 kb bin in Bartlow Combine and Kokstad populations, respectively. Variation in LD levels across autosomes was observed in both populations. The results showed higher levels of LD than previously reported in Nguni field populations and other South African breeds, especially at shorter marker distances of less than 20 kb. A total number of 77,305 and 66,237 haplotype blocks covering a total of 1570.09 Mb (61.99% genome coverage) and 1367.42 Mb (53.96% genome coverage) were detected in Bartlow Combine and Kokstad populations, respectively. A total of 18,449 haploblocks were shared between the two populations while 58,856 and 47,788 haploblocks were unique to Bartlow Combine and Kokstad populations, respectively. Effective population size (Ne) results demonstrated a rapid decrease in Ne across generations for both Bartlow Combine and Kokstad conservation herds. Two complementary methods, integrated haplotype score (iHS) and Extend Haplotype Homozygosity Test (XP-EHH), were implemented in this study to detect the selection signatures in the two herds. A total of 553 and 166 selected regions were identified in Bartlow Combine and Kokstad populations, respectively. DAVID and GO terms analysis of the regions under selection reported genes/QTLs associated with fertility, carcass weight, coat colour, immune response, and eye area pigmentation. Some genes, such as HCAR1, GNAI1, PIK3R3, WNT3, RAB5A, BOLA-N (Class IB MHC Antigen QA-2-Related), BOLA (Class IB MHC Antigen QA-2-Related), and Rab-8B, etc., were found in regions under selection in this study. Overall, the study implied reduced genetic diversity in the two herds calling for corrective measures to maintain the diversity of the South African Nguni cattle. This study presented a comprehensive analysis of the genomic architecture of South African Nguni cattle populations, providing essential genetic information of utility in the management of conservation flocks.

GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.).

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi , threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%–18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.

Fiducial marker position affects target volume in stereotactic lung irradiation.

PurposeReal‐time tracking systems of moving respiratory targets such as CyberKnife, Radixact, or Vero4DRT are an advanced robotic radiotherapy device used to deliver stereotactic body radiotherapy (SBRT). The internal target volume (ITV) of lung tumors is assessed through a fiducial marker fusion using four‐dimensional computed tomography (CT). It is important to minimize the ITV to protect normal lung tissue from exposure to radiation and the associated side effects post SBRT. However, the ITV may alter if there is a change in the position of the fiducial marker with respect to the tumor. This study investigated the relationship between fiducial marker position and the ITV in order to prevent radiation exposure of normal lung tissue, and correct target coverage.Materials and methodsThis study retrospectively reviewed 230 lung cancer patients who received a fiducial marker for SBRT between April 2015 and September 2021. The distance of the fiducial marker to the gross tumor volume (GTV) in the expiratory (d ex) and inspiratory (d in) CT, and the ratio of the ITV/V(GTVex), were investigated.ResultsUpon comparing each lobe, although there was no significant difference in the d diff and the ITV/V(GTVex) between all lobes for d ex < 10 mm, there was significant difference in the d diff and the ITV/V(GTVex) between the lower and upper lobes for d ex ≥ 10 mm (p < 0.05). Moreover, there was significant difference in the d diff and the ITV/V(GTVex) between d ex ≥10 mm and d ex < 10 mm in all lung regions (p < 0.05).ConclusionThe ITV that had no margin from GTVs increased when d ex was ≥10 mm for all lung regions (p < 0.05). Furthermore, the increase in ITV tended to be greater in the lower lung lobe. These findings can help decrease the possibility of adverse events post SBRT, and correct target coverage.