Linkage Groups Research Articles

Phenotypic features, transcriptomic signatures and genomic regions associated with body ellipticity in the flatfish Senegalese sole

Body shape is a complex and plastic trait with a high impact on fish performance and commercialization. Shape is particularly relevant in flatfish with highly asymmetric bodies. In this study we investigated the skeleton features, transcriptomic profiles and genomic regions in two Senegalese sole groups from a full-sib family with positive (named as HE) or negative (LE) breeding values for body ellipticity (ELL). Soles from HE group were heavier and displayed more elongated bodies than LE. A skeleton analysis showed that HE had a higher number of vertebrae, longer vertebral bodies and intervertebral spaces and a lower incidence of skeletal fusions than LE. With respect to the gender effect, females showed a higher height of ventral body and some differences in the ratio urostyle to skeleton length than males for similar ELL values. The PCA analysis using 28 dimensionless morphological traits indicated that PC1 and PC2 explained 51.3% of the total variance and they were mainly associated with ELL and gender variation, respectively. Expression analysis using two factors (ELL and gender) revealed a major effect of gender in muscle, pterygiophores and liver with 6764, 6506 and 7559 differentially expressed transcripts (DETs) between sexes, respectively. In brain, only 16 DETs were identified. When HE and LE were compared controlling by gender, we identified the subset of DETs with conserved responses in both sexes or those regulated in a sex-specific manner in each tissue. A comparison across tissues identified 31 ubiquitous transcripts as differentially expressed in at least two of them. Functional analysis showed that liver and pterygiophores had the highest number of enriched gene ontology categories (24 and 14, respectively). Some of these enriched pathways were related to regulation of cell cycle, cell structure and shape, locomotory behavior, immune system, hormonal responses and homeostasis. A BSR-Seq analysis confirmed five significant genomic windows associated with ELL by using the tricube-smoothed G' and Fst statistics. Windows located in linkage groups (LG) 5 and LG14 included the malt1 and vtg3 genes, respectively, that were also detected within the subset of ubiquitous DETs. Moreover, malt1 appeared located very close to the bmpr1b gene within the significance hotspot of LG5 indicating that mediators of the inflammatory responses and BMP signaling pathway could be responsible for the differences found in the skeleton features and body ellipticity.

Genome-wide association analysis to identify genomic regions and predict candidate genes for bunch traits in grapes (Vitis vinifera L.)

Grape quality traits like bunch and berry size are important as they influence consumer acceptance and marketability of the produce. Therefore, a deeper understanding of their genetic determinant is crucial for varietal improvement. In this study, association mapping was performed using SNP marker data and three season phenotyping data of 122 diverse grapevine genotypes. Genotyping by sequencing (GBS) identified 1,08,777 high quality SNPs distributed on all the chromosomes. A good correlation was observed across three seasons for berry size and bunch length. Genome-wide association analysis using six different models identified significantly associated SNPs for each of the traits. We identified 13 significant SNPs associated with bunch length, seven of them were located on linkage groups (LGs) 9 and 15. For berry diameter, 18 significantly associated markers located on LGs 4, 5, 17 and six other LGs were identified. Fourteen SNPs mainly on linkage groups 3 and 5 were identified for berry weight. Three closely linked markers on LG3 explaining about 20-25 % variation suggested presence of major QTL for berry weight on LG3. Candidate genes were mined in the genomic regions containing significant SNPs explaining large phenotypic variation. Twenty-one genes for bunch length, 28 genes for berry length, 22 genes for berry diameter and 25 genes for berry weight were predicted. Several predicted genes were found to have function related to cell enlargement, cell morphogenesis and other physiological processes required for cell growth and development.

LsMybW-encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed

Key messageWe identified LsMybW as the allele responsible for the shift in color from black to white seeds in wild ancestors of lettuce to modern cultivars.Successfully selected white seeds are a key agronomic trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black—in its wild ancestor—to white seeds remains uncertain. We aimed to identify the gene/s responsible for white seed trait in lettuce. White seeds accumulated less proanthocyanidins than black seeds, similar to the phenotype observed in Arabidopsis TT2 mutants. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F2 population derived from a cross between “ShinanoPower” (white) and “Escort” (black). The white seed trait was controlled by a single recessive locus (48.055–50.197 Mbp) in linkage group 7. Using five PCR-based markers and numerous cultivars, eight candidate genes were mapped in the locus. Only the LG7_v8_49.251Mbp_HinfI marker, employing a single-nucleotide mutation in the stop codon of Lsat_1_v5_gn_7_35020.1, was completely linked to seed color phenotype. In addition, the coding region sequences for other candidate genes were identical in the resequence analysis of “ShinanoPower” and “Escort.” Therefore, we proposed Lsat_1_v5_gn_7_35020.1 as the candidate gene and designated it as LsMybW (Lactuca sativaMyb White seeds), an ortholog encoding the R2R3-MYB transcription factor in Arabidopsis. When we validated the role of LsMybW through genome editing, LsMybW knockout mutants harboring an early termination codon showed a change in seed color from black to white. Therefore, LsMybW was the allele responsible for the shift in seed color. The development of a robust marker for marker-assisted selection and identification of the gene responsible for white seeds have implications for future breeding technology and physiological analysis.

Identification of sex locus and a male-specific marker in blunt-snout bream (Megalobrama amblycephala) using a whole genome resequencing method

Fish sex is often associated with its economic traits, such as growth and body color. The mechanism of fish sex determination is always a hot spot for scientific research. Fish is one of the most diverse groups of vertebrates, and its sex determination mechanism is diverse and complex. Blunt-snout bream (BSB), belonging to Cyprinidae and the genus Megalobrama, is an important economic fish in China. Ordinary consumers are more inclined to buy male fish that does not carry eggs, hence the preparation of this all-male group of BSB meets the needs of the industry. In this study, we applied a whole genome resequencing approach to search sex-linked markers and better characterized sex determination in this fish. Our results confirmed that BSB uses a male heterogametic (XX/XY) system. Individuals from two populations including 10 males and 10 females were sequenced using a whole genomic sequencing method. A large potential sex differentiated region with approximately 6 Mb at the beginning of linkage group (LG) 9 of female BSB genome was identified using genome comparative analysis. This region contained a high density of male-biased genetic polymorphisms and harbored 275 genes, whereas reported sex-related genes didn't exist in this region. With the help of male genome, some male-biased sequences were identified using genome-wide associated analysis, and subsequently a male-specific marker was developed. Our results exhibited that BSB had a considerably large sex locus on LG9, which was likely sex chromosome of this species. Moreover, we developed a male-specific marker for BSB. Our study not only is of great practical significance to the development of sex-controlled breeding technology, but also is of theoretical significance to further explore the sex determination mechanism in fish.

Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors.

Living in the intertidal environment, littorinid snails are excellent models for understanding genetic mechanisms underlying adaptation to harsh fluctuating environments. Furthermore, the karyotypes of littorinid snails, with the same chromosome number as the presumed bilaterian ancestor, make them valuable for investigating karyotype evolution from the bilaterian ancestor to mollusks. Here, we generated high-quality, chromosome-scale genome assemblies for 2 littorinid marine snails, Littorina brevicula (927.94 Mb) and Littoraria sinensis (882.51 Mb), with contig N50 of 3.43 Mb and 2.31 Mb, respectively. Comparative genomic analyses identified 92 expanded gene families and 85 positively selected genes as potential candidates possibly associated with intertidal adaptation in the littorinid lineage, which were functionally enriched in stimulus responses, innate immunity, and apoptosis process regulation and might be involved in cellular homeostasis maintenance in stressful intertidal environments. Genome macrosynteny analyses indicated that 4 fissions and 4 fusions led to the evolution from the 17 presumed bilaterian ancestral chromosomes to the 17 littorinid chromosomes, implying that the littorinid snails have a highly conserved karyotype with the bilaterian ancestor. Based on the most parsimonious reconstruction of the common ancestral karyotype of scallops and littorinid snails, 3 chromosomal fissions and 1 chromosomal fusion from the bilaterian ancient linkage groups were shared by the bivalve scallop and gastropoda littorinid snails, indicating that the chromosome-scale ancient gene linkages were generally preserved in the mollusk genomes for over 500 million years. The highly conserved karyotype makes the littorinid snail genomes valuable resources for understanding early bilaterian evolution and biology.

Narrowing down a major QTL region reveals Phytochrome E (PHYE) as the candidate gene controlling flowering time in mungbean (Vigna radiata).

Flowering time is an important agronomic trait that is highly correlated with plant height, maturity time and yield in mungbean. Up to present, however, molecular basis of flowering time in mungbean is poorly understood. Previous studies demonstrated that flowering time in mungbean is largely controlled by a major QTL on linkage group 2 (LG2). In this study, the QTL on the LG2 in mungbean was investigated using F2 and F2:3 populations derived from a cross between mungbean cultivar Kamphaeng Saen 2 (KPS2) and wild mungbean accession ACC41. The QTL was narrowed down to a genome region of 164.87 Kb containing a phytochrome gene, designated VrPHYE, encoding phytochrome E (phyE), a known photoreceptor modulating flowering time. Compared to VrPHYE of the wild ACC41, VrPHYE of KPS2 contained several single nucleotide polymorphisms (SNPs) causing amino acid changes. Those SNPs were also found in other mungbean cultivars. Some amino acid changes were predicted to occur in the regulatory region of phytochromes. Gene expression analysis revealed that VrPHYE in KPS2 was expressed significantly higher than that in ACC41. These results showed that VrPHYE is the candidate gene controlling flowering time in the mungbean.

Linkage Group and Segregation Analyses of Fingerprint and Foot Patterns in the Yoruba, Igbo and Ibibio Populations of Nigeria

Linkage Group and Segregation Analyses of Fingerprint and Foot Patterns in the Yoruba, Igbo and Ibibio Populations of Nigeria

Organofunctionalized Nb2O5 Nanoparticles for Photodynamic Therapy against A549 Cancer Cells

Niobium pentoxide shows an interesting reactivity that allows the control of different aspects of its morphology and chemistry. In this study, Nb2O5 nanoparticles were modified with protoporphyrin IX (PPIX) and tris(ethynylphenyl) pyrene derivative (PyPh3) by using 3-aminopropyltriethoxysilane as linkage group and used as photosensitizers against lung cancer. The antitumor photoactivity against the A549 tumor cell line as a model of in vitro study showed half maximal inhibitory concentration (IC50) ca. 15 μmol L-1 for both materials and the absence of dark activity, indicating the viability of dye-modified Nb2O5 as a photodynamic therapy (PDT) agent.

QTL Mapping Using RIL Population.

Genetic maps are an excellent tool for the analysis of important traits, the development of which is the result of the combined expression of several genes, enabling the genomic localization of the factors determining them. Such features, characterized by a normal distribution of values, are referred to as quantitative or polygenic. The analysis of their genetic background using a chromosome map is called the mapping of quantitative traits loci (QTL). QTL analysis is a statistical method of determining the genetic association of phenotypic data (trait measurements) with genotypic data (DNA markers assigned to linkage groups).There are numerous tools developed for QTL mapping. This chapter introduces Windows QTL Cartographer with Composite Interval Mapping (CIM) method, which estimates the QTL position by combining interval mapping with multiple regression. The genotypic and phenotypic data used in the exemplary QTL mapping procedure were obtained for the recombinant inbred line (RIL) population of rye. Plant height, assessed in three seasons, was the exemplary trait under study.

High-density genetic map and quantitative trait loci map of skin color in hawthorn (Crataegus pinnatifida bge. Var. major N.E.Br.).

Fruit skin color is an important trait of the hawthorn tree, which has an important influence on fruit quality. Crataegus pinnatifida Bge. var. Major N.E.Br. Is one of the most widely cultivated varieties in China and has a long history of medicinal use. In recent years, it has attracted the attention of the world due to its nutritional and medicinal values. Skin color is the focus of breeders and food processors. At present, skin color-related genes have still not been mapped. In this study, "Shandong Da Mianqiu" (♀, red skin color), "Da Huang Mianzha" (♂, yellow skin color) and 131 F1 hybrids were used to construct genetic map of hawthorn by RAD-seq, and QTL mapping was performed by combining these features with the hue angle and the observed color. In this study, 13,260 SNP was assigned to 17 linkage groups, with an integrated map covering 2,297.75cM was constructed. A total of 5 QTLs related to hawthorn skin color were detected on LG1, LG3 and LG15. Whether hue angle or pericarp color acts as phenotype for QTL mapping, the candidate genes include bHLH086, WD repeat regions and Myb-like. bHLH, WD and Myb play an important role in the color regulation of Hawthorn skin color. These results lay a solid foundation for QTL mapping and molecular marker-assisted breeding of hawthorn.

Scalable High‐Permittivity Polyimide Copolymer with Ultrahigh High‐Temperature Capacitive Performance Enabled by Molecular Engineering

AbstractPolymer capacitors are essential components of advanced electronic and power systems. However, the deficient high‐temperature capacitive performance of polymer dielectrics fails to meet the demand for harsh condition applications, due to the mutually restrictive relationships in permittivity (εr), glass transition temperature (Tg), and bandgap (Eg). Here, a modularized molecular engineering strategy is reported to enhance the high‐temperature capacitive performance of polymer dielectrics. First, the potential influences of multiple structural units on εr, Tg, and Eg of polymers are elucidated by comparing a set of polyimides (PIs). After screening out an excellent sulfonated PI with concurrently high εr (4.2), Eg (3.4 eV), and Tg (311.2 °C), a semi‐alicyclic sulfonyl‐containing PI copolymer is further synthesized that exhibits a superior discharged energy density of 4.3 J cm−3 above 90% efficiency at 200 °C and 485 MV m−1. Density functional theory calculations demonstrate that the combination of polar sulfonyl group, ether linkage, and alicyclic group in the backbones of the copolymer decouples the dipole orientation and the segmental motion of backbones, and reduces conjugation effects of aromatic groups, thereby minimizing the polarization relaxation loss and the conduction loss while retaining excellent thermal stability and high permittivity.

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

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

QTL Mapping and Genetic Map for the Ornamental Sunflower in China

Quantitative trait locus (QTL) mapping and genetic map are of great significance for ornamental sunflowers in China. In this study, a total of 956.50 Mbp data were obtained, the average Q30 was 93.76%, the average GC content was 42.43%, and the GC distribution of the parents and F2 population of the ornamental sunflowers was normal. At the same time, the double-end comparison efficiency of control data was 90.28%, and the enzyme digestion efficiency was 92.01%. The Specific-Locus Amplified Fragment (SLAF) library construction was normal. Furthermore, a total of 734,893 SLAF markers were obtained, among which 127,855 were polymorphic SLAF markers and 38,908 could be used for genetic map construction, and the effective polymorphism of the parents was 5.29%. Moreover, we constructed a total of 17 linkage groups, with 6181 markers in the QTL mapping, the total map distance was 2608.66 cM, the marker integrity in the figure above was 99%, the proportion of double exchange was 0.05, the sequencing depth of the parents was 42.455 × , and the progeny was 9.24 × . The relationship of traits (plant height, stem diameter, disk diameter, number of petals, leaf number, stigma color, petal color, petiole color) and QTL mapping was closely related to show the best of ornamental effect.

Genetic Architecture of Body Fat Composition in Mice

Body fat composition is a quantitative measure of obesity, a major health concern in humans. Laboratory mice are considered an excellent model for dissecting the genetic basis of obesity due to the genetic variation present in inbred strains for body size and fat composition, as well as their historical use as a model organism for human disease studies. To identify the loci controlling fat pad weights and body weight in mice, we performed a quantitative trait loci (QTL) analysis of 513 (SM/J x NZB/BINJ) F2 individuals fed a high-fat diet for 14 weeks. Our analysis separated fat composition genetic effects from those affecting overall body sizes in mouse. Composite interval mapping (CIM) results showed that body weight was conditioned by three major additive QTLs, explaining 3 to 30% of the phenotypic variation. One significant QTL on chromosome 19 conditioned all fat pads with the exception of the inguinal fat weight, which was controlled by a different QTL also on chromosome 19. Significant QTLs associated with fat compositions were detected on chromosomes 17 and 19 and differed from those of body weight. The fat pad QTLs also showed mainly additive gene effects and they explained 2 to 7% of variation in fat composition. Joint analysis of correlated traits detected five additional large effect QTLs on five different linkage groups. These findings have indicated that fat composition and body weight in mouse are conditioned by one to three major additive genes and can therefore be potentially manipulated in controlling obesity.

CmWAT6.1, mined by high-density genetic map-based QTL mapping, enhances waterlogging tolerance in chrysanthemum

High-density genetic maps are a valuable tool for quantitative trait locus (QTL) mapping and gene discovery for important traits in plants. However, such work in chrysanthemum remains largely unexplored, primarily owing to its large genome and complex genetic background. In this study, a high-density map containing 11,941 SNP bins spanning a total of 2967.76 cM in 27 linkage groups (LGs) with an average intermarker distance of 0.26 cM was developed with a genotyping by sequencing (GBS) approach. A total of 34 QTL clusters for waterlogging tolerance (WAT) were detected via multiple-QTL mapping (MQM) algorithms. A total of 186 candidate genes within these QTL clusters were mined in combination with transcriptome data. One key candidate gene within the QTL cluster cWAT6.1, which belongs to group VII ethylene response factors (CmWAT6.1), was proven to be a positive regulator of WAT in chrysanthemum. Furthermore, transcriptomic assays of transgenic and wild-type chrysanthemums under normal conditions as well as further experiments provided evidence that CmWAT6.1 regulated WAT by promoting cell wall formation and lignin biosynthesis and coordinating oligosaccharide metabolic processes. This study represents important progress in gene mining through forward genetics, provides valuable genetic resources for further WAT improvement and provides new insight into the molecular mechanism of WAT in chrysanthemum.

Design and rheological behaviour of lactic acid based cholesteric liquid crystalline materials with hydroquinone unit in the molecular core

In order to contribute to molecular structure – physical property relationship for chiral self-assembling materials, two chiral compounds derived from the lactic acid have been designed. Mesogenic core of materials consists of two benzoate units and one hydroquinone unit connected by the ester linkage groups and two flexible alkyl chains. Different lengths of the chiral alkyl chain were tested, while the length of the achiral alkyl was kept same for all materials. The mesomorphic properties were established by polarizing optical microscopy and differential scanning calorimetry. Both materials possess reasonably broad and stable cholesteric (N*) phase down to room temperature. The rheological characterisation was performed in the N* phase on the compound with shorter chiral alkyl chain using a rotational rheometer in a plate/plate geometry with and without external electric field applied perpendicularly to the flow direction. The results reveal a shear thinning behaviour, even without electric field applied. The N* phase exhibits a slight electrorheological effect, at low shear rates, that continuously decrease with the increase of the shear rate, due to the competition of the flow and electric fields. The mesomorphic behaviour of the designed materials was compared to structurally similar materials. Quite broad temperature range of the N* phase down to room temperature makes studied lactic acid derivatives as suitable chiral dopants for design of new multicomponent mixtures targeted for various applications in photonics and optoelectronics.

Analysis of chickpea (Cicer arietinum L.) genotypes by microsatellite loci of the QTL-hotspot-­region associated with drought tolerance

Purpose. To determine the polymorphism of microsa­tellite loci of the QTL-hotspot-region of linkage group 4, associated with drought tolerance in Ukrainian chickpea varieties. Methods. Extraction and purification of DNA from seedlings using the CTAB method; polymerase chain reaction; horizontal gel electrophoresis; determination of the size of amplification products using the “Image J” prog­ram. Results. Allelic combinations of microsatellite loci ICCM0249, NCPGR127, TAA170, NCPGR21, TA130, STMS11 of the QTL­hotspot­region of linkage group 4 of the chickpea genome were established. It was found that the loci STMS11, NCPGR127, NCPGR21 were not polymorphic within the sample of varieties analyzed, one allele was detected for each locus; two alleles were detected for the loci ICCM0249 and TAA170 and three alleles for the locus TAA130, indica­ting their polymorphism. Conclusions. Microsatellite loci STMS11, NCPGR127, NCPGR21 are non­polymorphic in seven Ukrainian chickpea varieties. Three loci are polymorphic with two alleles for ICCM0249 and TAA170 and three alleles for TAA130. According to the analysis of chickpea varie­ties, five types of allelic combinations of microsatellite loci ICCM0249, NCPGR127, TAA170, NCPGR21, TA130, STMS11 were established. An allele of 185 bp unique to the sample of cultivars studied was identified in the variety ‘Pamiat’

Genetic mapping of quantitative trait loci controlling smut resistance in Louisiana sugarcane using a bi-parental mapping population

Sugarcane smut, caused by Sporisorium scitamineum, is a major disease worldwide. Breeding resistant cultivars is the main management strategy. However, occasional failure to detect susceptible clones due to unfavorable environmental conditions, inconsistency in disease ratings between experiments, and continued clone losses due to pathogen adaptability are some of the challenges for this strategy. The development and use of molecular markers associated with smut resistance may overcome these limitations allowing more accurate identification of resistant parents and progeny. A genetic analysis was conducted using an inoculated population of 162 F1 progeny from a biparental cross between susceptible/female and resistant/male parents to identify quantitative trait loci (QTLs) associated with resistance. A total of 1574 single dose (SD) single-nucleotide polymorphisms (SNP) markers used to construct a genetic map resulted in 253 linkage groups (LGs) of which 150 LGs were assigned to the female parent and 204 LG to the male parent with a genome coverage of 24,580 cM. (Composite) interval mapping with selective sub-populations identified six consistent QTLs that cumulatively explained 25.74% of the phenotypic variance with LOD scores ranging from 3.17 to 23.7. Four out of 12 SNP markers closest to the QTL peaks had effect >10 for resistance in the heterozygous condition. Genes known to be involved in disease resistance, such as cellulose synthase, expansin, protein degradation, and receptor-kinase were linked to the genomic regions associated with smut resistance. The markers upon validation in different populations can be utilized for marker-assisted selection.

A High-Resolution Linkage Map Construction and QTL Analysis for Morphological Traits in Anthurium (Anthurium andraeanum Linden).

Anthurium andraeanum Linden is a prominent ornamental plant belonging to the family Araceae and is cultivated worldwide. The morphology characteristics are crucial because they significantly impact ornamental values, commercial properties, and the efficiency of space utilization in production. However, only a few related investigations have been conducted in anthurium to date. In this study, an F1 genetic segregation population containing 160 progenies was generated through hybridization between potted and cut anthurium varieties. Fifteen morphological traits were assessed and revealed substantial levels of genetic variation and widespread positive correlation. Based on specific length amplified fragment (SLAF) sequencing technology, 8171 single nucleotide polymorphism (SNP) markers were developed, and the high-density linkage map of 2202.27 cM in length distributed on 15 linkage groups was constructed successfully, with an average distance of 0.30 cM. Using the inclusive composite interval mapping (ICIM) method, 59 QTLs related to 15 key morphological traits were successfully identified, which explained phenotypic variance (PVE) ranging from 6.21% to 17.74%. Thirty-three of those associated with 13 traits were designated as major QTLs with PVE > 10%. These findings offer valuable insights into the genetic basis of quantitative traits and are beneficial for molecular marker-assisted selection (MAS) in anthurium breeding.

Genome-wide identification and expression analysis of C-type lectins in discus fish (Symphysodon aequifasciatus) during parental care

Discus fish (Symphysodon aequifasciatus) exhibit a unique parental care behavior: adult discus produces secretion through their skin, on which the larvae live after birth. The immune components in the skin mucus of parental discus would change during different parental care. C-type lectins (CTLs) could identify and eliminate pathogenic microorganisms and play important roles in innate immunity. Studies on CTLs of discus fish especially during parental care, however, are scarce. Here, we identified 186 CTL genes that distributed in 27 linkage groups based on discus genome. Phylogenetic analysis showed that S. aequifasciatus CTL (SaCTL) members were grouped into 14 subfamilies. A total of 80 gene replication events occurred, of which 15 pairs were subjected to segmental duplication and 65 pairs underwent tandem duplication. Ka/Ks ranged from 0.11 (SaCTL25/SaCTL158) to 0.68 (SaCTL36/SaCTL69), all undergoing purifying selection. RNA-seq analysis revealed that SaCTL members, including duplicated genes, in the skin of parental discus show distinct expression patterns in different care stages and between male and female parents. The SaCTL11 was differentially expressed in most care stages and reached the maximum after eggs spawned, but the expression of its paired SaCTL14 was low in each stage. The SaCTL39 increased first and then decreased, reaching a peak in eggs spawned, while paired SaCTL48 first decreased and then increased, reaching a peak in hatched eggs. The SaCTL50 was differentially expressed only in female fish during care, but not in male fish. These results provide new insights into the evolution and potential functional differentiation of CTLs in discus fish during parental care.