Linkage Groups Research Articles

Genetic Linkage Map Construction and QTL Mapping for Juvenile Leaf and Growth Traits in Camellia oleifera

Advancement of the oil tea industry requires the development of high-yielding and superior-quality varieties of Camellia oleifera, a major oilseed crop. However, traditional breeding methods, hampered by lengthy cycles and low selection accuracy, significantly constrain the breeding process. Identifying single nucleotide polymorphisms (SNPs) associated with target traits, and applying molecular marker-assisted selection (MAS) for these traits, can thereby shorten the breeding cycles and amplify the breeding efficiency. In this study, we utilized the hexaploid C. oleifera as the reference genome to identify high-quality SNPs and constructed a high-density genetic linkage map of C. oleifera that spanned 1566.733 cM, included 3097 SNPs, and was anchored to 15 linkage groups. Using interval mapping, we localized quantitative trait loci (QTLs) for 11 juvenile traits in C. oleifera, identifying 15 QTLs for growth traits and 24 QTLs for leaf traits, including 4 stable QTLs. The logarithm of odds (LOD) scores for individual QTLs ranged from 3.48 to 14.62, explaining 9.86–48.61% of the phenotypic variance. We further identified 2 SNPs associated with growth traits (marker11-951 and marker12-68) and 10 SNPs associated with leaf traits (marker11-276, marker11-410, marker11-560, marker13-16, marker13-39, marker13-110, marker13-731, marker14-701, marker14-910, and marker14-1331). These results provide valuable insights into the genetic mapping of key traits in C. oleifera and will contribute to the development of new varieties with high yield and superior quality in the future.

Eastern filbert blight resistant Corylus avellana identified from 20 years of germplasm introduction and evaluation at Rutgers University, New Jersey, USA

The stem canker disease eastern filbert blight (EFB), caused by Anisogramma anomala, is a major impediment of European hazelnut (Corylus avellana) production in the United States. While most European hazelnut cultivars are highly susceptible to the pathogen, which remains confined to North America, EFB resistant and tolerant genotypes occur in the gene pool at low frequency. At Rutgers University, New Brunswick, NJ, USA, 5,226 trees were grown from open pollinated seeds collected from Russia, Crimea, Poland, Turkey, Estonia, Latvia, Lithuania, Moldova, Azerbaijan, Italy, and the Republic of Georgia between 2002 to 2010. The trees were field planted, exposed to A. anomala under high pathogen pressure, and evaluated for disease response 5-6 years after their establishment. At this point, around four percent were found to be EFB resistant totaling 216 accessions that spanned a wide diversity of seedlots from most countries and regions. However, recent observations show many of these once-resistant selections have since succumbed to EFB. In this study, the long-term disease response of this germplasm was evaluated to identify trees remaining resistant and tolerant and document changes in EFB response over time in relation to their origin. All trees were rated for presence of EFB according to a scale of 0 to 5 where 0 = no EFB and 5 = all stems have cankers. Data were assembled from three sets: first reports from 5-6 years after each planting year, a reassessment in 2017, and a final evaluation in January 2024. Overall, the results showed a significant reduction in resistant individuals from the original reports. By 2017, the population of 216 trees was reduced to 154 and by 2024 it decreased further to 91. Notably, this shift from resistant to susceptible phenotype was severe and abrupt and patterns were observed within related seed lots. These patterns were also apparent in trees where their resistance (R) genes were mapped. Specifically, all selections with R genes mapped to linkage group (LG) 6 now expressed severe EFB, while those with R genes mapped to LG 2 or 7 remained free of disease. These results strongly suggest pathogenic variation present over time played a role in the breakdown of resistance. Fortunately, despite loss of some of the germplasm, a wide variety of trees spanning most collection origins still remain free of EFB. These 91 trees from 56 distinct seedlots originating from 7 countries are formally documented in this manuscript to facilitate their long-term preservation, continued evaluation and sharing, and to increase global awareness of this valuable genetic resource for future research and breeding.

Quantitative trait loci mapping for agronomic and leaf chemistry traits using high density linkage map in flue-cured tobacco (Nicotiana tabacum L.)

Flue-cured tobacco (Nicotiana tabacum L.) is one of the most important economic crops in the world, and is the most important raw material in the cigarette industry. Construction of a high-density linkage map and identification of agronomic and leaf traits quantitative trail loci (QTLs) are prerequisites for molecular marker-assisted selective breeding projects. In the present study, an integrated high-density linkage map for flue-cured tobacco was constructed using a doubled haploid (DH) population based on SSR and SNP markers. The integrated genetic map spans 2618.89 cM and contains 607 SSR marker loci, and 917 SNP marker loci. Using the newly constructed map, QTL mapping was performed using the method of composite interval mapping (CIM) for six plant and six leaf chemistry traits. A total of 102 QTLs associated with 1.77–27.65% of the phenotypic variation were identified on 22 linkage groups in two years (2021 and 2022). Eighty-four and 89 QTLs were detected using 2021 and 2022 field experiments, respectively. Seventy-one QTLs were detected in both years. Most QTLs presented small effects, but six QTLs presented relatively large effects in both two years, with each explaining 15–28% of the phenotypic variation in the DH population. The twelve measured traits were strongly correlated with each other. Consistent with this finding, many QTLs identified for one trait overlapped with those identified for alternative traits.

Construction of a high-density genetic map and QTL mapping of growth traits in kiwifruit

The trunk diameter (TD) and annual branch diameter (ABD) are closely associated with the growth vigor, abiotic resistance and fruit yield of kiwifruit. These traits are quantitative traits that are controlled by more than one quantitative trait loci (QTLs). However, QTLs for TD and ABD in kiwifruit remain unelucidated. In this study, we generated a cross of the diploid species Actinidia chinensis ‘Hongyang’ (♀) × ‘Boshanbiyu’ (♂) and performed restriction-site associated DNA sequencing on the parents and 173 F1 progeny to identify single-nucleotide polymorphisms (SNPs) in the population. A high-density linkage map spanning 2,548.97 cM was developed using 6,506 bin markers. This bin map consisted of 29 linkage group (LG), with an average genetic distance of 0.39 cM. A total of 8 QTLs were identified: four for TD and four for ABD, with the variance explained by these QTLs ranging from 4.43 % to 16.11 %. A total of 358 TD genes and 181 ABD genes were extracted from the mapped QTLs, and analyzed by KEGG enrichment. In addition, we developed a TD marker from LG23 and an ABD marker from LG10 which were significantly correlated with growth traits. The TD marker is associated with Actinidia22292, a gene involved in protein polar localization, while the ABD marker is linked to Actinidia40478, an Ein3-binding F-box protein. The two SNP markers developed in this study were further validated in a biparental population, indicating their potential use in predicting seedling growth vigor. In summary, these genetic findings deepen our understanding of the genetic basis of growth traits in kiwifruit, and provide valuable information to facilitate kiwifruit breeding.

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

BackgroundOver their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential.ResultsWe present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids, Acropora palmata and A. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genus Acropora exhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from one A. palmata family and 16 A. cervicornis families using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM for A. palmata and A. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps.ConclusionsTogether, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the Atlantic Acropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

The recombination landscape of the barn owl, from families to populations.

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and limited data. Frequently used approaches include linkage mapping based on familial data that provides sex-specific broad-scale estimates of realized recombination and inferences based on population LD that reveal a more fine scale resolution of the recombination landscape, albeit dependent on the effective population size and the selective forces acting on the population. In this study, we use a combination of these two methods to elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). We find subtle differences in crossover placement between sexes that leads to differential effective shuffling of alleles. LD based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates, while smaller chromosomes have a universally high rate which shapes the diversity landscape. We find that recombination rates are correlated with gene content, genetic diversity and GC content. We find no conclusive differences in the recombination landscapes between populations. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics.

Quantitative Trait Locus Mapping and Candidate Gene Analysis of the Contents of Three Tanshinone Components in Salvia miltiorrhiza Bunge.

Tanshinones are abietane diterpenoid quinone compounds with diverse biological activities and pharmacological effects found in Salvia miltiorrhiza. Leveraging the high-density genetic map established through our prior research endeavors, we conducted a quantitative trait locus (QTL) analysis pertaining to the concentrations of three major tanshinone components, cryptotanshinone, tanshinone I, and tanshinone IIA, in S. miltiorrhiza. This extensive investigation was conducted across three distinct planting environments, ultimately identifying a comprehensive repertoire of 27 discernible QTLs. These QTLs were mapped onto four distinct linkage groups (LG), namely LG1, LG5, LG6, and LG7, which explained 3.11%-37.85% phenotypic variation. Candidate genes were projected based on consistent QTLs detected for each active ingredient in three environments. Nineteen putative candidate genes involved in the regulation of tanshinone biosynthesis were identified. These genes participate in primary metabolic and multiple branching terpenoid biosynthesis pathways, forming a complex regulatory network. Our findings have the potential to offer novel insights into advancing the understanding of the regulatory mechanisms governing tanshinone biosynthesis. Furthermore, these results establish crucial groundwork for gene discovery, marker-assisted selection breeding, and map-based cloning of functional genes associated with tanshinone content in S. miltiorrhiza.

Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass.

Russian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass that plays a crucial role in foragaing and rangeland restoration due to its tiller producing capabilities, nevertheless, a genetic map has yet to be constructed due to a shortage of efficient and reliable molecular markers. This also limits the identification, localization, and cloning of economically important traits related to tiller density during breeding. Therefore, this study aimed to create a F1 mapping population with 147 individual lines and their two parents, which were selected based on varying tiller densities. We then used this mapping population to conduct specific-locus amplified fragment sequencing (SLAF-seq) to generate SLAF markers and discover single nucleotide polymorphisms (SNPs). Initially, we generated a total of 1,438.38 million pair-end reads with an average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F1 individual line, respectively. Following the filtering of low-depth SLAF tags, a total of 558,344 high-quality SLAFs were identified. A total of 1,519,903 SNP markers were obtained, and 62,424 polymorphic SNPs were discovered. From these, 4,644 polymorphic SNPs were selected and used for the construction of a genetic map encompassing seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance of 0.31 cM between adjacent markers. Comparative analysis between the seven linkage groups of RWR SLAF tag and the whole-genome sequences in barley (Hordeum vulgare L.) revealed homology values ranging from 17.5% to 34.6%, and the collinearity between the RWR linkage groups and the barley homology groups ranged from 0.6787 to 0.9234, with an average value of 0.8158. Additionally, 143 significant quantitative trait locus (QTLs) with Logarithm of Odds (LOD) value greater than 2.5 for five tiller related traits were detected using three consecutive years of phenotypic trait data from the F1 population, further verifying the map's reliability.

Genetic and QTL analysis of sugars and acids content in sweet cherry (Prunus avium L.)

Abstract Sweet cherry is very appreciated by consumers because of its attractive appearance and taste, which is determined by the balanced sweet-sour flavor. In this work, the genetics of soluble solid content (SSC), titratable acidity (TA), sugars and organic acids was investigated in sweet cherry to facilitate breeding improvement for fruit quality. The fruits of five sweet cherry populations (N = 372), three F1 and two F2, were sampled over two years to evaluate SSC, TA, and the content of individual sugars (glucose, fructose, sorbitol, and sucrose) and organic acids (malic, quinic, oxalic, citric and shikimic) by ultra-performance liquid chromatography (UPLC). Glucose, followed by fructose, was the most abundant sugar, while malic acid was the predominant acid. Sorbitol and malic acid were the most stable compounds between years, and had the highest heritability, being also the best correlated to SSC and TA respectively, revealing their relevance for breeding. Significantly positive correlations were observed among sugars and SSC, and acids and TA, but high interannual variability between years was observed for all traits. QTL mapping for SSC, sugars, TA, and organic acids was performed using a multi-family approach with FlexQTL™. Twenty QTLs were detected consistently during the two phenotyped years, and several relevant regions with overlapping QTLs for sugars and acids were also identified. The results confirmed major stable SSC and TA QTLs on the linkage groups 4 and 6, respectively. Within the main LG4 SSC QTL region, where maturity and fruit development time QTLs have been previously detected, three stable sugar (glucose, sorbitol, and sucrose) and two acid (quinic, shikimic) QTLs were also identified, suggesting a pleiotropic effect of ripening date on the content of these compounds. The major malic acid QTL overlapped with TA QTL on LG6, thus TA QTL mapping in LG6 may correspond to malic acid QTLs. Haplotype analyses of major SSC and sugars QTL in LG4, and TA and malic acid in LG6 revealed haplotypes of breeding interest. Several candidate genes previously identified in other Prunus fruit species, like peach, were found to collocate with the QTLs detected herein. This work reports QTLs regions and haplotypes of sugar and acid content in a Prunus non-climacteric stone fruit for the first time.

The constructed high-density genetic map helps to explore the genetic regulation of erucic acid, oleic acid, and linolenic acid contents in Brassica juncea

Rapeseed mustard (Brassica juncea L.) is the third most important oilseed crop in the world but the genetic mechanism underlying its massive phenotypic variation remains largely unexplored. In this study, specific length amplified fragment sequencing (SLAF-Seq) was used to resequence a population comprising 197 F8 recombinant inbred lines (RILs), derived from a cross between vegetable-type Qichi881 and oilseed-type YufengZC in B. juncea. In total, 438,895 high-quality SLAFs were discovered, of which 47,644 were polymorphic, and 3,887 of the polymorphic markers met the requirements for genetic map construction. The final map included 3,887 markers on 18 linkage groups and was 1,830.23 cM in length, with an average distance of 0.47 cM between adjacent markers. Using the newly constructed high-density genetic map, a total of 53 QTLs for erucic acid (EA), oleic acid (OA), and linolenic acid (LNA) were detected and integrated into 8 consensus QTLs with two for each of these traits. For each of these three traits, two candidate genes were cloned and sequence analyzed, indicating colocalization with their respective consensus QTLs. The co-dominant allele-specific markers for Bju.FAD3.A03 and Bju.FAD3.B07 were developed and showed co-localization with their consensus QTL and co-segregation with LNA content, further supporting the results of QTL mapping and bioinformatic analysis. The expression level for the cloned homologous genes was also identified, which was tightly correlated with the EA, OA and LNA contents of different lines. The results would facilitate the improvement of fatty acid traits and molecular breeding of B. juncea. More use of the high-density genetic map created in this study is also discussed.

Influence of gender, age, and body mass index on the gut microbiota of individuals from South China.

The symbiotic gut microbiota is pivotal for human health, with its composition linked to various diseases and metabolic disorders. Despite its significance, there remains a gap in systematically evaluating how host phenotypes, such as gender, age, and body mass index (BMI), influence gut microbiota. We conducted an analysis of the gut microbiota of 185 Chinese adults based on whole-metagenome shotgun sequencing of fecal samples. Our investigation focused on assessing the effects of gender, age, and BMI on gut microbiota across three levels: diversity, gene/phylogenetic composition, and functional composition. Our findings suggest that these phenotypes have a minor impact on shaping the gut microbiome compared to enterotypes, they do not correlate significantly within- or between-sample diversity. We identified a substantial number of phenotype-associated genes and metagenomic linkage groups (MLGs), indicating variations in gut microflora composition. Specifically, we observed a decline in beneficial Firmicutes microbes, such as Eubacterium, Roseburia, Faecalibacterium and Ruminococcus spp., in both older individuals and those with higher BMI, while potentially harmful microbes like Erysipelotrichaceae, Subdoligranulum and Streptococcus spp. increased with age. Additionally, Blautia and Dorea spp. were found to increase with BMI, aligning with prior research. Surprisingly, individuals who were older or overweight exhibited a lack of Bacteroidetes, a dominant phylum in the human gut microbiota that includes opportunistic pathogens, while certain species of the well-known probiotics Bifidobacterium were enriched in these groups, suggesting a complex interplay of these bacteria warranting further investigation. Regarding gender, several gender-associated MLGs from Bacteroides, Parabacteroides, Clostridium and Akkermansia were enriched in females. Functional analysis revealed a multitude of phenotype-associated KEGG orthologs (KOs). Our study underscores the influence of gender, age, and BMI on gut metagenomes, affecting both phylogenetic and functional composition. However, further investigation is needed to elucidate the precise roles of these bacteria, including both pathogens and probiotics.

Genetic Diversity and Forensic Utility of X-STR Loci in Punjabi and Kashmiri Populations: Insights into Population Structure and Ancestry.

Background: X-chromosomal short tandem repeats (X-STRs) are crucial in forensic applications, particularly in complex kinship cases, and play an important role in population genetics. However, there is limited data on X-STR variation in Pakistani populations, especially among ethnic groups like Kashmiri and Punjabi. Methodology: This study investigates the forensic and genetic properties of 12 X-STRs from the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 125 families (75 Kashmiri, 50 Punjabi) from Azad Jammu and Kashmir and Punjab, Pakistan. Results: In both populations, a total of 222 alleles were identified across the 12 X-STR loci (Punjabi 171 alleles, Kashmiri 161 alleles), with allele frequencies ranging from 0.0056 to 0.3033. DXS10148 was the most polymorphic locus with 28 alleles, while DXS7132 was the least polymorphic with 9 alleles. Most loci were in linkage equilibrium, except for the DXS10135/DXS10148 pair in males, with no loci exhibiting significant linkage disequilibrium in females. The combined power of discrimination was 0.999 999 9977 for Kashmiri males, 0.999 999 999 999 9746 for Kashmiri females, and 0.999 999 999 999 9781 for Punjabi females. In Kashmiri males, 34, 31, 28, and 32 haplotypes were observed across the four linkage groups (LG1, LG2, LG3, and LG4), though these groups did not form stable haplotypes, as indicated by Linkage Equilibrium within and significant Linkage Disequilibrium between groups. Conclusions: Genetic structure analysis using Principal Component Analysis and STRUCTURE revealed distinct clustering patterns for the Kashmiri and Punjabi populations, indicating unique genetic backgrounds and ancestry influences, particularly distinguishing them from East Asian populations. This study provides a comprehensive analysis of X-STR variation in Punjabi and Kashmiri populations, offering valuable insights for forensic and population genetic studies.

Experimental evaluation of effectiveness of genomic selection for resistance to northern corn leaf blight in maize.

Northern corn leaf blight (NLB) caused by Setosphaeria turcica (Luttrell) Leonard & Suggs is a severe foliar disease in maize. Resistance to NLB is complexly inherited and controlled by several quantitative trait loci (QTL) distributed across the genome. Phenotype and DNA marker-based selection for resistance to NLB is expected to be effective. Hence, an investigation was carried out to predict the genetic value of selection candidates for resistance to NLB and compare the accuracies of genomic prediction in two F2:3 populations of two crosses (CM212 × MAI172; CM202 × SKV50) derived from contrasting parents. Linkage analysis using 297 polymorphic SNPs in population-1 and 290 polymorphic SNPs in population-2 revealed ten linkage groups spanning 3623.88cM and 4261.92cM with an average distance of 12.40cM and 14.9cM in population-1 and population-2, respectively. Location-wise and pooled data across locations identified common QTLs on linkage groups 1 and 6 in population-1 and 3 and 8 in population-2. The prediction accuracy of the QTL mapping (9.92 and 9.10 for population-1 and population-2, respectively) was based on only a few markers, which explained higher percent phenotypic variation. The prediction accuracies of the genomic estimated breeding values in the present investigation were relatively low in population-1 (0.24 to 0.26) and population-2 (0.29-0.32) compared to the expected accuracies. This could be due to fewer polymorphic markers and a small training/population size. Though the GS prediction accuracies were relatively low, they were significantly higher than QTL mapping, which promises better genetic gain per cycle. The resistant progenies from both populations were advanced to derive inbred lines and crossed with four different testers in line × tester mating design to test for their combining ability and effectiveness of genomic selection. High overall general combining ability was exhibited by 21 inbred lines. Among F1s, 48% were assigned high overall specific combining ability status. Out of the 136 single crosses, seven recorded significant positive standard heterosis over the best check for grain yield. Twenty-five inbreds with high GEBVs were crossed with four testers to obtain 100 F1s and evaluated for their response to NLB. The majority of hybrids displayed moderate to resistant reaction to NLB either in combination with susceptible or resistant testers indicating the effectiveness of selection based on high GEBVs.

QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in Larimichthys polyactis.

Disease outbreaks in aquaculture have recently intensified. In particular, visceral white-nodules disease, caused by Pseudomonas plecoglossicida, has severely hindered the small yellow croaker (Larimichthys polyactis) aquaculture industry. However, research on this disease is limited. To address this gap, the present study employed a 100K SNP chip to genotype individuals from an F1 full-sib family, identify single nucleotide polymorphisms (SNPs), and construct a genetic linkage map for this species. A high-density genetic linkage map spanning a total length of 1395.72 cM with an average interval of 0.08 cM distributed across 24 linkage groups was obtained. Employing post-infection survival time as an indicator of disease resistance, 13 disease resistance-related quantitative trait loci (QTLs) were detected, and these regions included 169 genes. Functional enrichment analyses pinpointed 11 candidate disease resistance-related genes. RT-qPCR analysis revealed that the genes of chmp1a and arg1 are significantly differentially expressed in response to P. plecoglossicida infection in spleen and liver tissues, indicating their pivotal functions in disease resistance. In summary, in addition to successfully constructing a high-density genetic linkage map, this study reports the first QTL mapping for visceral white-nodules disease resistance. These results provide insight into the intricate molecular mechanisms underlying disease resistance in the small yellow croaker.

SSR markers based QTL mapping and genetic analysis for yield and yield-attributing traits in bitter gourd (Momordica charantia L.)

The present study was conducted for QTL mapping for yield and other yield attributing traits in bitter gourd using Simple Sequence Repeat (SSR) markers. A total of 630 SSR markers were screened for polymorphism in two contrasting parents (DBGS-2 and Pusa Purvi), out of which only 35 were polymorphic. F1 plants (10 individuals) in which hybridity was ascertained (using these polymorphic markers); were further employed for development of mapping population (F2) consisting of 120 plants. Higher variation was present in the mapping population as evident from the wider range value of the characters. Continuous frequency distribution classes combined with bell-shaped, symmetrical normal distribution curve, revealed the quantitative inheritance nature of the traits studied. Higher PCV than the GCV for all the traits, along with high difference between the PCV and GCV for majority of traits indicated higher influence of environment in expression of these traits in the mapping population. Presence of transgressive segregation was also noted for majority of the traits. Amongst the various linkage groups (LG), LG 4 had the maximum number of markers, covering 171.07 cM map distance. LG4 also possessed the maximum number (nine) of QTLs while LG1 had six. QTL mapping using polymorphic SSRs resulted in detection of a total of 28 QTLs for fourteen traits viz. yield per plant (kg), earliness or flower related traits (node to first female flower, node to first male flower, days to first male flower, male to female flower ratio), fruit traits (fruit number per plant, fruit diameter (cm), fruit length/ diameter ratio, pericarp thickness (mm) and number of seed per fruit) and vegetative traits (internodal length (cm), number of primary branches, leaf width (cm), length and width ratio). The LOD score of these QTLs ranged from 3.01 to 64.47, the total phenotypic variances (PVE) ranged from 1.52 to 34.57 % and additive effects ranged from –3.69 to 17.07. Of the total, nineteen were major QTLs, having PVE >10 %. Three QTLs were detected for yield per plant while a total of seven for the traits imparting earliness viz. days to first male flower, node to first female flower and node to first male flower. Amongst all the QTLs detected, qFrtLDR-4-1 (K) had the maximum LOD (64.47) and PVE (34.57 %) value. Two hotspots were detected with multiple QTLs clustered in the LG 1. The first hotspot possessed four QTLs [qLfW-1-1, qMFR-1-1 (K), qSPF-1-1, qNFmlF-1-1 (K)] while the second had two related to yield per plant [qYldpl-1-1 (K) and qYldpl-1-1]. Many of these QTLs are also being reported for the first time in bitter gourd. The findings of the present study can be used to fasten the bitter gourd improvement by utilizing these in MAS, DNA fingerprinting, genetic mapping, genomics analysis etc.

A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens).

The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.1% with respect to the Aves database. The annotated gene set has a BUSCO transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern.

Discovery of a major QTL for resistance to the guava root-knot nematode (Meloidogyne enterolobii) in ‘Tanzania’, an African landrace sweetpotato (Ipomoea batatas)

Sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is among the world’s most important food crops and is North Carolina’s most important vegetable crop. The recent introduction of Meloidogyne enterolobii poses a significant economic threat to North Carolina’s sweetpotato industry and breeding resistance into new varieties has become a high priority for the US sweetpotato industry. Previous studies have shown that ‘Tanzania’, a released African landrace, is resistant to M. enterolobii. We screened the biparental sweetpotato mapping population, ‘Tanzania’ x ‘Beauregard’, for resistance to M. enterolobii by inoculating 246 full-sibs with 10,000 eggs each under greenhouse conditions. ‘Tanzania’, the female parent, was highly resistant, while ‘Beauregard’ was highly susceptible. Our bioassays exhibited strong skewing toward resistance for three measures of resistance: reproductive factor, eggs per gram of root tissue, and root gall severity ratings. A 1:1 segregation for resistance suggested a major gene conferred M. enterolobii resistance. Using a random-effect multiple interval mapping model, we identified a single major QTL, herein designated as qIbMe-4.1, on linkage group 4 that explained 70% of variation in resistance to M. enterolobii. This study provides a new understanding of the genetic basis of M. enterolobii resistance in sweetpotato and represents a major step towards the identification of selectable markers for nematode resistance breeding.

High-density genetic map construction and QTL mapping to identify genes for blight defense- and yield-related traits in sesame (Sesamum indicum L.).

Sesame (Sesamum indicum L.) is an important oilseed crop widely cultivated in subtropical and tropical areas. Low genetic yield potential and susceptibility to disease contribute to low productivity in sesame. However, the genetic basis of sesame yield- and disease-related traits remains unclear. Here, we represent the construction of a high-density bin map of sesame using whole genome sequencing of an F2 population derived from 'Yizhi' and 'Mingdeng Zhima'. A total of 2766 Bins were categorized into 13 linkage groups. Thirteen significant QTLs were identified, including ten QTLs related to yield, two QTLs related to Sesame Fusarium wilt (SFW) disease, and one QTL related to seed color. Among these QTLs, we found that SFW-QTL1.1 and SFW-QTL1.2 were major QTLs related to Fusarium wilt disease, explaining more than 20% of the phenotypic variation with LOD > 6. SCC-QTL1.1 was related to seed coat color, explaining 52% of the phenotypic variation with LOD equal to 25.3. This suggests that seed color traits were controlled by a major QTL. Candidate genes related to Fusarium wilt disease and seed color in the QTLs were annotated. We discovered a significant enrichment of genes associated with resistance to late blight. These genes could be spectral disease resistance genes and may have a role in the regulation of Fusarium wilt disease resistance. Our study will benefit the implementation of marker-assisted selection (MAS) for the genetic improvement of disease resistance and yield-related traits in sesame.

Construction of the First High-Density Genetic Linkage Map and QTL Mapping of Shikimic Acid Content in Liquidambar

High-quality genetic maps are effective tools for elucidating the genetic mechanisms of complex quantitative traits and facilitating marker-assisted breeding. Species within the genus Liquidambar (commonly called sweetgum), particularly Liquidambar styraciflua and Liquidambar formosana, are significant forest resources worldwide. These sweetgum trees have been extensively utilized in medical and cosmetic applications for centuries as they contain large amounts of valuable secondary metabolites. Among these, shikimic acid is a notable metabolite with significant pharmaceutical applications. Despite advances in conventional breeding and propagation techniques for sweetgum, the genetic basis and regulatory mechanisms of valuable traits remain largely unexplored. In this study, we constructed the first high-density genetic map for sweetgum using whole-genome resequencing (WGR) of 220 progeny individuals derived from a cross of L. styraciflua × L. formosana. The genetic map spanned a total distance of 1428.51 centimorgans (cM) with an average inter-marker distance of 0.33 cM, incorporating 4268 bin markers across 16 linkage groups. To identify the genetic loci controlling the shikimic acid content, quantitative trait locus (QTL) mapping was carried out based on the genetic map. Two QTLs located on linkage group (LG) 12 were detected, encompassing a total of 213 genes within the QTL interval. Some of these genes are closely related to secondary metabolism in plants, including YUCCA and DXS genes. This study presents the first high-quality genetic map of sweetgum and provides a preliminary QTL analysis for shikimic acid content. Our findings establish a foundational framework for the genetic improvement of sweetgum through marker-assisted breeding and offer valuable insights for further research in sweetgum genetics.

Rpv10.2: A Haplotype Variant of Locus Rpv10 Enables New Combinations for Pyramiding Downy Mildew Resistance Traits in Grapevine.

In viticulture, pathogens like the oomycete Plasmopara viticola, the causal agent of downy mildew, can cause severe yield loss and require extensive application of plant protection chemicals. Breeders are generating pathogen-resistant varieties exploiting American and Asian wild Vitis germplasm as sources of resistance. Several loci mediating resistance to P. viticola have been identified in the past but may be overcome by specifically adapted strains of the pathogen. Aiming to find and characterize novel loci, a cross population with Vitis amurensis ancestry was investigated searching for resistance-correlated quantitative trait loci (QTL). As a prerequisite, a genetic map was generated by analyzing the 244 F1 individuals derived from a cross of the downy mildew susceptible Vitis vinifera cultivar 'Tigvoasa' and the resistant V. amurensis pBC1 breeding line We 90-06-12. This genetic map is based on the information from 627 molecular markers including 56 simple sequence repeats and 571 rhAmpSeq markers. A phenotypic characterization of the progeny showed a clear segregation of the resistance traits in the F1 population after an experimental inoculation of leaf discs with downy mildew. Combining genetic and phenotypic data, an analysis for QTL revealed a major locus on linkage Group 9 that correlates strongly with the resistance to downy mildew. The locus was mapped to a region of about 80 kb on the PN40024 (12x.V2) grapevine reference genome. This genomic region co-localizes with the formerly identified locus Rpv10 from the grapevine cultivar 'Solaris'. As we found different allele sizes of the locus-linked SSR markers than those characterizing the known Rpv10 locus and differences in the sequence of a candidate gene, it was regarded as a haplotype variant and named Rpv10.2.