Candidate Gene Analysis Research Articles

Analysis of QTLs and Candidate Genes for Tassel Symptoms in Maize Infected with Sporisorium reilianum.

Heat smut is a fungal soil-borne disease caused by Sporisorium reilianum, and affects the development of male and female tassels. Our previous research found that the tassel symptoms in maize infected with Sporisorium reilianum significantly differed in inbred lines with Sipingtou blood, and exhibited stable heredity over time at multiple locations. In this study, cytological analysis demonstrated that the cellular organization structures of three typical inbred lines (Huangzao4, Jing7, and Chang7-2) showed significant discrepancies at the VT stage. QTLs that control the different symptoms of maize tassels infected with Sporisorium reilianum were located in two F2 populations, which were constructed using three typical inbred lines. The BSA (bulked segregation analysis) method was used to construct mixed gene pools based on typical tassel symptoms. The QTLs of different symptoms of maize tassels infected with Sporisorium reilianum were detected with 869 SSR markers covering the whole maize genome. The mixed gene pools were screened with polymorphic markers between the parents. Additional SSR markers were added near the above marker to detect genotypes in partially single plants in F2 populations. The QTL controlling tassel symptoms in the Huangzao4 and Jing7 lines was located on the bin 1.06 region, between the markers of umc1590 and bnlg1598, and explained 21.12% of the phenotypic variation with an additive effect of 0.6524. The QTL controlling the tassel symptoms of the Jing7 and Chang7-2 lines was located on the bin 2.07 region, between the markers of umc1042 and bnlg1335, and explained 11.26% phenotypic variation with an additive effect of 0.4355. Two candidate genes (ZmABP2 and Zm00001D006403) were identified by a conjoint analysis of label-free quantification proteome sequencings.

GENETIC VARIANTS AND SERUM PROFILES OF CYTOKINES IN COVID-19 SEVERITY.

Background: Patients with severe coronavirus disease 2019 (COVID-19) are at an increased risk of acute respiratory distress syndrome and mortality. This is due to the increased levels of pro-inflammatory cytokines that amplify downstream pathways that are controlled by immune regulators. Objective: This study aimed to investigate the association between cytokine genetic variants, cytokine serum levels/profiles, and disease severity in critically and noncritically ill COVID-19 patients. Methods: This cross-sectional study recruited 646 participants who tested positive for severe acute respiratory syndrome coronavirus 2 from six collection sites across the United Arab Emirates. Medical files were accessed to retrieve clinical data. Blood samples were collected from all participants. Patients were divided into two clinical groups, noncritical (n = 453) and critical (n = 193), according to World Health Organization classification guidelines for COVID-19 patients. Cytokine analyses were conducted on serum of a subset of the cohort, specifically on 426 participants (noncritical, 264; critical, 162). Candidate gene analyses of 33 cytokine-related genes (2,836 variants) were extracted from a genome-wide association study to identify genetic variants with pleiotropic effects on a specific cytokine and the severity of COVID-19 disease. Results: Age, body mass index (BMI), and pre-existing medical conditions were found to be significant risk factors that contribute to COVID-19 disease severity. After correcting for age, sex, and BMI, IP-10 ( P < 0.001), IFN ( P = 0.001), IL-6 ( P < 0.001), and CXCL-16 ( P < 0.001) serum levels were significantly higher among critical COVID-19 cases, when compared with noncritically ill patients. To investigate if the genetic variants involved in the serum cytokine levels are associated with COVID-19 severity, we studied several genes. Single nucleotide polymorphisms in IL6 (rs1554606; odd ratio (OR) G = 0.67 [0.66, 0.68]; P = 0.017), IFNG (rs2069718; OR G = 0.63 [0.62, 0.64]; P = 0.001), MIP (rs799187; OR A = 1.69 [1.66, 1.72]; P = 0.034), and CXCL16 (rs8071286; OR A = 1.42 [1.41, 1.44]; P = 0.018) were found to be associated with critically ill patients. Polymorphisms in the CXCL10 , CCL2 , IL1 , CCL7 , and TNF genes were not associated with the COVID-19 critical phenotype. The genotypes of IL-6 (gene, IL6 [7p15.3]) and CXCL-16 (gene, CXCL16 [17p13.2]) were significantly associated with the serum levels of the respective cytokine in critical cases of COVID-19. Conclusion: Data obtained from measuring cytokine levels and genetic variant analyses suggest that IL-6 and CXCL-16 could potentially be used as potential biomarkers for monitoring disease progression of COVID-19 patients. The findings in this study suggest that specific cytokine gene variants correlate with serum levels of the specific cytokine. These genetic variants could be of assistance in the early identification of high-risk patients on admission to the clinic to improve the management of COVID-19 patients and other infectious diseases.

Association between the LRP1B and APOE loci in the development of Parkinson's disease dementia.

Parkinson's disease is one of the most common age-related neurodegenerative disorders. Although predominantly a motor disorder, cognitive impairment and dementia are important features of Parkinson's disease, particularly in the later stages of the disease. However, the rate of cognitive decline varies among Parkinson's disease patients, and the genetic basis for this heterogeneity is incompletely understood. To explore the genetic factors associated with rate of progression to Parkinson's disease dementia, we performed a genome-wide survival meta-analysis of 3,923 clinically diagnosed Parkinson's disease cases of European ancestry from four longitudinal cohorts. In total, 6.7% of individuals with Parkinson's disease developed dementia during study follow-up, on average 4.4 ± 2.4 years from disease diagnosis. We have identified the APOE ε4 allele as a major risk factor for the conversion to Parkinson's disease dementia [hazards ratio = 2.41 (1.94-3.00), P = 2.32 × 10-15], as well as a new locus within the ApoE and APP receptor LRP1B gene [hazards ratio = 3.23 (2.17-4.81), P = 7.07 × 10-09]. In a candidate gene analysis, GBA variants were also identified to be associated with higher risk of progression to dementia [hazards ratio = 2.02 (1.21-3.32), P = 0.007]. CSF biomarker analysis also implicated the amyloid pathway in Parkinson's disease dementia, with significantly reduced levels of amyloid β42 (P = 0.0012) in Parkinson's disease dementia compared to Parkinson's disease without dementia. These results identify a new candidate gene associated with faster conversion to dementia in Parkinson's disease and suggest that amyloid-targeting therapy may have a role in preventing Parkinson's disease dementia.

Whole Exome-Sequencing Identifies Variants Associated with Harris Platelet Syndrome

Abstract Introduction/Objective Introduction: Harris platelet syndrome (HPS) is an autosomal dominant giant platelet disorder characterized by normal platelet function with varying degrees of thrombocytopenia. HPS was initially reported in healthy blood donors from West Bengal, and subsequent studies showed it is prevalent in healthy blood donors from the northeastern part of the Indian subcontinent. Objective: Whole-exome sequencing was performed to identify single-nucleotide polymorphisms in protein-coding genes and the associated pathways between the cases and controls. Methods/Case Report Methods: HPS is defined as healthy blood donors having a mean platelet volume (MPV) greater than 12 fL (normal &amp;lt;10 fL) with or without concomitant thrombocytopenia in the absence of any significant past history of bleeding disorder in either themselves or their first-degree relatives. HPS and control healthy donors were enrolled in the study with proper consent. Plasma is extracted from 15 ml of blood samples that were drawn from subjects, and whole-exome sequencing was done on the samples. Pathway analysis of candidate genes and interaction mapping was done using Reactome Pathway Database and STRING, respectively. Results (if a Case Study enter NA) Results: Whole-exome sequencing from the plasma from HPS and non-HPS subjects (n=5 in each group) identified 1374 differentially expressed genes between the two groups. There was a total of 42 single nucleotide polymorphisms (SNPs), (5 deletions and 1 insertion) in the cases (either heterozygous or homozygous) but not in controls. 13 pathways were associated with these variants, and iron homeostasis and defective Cubulin (CUBN) were the top among the predicted pathways. HDL clearing, vitamin and cofactor transport, metabolism, and cardiac conduction defects were among the significantly predicted pathways affected by the variants in HPS patients. An interaction map of the 25 differentially expressed genes where the variants can be mapped is prepared. Conclusion Conclusion: This study shows that SNP variants in HPS may be associated with pathways related to iron homeostasis, HDL clearing, vitamin metabolism and transport and cardiac conduction defects. Phenomapping of HPS patients with detailed genotyping in large population cohort studies are necessary to validate and characterize the functional effect of HPS variants.

Evidence for the Growth Superiority and Delayed Ovarian Development in Tetraploid Loach Misgurnus anguillicaudatus

The diploids and tetraploids of cyprinid loach Misgurnus anguillicaudatus coexist in many natural habits. The tetraploids generally exhibit superior growth performance and delayed gonadal development compared with diploids. To investigate the regulation mechanism of growth superiority and ovarian development in tetraploids, we first conducted a long-term culture experiment and histological observation. The tetraploids exhibited a higher growth performance and delayed ovarian development. Meanwhile, at a genetic level, an average of 6891 differentially expressed genes (DEGs) between diploids and tetraploids were identified from the brain, pituitary, liver, gonad and muscle using the RNA-seq method. Among these DEGs, as expected, some candidate genes, including IGF family genes, somatostatin, leptin, cyp19a1b, gthα, lhβ and fshβ, were detected, which play critical roles in the regulation of growth and gonad development of fish. In particular, the genes related to GH/IGF axis and growth factors, signal transduction, gonadal hormone and appetite were significantly increased in tetraploids. The clustering analyses of the key candidate genes showed that most key genes were up-regulated in the pituitary and gonad of tetraploids instead of other tissues. The dynamics of these key genes provide valuable genetic evidence for clarifying the growth superiority and delayed gonadal development of tetraploids. Moreover, this study also provides some clues for unveiling the genetic superiority of polyploidy species in other phenotypes.

Fine Mapping and Candidate Gene Analysis of Pm36, a Wild Emmer-Derived Powdery Mildew Resistance Locus in Durum Wheat.

Powdery mildew (PM) is an economically important foliar disease of cultivated cereals worldwide. The cultivation of disease-resistant varieties is considered the most efficient, sustainable and economical strategy for disease management. The objectives of the current study were to fine map the chromosomal region harboring the wild emmer PM resistance locus Pm36 and to identify candidate genes by exploiting the improved tetraploid wheat genomic resources. A set of backcross inbred lines (BILs) of durum wheat were genotyped with the SNP 25K chip array and comparison of the PM-resistant and susceptible lines defined a 1.5 cM region (physical interval of 1.08 Mb) harboring Pm36. The genetic map constructed with F2:3 progenies derived by crossing the PM resistant line 5BIL-42 and the durum parent Latino, restricted to 0.3 cM the genetic distance between Pm36 and the SNP marker IWB22904 (physical distance 0.515 Mb). The distribution of the marker interval including Pm36 in a tetraploid wheat collection indicated that the positive allele was largely present in the domesticated and wild emmer Triticum turgidum spp. dicoccum and ssp. dicoccoides. Ten high-confidence protein coding genes were identified in the Pm36 region of the emmer, durum and bread wheat reference genomes, while three added genes showed no homologous in the emmer genome. The tightly linked markers can be used for marker-assisted selection in wheat breeding programs, and as starting point for the Pm36 map-based cloning.

Weighted Gene Coexpression Network Analysis of Candidate Pathways and Genes in Soft Rot Resistance of Amorphophallus

Amorphophallus species are one of the main economic crops in the mountainous areas of southwest China. However, soft rot disease (Pectobacterium carotovorum ssp. carotovorum) is devastating for this crop. This study explored the Amorphophallus resistance mechanism against soft rot disease by analyzing transcriptome data using a weighted gene coexpression network analysis. The RNA sequencing of plants infected for 0, 12, 24, and 48 hours produced a total of 52.25 Gb of clean reads. A total of 29,096 genes were divided into 34 modules. Six modules of interest with the highest correlation with the target traits were selected to elucidate the resistance genes and pathways. The selected modules were enriched in the α-linolenic acid metabolism, phenylpropane biosynthesis, plant hormone signal transduction, and plant pathogen interaction pathways. Ultimately, AmBGLU, AmCAML, AmCDPK, AmLOX, and AmRBOHD were identified as genes of interest in the four significantly related metabolic pathways for real-time fluorescence quantitative polymerase chain reaction verification. The determination of salicylic acid (SA) and jasmonic acid (JA) in Amorphophallus muelleri and Amorphophallus konjac that suffered from soft rot disease showed that SA and JA were involved in the A. muelleri and A. konjac defense response against soft rot disease. Methyl jasmonate treatment delayed the onset of A. konjac soft rot disease. This study provides a reference for the interaction between Amorphophallus species and soft rot disease and the breeding of broad-spectrum and specific Amorphophallus cultivars that are resistant to soft rot disease.

Investigating Genetic Determinants of Plasma Inositol Status in Adult Humans

Myo-inositol (MI) is incorporated into numerous biomolecules, including phosphoinositides and inositol phosphates. Disturbance of inositol availability or metabolism is associated with various disorders, including neurological conditions and cancers, whereas supplemental MI has therapeutic potential in conditions such as depression, polycystic ovary syndrome, and congenital anomalies. Inositol status can be influenced by diet, synthesis, transport, utilization, and catabolism. We aimed to investigate potential genetic regulation of circulating MI status and to evaluate correlation of MI concentration with other metabolites. GC-MS was used to determine plasma MI concentration of >2000 healthy, young adults (aged 18-28 y) from the Trinity Student Study. Genotyping data were used to test association of plasma MI with single nucleotide polymorphisms (SNPs) in candidate genes, encoding inositol transporters and synthesizing enzymes, and test for genome-wide association. We evaluated potential correlation of plasma MI with d-chiro-inositol (DCI), glucose, and other metabolites by Spearman rank correlation. Mean plasma MI showed a small but significant difference between males and females (28.5 and 26.9 μM, respectively). Candidate gene analysis revealed several nominally significant associations with plasma MI, most notably for SLC5A11 (solute carrier family 5 member 11), encoding a sodium-coupled inositol transporter, also known as SMIT2 (sodium-dependent myo-inositol transporter 2). However, these did not survive correction for multiple testing. Subsequent testing for genome-wide association with plasma MI did not identify associations of genome-wide significance (P < 5 × 10-8). However, 8 SNPs exceeded the threshold for suggestive significant association with plasma MI concentration (P < 1 × 10-5), 3 of which were located within or close to genes: MTDH (metadherin), LAPTM4B (lysosomal protein transmembrane 4 β), and ZP2 (zona pellucida 2). We found significant positive correlation of plasma MI concentration with concentration of dci and several other biochemicals including glucose, methionine, betaine, sarcosine, and tryptophan. Our findings suggest potential for modulation of plasma MI in young adults by variation in SLC5A11, which is worthy of further investigation.

Copy number variant analysis for syndromic congenital heart disease in the Chinese population

BackgroundSyndromic congenital heart disease (CHD) is among the most severe conditions in the pediatric population. Copy number variant (CNV) is an important cause of syndromic CHD, but few studies focused on CNVs related to these patients in China. The present study aimed to identify pathogenic CNVs associated with syndromic CHD in the Chinese population.MethodsA total of 109 sporadic patients with syndromic CHD were applied chromosomal microarray analysis (CMA). Phenotype spectrum of pathogenic or likely pathogenic CNVs was analyzed. CHD-related genes were prioritized from genes within pathogenic or likely pathogenic CNVs by VarElect, OVA, AMELIE, and ToppGene.ResultsUsing CMA, we identified 43 candidate CNVs in 37/109 patients. After filtering CNVs present in the general population, 29 pathogenic/likely pathogenic CNVs in 24 patients were identified. The diagnostic yield of CMA for pathogenic/likely pathogenic CNVs was 23.1% (24/104), excluding 5 cases with aneuploidies or gross chromosomal aberrations. The overlapping analysis of CHD-related gene lists from different prioritization tools highlighted 16 CHD candidate genes.ConclusionAs the first study focused on CNVs in syndromic CHD from the Chinese population, this study reveals the importance of CMA in exploring the genetic etiology of syndromic CHD and expands our understanding of these complex diseases. The bioinformatic analysis of candidate genes suggests several CHD-related genes for further functional research.

Transcriptome and Metabolome Combined to Analyze Quinoa Grain Quality Differences of Different Colors Cultivars.

Quinoa (Chenopodium quinoa Wild.) has attracted considerable attention owing to its unique nutritional, economic, and medicinal values. Meanwhile, quinoa germplasm resources and grain colors are rich and diverse. In this study, we analyzed the composition of primary and secondary metabolites and the content of the grains of four different high-yield quinoa cultivars (black, red, white, and yellow) harvested 42 days after flowering. The grains were subjected to ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and transcriptome sequencing to identify the differentially expressed genes and metabolites. Analysis of candidate genes regulating the metabolic differences among cultivars found that the metabolite profiles differed between white and black quinoa, and that there were also clear differences between red and yellow quinoa. It also revealed significantly altered amino acid, alkaloid, tannin, phenolic acid, and lipid profiles among the four quinoa cultivars. Six common enrichment pathways, including phenylpropane biosynthesis, amino acid biosynthesis, and ABC transporter, were common to metabolites and genes. Moreover, we identified key genes highly correlated with specific metabolites and clarified the relationship between them. Our results provide theoretical and practical references for breeding novel quinoa cultivars with superior quality, yield, and stress tolerance. Furthermore, these findings introduce an original approach of integrating genomics and transcriptomics for screening target genes that regulate the desirable traits of quinoa grain.

Fine Mapping and Candidate-Gene Analysis of an open glume multi-pistil 3 (mp3) in Rice (Oryza sativa L.)

The rice mutant mp3 was derived from an indica–japonica cross between Rejing35 and XieqingzaoB, producing an inconstant number of pistils ranging from one to four pistils in a floret at heading stage, which also developed an open-glume with one or two seeds and twin seedlings at mature and seedling stage. Several altered characteristics, including filling grain panicle–1 (62.90), grain-setting rate (60.48%) and grain yield plant–1 (13.42 g), decreased but an increase in 1000-grain weight (36.87 g) was observed. Genetic analysis revealed that the mp3 mutant phenotype was controlled by a single recessive gene. Using a chromosome walking strategy in the F2 population of 02428/mp3, the mp3 gene was fine mapped between L3-135 and RM7576, with a physical distance of 30.617 kb on rice chromosome 3. Four candidate genes were found in this region referred to the rice genome annotations. LOC_Os03g11614/OsMADS1 corresponded with the mutant mp3 phenotype. Sequencing showed no sequence alterations in the coding and promoter sequence of the LOC_Os03g11614/OsMADS1 of mp3. The mp3 gene may be an allelic gene with three previously reported genes but controlled different mutant floral organ phenotypes in rice. Therefore, this mp3 gene provided a novel perspective on the biological function of OsMADS1 in the development of rice floral organ.

Genome-wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments.

Improving seed yield is one of the main targets of soybean [Glycine max (L.) Merr.] breeding. Identification of loci that influence productivity and understanding their genetic mechanism will help marker-assisted trait introgression. The present study evaluated a diverse panel of 541 soybean genotypes consisting of three maturity groups (MGs III-V) in four environments in Kansas, U.S. Data on seed yield, seed weight, shattering resistance, days to maturity, and plant height showed significant genotype, environmental, and genotype × environment interaction variations. Seed yield and shattering had moderate broad-sense heritability (<85%), while the rest of the traits showed high broad-sense heritability (>90%). The SoySNP50K iSelect BeadChip dataset was used to identify significantly associated loci via genome-wide association studies (GWAS). A total of 19 single-nucleotide polymorphisms (SNPs) were significantly associated with seed yield. Particularly, two stable seed yield quantitative trait loci (QTL) on chromosomes 9 and 17 were consistently detected in at least three out of four environments. Candidate gene analysis surrounding seed yield QTL on chromosome 9 showed that Glyma.09G048900, an oxygen binding protein, was the closest to the QTL peak. Similarly, Glyma.17G090200 and Glyma.17G090400 were within 20-kb region of the seed yield QTL on chromosome 17. The candidate genes warrant further analysis to determine their functional mechanisms and develop markers for seed yield improvement.

Fine mapping and candidate gene analysis of CRA3.7 conferring clubroot resistance in Brassica rapa.

In this study, we fine-mapped a clubroot resistance gene CRA3.7 in Chinese cabbage and developed its closely linked marker syau-InDel3008 for marker-assisted selection in CR cultivars breeding. Chinese cabbage is an important leafy vegetable rich in many nutrients widely grown in China. Clubroot disease caused by an obligate biotrophic pathogen Plasmodiophora brassicae was rapidly spread and challenged to Chinese cabbage production. A clubroot resistance (CR) gene, CRA3.7, was mapped on chromosome A03 of Brassica rapa. A Chinese cabbage line 'CR510', which harbor homozygous resistance locus CRA3.7 was selected from a BC4F3 family. 'CR510' was crossed with a clubroot susceptible Chinese cabbage inbred line '59-1'. Total 51 recombinant plants were identified from an F2 population including 3000 individuals. These recombinants were selfed and the clubroot resistance of F2/3 families was evaluated. Finally, a clubroot resistance gene CRA3.7 was fine-mapped to an interval of approximately 386 kb between marker syau-InDel3024 and syau-InDel3008. According to the reference genome, total 54 genes including five encoding the TIR-NBS-LRR proteins was annotated in the fine-mapped region. Further, nine candidate's gene expression in parental lines at 7, 14 and 21 days after inoculation of P. brassicae were evaluated. Bra019376, Bra019401, Bra019403 and Bra019410 are highly expressed in 'CR510' than '59-1'. Gene sequence of Bra019410 from 'CR510' was cloned and identified different from CRa. Therefore, Bra019376, Bra019401, Bra019403 and Bra019410 are the most likely candidates for CRA3.7. Our research provides a valuable germplasm resource against P. brassicae Pb3 and CRA3.7 closely linked marker for marker-assisted selection in CR cultivars breeding.

RNA-sequencing analysis of candidate genes involved in berry development in 'Summer Black' grapes and its early bud mutants varieties

Berry development time and early maturity are important breeding traits in grapes. The mechanisms for early grape bud mutants remain unclear. Grape development is divided into three major phases known as the modified E–L system. This study measured fructose, glucose, tartaric acid, gallic acid, malic acid, and dihydroquercetin of ‘Summer Black’ and its bud mutants cultivars ‘Chunxiangwuhe,’ ‘Zaoxiaxiang,’ and ‘Sanbenti’ at different fruit development stages to determine their role in fruit maturity. RNA-sequencing analysis was used to identify the genes involved in fruit ripening. The results showed that fructose and glucose were accumulatedearlier during the EL-34 stage of the early bud mutants cultivars, whereas malic and tartaric acids levels showed a significant downward trend. Gene set enrichment analysis and weighted gene co-correlation network analysis showed that the differentially expressed genes were primarily enriched in flavonoid biosynthesis and galactose metabolism. Some candidate genes, including GAST1, APX2, ATHB-12, and AOS1, were identified via DEG and transcription factor prediction analyses. These genes play an essential role in the development of grape berries. The role of these genes was verified via qRT-PCR. The results of this study provide a theoretical basis for the genetic improvement of grapes.

Fine-mapping and candidate gene analysis of qFL-c10-1 controlling fiber length in upland cotton (Gossypium hirsutum L.).

A fiber length QTL, qFL-c10-1, was fine-mapped to a 96.5-kb region containing one gene that has not been characterized in plants. Fiber length is an important component of cotton fiber quality, which is associated with other quality properties such as fiber strength, fiber maturity, and fineness. In our previous studies, a stable QTL qFL-c10-1 controlling fiber length had been identified on chromosome A10 in an upland cotton recombinant inbred line (RIL) population from a cross between Jimian5 and DH962. To fine-map qFL-c10-1, an F2 population with 1081 individual plants from a cross between a recombinant line DJ61 and Jimian5 was established. Using linkage analysis and progeny recombination experiment, qFL-c10-1 was mapped into a 96.5-kb genomic region that just contained one proper transcript Ghir_A10G022020 (described as GhFL10), an undescribed gene in plants. One 214-bp deletion was identified in the promoter region of DJ61 compared with Jimian5. Quantitative real-time PCR (qRT-PCR) and comparative analysis of parental sequences suggested that GhFL10 was the most promising candidate gene for qFL-c10-1. According to RNA-seq, yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC), we speculate that GhFL10 interacts with NF-YA transcription factors to negatively regulate fiber elongation.

Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.).

Identification and genomic characterization of major resistance locus against cotton bacterial blight (CBB) using GWAS and linkage mapping to enable genomics-based development of durable CBB resistance and gene discovery in cotton. Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm), has periodically been a damaging disease in the USA. Identification and deployment of genetic resistance in cotton cultivars is the most economical and efficient means of reducing crop losses due to CBB. In the current study, genome-wide association study (GWAS) of CBB resistance using an elite diversity panel of 380 accessions, genotyped with the cotton single nucleotide polymorphism (SNP) 63K array, and phenotyped with race-18 of CBB, localized the CBB resistance to a 2.01-Mb region in the long arm of chromosome D02. Molecular genetic mapping using an F6 recombinant inbred line (RIL) population showed the CBB resistance in cultivar Arkot 8102 was controlled by a single locus (BB-13). The BB-13 locus was mapped within the 0.95-cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i04890Gh and i04907Gh of the BB-13 locus, identified from the combined linkage analysis and GWAS, targeted it to a 371-Kb genomic region. Candidate gene analysis identified thirty putative gene sequences in the targeted genomic region. Nine of these putative genes and two NBS-LRR genes adjacent to the targeted region were putatively involved in plant disease resistance and are possible candidate genes for BB-13 locus. Genetic mapping and genomic targeting of the BB13 locus in the current study will help in cloning the CBB-resistant gene and establishing the molecular genetic architecture of the BB-13 locus towards developing durable resistance to CBB in cotton.

Genetic mapping and meta-analysis identifies several candidate genes for watermelon (Citrullus lanatus) fruit quality traits

Citron (Citrullus amarus), a wild relative of watermelon possesses white flesh with coarse texture and bland/bitter taste; this may cause undesirable effect on quality in watermelon breeding. It is therefore important to understand the genomic regions/genes governing fruit quality, while using this species in introgressive breeding to avoid linkage drag. Hence, in the current experiment an attempt has been made to understand genes/QTLs governing important fruit quality traits in an inbred line derived from C. amarus. BIL-53 (P1) characterized by creamish white flesh, low TSS, red colored seeds and flat fruit shape; and ice box type inbred line, IIHR-140–152 (P2) characterized by dark red colored flesh, high TSS, black colored seeds and oblong fruit shape were used as parents for this QTLs study. Among 693 markers screened, 202 (29.14%) markers were found to be polymorphic and were used for linkage map construction and QTL mapping. QTL mapping identified eleven major QTLs for fruit shape on chromosome 3, 4 and 11. Candidate gene analysis in these regions validated Cla011257 gene on chromosome 3 and predicted Cla016683 gene in a novel QTL region on chromosome 11 as a putative candidate for fruit shape. Similarly, one novel QTL was identified for total soluble solids on chromosome 11, candidate gene analysis in this region predicted Cla016890 and Cla016891 genes as putative candidates. For flesh color, this is the first attempt to map the genes/QTLs governing flesh color at the different regions of fruit through visual and colorimetric analysis. Results revealed fifteen major QTLs on chromosome 2, 4, 5, 6, 7 and 10 for flesh color at different regions. Candidate gene analysis predicted Cla020214 and Cla020121 on chromosome 2; Cla005011 on chromosome 4; Cla018767, Cla018768, Cla018769, Cla018770, Cla018771 on chromosome 6; Cla017416 and Cla017593 on chromosome 10 as a probable candidates genes governing flesh color at different regions. The results presented here provide valuable information for future studies on functional validation of putative candidate genes and breeding of important fruit quality traits in watermelon.

Polygenic plague resistance in the great gerbil uncovered by population sequencing.

Pathogens can elicit high selective pressure on hosts, potentially altering genetic diversity over short evolutionary timescales. Intraspecific variation in immune response is observable as variable survivability from specific infections. The great gerbil (Rhombomys opimus) is a rodent plague host with a heterogenic but highly resistant phenotype. Here, we investigate the genomic basis for plague-resistant phenotypes by exposing wild-caught great gerbils to plague (Yersinia pestis). Whole genome sequencing of 10 survivors and 10 moribund individuals revealed a subset of genomic regions showing elevated differentiation. Gene ontology analysis of candidate genes in these regions demonstrated enrichment of genes directly involved in immune functions, cellular metabolism and the regulation of apoptosis as well as pathways involved in transcription, translation, and gene regulation. Transcriptomic analysis revealed that the early activated great gerbil immune response to plague consisted of classical components of the innate immune system. Our approach combining challenge experiments with transcriptomics and population level sequencing, provides new insight into the genetic background of plague-resistance and confirms its complex nature, most likely involving multiple genes and pathways of both the immune system and regulation of basic cellular functions.

Research Progressin Single Nucleotide Polymorphism of Vitiligo Susceptibility Gene

Vitiligo is a depigmentation disease affected by a variety offactors,of which genetic factors play a key role.Single nucleotide polymorphism as a common type of genetic variation can be detected by candidate gene analysis and genome-wide association study.The recent studies have demonstrated that multiple susceptibility genes play a vital role in the occurrence and development of vitiligo.This article introduces the single nucleotide polymorphisms of vitiligo susceptibility genes according to the gene functions.

Role of 19 SNPs in 10 genes with type 2 diabetes in the Pakistani population

Meta-GWAS report numerous variants associated with type 2 diabetes (T2D), however, for diabetic retinopathy (DR) no loci achieved genome-wide significance. There are limited candidate gene analyses for T2D and/or DR reported from the Pakistani population. Therefore, the current study was designed to evaluate the genetic association of 10 loci with T2D, non-proliferative DR (NPDR), and proliferative DR (PDR). In total 375 T2D cases and 205 controls were collected. The T2D cases included diabetic no retinopathy (n = 196), NPDR (n = 95), and PDR (n = 84). Genomic DNA was isolated, and 19 SNPs were genotyped. To determine association of SNPs with T2D, logistic regression analyses were performed adjusting for age and sex. Moreover, for association of SNPs with NPDR and PDR logistic regression analyses adjusting for diabetes duration and age of T2D onset were performed. In multivariate analysis, the minor alleles of rs1043618 [G > C, odds ratio (OR) 95% confidence interval (CI) = 1.45 (1.13–1.87), p = 4.00E-3], rs3807987 [G > A, 1.87 (1.22–2.94), p = 0.01], rs12672038 [G > A, 1.53 (1.04–2.30), p = 0.03] and rs2055858 [G > C, 1.70 (1.20–2.43), p = 3.00E-3] were associated with higher risk while rs1801133 (C > T, 0.59 (0.42–0.83), p = 2.28E-3) was associated with a lower risk of T2D. Moreover, minor alleles of rs2055858 [G > C, 1.77 (1.17–2.68), p = 0.02], and rs3759890 [C > G, 2.17 (1.39–3.39), p = 4.00E-3] showed an association with PDR when compared with DNR. However, only the association of rs1801133 survived multiple test correction. Hence, we report that rs1801133 is associated with T2D in the Pakistani population. In addition, out of studied 10 genes 8 proteins had higher interactions among themselves that are predicted to be partially biologically connected, as a group.