Polymorphic Sequence Research Articles

Fine mapping and candidate gene analysis of a major QTL for grain length on chromosome 5BS in bread wheat

Large grain is a favorable trait for appearance quality and large sink potential in wheat breeding. A stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895). Here, a BC1F6 residual heterozygous line was selected from the cross of ZM871/ZM895//ZM871 population, and six heterozygous recombinant plants were identified in the BC1F7 population from self-pollination of the heterozygous line. QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2 (25.3-27.5 Mb) through phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants. Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses. Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS. A gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed, and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population including 166 cultivars using the marker. These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.

Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes.

Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.

Eggplant Little Leaf-Associated Phytoplasma Detection in Seedlings under Insect-Proof Conditions

Eggplant, or brinjal, is one of the most consumed and important tropical solanaceous vegetable crops grown worldwide. Little leaf is a disease associated with the presence of phytoplasmas especially widespread in brinjal in India. To clarify the epidemiology of this disease, a verification of its transmission through seeds to seedlings and their progeny derived from symptomatic mother plants was performed. Brinjal seeds field-collected in the Dharwad district of Karnataka State, India, were sowed in a greenhouse under insect-proof conditions. DNA was extracted from seedlings and their progeny and from symptomatic plant samples collected in the field. The first- and second-generation seedlings obtained *under these conditions were tested at various time points after germination by amplification of the 16S rRNA gene of phytoplasmas. The amplicons obtained were subjected to restriction fragment length polymorphism (RFLP) analysis and sequencing for the identification of detected phytoplasmas. Ribosomal groups 16SrI, 16SrII, 16SrIII, 16SrV, 16SrVI, and 16SrXII were identified. Moreover, a number of fruits produced from the first-generation seedlings showed precocious seed germination, and the young seedlings resulted as phytoplasma-positive. The seed transmission of phytoplasmas in eggplants for two subsequent generations highlights the risk of additional sources of infection of the disease represented by asymptomatic and infected seedlings in the presence of insect vectors. The seed transmission could explain the continuous presence of epidemic outbreaks of phytoplasmas in brinjal cultivations in several cultivation areas.

Production performance analysis of sheep MSTN gene C2361T locus

The myostatin (MSTN) gene exhibits significant nucleotide sequence variations in sheep, impacting growth characteristics and muscular traits of the body. However, its influence on specific growth traits in some sheep remains to be further elucidated. This study utilized single nucleotide polymorphism sequence analysis to investigate the role of the MSTN gene in meat production performance across four sheep breeds: Charolais sheep, Australian White sheep, crossbreeds of Australian White and Small-tailed Han, and crossbreeds of Charolais and Small-tailed Han. At a SNP locus of the MSTN gene, the C2361T site was identified, with three genotypes detected: CC, CT, and TT, among which CC predominated. Gene substitution effect analysis revealed that replacing C with T could elevate the phenotypic value. Comparative analysis of data from different genotypes within the same breed highlighted the superiority of CC and TT genotypes in phenotypic values, underscoring the significance of specific genotypes in influencing key traits. Contrasting the performance of different genotypes across breeds, Charolais sheep and Charolais Han hybrids demonstrated superiority across multiple indicators, offering valuable insights for breeding new sheep varieties. Analysis of gender effects on growth characteristics indicated that ewes exhibited significantly wider chest, waist, and hip widths compared to rams, while rams displayed better skeletal growth and muscle development. Additionally, the MSTN gene also exerted certain effects on lamb growth characteristics, with the CC genotype closely associated with weight. These findings not only contribute crucial insights for sheep breeding but also pave the way for future research exploring the interaction of this gene with others.

Molecular marker-assisted genetic diversity analysis in soybean cultivars from Himalayan region of Uttarakhand, India

‘Bhat’ is the soybean variety highly valued in the traditional food and therapeutic system of Uttarakhand state in the Indian Himalayan region. It is available in diverse colors, shapes, and sizes, often linked to their nutritional parameters. The present investigation was conducted to assess the diversity and genetic relatedness in ‘bhat’ genotype indigenous to the Garhwal division of Uttarakhand. 25 polymorphic simple sequence repeats (SSR) markers were used to determine the genetic diversity and varietal identification among the 45 genotypes collected from the different villages of Uttarakhand. Out of the different markers assessed only 13 primers showed amplification with the maximum of 2–4 alleles obtained with each primer with the molecular weight ranging between 80 and 400 kb. The highest band amplification was observed in Satt 257 and Satt 197. The allelic frequencies of amplified primers ranged from 0.5 to 0.833 with a mean value of 0.645 and the mean gene diversity and PIC value was found to be 0.43 and 0.33. Satt 183, Satt 288, and Satt 389 showed the highest polymorphism, while Satt257 and Satt245 exhibited the presence of unique alleles in some samples. The phylogenetic analysis grouped the genotypes into 4 major clusters having visually distinct phenotypes in each group, indicating the mixing of population and loss of authenticity also confirming that phenotypic attributes are not indicative of genetic relatedness among the genotype under study. The results indicate the need for the development of novel ‘bhat’ specific markers for more accurate genetic identification of the nutritionally rich indigenous soybean variety.

Epidemiología, clínica y prevención de la Viruela Símica. Revisión bibliográfica

Introduction: Monkeypox, or monkeypox, is a zoonosis endemic in the rural jungle areas of central and western Africa, in humans the first occurrence was in 1970 in the Democratic Republic of Congo. It is caused by a virus belonging to the genus Orthopoxvirus of the Poxviridae family. Objective: To determine the causes and predisposing factors to the outbreak of monkeypox, transmission routes, clinical manifestations, evolution, complications, diagnosis, therapeutic management, prevention and control of infection.Material and methods: A systematic review was carried out in the Medscape, Pubmed, Science Direct and Scielo databases. Thirty-one papers were used.Results: Monkeypox was discovered in 1958 in the city of Copenhagen, capital of Denmark, in monkeys used for research. In 1970, the first case of monkeypox in humans was reported in a child in the Democratic Republic of Congo. Once the diagnostic suspicion is determined, sampling is indicated to confirm infection by nucleic acid amplification test (NAAT) or real-time PCR. PCR is the definitive diagnostic test, can be alone or followed by restriction fragment length polymorphism (RFLP) analysis or sequencing, has high sensitivity and specificity; and a rapid turnaround time of about one day or less. Monkeypox is usually mild and most people recover without treatment.Conclusions: So far in Ecuador 421 cases of monkeypox have been reported, so it is important that public health officials and health care personnel receive training on the risk of the disease, recognition, treatment and isolation of cases. It is important that the country has sufficient PCR tests in public facilities for the confirmation of cases and as a method of prevention, citizens should maintain the biosecurity measures announced by the MSP.

Evolutionary analysis of LMP-1 genetic diversity in EBV-associated nasopharyngeal carcinoma: Bioinformatic insights into oncogenic potential

EBV latent membrane protein 1 (LMP-1) is an important oncogene involved in the induction and maintenance of EBV infection and the activation of several cell survival and proliferative pathways. The genetic diversity of LMP-1 has an important role in immunogenicity and tumorigenicity allowing escape from host cell immunity and more metastatic potential of LMP-1 variants. This study explored the evolutionary of LMP-1 in EBV-infected patients at an advanced stage of nasopharyngeal carcinoma (NPC). Detection of genetic variability in LMP-1 genes was carried out using Sanger sequencing. Bioinformatic analysis was conducted for translation and nucleotide alignment. Phylogenetic analysis was used to construct a Bayesian tree for a deeper understanding of the genetic relationships, evolutionary connections, and variations between sequences. Genetic characterization of LMP-1 in NPC patients revealed the detection of polymorphism in LMP-1 Sequences. Motifs were identified within three critical LMP-1 domains, such as PQQAT within CTAR1 and YYD within CTAR2. The presence of the JACK3 region at specific sites within CTAR3, as well as repeat regions at positions (122−132) and (133–143) within CTAR3, was also annotated. Additionally, several mutations were detected including 30 and 69 bp deletions, 33 bp repeats, and 15 bp insertion. Although LMP-1 strains appear to be genetically diverse, they are closely related to 3 reference strains: prototype B95.8, Med- 30 bp deletion, and Med + 30 bp deletion. In our study, one of the strains harboring the 30 bp deletion had both bone and bone marrow metastasis which could be attributed to the fact that LMP-1 is involved in tumor metastasis, evasion and migration of NPC cells. This study provided valuable insights into genetic variability in LMP-1 sequences of EBV in NPC patients. Further functional studies would provide a more comprehensive understanding of the molecular characteristics, epidemiology, and clinical implications of LMP-1 polymorphisms in EBV-related malignancies.

Comparative genomics analysis reveals sequence characteristics potentially related to host preference in Cryptosporidium xiaoi

Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi, which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis.

Genetic Diversity and Population Structure of Maize (Zea mays L.) Inbred Lines in Association with Phenotypic and Grain Qualitative Traits Using SSR Genotyping

Maize (Zea mays L.) is an important cereal and is affected by climate change. Therefore, the production of climate-smart maize is urgently needed by preserving diverse genetic backgrounds through the exploration of their genetic diversity. To achieve this, 96 maize inbred lines were used to screen for phenotypic yield-associated traits and grain quality parameters. These traits were studied across two different environments (Anand and Godhra) and polymorphic simple sequence repeat (SSR) markers were employed to investigate the genetic diversity, population structure, and trait-linked association. Genotype–environment interaction (GEI) reveals that most of the phenotypic traits were governed by the genotype itself across the environments, except for plant and ear height, which largely interact with the environment. The genotypic correlation was found to be positive and significant among protein, lysine and tryptophan content. Similarly, yield-attributing traits like ear girth, kernel rows ear−1, kernels row−1 and number of kernels ear−1 were strongly correlated to each other. Pair-wise genetic distance ranged from 0.0983 (1820194/T1 and 1820192/4-20) to 0.7377 (IGI-1101 and 1820168/T1). The SSRs can discriminate the maize population into three distinct groups and shortlisted two genotypes (IGI-1101 and 1820168/T1) as highly diverse lines. Out of the studied 136 SSRs, 61 were polymorphic to amplify a total of 131 alleles (2–3 per loci) with 0.46 average gene diversity. The Polymorphism Information Content (PIC) ranged from 0.24 (umc1578) to 0.58 (umc2252). Similarly, population structure analysis revealed three distinct groups with 19.79% admixture among the genotypes. Genome-wide scanning through a mixed linear model identifies the stable association of the markers umc2038, umc2050 and umc2296 with protein, umc2296 and umc2252 with tryptophan, and umc1535 and umc1303 with total soluble sugar. The obtained maize lines and SSRs can be utilized in future maize breeding programs in relation to other trait characterizations, developments, and subsequent molecular breeding performances for trait introgression into elite genotypes.

Novel electroporation-based genome editing of carnation plant tissues using RNPs targeting the anthocyanidin synthase gene.

A novel electroporation method for genome editing was performed using plant tissue samples by direct RNPs-introduction in carnation. Genome editing is becoming a very useful tool in plant breeding. In this study, a novel electroporation method was performed for genome editing using plant tissue samples. The objective was to create a flower color mutant using the pink-flowered carnation 'Kane Ainou 1-go'. For this purpose, a ribonucleoprotein consisting of guide RNA and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) was introduced into the stem tissue to induce mutations in the anthocyanidin synthase (ANS) gene, which is involved in anthocyanin biosynthesis. As the ANS of 'Kane Ainou 1-go' has not been previously isolated, we initially isolated the ANS gene from 'Kane Ainou 1-go' for characterization. Southern hybridization analysis confirmed that the ANS gene was present in the genome as a two-allele gene with a pair of homologous sequences (ANS-1 and 2); these sequences were used as the target for genome editing. Genome editing was performed by introducing #2_single-guide RNA into the stem tissue using the ribonucleoprotein. This molecule was used because it exhibited the highest efficiency in an analysis of cleavage activity against the target sequence in vitro. Cleaved amplified polymorphic sequence analysis of genomic DNA extracted from 85 regenerated individuals after genome editing was performed. The results indicated that mutations in the ANS gene may have been introduced into two lines. Cloning of the ANS gene in these two lines confirmed the introduction of a single nucleotide substitution mutation for ANS-1 in both lines, and a single amino acid substitution in one line. We discussed the possibility of color change by the amino acid substitution, and also the future applications of this technology.

Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing

Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.

Fhb9, a major QTL for Fusarium head blight resistance improvement in wheat

Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most devastating diseases of wheat worldwide. Identification and validation of major quantitative trait loci (QTLs) for FHB resistance without negative effects on agronomic traits is critical to success in breeding FHB-resistant cultivars. In this study, a stable major QTL on chromosome arm 2DL was identified by evaluating a recombinant inbred line (RIL) population derived from Shi4185×Shijiazhuang 8 in both field and greenhouse experiments. QTL mapping and pedigree analyses indicated that the 2DL QTL is the same QTL as QFhb-2DL previously identified in Ji5265, therefore, designated Fhb9. Four kompetitive amplicon sequence polymorphism (KASP) markers were developed based on exome capture sequencing data to enhance marker density in the Fhb9 region, and it was delimited to an interval between single nucleotide polymorphism (SNP) markers KASP-12056 (533.8) and KASP-525 (525.9 Mb) explained 26.0-30.1% of the phenotypic variation. Analysis of the geographic distribution of the Fhb9 resistance allele suggested that it originated from Huang-Huai winter wheat region in China, and very low frequency of Fhb9 in modern Chinese cultivars reveals that it has not been widely deployed in breeding programs. Field and greenhouse evaluation of yield-related traits of near-isogenic lines (NILs) contrasting in Fhb9 alleles indicated that Fhb9 resistance allele did not show any adverse effects on those traits. Fhb9 showed an additive effect on enhancing FHB resistance with Fhb1. Therefore, Fhb9 is a valuable major QTL for improving FHB resistance in wheat and the near-diagnostic markers developed in this study will facilitate its deployment in wheat breeding programs.

Characterization of a human H3N8 influenza virus

In 2022 and 2023, novel reassortant H3N8 influenza viruses infected three people, marking the first human infections with viruses of this subtype. Here, we generated one of these viruses (A/Henan/4-10CNIC/2022; hereafter called A/Henan/2022 virus) by using reverse genetics and characterized it. In intranasally infected mice, reverse genetics-generated A/Henan/2022 virus caused weight loss in all five animals (one of which had to be euthanized) and replicated efficiently in the respiratory tract. Intranasal infection of ferrets resulted in minor weight loss and moderate fever but no mortality. Reverse genetics-generated A/Henan/2022 virus replicated efficiently in the upper respiratory tract of ferrets but was not detected in the lungs. Virus transmission via respiratory droplets occurred in one of four pairs of ferrets. Deep-sequencing of nasal swab samples from inoculated and exposed ferrets revealed sequence polymorphisms in the haemagglutinin protein that may affect receptor-binding specificity. We also tested 90 human sera for neutralizing antibodies against reverse genetics-generated A/Henan/2022 virus and found that some of them possessed neutralizing antibody titres, especially sera from older donors with likely exposure to earlier human H3N2 viruses. Our data demonstrate that reverse genetics-generated A/Henan/2022 virus is a low pathogenic influenza virus (of avian influenza virus descent) with some antigenic resemblance to older human H3N2 viruses and limited respiratory droplet transmissibility in ferrets. This work was supported by the Japan Program for Infectious Diseases Research and Infrastructure (JP23wm0125002), and the Japan Initiative for World-leading Vaccine Research and Development Centers (JP233fa627001) from the Japan Agency for Medical Research and Development (AMED).

Development of a rapid detection assay for acetolactate synthase inhibitors resistance in three Amaranthus weed species through loop-mediated isothermal amplification.

The early detection of herbicide resistance in weeds is a key factor to avoid herbicide waste and improve agriculture sustainability. The present study aimed to develop and validate an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for the quick on-site detection of the resistance-endowing point mutation Trp-574-Leu in the acetolactate synthase (ALS) gene in three widely diffused Amaranthus weed species: Amaranthus retroflexus, Amaranthus hybridus and Amaranthus tuberculatus. The AS-LAMP protocol was developed on wild-type and ALS-mutant plants of the three species and revealed that the amplification approach with only the primer set specific for the mutant allele (574-Leu) was the most promising. The validation and estimation of the AS-LAMP performance evaluated by comparing the results with those of the molecular marker (cleaved amplified polymorphic sequences) indicated that, although the sensitivity and specificity were relatively high in all species (overall 100 and > 65%, respectively), precision was high for A. hybridus L. and A. retroflexus L. (75 and 79%, respectively), but quite low for A. tuberculatus (Moq.) J. D. Sauer (59%). The LAMP assay was also effective on crude genomic DNA extraction, allowing the quick detection of mutant plants in field situation (on site resistance detection). The proposed AS-LAMP method has proven to be a promising technique for rapid detection of resistance as a result of Trp-574-Leu on the two monoecious weedy Amaranthus species but resulted less effective in the genetically variable dioecious species A. tuberculatus. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings.

Ten stable loci for freezing tolerance (FT) in wheat were detected by genome-wide association analysis. The putative candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identified and validated. Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties and lines, and genotyped them using a Wheat 90K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 570.67-571.16Mb interval (0.49Mb) on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+1956, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (including the above 245 materials) and 318 F2 lines derived from the cross of 'Annong 9267' (freezing-tolerant) × 'Yumai 9' (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in 'Yumai 9' by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.

Fine mapping of ClLOX, a QTL for powdery mildew resistance in watermelon (Citrullus lanatus L.).

ClLOX, is located on chromosome 2 and encodes a lipoxygenase gene, which induced watermelon powdery mildew resistance by inhibiting pathogen spread. Powdery mildew is one of the most severe fungal diseases reducing yield and quality of watermelon (Citrullus lanatus L.) and other cucurbit crops. Genes responsible for powdery mildew resistance in watermelon are highly valuable. In this study, we first identified the QTL pm-lox for powdery mildew resistance in watermelon, located within a 0.93Mb interval of chromosome 2, via XP-GWAS method using two F2 populations. The F2:3 families from one of the F2 populations were then used for fine-mapping the pm-lox locus into a 9,883bp physical region between 29,581,906 and 29,591,789, containing only two annotated genes. Of these, only ClG42_02g0161300 showed a significant differential expression between the resistant and susceptible lines after powdery mildew inoculation based on RNA sequencing (RNA-seq) and qRT-PCR analysis, and is designated ClLOX. Derived Cleaved Amplified Polymorphic Sequence (dCAPs) markers were developed and validated. In addition, our tests showed that the resistance was anti-spread rather than anti-infection of the pathogen. This study identified a new resistance gene (ClLOX), provided insights into the mechanism of powdery mildew resistance, and developed a molecular marker for watermelon breeding.

Sequencing and characterizing short tandem repeats in the human genome.

Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.

Polymorphism rs5780218, rs12998 and rs10158616 in KISS1 gene among the Hubei province Chinese girls with the central precocious puberty.

Central precocious puberty (CPP) results from early activation of the hypothalamic-pituitary-gonadal (HPG) axis. To elucidate the molecular genetic basis of CPP, we here investigated the effects of polymorphism rs5780218, rs12998 and rs10158616 in KISS1 gene on CPP susceptibility. The three KISS1 gene polymorphisms were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Sanger sequencing in 422 healthy Hubei Chinese girls and 384 Hubei Chinese girls with CPP. Single-locus analysis demonstrated that rs5780218 and rs12998 were significantly associated with CPP susceptibility in Hubei Chinese girls. Haplotype analysis exhibited that the AGG carrying the risk allele A of rs5780218 and the -GG carrying the protective allele - of rs5780218 were associated with increased and decreased CPP susceptibility in Hubei Chinese girls, respectively. The following meta-analysis confirmed the contribution of rs5780218 and rs12998 on CPP susceptibility in Chinese girls. rs5780218 and rs12998 in the KISS1 gene may participate in genetic susceptibility to CPP in Chinese girls, and the KISS1 gene rs5780218 may serve as a genetic biomarker of CPP. However, the present findings should be validated in future studies with larger sample sizes in other ethnic populations.

Genetic characterization of new source of resistance for tomato leaf curl New Delhi virus (ToLCNDV) from snapmelon (C. melo var. momordica)

AbstractThis study aimed to understand the genetics of tomato leaf curl New Delhi virus (ToLCNDV) in the identified novel source of resistance from Indian melon germplasm DSM-19 (Cucumis melo var. momordica) as viral diseases in muskmelon cause significant economic yield loss. To achieve this, a cross was made between the highly susceptible genotype Pusa Sarda (C. melo var. inodorus), known for its desirable fruit characters, and the resistant source DSM-19 to generate the suitable populations for inheritance study. These populations were screened under natural epiphytotic conditions and further validated through challenge inoculation with viruliferous whiteflies. The inheritance of ToLCNDV resistance in snapmelon germplasm DSM-19 was identified as monogenic recessive in both the screening methods. Moreover, a cleaved amplified polymorphic sequence (CAPS) marker named ‘CAPS 16 (2)’ was designed near to SNP marker D16 located on chromosome 11 of melon, and it was found to be linked to the ToLCNDV resistance gene in DSM-19. This is the first report on genetics of ToLCNDV resistance in snapmelon germplasm from India. Snapmelon line DSM-19 can be used as a source for fine mapping and introgression of the ToLCNDV resistance into susceptible muskmelon cultivars.

The Resistance of Soybean Variety Heinong 84 to Apple Latent Spherical Virus Is Controlled by Two Genetic Loci.

Apple latent spherical virus (ALSV) is widely used as a virus-induced gene silencing (VIGS) vector for function genome study. However, the application of ALSV to soybeans is limited by the resistance of many varieties. In this study, the genetic locus linked to the resistance of a resistant soybean variety Heinong 84 was mapped by high-throughput sequencing-based bulk segregation analysis (HTS-BSA) using a hybrid population crossed from Heinong 84 and a susceptible variety, Zhonghuang 13. The results showed that the resistance of Heinong 84 to ALSV is controlled by two genetic loci located on chromosomes 2 and 11, respectively. Cleaved amplified polymorphic sequence (CAPS) markers were developed for identification and genotyping. Inheritance and biochemical analyses suggest that the resistance locus on chromosome 2 plays a dominant dose-dependent role, while the other locus contributes a secondary role in resisting ALSV. The resistance locus on chromosome 2 might encode a protein that can directly inhibit viral proliferation, while the secondary resistance locus on chromosome 11 may encode a host factor required for viral proliferation. Together, these data reveal novel insights on the resistance mechanism of Heinong 84 to ALSV, which will benefit the application of ALSV as a VIGS vector.