Meta-QTL analysis in wheat: progress, challenges and opportunities

Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.

Isolation and genetic analysis of Porcine circovirus 2 in southern India evidences high circulation of Porcine circovirus 2d genotype

BACKGROUND

Porcine circovirus 2 is globally noted swine pathogen with multiple genotypes associated with vast clinical and subclinical outcomes. This study aimed to isolate and characterize PCV2 genotypes circulating in southern states of India.

METHODS AND RESULTS

A total of 434 field samples comprising of serum (n = 273), tissues (n = 109) and swabs (n = 52) collected from swine during 2019 to 2021 from southern states of India were screened for PCV2 by specific polymerase chain reaction (PCR) assay. Molecular prevalence of PCV2 in southern India was found to be 12.21% (n = 53). All the 53 PCV2 positive samples were further subjected to the PCR assay with designed primers targeting full length amplification of ORF2 gene of PCV2 for molecular characterization. Randomly 32 positive samples by full length PCV2-ORF2 gene PCR were sequenced for genotyping. Signature motif and phylogenetic analysis of 32 PCV2 sequences revealed 62.5% (n = 20) prevalence of PCV2d genotype followed by 21.8% (n = 7) of PCV2h or PCV2-IM1 and 15.6% (n = 5) of PCV2b genotypes. Twenty five PCR positive field samples were subjected for virus isolation in PK15 cells and characterized. Out of 25 samples processed 5 (20%) PCV2 isolates obtained in this study were confirmed by PCR and immune fluorescence assay. Molecular characterization of PK15 adapted five PCV2 isolates confirmed circulation of PCV2d, PCV2h and PCV2b genotypes in pigs under field conditions in southern India.

CONCLUSIONS

Isolation and molecular epidemiological study of PCV2 in southern states of India evidences high circulation of PCV2d genotypes in field conditions in comparison to other genotypes.

Molecular evidence of porcine circovirus 3 infection in swine: first report in southern India

The present study examined 434 field samples including serum (n = 273), swabs from natural orifices (n = 52) and postmortem tissue samples (n = 109) from both suspected and asymptomatic swine from Andhra Pradesh, Karnataka, Kerala, Pondicherry, Tamil Nadu, and Telangana states in southern India. All the samples were processed for molecular screening of PCV3 by specific PCR assay. Overall molecular positivity rate of PCV3 was found to be 0.7% in southern India with one sample positive from each state of Tamil Nadu, Kerala and Telangana. All the three PCR positive PCV3 samples are detected from reproductive failures and were processed and propagated in PK15 cell line for virus isolation. Out of 3 samples processed, one (INDKL9PK76) PCV3 isolate could be obtained in this study and it was confirmed by specific PCR at third and fifth passage levels. Sequencing of PCV3 positive PCR amplicon (INDKL9PK76) revealed 1004 nucleotides and BLAST analysis confirmed partial sequence of the PCV3 genome. The aligned contig sequence was submitted to GenBank under the accession number of MW627201. PCV3 sequence in this study revealed 99% homology with PCV3 isolates from Europe and China. Phylogentic analysis of the PCV3 isolate-INDKL9PK76 sequence along with established PCV3 genotypes revealed clustering within PCV3 genotypes. Characterization of PCV3 (INDKL9PK76) isolate based on deduced amino acid composition of PCV3-capsid protein revealed "A" (alanine) and "R" (arginine) at 24th and 27th residues respectively confirming the incidence of PCV3a genotype. This study evidences PCV3 associated reproductive failure in domestic pigs for the first time in southern India.

Molecular detection of porcine parvovirus 1-associated reproductive failure in southern India

This study used 56 aborted and stillborn fetuses from organized swine farms in Tamil Nadu and Kerala, southern states of India. All samples were screened by using a PCR assay that targets the NS1 gene for PPV. Furthermore, the PCR positive samples were subjected to amplification of the VP2 gene of PPV1 with designed primers and sequenced for further study. The PCR screening of 56 samples found that 14.3% (n = 8) were positive for PPV genome. According to VP2 gene–based PCR for PPV1, 897 bp specific amplicons were detected in all eight of the samples. Two of the eight positive samples (L17 and T5) were sequenced and annotated randomly. The BLAST analysis of contig sequence INDTNCHN-T5 revealed 100% sequence homology with Chinese PPV1genome, whereas sequence from INDTNCHN-L17 revealed 99.43% sequence homology with Spain, Chinese, and German. PPV1 sequences and both the sequences INDTNCHN-T5 and INDTNCHN-L17 were submitted to the GenBank under the accession numbers MW822566 and MW822567 respectively. A phylogenetic analysis of the sequences in this study revealed specific grouping along with PPV1 strains in cluster E. Amino acid analysis of both isolated sequences in addition to the reference sequence from PPV1 showed variations in position 215 (I to T) in both the isolates, variation at position 228 (Q to E) in T5 isolate and variations at position 59 (L to M) and 314 (K to E) in L17 isolate. This study represents the first report of PPV1 cluster E in Tamil Nadu, southern India.

Sequence analysis of VP2 hypervariable region of the field isolates of infectious bursal disease viruses from southern region of India

Infectious bursal disease virus isolates obtained from southern parts of India were subjected to comparative sequencing and phylogenetic analysis of 743bp hypervariable region of VP2. The sequence analysis showed that among eight isolates, only HY12 showed the characteristic conserved amino acid residues at 256I, 294I, and 299S of vvIBDV. Six isolates BGE14, PY12, NKL14, VCN14, RPM14 and EDE14 had conserved amino acid residues at 256I and 299S, whereas at residue 294, isoleucine was substituted by valine. The remaining isolate MB11 had leucine at residue 294 and asparagine at residue 299 similar to classical strain 52/70. The serine-rich heptapeptide sequence SWSASGS adjacent to the second hydrophilic region was conserved in all seven Indian IBDV isolates except isolate MB11. Conservation of this sequence was earlier reported to be an indication of a virus isolate being pathogenic in nature. The reported heptapeptide sequence of the classical strain is 'SWSARGS'. In the present study, 'SWSARGS' heptapeptide sequence was observed in MB11 isolate. The pathogenicity trials conducted with these isolates further confirmed the genome analysis in classification. This study further reveals that the circulating IBDV strains in India could be diverse in nature.

Prevalence of enteropathogens and their antibiotic sensitivity pattern in puppies with hemorrhagic gastroenteritis

AIM

Hemorrhagic gastroenteritis (HGE) ranging from mild to severe forms is commonly encountered in puppies. The aim of the study was to identify the prevalence of common enteropathogens and the antibiotic sensitivity pattern in puppies reported with HGE.

MATERIALS AND METHODS

The canine HGE activity index, with little modification, was adopted to identify Grade III/severely affected puppies below 6 months of age. Fecal polymerase chain reaction (PCR) assay was employed to screen and compare the enteropathogens in puppies with hemorrhagic diarrhea and healthy control.

RESULTS

Canine parvovirus 2b was identified in 90.3% of the diarrheic and 10% of the non-diarrheic healthy puppies. Clostridium difficile was identified in all the diarrheic puppies and in 80% of the healthy puppies. Among the diarrheic puppies, 17.7% were positive for Clostridium perfringens enterotoxin, 9.7% were positive for C. perfringens alpha toxin, 6.4% were positive for Escherichia coli shiga toxin, 6.4% were positive for E. coli enterotoxin (LT), and 3.2% were positive for canine distemper virus. Whereas, none of the healthy puppies were positive for these bacteria and toxins. Fecal antibiotic sensitivity test pattern revealed gentamicin to be sensitive in 95% of the cases, azithromycin in 50%, enrofloxacin in 25%, cefotaxime in 20%, and tetracycline in 5% of the cases.

CONCLUSION

Parvoviral enteritis is predominant among puppies. Yet, bacteria and their toxins also play an important role in HGE. Gentamicin has higher sensitivity against the enteropathogens associated with the condition.

Comparison of Immunoprotection of Leptospira Recombinant Proteins with conventional vaccine in experimental animals

Leptospirosis is a bacterial disease caused by bacteria of the genus Leptospira affecting humans and animals. Untreated leptospirosis may result in severe kidney damage, meningitis, liver failure, respiratory distress, and even death. Virulent leptospirosis can rapidly enter kidney fibroblasts and induce a programmed cell death. Thus, it is a challenge for immunologists to develop an effective and safe leptospirosis vaccine. Here, we compared the commercial canine leptospira vaccine and recombinant proteins (OmpL1 and LipL41) with and without adjuvant in terms of immune response and challenge studies in hamsters and immune response studies alone in experimental dogs. The outer membrane proteins viz., lipL41 and OmpL1 of leptospira interrogans serovars icterohaemorrhagiae were amplified. The primers were designed in such a way that amplified products of OmpL1 and lipL41 were ligated and cloned simultaneously into a single vector. The cloned products were expressed in E. coli BL21 cells. The immunoprotection studies were conducted for both recombinant proteins and commercial vaccine. The challenge experiment studies revealed that combination of both rLip41 and rOmpL1 and commercial vaccine gave 83% and 87% protection, respectively. Histopathological investigation revealed mild sub lethal changes were noticed in liver and kidney in commercially vaccinated group alone. The immune responses against recombinant leptospiral proteins were also demonstrated in dogs.

Nucleotide sequence analysis of the L1 loop variable region of hexon gene of fowl adenovirus 4 isolates from India

Three fowl adenovirus 4 (FAV4) isolates from chicken and one from quail, all from Tamil Nadu, India were analyzed. The L1 loop variable region of hexon gene of these isolates was amplified by PCR and sequenced. The nucleotide sequences (442 bp) and deduced amino acid sequences of the four isolates were compared with those of other isolates of FAV4. The nucleotide sequences of the four isolates had a 98% homology with other Indian isolates and a 96% homology with Belgian and Russian isolates. The amino acid sequences of the four Indian isolates had a more than 98% homology with other Indian isolates and a more than 92% homology with Belgian and Russian isolates. Hence, the variable of L1 loop region of hexon gene was found to be highly homologous in all the FAV4 isolates tested both at nucleotide and amino acid level.

Rapid serological profiling by an immunocomb-based dot-enzyme-linked immunosorbent test for three major poultry diseases

An immunocomb-based dot-ELISA, employing specially designed apparatus, was used to measure the antibody status for the three major poultry diseases--Newcastle disease, infectious bursal disease and infectious bronchitis--in single test sera. Positive samples could be classified into strong, moderate and weak positives by comparison with the colour reaction given by known strong and weak positive serum controls. The simultaneous dot-immunobinding assay gave reproducible results and allowed considerable savings on the cost of reagents compared to liquid ELISA. The antigen-coated immunocomb can be stored under refrigeration and the test can be performed rapidly under field conditions by trained personnel.

Sequence analysis of infectious bursal disease virus isolates from India: phylogenetic relationships

Prevalence of infectious bursal disease (IBD) among chickens in different parts of Tamil Nadu, India, has been studied by collection of bursal samples from suspected flocks and by performing reverse transcription-polymerase chain reaction (RT-PCR) for amplification of a specific product of 474 bp from the variable region of the VP2 gene. Among 53 bursal samples examined by RT-PCR, 40 showed a positive reaction. The amplified products were subjected to nucleotide sequencing and the obtained sequences were compared with those of IBD virus (IBDV) vaccine strain Georgia, the classical virulent strain 52/70 and the very virulent Japanese OKYM strain. Nucleotide homology data indicated that all the Tamil Nadu isolates showed homology ranging from 91 to 99.6% among themselves. When compared with the very virulent Japanese OKYM strain, four isolates grouped with that strain. Majority of the isolates clustered with the very the virulent OKYM strain as evident from phylogenetic analysis performed using the MEGA program. Comparison of the deduced amino acid sequences of IBDV isolates with those of the vaccine strain Georgia, the classical virulent strain 52/70 and the very virulent strain OKYM also revealed the presence of conserved serine-rich heptapeptide sequence in most of the isolates. Results of this study indicate that majority of the IBDV isolates are very virulent, which is evident from heavy mortality that has been reported in few flocks of poultry in spite of regular vaccination.

Clinical spectrum of inflammatory myositis in South India--a ten year study

OBJECTIVE

To describe the clinical spectrum of inflammatory myopathies at a referral hospital in South India.

METHODS

Patients were assessed for the pattern of muscle involvement, for the presence of arthritis, Raynaud's phenomenon, interstitial lung disease (ILD) and cardiac involvement. Muscle enzymes, electromyogram (EMG) and muscle biopsies were done.

RESULTS

Eighty seven patients with inflammatory myopathies were encountered over 10 years. These included 24 with adult polymyositis, 26 with adult dermatomyositis, one with amyopathic dermatomyositis, five with juvenile myositis, one with dermatomysitis following carcinoma breast and 30 with overlap with other connective tissue diseases. There was a female preponderance (M:F = 1:2.35) except in juvenile myosits group (M:F = 1.5:1). The mean age of onset in years was 33.26 in adult polymyositis, 35.03 in adult dermatomyositis, 7.4 in juvenile dermatomyositis, 42 in malignancy-associated dermatomyositis and 25.51 in the overlap group. Proximal muscle weakness was seen in 98.8% patients, dysphagia in 33.3%, distal muscle weakness in 12.5%, respiratory muscle weakness in 9.2% and dysphonia in 4.6%. Other features included arthritis 35.63%, interstitial lung disease (ILD) 9.2%, Raynaud's 5.7%, myocarditis 4.6% and conduction disturbances 1.15%. Eleveated muscle enzymes were seen in 85.1% patients. Eletromyogram was positive in 66.6%. Muscle biopsy was positive in 85.29%. Anti-nuclear antibody was positive in 67.24%. All received steroids, non-responders needed methotrexate (13 patients) or azathioprine (11 patients). Death occurred in 10 (seven with dermatomyositis predominantly due to respiratory involvement and three with overlap).

CONCLUSION

There was female preponderance except in juvenile myositis group. Proximal muscle weakness was the commonest feature. ILD was the commonest respiratory problem, while myocarditis was the commonest cardiac problem seen. Response to therapy and prognosis in polymyositis were good with no mortality during the study period. Death in the dermatomyositis group was mainly due to respiratory involvement.

The value of tissue imprint hybridization for rapid detection of infectious bursal disease virus from field outbreaks

The use of a peroxidase labelled PCR generated probe followed by enhanced chemiluminescence hybridization assay detected infectious bursal disease virus directly from bursal imprints on a nylon membrane. Tissue imprint hybridization proved to be a simple, rapid and safe means of detecting IBD virus for screening large numbers of field samples. The PCR generated probe was highly specific for IBD virus and did not hybridize with cellular nucleic acids in control imprints. Tissue imprint hybridization was found to be a more sensitive method than conventional antigen detection assays.

HLA class I and class II association with ankylosing spondylitis in a southern Indian population

Ankylosing spondylitis (AS) is a chronic inflammatory condition associated with HLA B27. But the association is not absolute. Hence association with other HLA class I antigens and class II alleles was studied in a southern Indian population. Sixty-five patients with primary AS were typed serologically for HLA class I antigens. Age- and sex-matched disease controls (37 with enterogenic reactive arthritis [ReA] and 25 with undifferentiated spondyloarthropathy [UnSpA]) and 124 healthy controls were studied. PCR-based DNA-SSO typing for DQA1 and DQB1 was performed on 20 patients with AS and 38 healthy controls. Twenty-three patients with AS and 39 controls were typed for DRB1 alleles. HLA B27 was positive in 76.9 % of the cases of AS (RR 811), 59.5% of those with ReA (RR 9.3), and 40% of the patients with UnSpA (RR 9.3), while none of the controls were B27 positive. The P value for positive association was highly significant for B27 in all the three groups. B27 positivity was associated with earlier age of onset of disease in all the diseases compared to the B27-negative group. HLA Cw2 was positively associated with AS (P highly significant; OR 52) and ReA (P = 0.0003; OR 14.2). HLA A1 and CW6 were significantly negatively associated only with AS (P = 0.0001 and 0.00004 and OR 0.25 and 0.02, respectively). None of the HLA class II alleles were significantly associated with AS. The apparent association with DRB1*11 (P = 0.03) was lost after Yates correction.

Class II MHC alleles in rheumatoid arthritis in Tamilnadu, India: is there an association?

Rheumatoid arthritis (RA) was reported to be associated with class II MHC alleles in different ethnic populations. A similar study was undertaken to determine the association of class II MHC with RA patients of Tamilnadu (Tamil-speaking Hindus), India. Thirty patients with RA and 39 healthy controls were included. Polymorphic second exons of the DRB1, DQA1, and DQB1 genes were amplified and subjected to SSOP typing. No allele was found to be significantly associated with RA. However DRB1*11 (P = 0.01) and DQB1*0302 (P = 0.02) were significantly associated with rheumatoid factor-positive RA patients. (All the DRB1*11-positive RA patients had either *04 or *10 allele as their second allele. This study is first of its kind in this population.

Childhood systemic lupus erythematosus in south India

Out of 330 adult Systemic Lupus Erythematosus (SLE) cases who attended the Rheumatic Care Centre, Government General Hospital, 59 children were analysed. There was no case with onset before the age of 5 years. There were 49 females and 110 males (M:F = 1:4.9). The initial manifestations were fever (67%), arthritis (61%), skin rash (59%) and lymphadenopathy (27.1%). There was no case of Raynaud's phenomenon. Only 10.1% of patients presented with thrombocytopenic purpura. In the cumulative clinical features, arthritis in 86.6%, fever in 79.8%, skin rash in 69.4%, lymphadenopathy in 61% and hepatosplenomegaly in 39.9% were observed. Renal involvement was seen in 49.1%, neuropsychiatric manifestations in 27.1%, pleuropulmonary in 22% and cardiac manifestations in 10.2%. Anaemia was seen in 50.8%, leukopenia in 18.4%, thrombocytopenia in 11.8%, ANA in 100%, anti-dsDNA in 92.3%, anti-Sm in 34.7%, anti-SSA in 38.5%, anti-SSB in 15.4%, ACL in 30.8%, low C3 in 50% and false positive VDRL in 3.3%. Death occurred in 8 children, 3 due to infection, 2 due to renal causes, 1 due to cardiac and 2 due to central nervous system involvement.

Progressive systemic sclerosis in south India

Seventy eight patients with progressive systemic sclerosis (PSS) were seen over a period of 14 years. They were analysed after clinical, haematological, biochemical, immunological and radiological investigations for comparison with other Indian and Western studies. Nine of the 78 were cases of childhood PSS. There was a female preponderance (3.9:1) and the peak age of occurrence was the 4th decade (32.1%). Arthralgia (53.8%) and skin thickening (70.5%) were the common presenting symptoms. Raynaud's phenomenon (28.2%) was less common. Involvement of the skin was present in all the patients and skin biopsy was positive in 96% of the cases. Joints were affected in 66.7%; internal organs were involved in 52.6%. Antinuclear antibody was positive in 56.8%. Abnormal echocardiography (37.6%) and barium studies (20.4%) were seen. Restrictive airway pattern by pulmonary function test was present in 55%. Death occurred in 5 patients, of whom 3 died of severe pulmonary hypertension.

Pattern of rheumatic diseases in south India. IV. Clinical profile of juvenile rheumatoid arthritis

An analysis of 100 consecutive cases of juvenile rheumatoid arthritis from South India revealed a male preponderance (62%), a lower incidence of the systemic onset variety (10%) and equal incidence of systemic features when compared with the West. Knees and ankles were the joints commonly involved. The incidence of elevated erythrocyte sedimentation rate and C reactive protein, with haemoglobin levels below 10 g/dl was highest in the systemic onset variety. The polyarticular and systemic onset group responded well to aspirin, while the pauciarticular group responded well to indomethacin.

Pattern of rheumatic diseases in south India. V. Ankylosing spondylitis. A clinical and radiological study

One hundred and two patients from South India with primary ankylosing spondylitis (AS) were analysed clinically and radiologically. The mean age of onset was 26 years, with a male to female ratio of 16:1. Eleven patients presented as juvenile ankylosing spondylitis. The mode of presentation of AS included axial involvement in 59, peripheral arthritis in 38, heel pain in 18 and acute anterior uveitis (AAU) in 11. The overall incidence of extra axial features was high (90 patients). These included subjects with peripheral arthritis (49), heel pain (35), AAU (14), rib pain (11), aortic regurgitation (8), apical pulmonary fibrosis (5), mitral regurgitation (2) and conduction defects (2). Peripheral arthritis was characteristically asymmetrical and oligo articular, and involved lower limb joints. No renal involvement was noticed. Radiologically, bilateral sacroilitis was seen in 80% of cases.