• Sushil Kumar

      Articles written in Journal of Genetics

    • Isolation and characterization ofgsv mutants of grain pea (Pisum sativum) having white stem and green leaflets

      Sushil Kumar Raghuveer Polisetty Nam Prakash T. V. R. Nair

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      Two Gsv- mutants have been isolated in mutagenized grain pea (Pisum sativum). A nuclear gene is affected in each mutant. The Gsv- plants are recessive homozygotes (gsv/gsv). They bear white stems and green leaves; the petiole, rachis, and veins on stipules and leaflets are also white. In the Gsv- plants, the stem is devoid of chlorophylls, although normal amounts of chlorophylla andb are present in leaflets. Mature chloroplasts and CO2 reduction ability are present in mesophyll tissue of leaves but absent in stem. The characteristics of Gsv- mutants allow the conclusion that the genes involved in chloroplast development and photosynthetic functions are regulated by different nuclear genes in mesophyll leaf cells on the one hand and green cells of stem and related tissues in functionally different segments of shoot on the other. It is proposed that segment-wise genetic control of photosynthesis in shoot is a rule among higher plants.

    • Symbiotic and galactose utilization properties of phage RMP64-resistant mutants affecting three complementation groups inRhizobium meliloti

      S. P. S. Khanuja Sushil Kumar

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      Random Tn5 insertional mutants were induced inRhizobium meliloti Rmd201, a streptomycin-resistant mutant of AK631 (which is itself a compact colony morphology mutant of the wild-type strain Rm41), and screened for sensitivity to a set of 16 phages. Out of 3000 mutants 240 were found to be phage-resistant. The phage-resistant mutants were separable into six groups on the basis of their sensitivity pattern against test phages. Nodulation tests on alfalfa showed that although all the phage-resistant mutants induced root nodules, 7 mutants out of 12 of a class resistant to phage RMP64 (Sxf-) induced atypical nodules that were ineffective in nitrogen fixation (Fix-). The aberrant nodules were small, white, contained only a few bacteria and no bacteroids, and phenotypically resembled nodules elicited by already knownexoB, exoH, ndvA andndvB mutants ofR. meliloti. Spontaneous mutants selected for resistance to RMP64 also fell into two groups: Fix+ and Fix-. Genetic complementation tests between the Sxf- mutants defined three genessxfA, sxfB andsxfC, of whichsxfA andsxfB comprise an operon. These also demonstrated thatsxfA, sxfB andsxfC must be located on the same replicon. All the Sxf- mutants were Calcofluor-positive, like their parent strains Rmd201 and AK631. Characterization of carbohydrate metabolism of the mutants revealed that while thesxfA (Fix-) andsxfB (Fix+) mutants utilized galactose as sole carbon source,sxfC (Fix-) mutants did not. It has been concluded thatsxf A, sxfB andsxfC are new genetic loci and thatsxfA andsxfC have roles in nodule invasion and development.

    • Detection of loci in theleu region ofRhizobium meliloti chromosome

      U. G. Sathyanarayana S. P. S. Khanuja Aqbal Singh Sushil Kumar

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      A multi-marked strain ofRhizobium meliloti was developed by the co-mutation method and employed to contribute to the genetic map ofR. meliloti chromosome. Seven loci were placed at 5 sites in theleu region in the orderman-aba, fix, leu-cro-azt, ost-thi.

    • Induced mutation to monocotyledony in periwinkle,Catharanthus roseus, and suppression of mutant phenotype by kinetin

      Shashi Pandey Rai Sushil Kumar

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      A recessive EMS-induced mutation inherited in Mendelian fashion caused monocotyledonous embryo formation and seed germination on high salt medium inCatharanthus roseus. Availability during embryo development of exogenously supplied cytokinin kinetin suppressed the mutant phenotype. These observations suggest that, inC. roseus, (i) insufficiency in endogenous kinetin may lead to monocotyledonous embryo patterning and (ii) dicotyledonous embryo formation requires a critical amount of kinetin in certain cells of early embryos.

    • Construction of genetic linkage map of the medicinal and ornamental plant Catharanthus roseus

      Sarika Gupta Sashi Pandey-Rai Suchi Srivastava Subhas Chandra Naithani Manoj Prasad Sushil Kumar

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      An integrated genetic linkage map of the medicinal and ornamental plant Catharanthus roseus, based on different types of molecular and morphological markers was constructed, using a F2 population of 144 plants. The map defines 14 linkage groups (LGs) and consists of 131 marker loci, including 125 molecular DNA markers (76 RAPD, 3 RAPD combinations; 7 ISSR; 2 EST-SSR from Medicago truncatula and 37 other PCR based DNA markers), selected from a total of 472 primers or primer pairs, and six morphological markers (stem pigmentation, leaf lamina pigmentation and shape, leaf petiole and pod size, and petal colour). The total map length is 1131.9 cM (centiMorgans), giving an average map length and distance between two markers equal to 80.9 cM and 8.6 cM, respectively. The morphological markers/genes were found linked with nearest molecular or morphological markers at distances varying from 0.7 to 11.4 cM. Linkage was observed between the morphological markers concerned with lamina shape and petiole size of leaf on LG1 and leaf, stem and petiole pigmentation and pod size on LG8. This is the first genetic linkage map of C. roseus.

    • Mapping of the multifoliate pinna (mfp) leaf-blade morphology mutation in grain pea Pisum sativum

      Raghvendra Kumar Mishra Anil Kumar Swati Chaudhary Sushil Kumar

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      The multifoliate pinna (mfp) mutation alters the leaf-blade architecture of pea, such that simple tendril pinnae of distal domain are replaced by compound pinna blades of tendrilled leaflets in mfp homozygotes. The MFP locus was mapped with reference to DNA markers using F2 and F2:5 RIL as mapping populations. Among 205 RAPD, 27 ISSR and 35 SSR markers that demonstrated polymorphism between the parents of mapping populations, three RAPD markers were found linked to the MFP locus by bulk segregant analyses on mfp/mfp and MFP/MFP bulks assembled from the F2:5 population. The segregational analysis of mfp and 267 DNA markers on 96 F2 plants allowed placement of 26 DNA markers with reference to MFP on a linkage group. The existence of common markers on reference genetic maps and MFP linkage group developed here showed that MFP is located on linkage group IV of the consensus genetic map of pea.

    • Genetic control of leaf-blade morphogenesis by the INSECATUS gene in Pisum sativum

      Sushil Kumar Swati Chaudhary Vishakha Sharma Renu Kumari Raghvendra Kumar Mishra Arvind Kumar Debjani Roy Choudhury Ruchi Jha Anupama Priyadarshini Arun Kumar

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      To understand the role of INSECATUS (INS) gene in pea, the leaf blades of wild-type, ins mutant and seven other genotypes, constructed by recombining ins with uni-tac, af, tl and mfp gene mutations, were quantitatively compared. The ins was inherited as a recessive mutant allele and expressed its phenotype in proximal leaflets of full size leaf blades. In ins leaflets, the midvein development was arrested in distal domain and a cleft was formed in lamina above this point. There was change in the identity of ins leaflets such that the intercalary interrupted midvein bore a leaf blade. Such adventitious blades in ins, ins tl and ins tl mfp were like the distal segment of respective main leaf blade. The ins phenotype was not seen in ins af and ins af uni-tac genotypes. There was epistasis of uni-tac over ins. The ins, tl and mfp mutations interacted synergistically to produce highly pronounced ins phenotype in the ins tl mfp triple mutant. The role(s) of INS in leaf-blade organogenesis are: positive regulation of vascular patterning in leaflets, repression of UNI activity in leaflet primordia for ectopic growth and in leaf-blade primordium for indeterminate growth of rachis, delimitation of proximal leaflet domain and together with TL and MFP homeostasis for meristematic activity in leaflet primordia. The variant apically bifid shape of the affected ins leaflets demonstrated that the leaflet shape is dependent on the venation pattern.

    • Interaction between COCHLEATA and UNIFOLIATA genes enables normal flower morphogenesis in the garden pea, Pisum sativum

      Sushil Kumar Vishakha Sharma Swati Chaudhary Renu Kumari Nisha Kumari Poonam Mishra

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    • Genetics of flowering time in bread wheat Triticum aestivum: complementary interaction between vernalization-insensitive and photoperiod-insensitive mutations imparts very early flowering habit to spring wheat

      Sushil Kumar Vishakha Sharma Swati Chaudhary Anshika Tyagi Poonam Mishra Anupama Priyadarshini Anupam Singh

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      Time to flowering in the winter growth habit bread wheat is dependent on vernalization (exposure to cold conditions) and exposure to long days (photoperiod). Dominant Vrn-1 (Vrn-A1, Vrn-B1 and Vrn-D1) alleles are associated with vernalization-independent spring growth habit. The semidominant Ppd-D1a mutation confers photoperiod-insensitivity or rapid flowering in wheat under short day and long day conditions. The objective of this study was to reveal the nature of interaction between Vrn-1 and Ppd-D1a mutations (active alleles of the respective genes vrn-1 and Ppd-D1b). Twelve Indian spring wheat cultivars and the spring wheat landrace Chinese Spring were characterized for their flowering times by seeding them every month for five years under natural field conditions in New Delhi. Near isogenic Vrn-1 Ppd-D1 and Vrn-1 Ppd-D1a lines constructed in two genetic backgrounds were also phenotyped for flowering time by seeding in two different seasons. The wheat lines of Vrn-A1a Vrn-B1 Vrn-D1 Ppd-D1a, Vrn-A1a Vrn-B1 Ppd-D1a and Vrn-A1a Vrn-D1 Ppd-D1a (or Vrn-1 Ppd-D1a) genotypes flowered several weeks earlier than that of Vrn-A1a Vrn-B1 Vrn-D1 Ppd-D1b, Vrn-A1b Ppd-D1b and Vrn-D1 Ppd-D1b (or Vrn-1 Ppd-D1b) genotypes. The flowering time phenotypes of the isogenic vernalization-insensitive lines confirmed that Ppd-D1a hastened flowering by several weeks. It was concluded that complementary interaction between Vrn-1 and Ppd-D1a active alleles imparted super/very-early flowering habit to spring wheats. The early and late flowering wheat varieties showed differences in flowering time between short day and long day conditions. The flowering time in Vrn-1 Ppd-D1a genotypes was hastened by higher temperatures under long day conditions. The ambient air temperature and photoperiod parameters for flowering in spring wheat were estimated at 25°C and 12 h, respectively.

    • Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of Catharanthus roseus

      Vishakha Sharma Swati Chaudhary Suchi Srivastava Richa Pandey Sushil Kumar

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      Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.

    • Genetic interaction and mapping studies on the leaflet development (lld) mutant in Pisum sativum

      Sushil Kumar Raghvendra Kumar Mishra Arvind Kumar Swati Chaudhary Vishakha Sharma Renu Kumari

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      In Pisum sativum, the completely penetrant leaflet development (lld) mutation is known to sporadically abort pinnae suborgans in the unipinnate compound leaf. Here, the frequency and morphology of abortion was studied in each of the leaf suborgans in 36 genotypes and in presence of auxin and gibberellin, and their antagonists. Various lld genotypes were constructed by multifariously recombining lld with a coch homeotic stipule mutation and with af, ins, mare, mfp, tl and uni-tac leaf morphology mutations. It was observed that the suborgans at all levels of pinna subdivisions underwent lld-led abortion events at different stages of development. As in leafblades, lld aborted the pinnae in leaf-like compound coch stipules. The lld mutation interacted with mfp synergistically and with other leaf mutations additively. The rod-shaped and trumpet-shaped aborted pea leaf suborgans mimicked the phenotype of aborted leaves in HD-ZIP-III-deficient Arabidopsis thaliana mutants. Suborganwise aborted morphologies in lld gnotypes were in agreement with basipetal differentiation of leaflets and acropetal differentiation in tendrils. Altogether, the observations suggested that LLD was the master regulator of pinna development. On the basis of molecular markers found linked to lld, its locus was positioned on the linkage group III of the P. sativum genetic map.

    • Auxin transport inhibitor induced low complexity petiolated leaves and sessile leaf-like stipules and architectures of heritable leaf and stipule mutants in Pisum sativum suggest that its simple lobed stipules and compound leaf represent ancestral forms in angiosperms

      Arvind Kumar Vishakha Sharma Moinuddin Khan Mali Ram Hindala Sushil Kumar

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      In angiosperms, leaf and stipule architectures are inherited species-specific traits. Variation in leaf and stipule sizes, and forms result from the interaction between abiotic and biotic stimuli, and gene regulatory network(s) that underlie the leaf and stipule developmental programme(s). Here, correspondence between variation in leaf and stipule architectures described for extant angiosperms and that induced mutationally and by imposition of stress in model angiosperm species, especially in Pisum sativum, was detected. Following inferences were drawn from the observations.

      Several leaf forms in P. sativum have origin in fusion of stipule and leaf primordia. Perfoliate (and amplexicaul and connate) simple sessile leaves and sessile adnate leaves are the result of such primordial fusions. Reversal of changes in the gene regulatory network responsible for fusion products are thought to restore original stipule and leaf conditions.

      Compound leaf formation in several different model plants, is a result of promotion of pathways for such condition by gene regulatory networks directed by KNOX1 and LEAFY transcription factors or intercalation of the gene networks directed by them.

      Gene regulatory network for compound leaves in P. sativum when mutated generates highly complex compound leaves on one hand and simple leaves on other hand. These altered conditions are mutationally reversible.

      Simple leaves in model plants such as Arabidopsis thaliana despite overexpression of KNOX1 orthologues do not become compound.

      All forms of leaves, including simple leaf, probably have origins in a gene regulatory network of the kind present in P. sativum.

    • Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance

      Renu Kumari Vishakha Sharma Vinay Sharma Sushil Kumar

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      In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants ofMendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein-coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed.

    • Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus

      Renu Kumari Gitanjali Yadav Vishakha Sharma Vinay Sharma Sushil Kumar

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      The 5S and 18S rDNA sequences of Catharanthus roseus cv ‘Nirmal’ (wild type) and its leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill) single mutants and lli egd, lli ill and egd ill double mutants were characterized. The lli, egd and ill mutants of Mendelian inheritance bore the names after their most conspicuous morphological feature(s). They had been chemically induced and isolated for their salt tolerance. The double mutants were isolated as morphological segregants from crosses between single mutants. The morphological features of the two parents accompanied salt tolerance in the double mutants. All the six mutants were hypomethylated at repeat sequences, upregulated and downregulated for many genes and carried pleiotropic alterations for several traits. Here the 5S and 18S rDNAs of C. roseus were found to be relatively low in cytosine content. Cytosines were preponderantly in CG context (53%) and almost all of them were methylated (97%). The cytosines in CHH and CHG (where H = A, T or C) contexts were largely demethylated (92%) in mutants. The demethylation was attributable to reduced expression of RDR2 and DRM2 led RNA dependant DNA methylation and CMT3 led maintenance methylation pathways. Mutants had gained some cytosines by substitution of C at T sites. These perhaps arose on account of errors in DNA replication, mediated by widespread cytosine demethylation at CHG and CHH sites. It was concluded that the regulation of cytosine methylation mechanisms was disturbed in the mutants. ILL, EGD and LLI genes were identified as the positive regulators of other genes mediating the RdDM and CMT3 pathways, for establishment and maintenance of cytosine methylation in C. roseus.

    • Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

      Sushil Kumar Renu Kumari Vishakha Sharma Vinay Sharma

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      Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants.

    • Genetics of dioecy and causal sex chromosomes in plants

      Sushil Kumar Renu Kumari Vishakha Sharma

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      Dioecy (separate male and female individuals) ensures outcrossing and is more prevalent in animals than in plants. Although it is common in bryophytes and gymnosperms, only 5% of angiosperms are dioecious. In dioecious higher plants, flowers borne on male and female individuals are, respectively deficient in functional gynoecium and androecium. Dioecy is inherited via three sex chromosome systems: XX/XY, XX/X0 and WZ/ZZ, such that XX or WZ is female and XY, X0 or ZZ are males. The XX/XY system generates the rarer XX/X0 andWZ/ZZ systems. An autosome pair begets XY chromosomes. A recessive loss-of-androecium mutation (ana) creates X chromosome and a dominant gynoecium-suppressing (GYS) mutation creates Y chromosome. The ana/ANA and gys/GYS loci are in the sex-determining region (SDR) of the XY pair. Accumulation of inversions, deleterious mutations and repeat elements, especially transposons, in the SDR of Y suppresses recombination between X and Y in SDR, making Y labile and increasingly degenerate and heteromorphic from X. Continued recombination between X and Y in their pseudoautosomal region located at the ends of chromosomal arms allows survival of the degenerated Y and of the species. Dioecy is presumably a component of the evolutionary cycle for the origin of new species. Inbred hermaphrodite species assume dioecy. Later they suffer degenerate-Y-led population regression. Cross-hybridization between such extinguishing species and heterologous species, followed by genome duplication of segregants from hybrids, give rise to new species.

    • Overlap of Patau and Pierre Robin syndromes along with abnormal metabolism: an interesting case study

      Sushil Kumar Jaiswal Krishna Kishore Sukla Vineeta Gupta Amit Kumar Rai

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    • SNPs at exonic region of aquaporin-7 (AQP7) gene may affect semen quality parameters among crossbred bulls

      Sushil Kumar Rajib Deb Umesh Singh Indrajit Ganguly D. K. Mandal Rupali Singh Sheetal Sharma Gyanendra Sengar Rani Singh Mahesh Kumar Arjava Sharma

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    • Origin, structure and function of millions of chromosomes present in the macronucleus of unicellular eukaryotic ciliate, Oxytricha trifallax: a model organism for transgenerationally programmed genome rearrangements

      Sushil Kumar Renu Kumari

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    • Cytosine deletion at AP2-box region of HSP70 promoter and its influence on semen quality traits in crossbred bulls


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    • Single-nucleotide polymorphisms in CLEC7A, CD209 and TLR4 gene and their association with susceptibility to paratuberculosis in Indian cattle


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      The aim of this study was to identify the single-nucleotide polymorphisms (SNPs) in bovine candidate genes CLEC7A, CD209 and TLR4, and explore the association between these SNPs with the occurrence of bovine paratuberculosis (PTB) disease. For this purpose, 549 animals were screened by a panel of four diagnostic tests, namely Johnin PPD test, ELISA test, faecal microscopy and IS900 blood PCR against Mycobacterium avium ssp. paratuberculosis (MAP) to develop case–control populations. SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism method. Genotypic–phenotypic associations were assessed by the PROCLOGISTIC procedure of SAS 9.3. Of the seven SNPs; rs110353594 in CLEC7A gene and rs8193046 in TLR4 gene were found to be associated with PTB. For SNP rs110353594, odds of CC and CT genotypes vs TT genotype was 1.543 (0.420–5.667; 95% CI) and 0.284 (0.104–0.774; 95% CI), respectively which means that CT genotype was more resistant than TT and CC genotypes against bovine PTB. For SNP rs8193046, odds of AA and AG genotypes versus GG genotype was 0.947 (0.296–3.034; 95% CI) and 3.947 (1.555–10.022; 95% CI), respectively, i.e. probability for getting an infection in animals with AG genotype was 3.94 times more as compared to GG genotype. Hence, a selection programme favouring CT genotype for rs110353594 and against AG genotype for rs8193046 may be beneficial for conferring resistance against bovine PTB.

    • Coevolution mechanisms that adapt viruses to genetic code variations implemented in their hosts


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