Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers          下载免费PDF全文

Kapil K. Tiwari  Anshuman Singh  Sasmita Pattnaik  Maninder Sandhu  Sukhdeep Kaur  Sourabh Jain  Sushma Tiwari  Shweta Mehrotra  Mahender Anumalla  Rashmita Samal  Jyoti Bhardwaj  Neha Dubey  Vikrant Sahu  Gayle A. Kharshing  Patu K. Zeliang  Kadiri Sreenivasan  Pankaj Kumar  Swarup K. Parida  Sevanthi V. A. Mithra  Vandana Rai  Wricha Tyagi  Pawan K. Agrawal  Atmakuri R. Rao  Arunava Pattanayak  Girish Chandel  Ashok K. Singh  Ishwari S. Bisht  Kangila V. Bhat  Gundimeda J. N. Rao  Jitendra P. Khurana  Nagendra K. Singh  Trilochan Mohapatra 《Plant Breeding》2015,134(2):164-171

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini‐core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini‐core consisting of 98 genotypes was identified. Ninety‐four per cent of the alleles present in the core set were present in the mini‐core. The identified small but diverse panel will be useful for further intensive trait‐specific evaluation and utilization in allele mining.  相似文献   

Genetic association of polymorphisms in bovine TLR2 and TLR4 genes with Mycobacterium avium subspecies paratuberculosis infection in Indian cattle population     

Kumar  Satish  Kumar  Subodh  Singh  Ran Vir  Chauhan  Anuj  Kumar  Amit  Sulabh  Sourabh  Bharati  Jaya  Singh  Shoor Vir 《Veterinary research communications》2019,43(2):105-114

Toll like receptors (TLRs) are pattern recognition molecules involved in cellular recognition of Mycobacterium avium subspecies paratuberculosis (MAP), the infectious agent causing Paratuberculosis (PTB), a notified disease of domestic and wild ruminants. The present study was undertaken to investigate the presence of single nucleotide polymorphisms (SNPs) in TLR2 and TLR4 gene and to evaluate association of these SNPs with occurrence of PTB in Indian cattle. A total of 213 cattle, were subjected to multiple diagnostic tests viz. Johnin PPD, ELISA test (Indigenous and Parachek kit method), fecal microscopy and fecal culture for detection of MAP infection. Based on screening results 51 animals each were assigned to case and control population. Two SNPs viz. rs55617172, rs41830058 in TLR2 gene and two SNPs viz. rs8193046, rs8193060 in TLR4 gene and were genotyped by PCR-RFLP method. All SNPs were found to be polymorphic except rs41830058 in the case-control population. Both SNPs in TLR4 gene but none in TLR2 genes were significantly associated with the occurrence of PTB in our population. The genotypes in SNP rs8193046 and SNP rs8193060 were significantly (P?<?0.01) different in case-control population. These findings suggest that SNPs rs8193046 and rs8193060 are likely a potential marker against MAP infection and a selection programme eliminating AG genotype for rs8193046 and CT genotype for rs8193060 might be beneficial in conferring resistance to MAP infection in Indian cattle population.

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Endometrial transcript profile of progesterone‐regulated genes during early pregnancy of Water Buffalo (Bubalus bubalis)     

Naseer A. Baba  Manjit Panigrahi  Ankita D. Verma  Abdul Sadam  Sourabh Sulabh  Supriya Chhotaray  Subhashree Parida  Narayanan Krishnaswamy  Bharat Bhushan 《Reproduction in domestic animals》2019,54(1):100-107

Progesterone (P₄) plays a key role in the establishment and maintenance of pregnancy in most mammals. Unravelling the expression of progesterone‐regulated genes can expand the understanding of the embryonic mortality. Accordingly, we studied the relative mRNA expression of the P₄‐regulated genes in the buffalo. Uteri were collected from the abattoir and categorized into nonpregnant late luteal phase, stage I (28–38th days of gestation) and stage II (48–56th days of gestation) of pregnancy (n = 6/group). After extraction of total RNA from the endometrial tissues, we carried out qRT‐PCR for determining the relative mRNA expression of the P₄‐regulated genes using nonpregnant late luteal phase as calibrator group. The expression of LGALS3BP (essential for maternal recognition of pregnancy) gene was found to be significantly upregulated (p < 0.05), while MUC1 (important for embryo attachment) gene was downregulated in stage I and II of pregnancy. We observed no significant change in the expression of LGALS1, LGALS9 and CTSL genes. The SLC5A11 and SLC2A1 genes (involved in the transport of glucose to endometrium) in early pregnancy were upregulated in the pregnancy stage I (p < 0.05) relative to nonpregnant late luteal phase. The CST3 gene was significantly upregulated in pregnancy stage II (p < 0.01). These results provide molecular insights into the specific pathways involved in foeto‐maternal communication during early pregnancy in buffaloes.  相似文献   

Bayesian analysis of semiparametric linear-circular models     

Sourabh Bhattacharya  Ashis Sengupta 《Journal of Agricultural, Biological & Environmental Statistics》2009,14(1):33-65

In many environmental and agricultural studies, data are collected on both linear and circular random variables, with possible dependence between the variables. Classically, the analysis of such data has been carried out in a classical regression framework. We propose a Bayesian hierarchical framework to handle all forms of uncertainty arising in a linear-circular data set. One novelty of our multivariate linear-circular model is that, marginally, the circular component is assumed to be a mixture model with an unknown number of von Mises (or circular normal) distributions. We use the Dirichlet process to introduce variability in the model dimensionality, and develop a simple Gibbs sampling algorithm for simulating the mixture components. Although we illustrate our methodology on von Mises mixtures, it is widely applicable. We thus avoid complicated reversible-jump Markov chain Monte Carlo methods, which are considered ideal for analyzing mixtures of unknown number of distributions. We illustrate our methodologies with simulated and real data sets. Using pseudo-Bayes factors, we also compare different models associated with both fixed and variable numbers of von Mises distributions. Our findings suggest that models associated with varying numbers of mixture components perform at least as well as those with known numbers of mixture components. We tentatively argue that model averaging associated with variable number of mixture components improves the model’s predictive power, which compensates for the lack of knowledge of the actual number of mixture components.  相似文献   

Single Layer Centrifugation with 20% or 30% Porcicoll separates the majority of spermatozoa from a sample without adversely affecting sperm quality     

Sourabh Deori  Anders Johannisson  Jane Morrell 《Reproduction in domestic animals》2020,55(10):1337-1342

Centrifugation of boar semen through one layer of 40% colloid (Porcicoll) was previously shown to separate spermatozoa from bacteria without having a detrimental effect on sperm quality. However, some spermatozoa were lost. The purpose of the present study was to determine whether 20% or 30% Porcicoll could be used to recover most of the spermatozoa without impacting on sperm quality. Insemination doses (n = 10) from a commercial boar station were sent to the laboratory at the Swedish University of Agricultural Sciences and processed by Single Layer Centrifugation with 20% and 30% Porcicoll approximately 7 hr after semen collection. The resulting sperm samples and controls were evaluated for sperm quality immediately and again after storage at 16–18°C for 4 and 7 days. Sperm recovery was 94 ± 18% and 87 ± 15% for 20% and 30% Porcicoll, respectively (p > .05). Sperm mitochondrial membrane potential and chromatin integrity were unaffected (p > .05). The proportion of live spermatozoa producing superoxide (9 ± 8%, 7 ± 6% and 3 ± 1%; p < .05), and the proportion of spermatozoa with high stainability DNA (0.68 ± 19%, 0.61 ± 0.22% and 0.96 ± 0.23%; p < .05- <0.01), were marginally increased whereas membrane integrity, although high, was lower in the centrifuged samples than in the controls (82 ± 8%, 83 ± 5% versus 92 ± 4%; p < .05). In conclusion, centrifugation through 20% or 30% Porcicoll enables most spermatozoa to be recovered, without having a major effect on sperm quality. These results are encouraging for further studies involving microbiological investigation of the processed samples, and scaling-up to process larger volumes of boar ejaculates.  相似文献