<div>Background: The beta-defensin family antigens present on sperm surface suggestively play pivotal role in sperm fertility by aiding in various steps of sperm maturation, motility, capacitation, immune recognition and sperm-oocyte interaction in female tract. It is imperative to explore genetic polymorphisms to build a better understanding of individual variation in male fertility. The experiment was designed to identify DNA polymorphism in Sperm Associated Antigen 11B (SPAG11B) gene and to analyze association between genetic variants with sperm quality traits in buffalo bulls (Murrah) in ICAR-National Dairy Research Institute, Karnal.&nbsp; 
 
Methods: Genomic DNA was extracted from hundred and thirty Murrah bulls. A 395 base pair region covering partial Intron 2, Exon 3 and Partial Intron 3 of bovine SPAG11 gene was amplified and genotyped using PCR-RFLP method. The PCR amplified product was purified, sequenced and further ClustalW analysis was done to align edited sequence with reported Bos taurus sequence (AC_000158.1). Gene and genotype frequencies, effective number of alleles, level of heterozygosity and polymorphic information content of various genotypes were estimated by standard procedure. Seminal parameters (Post thaw sperm motility, sperm viability, acrosomal integrity, HOST and abnormality) were estimated and statistical analysis was carried out.&nbsp; 
 
Result: A novel SNP (G&gt;A substitution) at 2266 base of the SPAG11B gene was identified by sequencing. The fragment of SPAG11 gene containing 395 base pairs was amplified using PCR and digested with restriction enzyme i.e. MunI which showed three distinct genotypes viz., AA (266 bp and 107 bp fragment), AG (307 bp, 266 bp and 107 bp) and GG (373 bp fragment). Least squares means of seminal parameters for the SNP was estimated and compared after correction for non-genetic factors. Between genotypes, significant differences were found only for acrosomal integrity and was highest in AG (74.22&plusmn;0.72) followed by AA (72.6&plusmn;0.89) and GG (71.12&plusmn;0.97), respectively. The identified novel SNP of SPAG11 gene showed significant association with acrosome integrity with genotype AG being superior to other genotypes. However, an association cannot be established with other seminal parameters with this SNP, further studies are required in order to validate the impact of g.2266G&gt;A on sperm quality traits in a large population.</div>

SNP Identification in Sperm Associated Antigen 11B Gene and Its Association with Sperm Quality Traits in Murrah Bulls

<div>Background: Pasteurella multocida is the causative agent of many economically important diseases in a wide range of hosts. The mechanisms by which these bacteria can invade the mucosa, evade innate immunity and cause systemic disease are slowly being elucidated. Many key virulence factors are yet to be identified, including those required for initial attachment and invasion of host cells and for persistence in a relatively nutrient poor and hostile environment. This has led to intensive research to understand host adaptation mechanisms and virulence factors in order to develop effective vaccines.&nbsp; 
 
Methods: The present study was carried out to know the distribution of virulence genes viz., haemoglobin binding proteins (hgbA and hgbB), outer membrane protein (ompH), fimbrial antigen (ptfA), filamentous haemagglutinin (pfhA) and transferrin binding protein (tbpA) by PCR in P. multocida CapA isolates from apparently healthy or carrier animals and CapB isolates from field Haemorrhagic septicemia (HS) cases to monitor the epidemiological associations of virulence genes in Cap A and Cap B isolates. 
 
Result: The study revealed that all the six virulence associated genes were present in Cap B isolates. None of the Cap A isolates harboured tbpA and pfhA genes. These two genes were closely related to serotype B causing Haemorrhagic septicemia and were epidemiologically associated with disease status.</div>

<div>Virulence Gene Pattern of Pasteurella multocida Isolates of Buffalo in Association to Capsule Biosynthesis Genes</div>

<div style="text-align: justify;">Polymorphic variants of keratin-associated protein (KAP) 6.1 gene with wool traits of Sandyno and Nilagiri breeds of sheep were investigated in this study. Genomic DNA was isolated from blood samples of 125 Sandyno, Nilagiri and Dorset x Nilagiri breeds of sheep along with 76 numbers of wool samples. A 528 bp segment was amplified by PCR using ovine specific primers for KAP 6.1 gene. SSCP analysis of KAP 6.1 gene in Dorset x Nilagiri crossbred sheep resulted in two genotypes for the A/B with no polymorphism. KAP 6.1 gene locus revealed allele frequencies of &nbsp;A, B, C, D and E in Sandyno sheep were 0.67, 0.23, 0.04, 0.01 and 0.04 and in Nilagiri were 0.75, 0.06, 0.11, 0.04 and 0.04 respectively. KAP 6.1 gene revealed departure from Hardy-Weinberg equilibrium. KAP 6.1 genes were found to have high degree of homozygosity (0.6667) in Nilagiri sheep. The effective number of alleles (Ne) for KAP 6.1 gene was 1.1690 and 1.7006 respectively in Sandyno and Nilagiri breeds of sheep. The PIC values for KAP 6.1 gene was 0.1341 and 0.3909 in Sandyno and Nilagiri breeds of sheep respectively. FIS values for KAP 6.1 gene was positive (0.1909) in Nilagiri breed and it was negative (&ndash; 0.0110) in Sandyno breed. Least squares analysis of variance showed significant (P&lt;0.05) effect between genotypes and between sexes for wool traits like GFW (kg), CWY (%) and FD (&micro;). Significant (P&lt;0.05) effect of breed (Sandyno and Nilagiri) was observed for all the wool traits (GFW, CWY, FD, SL and Medullation %). Significant (p&lt;0.05) higher CWY production was recorded for AC genotype (62.00 &plusmn; 1.73 %) while low value was recorded for BB genotype (56.25 &plusmn; 1.74 %). FD was found to be high in genotype AC (24.29 &plusmn; 1.17 &micro;) than in AA genotype (23.24 &plusmn; 0.49 &micro;). The homozygote AA was found to have more Medullation (%) and SL. Genotypes BB had higher GFW and lower CWY. The heterozygous genotype AC yielded more FD and CWY with lower most Medullation (%) and SL values. From the study, it may be concluded that KAP 6.1 gene might be a potential molecular marker for genetic selection of wool traits in Sandyno and Nilagiri breeds of sheep .</div>

<div style="text-align: justify;">Polymorphism of Keratin - Associated Protein (KAP) 6.1 gene and its association with wool traits of Sandyno and Nilagiri breeds of sheep</div>

<div>Background: Osmanabadi is the premium meat type goat breed of Maharashtra, known for its adaptability and reproductive efficiency. Identification of superior germplasm and incorporating them into breeding programme is the need of hour for augmenting productivity of Osmanabadi as well as other indigenous goat breeds. Hence, the present research was aimed to study Pituitary Specific Transcription Factor I (POU1F1) gene polymorphism and its associations with body weight of Osmanabadi goat.&nbsp; 
 
Methods: Genomic DNA was extracted from 217 blood samples of randomly selected Osmanabadi goats. The 450 bp fragment of POU1F1 gene encompassing exon-6 and its flanking region (3&rsquo;UTR) was PCR amplified.&nbsp;The PCR amplicon was subjected to RFLP using AluI and PstI restriction enzymes to identify polymorphism at nucleotide position 174 (T&gt;C) in exon 6 and at nucleotide position 110 (T&gt;C) in the 3&rsquo;UTR of POU1F1 gene, respectively. The association of the observed allelic variants / genotypes with body weight of the animals was performed using One-way ANOVA.&nbsp; 
 
Result: The AluI PCR-RFLP of 450 bp amplicon of POU1F1 gene in Osmanabadi goats revealed polymorphism with three different genotypes viz., &lsquo;CC&rsquo;, &lsquo;TT&rsquo; and &lsquo;TC&rsquo;. The observed frequencies for TT, TC and CC genotypes were 0.604, 0.355 and 0.041 respectively. The frequencies of T and C alleles were found to be 0.781 and 0.219, respectively. However, PstI PCR-RFLP revealed monomorphic 3&rsquo;UTR of POU1F1 gene with single TT genotype. We observed significant differences (P&lt;0.01) between various genotypes at AluI exon-6 locus of POU1F1 gene and body weights at birth, 3 and 6 months of Osmanabadi goat. Highest body weight was recorded for TT genotype followed by TC and CC genotypes in all three age groups. Our findings indicate that the AluI PCR-RFLP locus of the exon-6 of POU1F1 gene can be used as a potent molecular marker for selection of superior stock of Osmanabadi goats.&nbsp;&nbsp;</div>

​POU1F1 Gene Polymorphism and its Associations with Body Weight of Osmanabadi Goat

<div>This study was conducted in Mia chicken breed to evaluate the association between four single nucleotide polymorphisms (SNPs), in insulin (INS) and growth hormone (GH) genes, with growth traits. Three genotypes for the SNP A3971G of INS gene and the SNP G662A and C423T of GH gene were present in the population while only two genotypes were found in the Mia chicken breed for SNP T3737C of INS gene (TT and TC). The SNP T3737C INS gene and G662A GH gene had significant association with growth traits (P &lt; 0.05). A significant association of T3737C INS gene with body weight (BW) was observed at 10 to 12 weeks of age and average daily gain (ADG) at 6-8 weeks of age. The SNP G662A of the GH gene was significantly associated (P &lt; 0.05) with BW of Mia chicken at ages from 7 to 14 weeks and with ADG (4-6; 6-8; 8-10; 10-12 and 2-16 weeks). Chicken with the GG genotype had greater BW and ADG compared to the other genotypes. The results demonstrated that this SNP G662A GH gene may be used as a candidate marker gene for genetic improvement of growth traits in Mia chicken breed.</div>

<div>Association of single nucleotide polymorphisms in the insulin and growth hormone gene with growth traits of Mia Chicken</div>

The polymorphisms of A-FABP gene which associated with meat quality traits of beef cattle divided in five groups(Qingyang native beef cattle group, Pingliang native beef cattle group, Qinchuan beef cattle group, South Devon beef crossbreed group, Simmental beef crossbreed group) in Gansu was studied. Three types of bands defined as genotypes GG, GC and CC were discovered in the study. According to the results we could find the mutation of c. 408 g &gt; c existed in A- FABP gene&rsquo;s exon3 area by sequencing analysis of gene in three different kinds. The analysis of A-FABP gene polymorphisms associated with meat quality traits like pressing lose, shear force, cooking loss, marbling score, meat color and pH value, showed that pressing loss with genotype GG was significantly greater than genotype CC (P&lt;0.05), shear force with genotype GG was significantly greater than genotype GC and genotype CC (P&lt;0.01), cooking loss and pH value with genotype GG were significantly greater than genotype GC (P&lt;0.05) and genotype CC (P&lt;0.01). This mutation of A-FABP gene could be considered as a locus associated with meat quality traits.

Polymorphisms in A-FABP gene associated with meat&nbsp;quality traits of beef cattle in Gansu

Background: The experiment aimed to investigate polymorphisms in exon 2 of the PHKA2 gene and investigate the relationship between identified single nucleotide polymorphism and udder type traits in Sahiwal cows. Udder morphometry is being used as a forecaster of production performance in cows since older times. Finding the variants associated with these traits in largely variable region of PHKA2 gene can prove to be highly beneficial.&nbsp; 
 
Methods: DNA isolated from Sahiwal cows was analysed by DNA sequencing. Nine udder type and five teat types were measured for each animal according to procedure followed by International committee of animal recording (2012). 
 
Result: Three SNPs g.124497381C&gt;T, X:124497248 G&gt;A and X:124497189 C&gt;T were identified. Recessive homozygotes were negligible as mutant allele exhibited very low ranging frequency (from 0.02 to 0.08) for the targeted loci. Identified point mutation g.124497381C&gt;T was found to be significantly (p&lt;0.05) associated with distance between teats and central ligament, SNP X: 124497248G&gt;A with rear udder width, fore udder attachment, udder depth, udder length and teat length (p&lt;0.05) and SNP X: 124497189 C&gt;T with udder length and rear udder height (p&lt;0.05). Interaction of identified SNPs and udder traits highlighted the gene&rsquo;s potential as a candidate gene for selecting for conformation traits in Indian Sahiwal cattle.

Genetic Profiling of PHKA2 Gene and its Association with Udder Type Traits in Indian Dairy Cattle

<div style="text-align: justify;">Bull fertility is an important component of reproductive efficiency in dairy cattle. PPP1R11 is a potent candidate gene for bull fertility being involved in the pathway of spermatogenesis. Present investigation was carried out in twenty Karan Fries (KF) bull to identify SNPs of PPP1R11 gene and their association with conception rate. Genomic DNA was extracted from frozen semen straws by phenol-chloroform method. Primer pair targeted to exonic II region of PPP1R11 gene was designed using Primer 3.1 software. PCR reactions were carried out in thermal cycler after optimizing. The PCR product was checked on 1.5% horizontal agarose gel electrophoresis to verify the amplification of target region. Samples were sequenced and SNPs were identified using multiple alignment programme with respect to reference sequence and visual inspection of chromatograms. Sequencing results revealed only two SNPs [G28708846A, T28708860C] at exonic II region of PPP1R11 gene in KF bulls. Each bull was genotyped with respect to each of the two identified SNPs. Association of SNP genotype with conception rate was analyzed using least square ANOVA taking genotypes as fixed effect. The result indicated that, only one SNP [T28708860C] had significant (p&lt;0.01) effect on conception rate. The bulls with TT genotype revealed significantly (p&lt;0.01) highest conception rate (53.20&plusmn;2.96%) followed by bulls with TC (43.12&plusmn;2.39%) and the lowest in bulls with CC (34.59&plusmn; 2.28%) genotypes. The results of present finding suggested that association of SNPs with conception rate after validation on large population might be useful in marker assisted selection for selection of bull with high fertility in future.</div>

Association of single nucleotide polymorphisms of PPP1R11 gene with conception rate in Karan Fries bull

<div>Background: Natural resistance associated macrophage protein 1 (Nramp1) is a relatively conservative gene that plays a crucial role in swine immune response and disease resistance.&nbsp; 
 
Methods: We identified the polymorphisms and gene variations in the exon 2 of Nramp1 using polymerase chain reaction&ndash;restriction fragment length polymorphism and investigated the correlation between the polymorphisms and piglet diarrhea in four pig breeds (Bamei, Duroc, Landrace, and Large White pigs).&nbsp; 
 
Result: The results showed that two alleles (A and B) were identified in all the pig breeds, three genotypes (AA, BB, and AB) were detected in Bamei and Large White breeds, and two genotypes (AA and AB) were detected in Landrace and Duroc breeds. Allele A and genotype AB were dominant in Bamei, Large White, and Landrace breeds, whereas genotype AA was dominant in Duroc pigs. A moderate polymorphism was observed in Landrace and Large White pigs, and polymorphism was abundant in Bamei pigs and low in Duroc pigs. The Chi-square test for Hardy&ndash;Weinberg equilibrium disclosed that the exon 2 of Nramp1 in the four breeds of pigs did not deviate from the Hardy&ndash;Weinberg balance (P&gt;0.05). The results of association analysis showed a significant correlation between breed and piglet diarrhea (P&lt;0.05), and the diarrhea score of Bamei pigs was much lower than those of the other breeds. The study could supply theoretical references for further functional research on Nramp1 gene and for screening genes related to disease-resistance breeding.</div>

<div>Polymorphism of Nramp1 Gene and Its Association with Diarrhea in Pigs</div>

Heat Shock Proteins (HSPs) are expressed in response to heat stress and the polymorphism in HSP genes at single nucleotide level is reported to be associated with heat tolerance and production performance traits in cattle. ATP1B2 gene was mapped to Bos taurus autosome 19 (BTA 19) spanning nearly 4310bp, comprising 7 Exons and 6 Introns. The present study was conducted in Sahiwal cows (n=108) raised under sub-tropical climate with the objectives to identify SNPs in targeted regions (Intron 2, 4 and Exon 3, 5) of ATP1B2 gene and to analyze their association with heat tolerance traits in Sahiwal cows. Respiration rate (RR) and rectal temperature (RT) were recorded during probable extreme hours in winter, spring and summer seasons. Heat tolerance coefficient (HTC) was also calculated to check the adaptability of the animals during the period of heat stress. The comparative sequence analysis revealed a total of two SNPs in Intron 2 of ATP1B2 gene i.e. g.2243G&gt;A and g.2366T&gt;C. Out of these two identified SNPs, only one SNP i.e. g.2243G&gt;A was found to be significantly (PC, RR, RT and HTC were having non-significant association with the different genotypes i.e. TT and TC. These findings suggest that AA and GA genotype of SNP g.2243G&gt;A of ATP1B2 gene can be utilized as potential marker for propagating thermo-tolerant cattle.

SNP Identification in Sperm Associated Antigen 11B Gene and Its Association with Sperm Quality Traits in Murrah Bulls

Virulence Gene Pattern of Pasteurella multocida Isolates of Buffalo in Association to Capsule Biosynthesis Genes

Polymorphism of Keratin - Associated Protein (KAP) 6.1 gene and its association with wool traits of Sandyno and Nilagiri breeds of sheep

POU1F1 Gene Polymorphism and its Associations with Body Weight of Osmanabadi Goat

Association of single nucleotide polymorphisms in the insulin and growth hormone gene with growth traits of Mia Chicken

Polymorphisms in A-FABP gene associated with meat quality traits of beef cattle in Gansu

Genetic Profiling of PHKA2 Gene and its Association with Udder Type Traits in Indian Dairy Cattle

Association of single nucleotide polymorphisms of PPP1R11 gene with conception rate in Karan Fries bull

Polymorphism of Nramp1 Gene and Its Association with Diarrhea in Pigs

Novel SNPs in ATP1B2 Gene and their Association with Heat Tolerance Indicator Traits in Sahiwal Cattle