Performance of using opposing homozygotes for paternity testing in Japanese Black cattle

2021 ◽  
Author(s):  
Ryota Komiya ◽  
Shinichiro Ogawa ◽  
Tatsuya Aonuma ◽  
Masahiro Satoh
Keyword(s):  
Paternity Testing ◽  
Japanese Black Cattle

Individual identification and paternity testing of bulls using microsatellite

2009 ◽  
Vol 31 (3) ◽  
pp. 285-289 ◽  
Author(s):  
Jing WANG ◽  
Chou-Sheng LIU ◽  
Li-Ping ZHANG ◽  
Zhi-Gang WANG ◽  
Fu-Qing YU ◽  
...  
Keyword(s):  
Paternity Testing ◽  
Individual Identification

Perception of the general public towards the ethical and legal issues surrounding DNA paternity testing in Lebanon

2021 ◽  
Vol 17 ◽  
pp. 100640
Author(s):  
M. Azoury ◽  
F.A. Mrad ◽  
I. Mansour ◽  
J.-N. Ibrahim ◽  
Z.A. Rjeily ◽  
...  
Keyword(s):  
General Public ◽  
Legal Issues ◽  
Paternity Testing ◽  
Ethical And Legal Issues

scholarly journals 353 ASAS-EAAP Talk: Low-coverage whole-genome sequencing in local livestock breeds

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 81-82
Author(s):  
Joaquim Casellas ◽  
Melani Martín de Hijas-Villalba ◽  
Marta Vázquez-Gómez ◽  
Samir Id Lahoucine
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Error Rate ◽  
Allele Frequencies ◽  
Paternity Testing ◽  
Sequencing Error ◽  
Whole Genome ◽  
Genomic Evaluation ◽  
Sequencing Error Rate ◽  
Low Coverage

Abstract Current European regulations for autochthonous livestock breeds put a special emphasis on pedigree completeness, which requires laboratory paternity testing by genetic markers in most cases. This entails significant economic expenditure for breed societies and precludes other investments in breeding programs, such as genomic evaluation. Within this context, we developed paternity testing through low-coverage whole-genome data in order to reuse these data for genomic evaluation at no cost. Simulations relied on diploid genomes composed by 30 chromosomes (100 cM each) with 3,000,000 SNP per chromosome. Each population evolved during 1,000 non-overlapping generations with effective size 100, mutation rate 10–4, and recombination by Kosambi’s function. Only those populations with 1,000,000 ± 10% polymorphic SNP per chromosome in generation 1,000 were retained for further analyses, and expanded to the required number of parents and offspring. Individuals were sequenced at 0.01, 0.05, 0.1, 0.5 and 1X depth, with 100, 500, 1,000 or 10,000 base-pair reads and by assuming a random sequencing error rate per SNP between 10–2 and 10–5. Assuming known allele frequencies in the population and sequencing error rate, 0.05X depth sufficed to corroborate the true father (85,0%) and to discard other candidates (96,3%). Those percentages increased up to 99,6% and 99,9% with 0,1X depth, respectively (read length = 10,000 bp; smaller read lengths slightly improved the results because they increase the number of sequenced SNP). Results were highly sensitive to biases in allele frequencies and robust to inaccuracies regarding sequencing error rate. Low-coverage whole-genome sequencing data could be subsequently integrated into genomic BLUP equations by appropriately constructing the genomic relationship matrix. This approach increased the correlation between simulated and predicted breeding values by 1.21% (h2 = 0.25; 100 parents and 900 offspring; 0.1X depth by 10,000 bp reads). Although small, this increase opens the door to genomic evaluation in local livestock breeds.

scholarly journals A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shinji Sasaki ◽  
Youko Miki ◽  
Takayuki Ibi ◽  
Hiroyuki Wakaguri ◽  
Yuichi Yoshida ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Copy Number Variation ◽  
Copy Number ◽  
Risk Allele ◽  
Wild Type ◽  
Japanese Black Cattle ◽  
Complement Activity ◽  
Categorical Trait ◽  
Number Variation ◽  
Calf Mortality

Abstract Background Calf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, whereas genetic factors affecting the susceptibility of calves to death are not well known. To identify variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait with a threshold model and performed a genome-wide copy number variation (CNV) association study on calf mortality. Results We identified a 44-kb deleted-type CNV ranging from 103,317,687 to 103,361,802 bp on chromosome 5, which was associated with the mortality of 1–180-day-old calves. The CNV harbored C1RL, a pseudogene, and an IncRNA localized in the C1R and C1S gene cluster, which is a component of the classical complement activation pathway for immune complexes for infectious pathogens. The average complement activity in CNVR_221 homozygotes at postnatal day 7 was significantly lower than that of wild-type animals and heterozygotes. The frequency of the risk allele in dead calves suffering from diarrhea and pneumonia and in healthy cows was 0.35 and 0.28, respectively (odds ratio = 2.2, P = 0.016), suggesting that CNVR_221 was associated with the mortality of Japanese Black calves suffering from an infectious disease. Conclusions This study identified a deleted-type CNV associated with the mortality of 1–180-day-old calves. The complement activity in CNVR_221 homozygotes was significantly lower than that in heterozygotes and wild type animals. The frequency of the risk allele was higher in dead calves suffering from an infectious disease than in healthy cows. These results suggest that the existence of CNVR_221 in calves could be attributed to a reduction in complement activity, which in turn leads to susceptibility to infections. Thus, the risk allele could serve as a useful marker to reduce the mortality of infected Japanese Black calves.

Systematic selection of microsatellite for paternity testing of yak

2021 ◽  
Author(s):  
Tong Chen ◽  
Ruilin Zeng ◽  
Wenyi Cai ◽  
Xianrong Xiong ◽  
Wei Fu ◽  
...  
Keyword(s):  
Paternity Testing ◽  
Systematic Selection ◽  
Selection Of

scholarly journals Long-term changes in plasma anti-Müllerian hormone concentration and the relationship with superovulatory response in Japanese Black cattle

2017 ◽  
Vol 63 (1) ◽  
pp. 95-100 ◽  
Author(s):  
Hiroki HIRAYAMA ◽  
Akira NAITO ◽  
Shigeo FUKUDA ◽  
Takashi FUJII ◽  
Masatsugu ASADA ◽  
...  
Keyword(s):  
Hormone Concentration ◽  
Japanese Black Cattle ◽  
Long Term Changes ◽  
The Relationship
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