Selection and implementation of single nucleotide polymorphism markers for parentage analysis in crossbred cattle population

Hu, Lirong; Li, Dan; Chu, Qing; Wang, Y.C.; Zhou, Lei; Yu, Ying; Zhang, Y.; Zhang, S.L.; Usman, Τahir; Xie, Zhenquan; Hou, Shiyu; Liu, L.; Shi, Wanhai

doi:10.1016/j.animal.2020.100066

Cited by 5 publications

(4 citation statements)

References 30 publications

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“…To assess the efficacy of our scheme in actual applications, we searched public data for datasets with known parent-child correspondences and the genotypes of SSR/SNP markers in each individual [5,8,20,26,[30][31][32][33] and found only one study [19] that met all the requirements. Thus, we used five datasets from this study for testing.…”

Section: The Efficacy Of the Low-redundancy Schemementioning

confidence: 99%

“…So, it is possible to be utilized in PMS screening for a wider range of species as long as the scenario meets the conditions mentioned above. For instance, parentage assignment has been widely used in diploid livestock breeding [5,8,19,24,32,40,41], where repeated use of artificial insemination leads to inaccurate pedigree records [42]. So, the scheme developed in this study has the ability to reduce the cost of parentage assignment, ensuring accuracy, in the same way as the fish breeding.…”

Section: Scalability Of the Schemementioning

confidence: 99%

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PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping

Xia,

Shi,

et al. 2024

Biology

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Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.

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Section: The Efficacy Of the Low-redundancy Schemementioning

confidence: 99%

Section: Scalability Of the Schemementioning

confidence: 99%

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping

Xia,

Shi,

et al. 2024

Biology

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“…Recently, interest in SNPs research has been increasing for forensic science (Lee et al 2005;Lessig et al 2005) and parentage testing of domestic animals (Werner et al 2004;Rohrer et al 2007;Hirota et al 2010;Lopes et al 2018;Browning et al 2018;Pook 2019;Randhawa et al 2020;Pook et al 2020. Přibáňová et al 2020Long 2021;Hu et al 2021;Gebrehiwot et al 2021;Nolte et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite Variation in Jeju and American horses and their Phylogenetic Relationship

2023

Int J Vet Sci

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The aim of this study was to evaluate the microsatellite (Ms) variation in Jeju and American horses and their phylogenetic relationship, and to establish a lineage-based breeding plan for domestic American miniature horse (AMH) and Quarter horse (QH) in Korea. A total of 83 horse samples (27 AMHs, 32 QHs, and 24 Jeju horses [JHs]) were genotyped with 17 Ms markers. The observed number of alleles per locus ranged from 4 (HTG7) to 12 (ASB17), with an average value of 7.71, 7.41, and 6.11 in AMH, QH, and JH, respectively. Of the 17 Ms markers, HTG4, HTG6, HTG7, HMS1 markers had relatively low PIC values (<0.6) in AMH and HMS1 in QH, and ASB2, HMS7, HTG4, ASB23, HMS1, HTG10 in JH. An average level of genetic variation was as follows: AMH, HE= 0.7300 and HO= 0.7317; QH, HE= 0.7505 and HO= 0.7011; and JH, HE = 0.6917 and HO= 0.7011. QH and JH had a genetic distance of 0.3831, and JH and AMH had a genetic distance of 0.2883. Of the three breeds, QH and JH formed clearly near groups and the AMH formed clearly different groups. This study is judged to be suitable for individual identification and parentage testing for registration of the lineage of AMH and QH. Therefore, the results of this study are an effective tool for genetic research and preservation of these horse breeds.

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“…In the previous decades, crossbreeding has been used worldwide to improve milk production, milk composition, and reproduction performance [ 7 ]. The Simmental and Holstein crossbreeding is one of the most common crossbreeding patterns, which has shown efficient herd improvement and reduced inbreeding coefficients in several studies [ 8 , 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Microbial Communities along the Gastrointestinal Tract in Crossbred Cattle

Wang

Zhang

et al. 2022

Animals

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The gastrointestinal microbiota greatly affects the health status and production performance of bovines. Presently, many studies have used high-throughput sequencing methods to investigate the gastrointestinal microbiome in bovines. However, the microbiome profile of crossbred cattle across the whole gastrointestinal tract (GIT) has not been thoroughly reported. In this study, the digesta at ten regions (including the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum) of the GIT were collected in three Simmental × Holstein crossbred heifers aged 17 months, and microbial DNA was extracted and amplified for sequencing of the V3–V4 regions of the 16S rRNA gene. Functional orthologs of the microbiota genome were predicted and analyzed. We found that samples were categorized into three groups (the stomach, small intestine, and large intestine) by principal coordinate analysis (PCoA) based on Bray–Curtis dissimilarity in both the bacterial composition and functional profile. Samples from small intestine had the lowest alpha diversity of bacteria composition and highest alpha diversity of the functional composition. Three groups of GIT regions were characterized by several microbiome features. The stomach was characterized by Bacteroidetes and Fibrobacteres at the phylum level, and KEGG pathways related to the metabolism of cofactors and vitamins, glycan biosynthesis, and metabolism were enriched in the stomach. The small intestine was characterized by Actinobacteria and Patescibacteria at the phylum level, and KEGG pathways related to xenobiotics biodegradation and metabolism were enriched in the small intestine. The large intestine featured Ruminococcaceae, Rikenellaceae, and Bacteroidacea at the family level, and KEGG pathways, including steroid hormone biosynthesis, linoleic acid metabolism, and cysteine and methionine metabolism were enriched in the large intestine. The results of the current study revealed the spatial heterogeneity of microbiota across the GIT in Simmental × Holstein crossbreeds and identified microbial biomarkers of different regions. The results can provide useful information for the study of the gastrointestinal microbiome in bovines.

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Selection and implementation of single nucleotide polymorphism markers for parentage analysis in crossbred cattle population

Cited by 5 publications

References 30 publications

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping

Microsatellite Variation in Jeju and American horses and their Phylogenetic Relationship

Characterization of the Microbial Communities along the Gastrointestinal Tract in Crossbred Cattle

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