A novel (ATC)<sub>n</sub> microsatellite locus is associated with litter size in an indigenous Chinese pig

Wu, Guofang; Shen, Wenjuan; Xue, Xingxing; Wang, Lei; Ma, Yuhong; Zhou, Jack G.

doi:10.1002/vms3.371

Cited by 2 publications

(1 citation statement)

References 38 publications

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“…G. gallus had the highest percentage for mono repeats, whereas F. catus had the lowest number of mono repeats; B. grunniens, F. catus, C. lupus familiaris, and A. melifera had more dimeric repeats than monomeric repeats (Figure 2). Almost all genomes have a significant abundance of monomeric repeats, which may be related to the inherent limits of next-generation sequencing (NGS) technologies used for data creation [29]. Similarly, dimeric repeats also recorded a higher abundance in animal genomes [27,[30][31][32].…”

Section: Ssrs Characterization By Motif Typementioning

confidence: 99%

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

Duhan

Kaur

Kaundal

2023

Genes

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Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface allows users to browse SSRs by genomic coordinates, repeat motif sequence, chromosome, motif type, motif frequency, and functional annotation. Users may enter their preferred flanking area around the repeat to retrieve the nucleotide sequence, they can investigate SSRs present in the genic or the genes between SSRs, they can generate custom primers, and they can also execute in silico validation of primers using electronic PCR. For customized sequences, an SSR prediction pipeline called miSATminer is also built. New species will be added to this website’s database on a regular basis throughout time. To improve animal health via genomic selection, we hope that ranchSATdb will be a useful tool for mapping quantitative trait loci (QTLs) and marker-assisted selection. The web-resource is freely accessible at https://bioinfo.usu.edu/ranchSATdb/.

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Section: Ssrs Characterization By Motif Typementioning

confidence: 99%

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

Duhan

Kaur

Kaundal

2023

Genes

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Genetic Divergence of Thai Indigenous Pigs from Three Distinct Geographic Regions Revealed by Microsatellite Marker Analysis

Chaweewan

Mahinchai²,

Kongsook³

et al. 2023

Animals

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Thai indigenous pigs (TIPs) are important genetic resources. Crosses with exotic pig breeds and wild boars may cause genetic losses. To date, the physical characteristics of TIPs have been inconsistent. The classification of TIPs by genetic information is needed to pursue an appropriate conservation program. In this study, the genetic diversity, cluster analysis, and phylogenetic relationship of TIPs were investigated using twenty-nine pig microsatellite markers. Blood samples were collected from TIPs from three regions of Thailand: north (NT, n = 118), northeast (NE, n = 61), and south (ST, n = 75). The mean total number of distinct alleles and the effective number of alleles per locus were 11.851 and 5.497, respectively. The mean observed heterozygosity (Ho) and mean expected heterozygosity (He) were 0.562 and 0.837, respectively. The F values of the microsatellite loci were positive under Hardy–Weinberg Equilibrium at p < 0.001, with overall mean values of Fis, Fit, and Fst of 0.247, 0.281, and 0.046, respectively. A total of 5, 5, and 17 private alleles were found at frequencies greater than 0.050 in the NT, NE, and ST pigs, respectively. Three optimal clusters (K = 3) were proposed within the TIP populations. Pigs from the NT and NE regions were mixed in two clusters, while members of the ST region were clearly separated. The phylogenetic tree confirmed that the pigs from NT and NE were each divided into two subgroups, while the pigs from ST were clustered into one group. A microsatellite analysis revealed the high genetic diversity of the TIP populations and confirmed the genetic divergence of the TIPs from the European and Chinese breeds. A genetic admixture of the TIP with the local wild boars was detected.

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A novel (ATC)_n microsatellite locus is associated with litter size in an indigenous Chinese pig

Cited by 2 publications

References 38 publications

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

Genetic Divergence of Thai Indigenous Pigs from Three Distinct Geographic Regions Revealed by Microsatellite Marker Analysis

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A novel (ATC)n microsatellite locus is associated with litter size in an indigenous Chinese pig

Cited by 2 publications

References 38 publications

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health

Genetic Divergence of Thai Indigenous Pigs from Three Distinct Geographic Regions Revealed by Microsatellite Marker Analysis

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A novel (ATC)_n microsatellite locus is associated with litter size in an indigenous Chinese pig