scholarly journals Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms

2014 ◽  
Vol 27 (9) ◽  
pp. 1263-1269 ◽  
Author(s):  
Zewdu Edea ◽  
Sang-Wook Kim ◽  
Kyung-Tai Lee ◽  
Tae Hun Kim ◽  
Kwan-Suk Kim
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pig Breeds ◽  
Korean Native Pig

scholarly journals The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

2019 ◽  
Author(s):  
James Worth ◽  
Luxian Liu ◽  
Nobuhiro Tomaru
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Chloroplast Genome ◽  
Tree Species ◽  
Fagus Crenata ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Genetic Structure And Diversity

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psbK-psbI, trnG-psbfM, trnV, rpl32, ndhD-psaC and ndhI-ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

Single nucleotide polymorphisms of the prion protein gene (PRNP) in Chinese pig breeds

2005 ◽  
Vol 12 (4) ◽  
pp. 324-326 ◽  
Author(s):  
Liping Meng ◽  
Deming Zhao ◽  
Hongxiang Liu ◽  
Jianmin Yang ◽  
Zhangyong Ning
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Prion Protein ◽  
Protein Gene ◽  
Prion Protein Gene ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pig Breeds

scholarly journals Single Nucleotide Polymorphisms of Porcine lncMGPF Regulate Meat Production Traits by Affecting RNA Stability

2021 ◽  
Vol 9 ◽  
Author(s):  
Wei Lv ◽  
Shiyu Zhao ◽  
Yunqing Hou ◽  
Qian Tong ◽  
Yaxin Peng ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Myogenic Differentiation ◽  
Muscle Growth ◽  
Backfat Thickness ◽  
Meat Production ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Muscle Area ◽  
Single Nucleotide ◽  
Pig Breeds

lncMGPF is a novel positive regulator of myogenic differentiation, muscle growth and regeneration in mouse, pig, and human. But whether natural mutations within lncMGPF gene regulate animal meat production traits is unclear. In this study, ten single nucleotide polymorphisms (SNPs) of pig lncMGPF (plncMGPF) gene were identified among commercial pig breeds and Chinese local pig breeds. These SNPs are highly linked and constructed into multiple haplotypes, and haplotype ATTCATGTTC (H1) mainly exists in commercial pig breeds while haplotype GCCTGCACCT (H3) is more frequent in Chinese local pig breeds. Association analysis indicated that all SNPs are significantly associated with the backfat thickness and loin muscle area (P < 0.05), respectively, and homologous H1 individuals have higher loin muscle area and lower backfat thickness than H3 pigs. Bioinformatics and functional analysis showed that haplotype H1 has a longer half-life and more stable RNA secondary structure than haplotype H3. plncMGPF haplotype H1 has stronger effects on pig primary myogenic progenitor cells differentiation and muscle growth than haplotype H3. Further experiments showed that two SNPs (rs81403974 and rs325492834) function together to confer plncMGPF stability and function. Our observation suggested that the SNPs in lncMGPF can change the RNA stabilities and lncMGPF function, thereby affecting the porcine meat production traits.

scholarly journals Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 784 ◽  
Author(s):  
Katie E Fowler ◽  
Ricardo Pong-Wong ◽  
Julien Bauer ◽  
Emily J Clemente ◽  
Christopher P Reitter ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Copy Number ◽  
Copy Number Variants ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide Analysis ◽  
Pig Breeds ◽  
Genome Wide

scholarly journals Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding

PLoS ONE ◽  
2019 ◽  
Vol 14 (8) ◽  
pp. e0220981 ◽  
Author(s):  
Hiroto Yamashita ◽  
Hideyuki Katai ◽  
Lina Kawaguchi ◽  
Atsushi J. Nagano ◽  
Yoriyuki Nakamura ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Wing Geometric Morphometrics of Workers and Drones and Single Nucleotide Polymorphisms Provide Similar Genetic Structure in the Iberian Honey Bee (Apis mellifera iberiensis)

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 89 ◽  
Author(s):  
Dora Henriques ◽  
Julio Chávez-Galarza ◽  
Juliana S. G. Teixeira ◽  
Helena Ferreira ◽  
Cátia J. Neves ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Geometric Morphometrics ◽  
Geographical Information ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Processes ◽  
Single Nucleotide ◽  
Genetic Patterns ◽  
Wing Geometric Morphometrics

Wing geometric morphometrics has been applied to honey bees (Apis mellifera) in identification of evolutionary lineages or subspecies and, to a lesser extent, in assessing genetic structure within subspecies. Due to bias in the production of sterile females (workers) in a colony, most studies have used workers leaving the males (drones) as a neglected group. However, considering their importance as reproductive individuals, the use of drones should be incorporated in these analyses in order to better understand diversity patterns and underlying evolutionary processes. Here, we assessed the usefulness of drone wings, as well as the power of wing geometric morphometrics, in capturing the signature of complex evolutionary processes by examining wing shape data, integrated with geographical information, from 711 colonies sampled across the entire distributional range of Apis mellifera iberiensis in Iberia. We compared the genetic patterns reconstructed from spatially-explicit shape variation extracted from wings of both sexes with that previously reported using 383 genome-wide SNPs (single nucleotide polymorphisms). Our results indicate that the spatial structure retrieved from wings of drones and workers was similar (r = 0.93) and congruent with that inferred from SNPs (r = 0.90 for drones; r = 0.87 for workers), corroborating the clinal pattern that has been described for A. m. iberiensis using other genetic markers. In addition to showing that drone wings carry valuable genetic information, this study highlights the capability of wing geometric morphometrics in capturing complex genetic patterns, offering a reliable and low-cost alternative for preliminary estimation of population structure.

scholarly journals The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana)

2019 ◽  
Author(s):  
James Worth ◽  
Luxian Liu ◽  
Nobuhiro Tomaru
Keyword(s):  
Genetic Structure ◽  
Single Nucleotide Polymorphisms ◽  
Chloroplast Genome ◽  
Tree Species ◽  
Fagus Crenata ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Genetic Structure And Diversity

This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome was a total of 158,247 bp in length containing 111 genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed between them and differing by 311 single nucleotide polymorphisms. The six most variable regions between the two genomes were the psbK-psbI, trnG-psbfM, trnV, rpl32, ndhD-psaC and ndhI-ndh regions. These highly variable chloroplast regions and the identification of 42 variable chloroplast SSRs found to be shared between the two species will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus.

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