Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.

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Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

Frontiers in Genetics ◽

10.3389/fgene.2021.657282 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sèyi Fridaïus Ulrich Vanvanhossou ◽

Tong Yin ◽

Carsten Scheper ◽

Ruedi Fries ◽

Luc Hippolyte Dossa ◽

...

Keyword(s):

Production Systems ◽

Principal Component ◽

West African ◽

Economic Traits ◽

Selection Signatures ◽

Extended Haplotype ◽

Indigenous Cattle ◽

Environmental Pressures ◽

Inbreeding Coefficients ◽

Recent Selection

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

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Genetic Evaluation and Bi-plot Analysis in Okra Hybrids for Yield, Quality Components and YVMV Resistance

Journal of AgriSearch ◽

10.21921/jas.5.4.5 ◽

2018 ◽

Vol 5 (04) ◽

Author(s):

SS SOLANKEY ◽

ANIL K SINGH

Keyword(s):

Genetic Divergence ◽

Principal Component ◽

F1 Hybrids ◽

Genetic Advance ◽

Economic Traits ◽

Cross Combination ◽

Plot Analysis ◽

Eigen Value ◽

Coefficient Of Variability ◽

Yield Quality

Fifty one okra F1 hybrids (using 17 lines as female and 3 testers as male parent) were evaluated in RCBD design during two different consecutive seasons (summer and rainy). Phenotypic coefficient of variability (PCV) was higher than genotypic coefficient of variability (GCV) for all studied character exhibiting environmental effects on the expression of characters. Heritability (h2b) along with genetic advance per cent of mean was found highest for character YVMV (86.95% and 150.61%). All the 51 okra hybrids were grouped into 4 distinct clusters in which Cluster II was the largest cluster having 28 F1s (54.90% of total F1s) followed by Cluster I with 14 F1s (27.45% of total F1s). Out of the major 6 PCs, 4 principal components (PC1, PC2, PC3 and PC4) accounted with proportionate values of 22.61, 17.22, 11.87 and 10.63%, respectively and contributed 62.33 % of the cumulative variation having Eigen value more than one. Moreover, based on PCs and genetic divergence in Cluster I and Cluster IV for plant height, YVMV and number of fruit per plant is important to identify the best cross combination (Arka Abhay × Arka Anamika) in okra. Therefore, the best cross combinations for improvement in various economic traits can be recommended on the basis of genetic divergence and principal component analysis in okra.

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Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkab028 ◽

2021 ◽

Author(s):

Michael Brilhante ◽

Stefanie Gobeli Brawand ◽

Andrea Endimiani ◽

Helene Rohrbach ◽

Sonja Kittl ◽

...

Keyword(s):

High Risk ◽

Klebsiella Pneumoniae ◽

Genetic Relationships ◽

Clinical Environment ◽

Structural Variations ◽

Veterinary Clinic ◽

Antimicrobial Resistance Genes ◽

Carbapenemase Gene ◽

Genetic Features ◽

Almost All

Abstract Objectives Infections with carbapenem-resistant Enterobacterales (CRE) are an emerging problem in pets and a major threat to public health. We determined the genetic relationships among carbapenemase-producing Klebsiella pneumoniae (CPKp) strains causing infections in hospitalized pets in a veterinary clinic and those found in the environment. Methods WGS was performed with both the Illumina and Nanopore platforms. Searches of genetic features were performed using several databases and bioinformatics tools, and phylogeny was assessed by whole-genome MLST (wgMLST) using SeqSphere and SNP calling with Snippy. Results WGS analysis of the CPKp strains identified all environmental and almost all animal strains as the high-risk clone ST11, with the exception of two strains that belonged to ST307. All CPKp belonged to novel complex types (CTs) and carried a conjugative 63 kb IncL plasmid encoding the carbapenemase gene blaOXA-48, yersiniabactin and other virulence factors. Although all CPKp ST11 strains carried additional similar IncR plasmids harbouring multiple antimicrobial resistance genes (ARGs), such as the plasmid-mediated blaDHA-1 AmpC gene, some structural variations were observed. The two ST307 strains carried identical 156 kb MDR IncFIB(K) plasmids with several ARGs, including the blaCTX-M-15 ESBL gene. Both wgMLST and cgSNP analysis confirmed that CPKp strains of the same ST were genetically highly related independent of the source of isolation. Conclusions This study demonstrated that the clinical CPKp strains were highly related to those contaminating the clinical environment. These findings confirmed nosocomial spread and highlight veterinary hospitals as a source of CPKp, which may further spread to animals, the environment and humans.

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A case report and mechanism analysis of a normal phenotype mosaic 47, XXY complicated by paternal iUPD (9) who had a normal PGD result

BMC Medical Genetics ◽

10.1186/s12881-019-0897-5 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Dan Li ◽

Yun Wang ◽

Nan Zhao ◽

Liang Chang ◽

Ping Liu ◽

...

Keyword(s):

Case Report ◽

Karyotype Analysis ◽

Snp Array ◽

Uniparental Disomy ◽

Comparative Genomic ◽

Klinefelter’S Syndrome ◽

Mechanism Analysis ◽

Klinefelter's Syndrome ◽

Preimplantation Genetic Testing ◽

First Case

Abstract Background Uniparental disomy (UPD) refers to the situation in which two copies of homologous chromosomes or part of a chromosome originate from the one parent and no copy is supplied by the other parent. Case presentation Here, we reported a woman whose karyotype was 46, XX, t (1;17)(q42;q21), has obtained 5 embryos by intracytoplasmic sperm injection (ICSI) after one cycle of in vitro fertility (IVF). After microarray-based comparative genomic hybridization (array-CGH) for preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR), two embryos were balanced, one balanced embryo was implanted and the patient successfully achieved pregnancy. Amniocentesis was performed at the 19th week of gestation for karyotype analysis and single nucleotide polymorphism (SNP)-array test. The result of karyotype analysis was: mos 47, XXY [19]/46, XY [81]; SNP-array results revealed 46, XY, iUPD (9) pat. After full genetic counseling for mosaic Klinefelter’s syndrome and paternal iUPD (9), the couple decided to continue pregnancy, and the patient gave birth to a healthy boy. The newborn is now 3.5 years old, and developed normally. This case will provide counseling evidences of paternal iUPD (9) for doctors. Conclusions This is the first case report of paternal iUPD9 with mosaic Klinefelter’s syndrome, and no abnormality has been observed during the 3.5-year follow-up. Further observation is required to determine whether the imprinted genes on the chromosomes are pathogenic and whether recessive pathogenetic genes are activated.

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Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population

Genes ◽

10.3390/genes12010117 ◽

2021 ◽

Vol 12 (1) ◽

pp. 117

Author(s):

Donglin Ruan ◽

Zhanwei Zhuang ◽

Rongrong Ding ◽

Yibin Qiu ◽

Shenping Zhou ◽

...

Keyword(s):

Candidate Genes ◽

Bone Growth ◽

Genome Wide Association Study ◽

Growth Traits ◽

Average Daily Gain ◽

Snp Array ◽

Single Step ◽

Economic Traits ◽

Association Analyses ◽

Genealogical Information

Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

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ESTIMATION OF GENETIC DIVERGENCE IN CHILLI PEPPER (CAPSICUM ANNUUM L.) GENOTYPES FOR MORPHOLOGICAL AND FRUIT TRAITS UNDER HOT CLIMATE OF UMERKOT, SINDH

Pakistan Journal of Agriculture, Agricultural Engineering and Veterinary Sciences ◽

10.47432/2021.37.1.3 ◽

2021 ◽

Vol 37 (1) ◽

pp. 21-28

Author(s):

A. Memon ◽

R. Ahmad ◽

M. S. Depar ◽

A. K. Pathan ◽

D. Ibrar

Keyword(s):

Cluster Analysis ◽

Genetic Divergence ◽

Agricultural Research ◽

Arid Zone ◽

Principal Component ◽

Fruit Weight ◽

Economic Traits ◽

Chilli Pepper ◽

Hot Climate ◽

Improvement Programs

Thirty-two genotypes of chilli from three different sources (local dandicuts, AVRDC and PGRI PARC) were evaluated for the presence of genetic divergence among them for different agro-economic traits i.e., plant height, stem girth, fruit length, fruit girth, number of fruits per plant, number of seed per fruit, fresh fruit weight and dry fruit weight at Arid Zone Agricultural Research Institute, Umerkot, Sindh during 2018. All these genotypes were found to be significantly different from each other for all the studied traits. For further diversity analysis, multivariate analyses like principal component analysis (PCA) and Cluster analysis were also performed to figure out the traits responsible for maximum variability and grouping of genotypes according to their similarities and differences for their future utilization in chilli breeding programs. PCA analysis showed that first four PCs exhibited 82.79% of the total variability among these 32 chilli genotypes. Cluster analysis showed four different sub-clusters and the genotypes from every single source merge in each sub-cluster, thus showing that chilli genotypes are from different geographical backgrounds. Based on these results, the chilli genotypes can be further utilized in future chilli improvement programs in Pakistan. Genotypes AZRI-DS-14, AZRI-DS-01 and AVPP-9804 showed better performance.

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Detection and evaluation of selection signatures in sheep

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2018000500001 ◽

2018 ◽

Vol 53 (5) ◽

pp. 527-539 ◽

Cited By ~ 2

Author(s):

Tiago do Prado Paim ◽

Patrícia Ianella ◽

Samuel Rezende Paiva ◽

Alexandre Rodrigues Caetano ◽

Concepta Margaret McManus Pimentel

Keyword(s):

Statistical Methods ◽

Phenotypic Diversity ◽

Selection Process ◽

Genomic Data ◽

Research Field ◽

Economic Traits ◽

Selection Signatures ◽

Important Species ◽

Challenges And Opportunities ◽

Genomic Regions

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

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Clustering of immunological, metabolic and genetic features in latent autoimmune diabetes in adults: evidence from principal component analysis

Internal and Emergency Medicine ◽

10.1007/s11739-015-1352-z ◽

2015 ◽

Vol 11 (4) ◽

pp. 561-567 ◽

Cited By ~ 8

Author(s):

Giovanni Mario Pes ◽

Alessandro Palmerio Delitala ◽

Alessandra Errigo ◽

Giuseppe Delitala ◽

Maria Pina Dore

Keyword(s):

Principal Component Analysis ◽

Autoimmune Diabetes ◽

Principal Component ◽

Component Analysis ◽

Latent Autoimmune Diabetes ◽

Genetic Features

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Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽

10.3390/ani9060361 ◽

2019 ◽

Vol 9 (6) ◽

pp. 361 ◽

Cited By ~ 3

Author(s):

Shuqi Diao ◽

Shuwen Huang ◽

Zhiting Xu ◽

Shaopan Ye ◽

Xiaolong Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Conservation Status ◽

Snp Array ◽

Size Analysis ◽

Selection Signatures ◽

Effective Population ◽

Low Genetic Diversity ◽

Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes

BMC Genetics ◽

10.1186/s12863-020-0827-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Christina Marie Rochus ◽

Elisabeth Jonas ◽

Anna M. Johansson

Keyword(s):

Population Structure ◽

Snp Array ◽

Principal Component ◽

Northern Sweden ◽

The Baltic Sea ◽

Sheep Breeds ◽

The North ◽

South West ◽

Branch Lengths ◽

The Baltic

Abstract Background Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree. Results The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they’ve been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree. Conclusions We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.

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