scholarly journals Signatures of Selection in Composite Vrindavani Cattle of India

2020 ◽  
Author(s):  
Akansha Singh ◽  
Arnav Mehrotra ◽  
Cedric Gondro ◽  
Andrea Renata da Silva Romero ◽  
Ashwni Kumar Pandey ◽  
...  
Keyword(s):  
Cattle Breed ◽  
Selection Response ◽  
Fixation Index ◽  
Selection Signatures ◽  
Extended Haplotype ◽  
Signatures Of Selection ◽  
Selection For ◽  
Breed Selection ◽  
The 1960S ◽  
Selection Of

AbstractVrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle in the 1960s. About 190,000 semen doses of Vrindavani bulls have been distributed to the farmers till date. The animals are under artificial and natural selection for higher milk production and adaptation to the tropical climate, respectively. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). Vrindavani was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). Selection of signature identifies 11 common region identified by more than one harbouring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

scholarly journals Signatures of Selection in Composite Vrindavani Cattle of India

2020 ◽  
Vol 11 ◽  
Author(s):  
Akansha Singh ◽  
Arnav Mehrotra ◽  
Cedric Gondro ◽  
Andrea Renata da Silva Romero ◽  
Ashwni Kumar Pandey ◽  
...  
Keyword(s):  
Selective Pressure ◽  
Cattle Breed ◽  
Selection Response ◽  
Fixation Index ◽  
Genotype Data ◽  
Public Database ◽  
Selection Signatures ◽  
Extended Haplotype ◽  
Signatures Of Selection ◽  
Breed Selection

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

ESTIMASI NILAI HERITABILITAS BOBOT IKAN MAS VARIETAS PUNTEN DALAM PROGRAM SELEKSI INDIVIDU

2016 ◽  
Vol 11 (3) ◽  
pp. 217
Author(s):  
Estu Nugroho ◽  
Budi Setyono ◽  
Mochammad Su’eb ◽  
Tri Heru Prihadi
Keyword(s):  
Body Weight ◽  
Selection Response ◽  
Base Population ◽  
Breeding Programs ◽  
Male And Female ◽  
Body Weight Trait ◽  
Population Selection ◽  
Selection For ◽  
Weight Trait ◽  
Selection Of

Program pemuliaan ikan mas varietas Punten dilakukan dengan seleksi individu terhadap karakter bobot ikan. Pembentukan populasi dasar untuk kegiatan seleksi dilakukan dengan memijahkan secara massal induk ikan mas yang terdiri atas 20 induk betina dan 21 induk jantan yang dikoleksi dari daerah Punten, Kepanjen (delapan betina dan enam jantan), Kediri (tujuh betina dan 12 jantan), Sragen (27 betina dan 10 jantan), dan Blitar (15 betina dan 11 jantan). Larva umur 10 hari dipelihara selama empat bulan. Selanjutnya dilakukan penjarangan sebesar 50% dan benih dipelihara selama 14 bulan untuk dilakukan seleksi dengan panduan hasil sampling 250 ekor individu setiap populasi. Seleksi terhadap calon induk dilakukan saat umur 18 bulan pada populasi jantan dan betina secara terpisah dengan memilih berdasarkan 10% bobot ikan yang terbaik. Calon induk yang terseleksi kemudian dipelihara hingga matang gonad, kemudian dipilih sebanyak 150 pasang dan dipijahkan secara massal. Didapatkan respons positif dari hasil seleksi berdasarkan bobot ikan, yaitu 49,89 g atau 3,66% (populasi ikan jantan) dan 168,47 g atau 11,43% (populasi ikan betina). Nilai heritabilitas untuk bobot ikan adalah 0,238 (jantan) dan 0,505 (betina).Punten carp breeding programs were carried out by individual selection for body weight trait. The base population for selection activities were conducted by mass breeding of parent consisted of 20 female and 21 male collected from area Punten, eight female and six male (Kepanjen), seven female and 12 male (Kediri), 27 female and 10 male (Sragen), 15 female and 11 male (Blitar). Larvae 10 days old reared for four moths. Then after spacing out 50% of total harvest, the offspring reared for 14 months for selection activity based on the sampling of 250 individual each population. Selection of broodstock candidates performed since 18 months age on male and female populations separately by selecting based on 10% of fish with best body weight. Candidates selected broodstocks were then maintained until mature. In oder to produce the next generation 150 pairs were sets and held for mass spawning. The results revealed that selection response were positive, 49.89 g (3.66%) for male and 168.47 (11.43%) for female. Heritability for body weight is 0.238 (male) and 0.505 (female).

scholarly journals Response of Egg Number to Selection of Different Genotypes of 24-bp Insertion-Deletion Locus in the Promoter of Prolactin Gene of Papua Local Chickens

2021 ◽  
pp. 18-26
Author(s):  
Muhammad Affan Mu'in ◽  
Sintje Lumatauw
Keyword(s):  
Selection Response ◽  
Breeding Value ◽  
Prolactin Gene ◽  
Egg Number ◽  
Selection For ◽  
Actual Response ◽  
Actual Selection ◽  
Selection Of ◽  
Selection Generation ◽  
Local Chickens

This study aims to estimate the response of the number of eggs produced up to 240 days of age (EN240) to the selection of Papua local chickens (PLC) with different genotypes from the 24-bp Indel cPRLp locus. A total of 68 PLCs were taken randomly from several breeders in Manokwari as the basic population for selection (G0). Genotype identification of the 24-bp Indel cPRLp locus was performed G0. Based on the distribution of these genotypes, mating pairs were randomly formed G0-II, G0-DD and G0-ID to produce G1-II, G1-DD, and G1-Control (G0-ID offspring). Heritability of EN240 in G1-II and G1-DD populations were estimated in full-sib (single pairs mating). Individual selection based on breeding value EN240 was carried out on G1-II (♀) and G1-DD (♀) to form the selection generation (GS): GS-II (♀) and GS-DD (♀). Selection was also carried out on G1-II (♂) and G1-DD (♂) based on body weight at 240 days (BW240) to become selected GS-II (♀) and GS-DD (♀) mating partners. GS-Control was also formed through 25% random sampling from G1-Control (♂ and ♀). GS mating resulted in the second generation (G2): G2-II, G2-DD, and G2-Control. Age at first laying (AFL), EN240, and mean egg weight (EWA) in hens of G1, GS, and G2 were recorded. Response to selection for EN240 was calculated by two methods predicted selection response (Rp) and actual selection response (Rr). Both methods of calculation yield positive and high values. In actual response (Rr), PLC in II genotypes group are more responsive to the selection treatment than DD genotype group. Selection increase EN240 impact accelerate of AFL and lower the EWA, because of their negative genetic correlation.

scholarly journals Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 346
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zitao Chen ◽  
Jinyan Teng ◽  
Yunlong Ma ◽  
...  
Keyword(s):  
Meat Quality ◽  
South China ◽  
Coat Color ◽  
Reference Group ◽  
Fixation Index ◽  
Extended Haplotype ◽  
Genome Wide ◽  
High Altitude Area ◽  
Signatures Of Selection ◽  
Indigenous Pigs

South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (FST) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs.

scholarly journals Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 976 ◽  
Author(s):  
Michela Ablondi ◽  
Susanne Eriksson ◽  
Sasha Tetu ◽  
Alberto Sabbioni ◽  
Åsa Viklund ◽  
...  
Keyword(s):  
System Development ◽  
Genomic Structure ◽  
Fixation Index ◽  
Principal Coordinates Analysis ◽  
Extended Haplotype ◽  
Principal Coordinates ◽  
Genotype Information ◽  
Signatures Of Selection ◽  
Control Body ◽  
Show Jumping

The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010–2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.

scholarly journals Genetic Variation and Response to Selection for Early Season Fruit Production in California Strawberry Seedling (Fragaria ×ananassa Duch.) Populations

2005 ◽  
Vol 130 (1) ◽  
pp. 41-45 ◽  
Author(s):  
Douglas V. Shaw ◽  
Kirk D. Larson
Keyword(s):  
Genetic Variance ◽  
Total Yield ◽  
Selection Response ◽  
Fruit Production ◽  
Fragaria Ananassa ◽  
Early Season ◽  
Selection For ◽  
Selection Intensities ◽  
Opportunity For Selection ◽  
Selection Of

The genetic opportunity for selection of early fruiting strawberry cultivars was evaluated using seedling populations from the Univ. of California (UC) breeding program in three years. Narrow-sense heritabilities for early season yield and for the proportion of an individual's total yield expressed early were moderate (h2 = 0.24-0.53) and broad-sense heritabilities were slightly larger (H2 = 0.31-0.70), suggesting the presence of some nonadditive genetic variance for these traits. These two traits were genetically correlated with each other (rg = 0.78-0.98), but only early yield was consistently genetically correlated with seasonal yield (rg = 0.52-0.82). Selection was performed for each trait using an index on full-sib family means and individual phenotypic values in two of the three years, and predicted response was compared with that obtained using vegetatively propagated runner plants from selected genotypes in the subsequent fruiting season. Statistically significant (P < 0.05) selection response was obtained in one of two years for each trait, and combined analysis demonstrated highly significant (P < 0.01) response for both traits. However, realized response over all traits and years was just 27.3% of that predicted based on the estimated heritabilities and applied selection intensities. These results suggest that selection for early yield should be based at least in part on runner plant evaluations rather than exclusively on seedling performance.

scholarly journals Selection of Simmental cattle on beef and meatiness traits in Serbia

2005 ◽  
Vol 21 (3-4) ◽  
pp. 25-34 ◽  
Author(s):  
Vladan Bogdanovic ◽  
Radica Djedovic ◽  
Milan Petrovic
Keyword(s):  
Cattle Population ◽  
Selection Methods ◽  
Dual Purpose ◽  
Dual Purpose Cattle ◽  
Beef Herds ◽  
Simmental Cattle ◽  
Selection For ◽  
Breed Selection ◽  
Selection Of ◽  
Made In

Population of domestic Simmental breed represents a dominant population of cattle in Serbia. According to importance of this breed, selection so far has been made in order to improve milk production. In other hand, beef and meatiness traits almost were ignored. Selection of dual-purpose cattle requires combining a various breeding goals and selection methods that are very differ from those applied in pure dairy or beef herds. Improving of beef and meatiness traits in our dominant cattle population will have great importance in future. The aim of this paper is to show possibility of selection for beef and meatiness traits in Serbian Simmental cattle.

scholarly journals ANALYSIS OF POLYMORPHISM IN MUCIN 4 GENE ASSOCIATED WITH ANIMAL RESISTANCE TO COLIBACTERIOSIS IN PIGS OF DOMESTIC AND FOREIGN SELECTIONS

2018 ◽  
Vol 51 ◽  
pp. 200-205 ◽  
Author(s):  
H. Rudoman ◽  
V. Balatskyi ◽  
V. Nor
Keyword(s):  
Escherichia Coli ◽  
Genetic Structure ◽  
Genetic Resistance ◽  
Fixation Index ◽  
Large White ◽  
Selection For ◽  
Type 3 ◽  
Muc4 Gene ◽  
Selection Of

Nowadays one of the most common and critical problem in pig breeding is colibacteriosis. This infectious disease has acute course and it is caused by enteropathogenic strains of bacteria Escherichia coli. One of the recent and effective approaches to prevent colibacteriosis is using markers of selection; it involves pig genotyping by genome loci. The chosen loci are associated with animal sensitivity to the disease and selection of animals with increased resistance by the results of genotyping. According to several researches, one of such loci is Mucin 4 (MUC4) gene. MUC4 gene is located in the13-th chromosome (SSC13q41). Mucins (MUC) are macromolecular glycoproteins synthesized by goblet enterocytes and play main role in protecting the intestinal epithelium from pathogens, including adhesive strains of Escherichia coli. As a result of spot replacement g.1849 G>С in intron 7, structure of mucin protein encoded by gene is changing which leads to changes in the sensitivity of the intestinal mucosa to pathogenic Escherichia coli. G allele and respectively GG genotype determine the resistance of animals to colibacteriosis, while СС і GС genotypes are susceptible to this disease. In Ukraine, the studies of polymorphism MUC4 g.1849 G> C were held fragmentally and only at certain populations of Ukrainian Meat and Large White. The aim of the work was to determine the genetic structure of pig breeds of domestic and foreign selection for MUC4 gene and to establish the possibility of organizing marker associated selection for genetic improvement of resistance to colibacteriosis. For research the samples of blood and hair were used from the animals of Large White of English selection, Large White of Ukrainian selection Type 1 and Type 3, Red White-Belt, Mirgorod, Poltava Meat and Landrace breeds. DNA isolation from the samples of biomaterial were carried out using ion exchange resin Chelex-100. Genotyping was performed by PCR-RFLP by Jorgensen methods (2006) with own modifications, concerning the selection of primer annealing temperature and optimum concentration of the gel to separate the restriction fragments. Genetic structure was determined using DNA analysis of MUC4 locus at seven breeds and intrabreed types. Predominance of potentially beneficial G allele frequency over undesirable C allele was established in all the populations of the studied pigs. The highest frequencies of G allele were characterized for Mirgorod (0.795), Poltava Meat (0.740) and Red White-Belt (0.820) breeds. Analysis of the distribution of genotypes showed domination of genotypes GG and GC in all analysed populations. Positive Wright fixation index and predominance of expected heterozygosity (0.484) over actual one (0.460) for Large White of Ukrainian selection Type 3 indicate the existence of moderate inbreeding and selective pressure in this herd. Other populations were characterized by a negative value of fixation index, which is indicative of an excess of heterozygotes, these breeds are in outbreeding depression. Statically significant deviation of actual frequencies of genotypes from expected ones was identified using Hardy-Weinberg criterion for pig population of Large White of English selection and Large White of Ukrainian selection Type 1. This may indicate that these populations aren’t in condition of equilibrium and about inclusion of the chosen gene to the selection process. The valuation was performed by calculating the PIC (polymorphic information content) of the marker. Based on the calculated PIC index MUC4 locus could be perspective to be used in marker associated selection with improving genetic resistance to colibacteriosis. The data of Mucin 4 gene polymorphism at Ukrainian pig populations of different origins and productive direction show the possibility of marker selection to improve the genetic resistance of animals to colibacteriosis regardless of their belonging to breed. This creates prerequisites for the establishment and implementation of the early molecular diagnosis of carriers of harmful C allele in MUC4 gene in pig breeding.

scholarly journals Identifying Selection Signatures for Backfat Thickness in Yorkshire Pigs Highlights New Regions Affecting Fat Metabolism

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 254 ◽  
Author(s):  
Haoran Ma ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Huiwen Zhan ◽  
Xia Peng ◽  
...  
Keyword(s):  
Fat Metabolism ◽  
Backfat Thickness ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Selection Signatures ◽  
Extended Haplotype ◽  
Single Nucleotide ◽  
Fundamental Information ◽  
Yorkshire Pigs

Identifying the genetic basis of improvement in pigs contributes to our understanding of the role of artificial selection in shaping the genome. Here we employed the Cross Population Extended Haplotype Homozogysity (XPEHH) and the Wright’s fixation index (FST) methods to detect trait-specific selection signatures by making phenotypic gradient differential population pairs, and then attempted to map functional genes of six backfat thickness traits in Yorkshire pigs. The results indicate that a total of 283 and 466 single nucleotide polymorphisms (SNPs) were identified as trait-specific selection signatures using FST and XPEHH, respectively. Functional annotation suggested that the genes overlapping with the trait-specific selection signatures such as OSBPL8, ASAH2, SMCO2, GBE1, and ABL1 are responsible for the phenotypes including fat metabolism, lean body mass and fat deposition, and transport in mouse. Overall, the study developed the methods of gene mapping on the basis of identification of selection signatures. The candidate genes putatively associated with backfat thickness traits can provide important references and fundamental information for future pig-breeding programs.

Identifying Measurement Invariant Item Sets in Cross-Cultural Settings Using an Automated Item Selection Procedure

Methodology ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. 177-188 ◽  
Author(s):  
Martin Schultze ◽  
Michael Eid
Keyword(s):  
Measurement Invariance ◽  
Optimal Solution ◽  
Selection Procedure ◽  
Cross Cultural ◽  
Item Selection ◽  
Ant System ◽  
Item Quality ◽  
Ant System Algorithm ◽  
Selection For ◽  
Selection Of

Abstract. In the construction of scales intended for the use in cross-cultural studies, the selection of items needs to be guided not only by traditional criteria of item quality, but has to take information about the measurement invariance of the scale into account. We present an approach to automated item selection which depicts the process as a combinatorial optimization problem and aims at finding a scale which fulfils predefined target criteria – such as measurement invariance across cultures. The search for an optimal solution is performed using an adaptation of the [Formula: see text] Ant System algorithm. The approach is illustrated using an application to item selection for a personality scale assuming measurement invariance across multiple countries.

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