scholarly journals Development of a low-density panel for genomic selection of pigs in Russia1

2019 ◽  
Vol 4 (1) ◽  
pp. 264-274
Author(s):  
Tatiana I Shashkova ◽  
Elena U Martynova ◽  
Asiya F Ayupova ◽  
Artemy A Shumskiy ◽  
Polina A Ogurtsova ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Reference Population ◽  
Snp Markers ◽  
Full Potential ◽  
Low Density ◽  
Single Chip ◽  
Large White ◽  
Pork Production ◽  
Individual Snps ◽  
The Individual

Abstract Genomic selection is routinely used worldwide in agricultural breeding. However, in Russia, it is still not used to its full potential partially due to high genotyping costs. The use of genotypes imputed from the low-density chips (LD-chip) provides a valuable opportunity for reducing the genotyping costs. Pork production in Russia is based on the conventional 3-tier pyramid involving 3 breeds; therefore, the best option would be the development of a single LD-chip that could be used for all of them. Here, we for the first time have analyzed genomic variability in 3 breeds of Russian pigs, namely, Landrace, Duroc, and Large White and generated the LD-chip that can be used in pig breeding with the negligible loss in genotyping quality. We have demonstrated that out of the 3 methods commonly used for LD-chip construction, the block method shows the best results. The imputation quality depends strongly on the presence of close ancestors in the reference population. We have demonstrated that for the animals with both parents genotyped using high-density panels high-quality genotypes (allelic discordance rate < 0.05) could be obtained using a 300 single nucleotide polymorphism (SNP) chip, while in the absence of genotyped ancestors at least 2,000 SNP markers are required. We have shown that imputation quality varies between chromosomes, and it is lower near the chromosome ends and drops with the increase in minor allele frequency. Imputation quality of the individual SNPs correlated well across breeds. Using the same LD-chip, we were able to obtain comparable imputation quality in all 3 breeds, so it may be suggested that a single chip could be used for all of them. Our findings also suggest that the presence of markers with extremely low imputation quality is likely to be explained by wrong mapping of the markers to the chromosomal positions.

Choice feeding to characterise genotypes in pigs

1995 ◽  
Vol 1995 ◽  
pp. 210-210
Author(s):  
J.M.F. Wilson ◽  
O.I. Southwood ◽  
H.A.M. van der Steen
Keyword(s):  
Crude Protein ◽  
Energy Requirements ◽  
Full Potential ◽  
Large White ◽  
Feeding Regime ◽  
Dietary Crude Protein ◽  
And Performance ◽  
The Individual ◽  
Choice Feeding

The choice feeding of pigs has been shown in many experiments to allow the individual pig to express its own needs and thereby grow more efficiently and show its full potential.The objective of this experiment was to test whether pigs representing 7 distinct genotypes, including Large White, Landrace, Pietrain, Duroc and Meishan, were able to select their dietary crude protein (CP) in relation to energy requirements under a choice feeding regime, and whether these differences were related to growth and performance.

Choice feeding to characterise genotypes in pigs

1995 ◽  
Vol 1995 ◽  
pp. 210-210
Author(s):  
J.M.F. Wilson ◽  
O.I. Southwood ◽  
H.A.M. van der Steen
Keyword(s):  
Crude Protein ◽  
Energy Requirements ◽  
Full Potential ◽  
Large White ◽  
Feeding Regime ◽  
Dietary Crude Protein ◽  
And Performance ◽  
The Individual ◽  
Choice Feeding

The choice feeding of pigs has been shown in many experiments to allow the individual pig to express its own needs and thereby grow more efficiently and show its full potential.The objective of this experiment was to test whether pigs representing 7 distinct genotypes, including Large White, Landrace, Pietrain, Duroc and Meishan, were able to select their dietary crude protein (CP) in relation to energy requirements under a choice feeding regime, and whether these differences were related to growth and performance.

scholarly journals Genomic regions associated with resistance to Fusarium wilt in castor identified through linkage and association mapping approaches

Genome ◽  
2021 ◽  
Author(s):  
Ranjan K. Shaw ◽  
Mobeen Shaik ◽  
M. Santha Lakshmi Prasad ◽  
R.D. Prasad ◽  
manmode darpan mohanrao ◽  
...  
Keyword(s):  
Association Mapping ◽  
Fusarium Wilt ◽  
Gene Diversity ◽  
Snp Markers ◽  
Phenotypic Variance ◽  
Wilt Resistance ◽  
Individual Snps ◽  
Efficiency And Effectiveness ◽  
The Individual ◽  
Genomic Regions

Fusarium wilt caused by <i>Fusarium oxysporum</i> f. sp <i>ricini</i> is the most destructive disease in castor. Host plant resistance is the best strategy for management of wilt problem. Identification of molecular markers linked to wilt resistance will enhance the efficiency and effectiveness of breeding for wilt resistance. In the present study, mapping of genomic regions linked to wilt resistance was attempted using a bi-parental population of 185 F<sub>6</sub>- RILs and a genetically diverse panel of 300 germplasm accessions. Quantitative trait loci (QTL) analysis performed using a linkage map consisting of 1,090 SNP markers identified a major QTL on chromosome-7 with LOD score of 18.7, which explained 44 per cent of phenotypic variance. The association mapping performed using genotypic data from 3,465 SNP loci revealed 69 significant associations (p <1×10-4) for wilt resistance. The phenotypic variance explained by the individual SNPs ranged from 0.063 to 0.210. The QTL detected in the bi-parental mapping population was not identified in the association analysis. Thus, the results of this study indicate the possibility of vast gene diversity for Fusarium wilt resistance in castor.

scholarly journals Genomic selection in French dairy cattle

2012 ◽  
Vol 52 (3) ◽  
pp. 115 ◽  
Author(s):  
D. Boichard ◽  
F. Guillaume ◽  
A. Baur ◽  
P. Croiseau ◽  
M. N. Rossignol ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Reference Population ◽  
Specific Reference ◽  
Nucleotide Polymorphisms ◽  
Genomic Evaluation ◽  
Linear Unbiased Prediction ◽  
Best Linear Unbiased ◽  
Estimated Breeding Values ◽  
Restricted Use

Genomic selection is implemented in French Holstein, Montbéliarde, and Normande breeds (70%, 16% and 12% of French dairy cows). A characteristic of the model for genomic evaluation is the use of haplotypes instead of single-nucleotide polymorphisms (SNPs), so as to maximise linkage disequilibrium between markers and quantitative trait loci (QTLs). For each trait, a QTL-BLUP model (i.e. a best linear unbiased prediction model including QTL random effects) includes 300–700 trait-dependent chromosomal regions selected either by linkage disequilibrium and linkage analysis or by elastic net. This model requires an important effort to phase genotypes, detect QTLs, select SNPs, but was found to be the most efficient one among all tested ones. QTLs are defined within breed and many of them were found to be breed specific. Reference populations include 1800 and 1400 bulls in Montbéliarde and Normande breeds. In Holstein, the very large reference population of 18 300 bulls originates from the EuroGenomics consortium. Since 2008, ~65 000 animals have been genotyped for selection by Labogena with the 50k chip. Bulls genomic estimated breeding values (GEBVs) were made official in June 2009. In 2010, the market share of the young bulls reached 30% and is expected to increase rapidly. Advertising actions have been undertaken to recommend a time-restricted use of young bulls with a limited number of doses. In January 2011, genomic selection was opened to all farmers for females. Current developments focus on the extension of the method to a multi-breed context, to use all reference populations simultaneously in genomic evaluation.

Packaging the Promise: Money, Messaging, and Misalignment

2021 ◽  
Vol 123 (6) ◽  
pp. 1-38
Author(s):  
Debbie H. Kim ◽  
Kelly Krupa Rifelj
Keyword(s):  
Public Schools ◽  
Theory Of Change ◽  
Organizational Level ◽  
School Staff ◽  
Full Potential ◽  
Financial Barriers ◽  
Structural Support ◽  
Exit Survey ◽  
Policy Tool ◽  
The Individual

Background Promise programs are a quickly spreading policy tool in the free college movement. Despite their rapid spread, promise programs remain generally untested and there is even less information about how they are implemented. Research Questions (1) In what ways were The Degree Project's (TDP) theory of change and intents represented in messaging materials to students and to school staff? 1(a) In what ways did these messages shape conditions (or not) for sensemaking? (2) In what ways did these messages support (or not) students and school staff in changing their practice? (2a) What changes in practice did we see (or not) for students and school staff? Intervention TDP, which was implemented in Milwaukee Public Schools between 2011–15, is the nation's first randomized control trial of a promise program. Freshmen in the treatment group were offered $12,000 for college if they met particular requirements (e.g., average 2.5 GPA, 90% attendance). TDP leaned heavily on marketing materials and personalized letters to students, families, and school staff to communicate its requirements and to provide college access tips. Research Design We analyze messaging materials, climate and exit survey data, and student and school staff interviews to understand how TDP's theory of change and intents were packaged into messaging materials and ultimately enacted among target students and staff. Findings TDP implementation was successful to a point. School staff handed out messaging materials; students understood the requirements and demonstrated an increase in motivation and desire to go to college. However, TDP failed to meet its goal of sending more students to college. Expectations for school staff (hand out flyers and speak to students) versus students were misaligned, contributing to a lack of substantive conversation and structures for students to convert their increased motivation to go to college into actionable practices over time. School staff were already stretched thin and, with no added structural support, were unable to interact more meaningfully with students. Conclusion TDP failed to send more students to college because it targeted change at the individual rather than organizational level. Students exhibited change in their motivation to attend college, but this was not met with the support needed to convert this motivation to meaningful action. To achieve their full potential, such programs will have to not only address financial barriers, but also leverage broader structural supports in schools to help channel increased student motivation in more productive directions.

scholarly journals Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

2019 ◽  
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Fengmin Wang ◽  
Yan Feng ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Candidate Genes ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

scholarly journals Association of non-synonymous SNPs of <i>OPN</i> gene with litter size traits in pigs

2015 ◽  
Vol 58 (2) ◽  
pp. 317-323 ◽  
Author(s):  
T. Kumchoo ◽  
S. Mekchay
Keyword(s):  
Litter Size ◽  
Reproductive Traits ◽  
Snp Markers ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Acid Exchange

Abstract. Osteopontin (OPN) gene is a secreted phosphoprotein which appears to play a key function in the conceptus implantation, placentation and maintenance of pregnancy in pigs. The objectives of this study were to verify the non-synonymous single nucleotide polymorphisms (SNPs) and their association with litter size traits in commercial Thai Large White pigs. A total of 320 Thai Large White sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three SNPs at c.425G> A, c.573T> C and c.881C> T revealed amino acid exchange rates of p.110Ala> Thr, p.159Val> Ala and p.262Pro> Ser, respectively, and were then segregated. These three SNPs were significantly associated with total number born (TNB) and number born alive (NBA) traits. No polymorphisms of the two SNP markers (c.278A> G and c.452T> G) were observed in this study. Moreover, the SNPs at c.425G> A and c.573T> C were found to be in strong linkage disequilibrium. The association of OPN with litter size emphasizes the importance of porcine OPN as a candidate gene for reproductive traits in pig breeding.

scholarly journals Application of Genomic Selection Using an Evenly Spaced Low-density Marker Panel in Broiler Chickens

2013 ◽  
Author(s):  
Chunkao Wang ◽  
David Habier ◽  
Anna Wolc ◽  
Dorian J. Garrick ◽  
Rohan L. Fernando ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Broiler Chickens ◽  
Low Density ◽  
Marker Panel ◽  
Density Marker

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

Abstract 2516: Primary Aldosteronism And Inappropriateness Of Left Ventricular Mass

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Maria Lorenza Muiesan ◽  
Massimo Salvetti ◽  
Anna Paini ◽  
Claudia Agabiti Rosei ◽  
Cristina Monteduro ◽  
...  
Keyword(s):  
Left Ventricular Mass ◽  
Primary Aldosteronism ◽  
Adrenal Adenoma ◽  
Blood Pressure Measurement ◽  
Reference Population ◽  
Left Ventricular ◽  
The Body ◽  
Stroke Work ◽  
Ventricular Mass ◽  
The Individual

Background: The calculation of values of left ventricular mass (LVM) exceeding individual needs to compensate haemodynamic load (inappropriate LVM) can identify patients with high CV risk (de Simone J. Hypertens 2001, Muiesan Hypertens 2007). However, a substantial percentage of LVM variance remains unexplained, even when the influence of cardiac workload, of the body size and gender are taken into account. It is possibile that other factors, non hemodynamic (genetic) or neurohumoral (renin-angiotensin-aldosterone system) may explain the individual LVM. Aim of this study to evaluate the prevalence of inappropriate LVM (iLVM) in patients with primary aldosteronism (PA). Methods 94 PA (51 with adrenal hyperplasia and 43 with adrenal adenoma), (age 49 ± 11 years, 41 F) and in 94 essential hypertensives (EHT) matched for age and sex, underwent echocardiography. The appropriateness of LVM to cardiac workload was calculated by the ratio of observed LVM to the value predicted for an individual gender, height, and stroke work at rest, from a reference population (de Simone et al, 1998). All subjects underwent laboratory examinations, including PRA and plasma aldosterone, and clinic and 24 hours blood pressure measurement. Results No significant differences were observed for clinic and 24 hours BP, clinic and 24 hours heart rate, glucose and lipids between PA and EHT. The prevalence of traditionally defined LV hypertrophy (LVMI ≥ 47 g/m 2.7 in F and 50g/m 2.7 in M) was greater in PA patients than in EHT (48 vs 19 % chi 2 = 0.02). In patients without LVH, the prevalence of iLVM (> 128% of predicted) was also greater in patients with PA than in EHT controls, (14 % vs 2.5 %, chi 2 p = 0.012). Among PA those with iLVM had a higher BMI, increased uric acid, lower midwall fractional shortening, and prolonged isovolumic relaxation time (p < 0.05 at least). In all patients a small, albeit statistically significant, correlation was observed between the Aldosterone/PRA levels and the ratio of observed/predicted LVM (r = 0.18, p < 0.02). Conclusions: In patients with PA the prevalence of iLVM is increased, even in the absence of traditionally defined LVH. The increase in aldosterone levels could contribute to the increase of LV mass exceeding the amount needed to compensate hemodynamic load.

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