scholarly journals Efficiency of bovine IGF-i gene in the improvement of milk productivity using marker-assisted selection (MAS)

2011 ◽  
Vol 27 (2) ◽  
pp. 159-169
Author(s):  
S.M. Abdel-Rahman ◽  
S.A. Hemeda ◽  
M.M. Fouda ◽  
A.I. Ateya
Keyword(s):  
Marker Assisted Selection ◽  
Breeding Value ◽  
Regulatory Function ◽  
Milk Production Trait ◽  
Holstein Cattle ◽  
Nucleotide Polymorphisms ◽  
Milk Productivity ◽  
Igf I ◽  
Trait Locus ◽  
I Gene

Because of insulin-like growth factor-I (IGF-I) gene plays an important regulatory function in milk secretion in cattle, IGF1 gene is potential quantitative trait locus and genetic marker (i.e, SNP) associated with milk production trait in cattle. Consequently, marker-assisted selection (MAS) will be useful to increase and accelerate the rate of genetic improvement on milk productivity. In this study, 48 female Holstein cattle reared under Egyptian conditions were selected based on their milk productivity and DNA from blood was extracted to amplify 249-bp of the gene encoding IGF-I. According to the breeding value, PCR products of IGF-I gene (249-bp) were sequenced only in the 15 highest and lowest milk productivity animals (GenBank accession numbers from gb|HQ183710| to gb|HQ183724|, sequentially). The result indicated that two single nucleotide polymorphisms (SNP?s) at two different positions were observed in one of the highest milk productivity animals. Where, all 15 animals have adenine (A) and cytosine (C) bases at the positions 33 and 63, respectively, except, one animal (GenBank Acc. No. gb|HQ183711|) has thymine (T) and guanine (G) bases at the same positions (33 and 63, respectively). Thus, this finding can be used as marker-assisted selection (MAS) for high milk productivity in Holstein cattle.

Effects of polymorphism in the 5′-flanking region of the IGF-I gene on milk-production traits in Chinese Holstein cattle

2012 ◽  
Vol 52 (9) ◽  
pp. 795 ◽  
Author(s):  
M. A. Alim ◽  
Yan Xie ◽  
Yipeng Fan ◽  
Xiaoping Wu ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Milk Production ◽  
Holstein Cattle ◽  
Production Traits ◽  
Milk Production Traits ◽  
Chinese Holstein ◽  
Chinese Holstein Cattle ◽  
Igf I ◽  
Flanking Region ◽  
Fat Yield ◽  
I Gene

Milk and milk products are major components of human dietary intake and have a potential influence on health. In our experiment, associations between insulin-like growth factor 1 (IGF-I) gene polymorphism and milk-production traits were analysed in Chinese Holstein cattle. A polymorphism, transition at position g.1407 T > C, was identified in the 5′-flanking region of the IGF-I gene by pooled DNA sequencing. The identified single-nucleotide polymorphism (SNP) was genotyped by matrix-assisted laser desorption–ionisation time-of-flight mass spectrometry (MALDI–TOF MS) methods from 752 individuals. Significant associations between IGF-I genotypes and 305-day milk yield, fat yield and protein yield were found. Homozygous cows with TT genotype showed the highest milk, fat and protein yields, with increases of 532.75 kg, 23.57 kg and 14.69 kg, respectively, as compared with homozygous CC cows. Heterozygous CT cows had intermediate yields. Allele substitution showed that the C allele decreased milk yield (255.23 kg), fat yield (11.37 kg) and protein yield (7.05 kg), whereas it increased protein percentage (0.01%). The results suggest that IGF-I is a candidate gene that influences milk-production traits, and provides useful information to be implemented in breeding programs to improve the performance of the Chinese Holstein.

Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits

2011 ◽  
Vol 43 (21) ◽  
pp. 1185-1197 ◽  
Author(s):  
Miri Cohen-Zinder ◽  
Ravikiran Donthu ◽  
Denis M. Larkin ◽  
Charu Gupta Kumar ◽  
Sandra L. Rodriguez-Zas ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Critical Region ◽  
Complex Traits ◽  
Association Studies ◽  
Dna Polymorphisms ◽  
Breeding Value ◽  
Chromosome 3 ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Trait Locus

The goal of this study was to identify candidate genes and DNA polymorphisms for quantitative trait loci (QTL) affecting milk yield (MY), fat yield (FY), and protein yield (PY) previously mapped to bovine chromosome 3 (BTA3). To accomplish this, 373 half-siblings sired by three bulls previously shown to be segregating for lactation trait QTL, and 263 additional sires in the U.S. Dairy Bull DNA Repository (DBDR) were genotyped for 2,500 SNPs within a 16.3 Mbp QTL critical region on BTA3. Targeted resequencing of ∼1.8 Mbp within the QTL critical region of one of the QTL heterozygous sires identified additional polymorphisms useful for association studies. Twenty-three single nucleotide polymorphisms (SNPs) within a fine-mapped region were associated with effects on breeding values for MY, FY, or PY in DBDR sires, of which five SNPs were in strong linkage disequilibrium in the population. This multisite haplotype included SNPs located within exons or promoters of four tightly linked genes: RAP1A, ADORA3, OVGP1, and C3H1orf88. An SNP within RAP1A showed strong evidence of a recent selective sweep based on integrated haplotype score and was also associated with breeding value for PY. Because of its known function in alveolar lumen formation in the mammary gland, RAP1A is thus a strong candidate gene for QTL effects on lactation traits. Our results provide a detailed assessment of a QTL region that will be a useful guide for complex traits analysis in humans and other noninbred species.

scholarly journals Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms

2007 ◽  
Vol 89 (1) ◽  
pp. 1-6 ◽  
Author(s):  
H. ZHAO ◽  
D. NETTLETON ◽  
J. C. M. DEKKERS
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Qtl Mapping ◽  
Marker Assisted Selection ◽  
Nucleotide Polymorphisms ◽  
Chi Square ◽  
Single Nucleotide ◽  
Standardized Measures ◽  
Trait Locus ◽  
Standardized Measure

Effectiveness of marker-assisted selection (MAS) and quantitative trait locus (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTLs depends on the extent of LD and how it declines with distance between markers and QTLs in a population. Marker–QTL LD can be predicted from LD between markers. Our previous work evaluated LD measures between multi-allelic markers as predictors of usable LD of multi-allelic markers with QTLs. Since single nucleotide polymorphisms (SNPs) are the current marker of choice for high-density genotyping and LD-mapping of QTLs, the objective of this study was to use LD between multi-allelic markers to predict LD among biallelic SNPs or between SNPs and QTLs. Observable LD between multi-allelic markers was evaluated using nine measures. These included two pooled and standardized measures of LD between pairs of alleles at two markers based on Lewontin's LD measure, two pooled measures of squared correlations between alleles, one standardized measure using Hardy–Weinberg heterozygosities, and four measures based on the chi-square statistic for testing for association between alleles at two loci. The standardized chi-square measure that best predicted usable LD between multi-allelic markers and QTLs, based on our previous work, overestimated usable SNP–SNP or SNP–QTL LD. Instead, three other measures were found to be good predictors of usable SNP–SNP or SNP–QTL LD when LD is generated by drift. Therefore, the LD measure between multi-allelic markers that is best for predicting usable LD in a population depends on the type of markers (i.e. multi-allelic or biallelic) that will eventually be used for QTL mapping or MAS.

scholarly journals Assessing haplotype-based models for genomic evaluation in Holstein cattle

2018 ◽  
Vol 98 (4) ◽  
pp. 750-759 ◽  
Author(s):  
Z. Karimi ◽  
M. Sargolzaei ◽  
J.A.B. Robinson ◽  
F.S. Schenkel
Keyword(s):  
Breeding Value ◽  
Validation Dataset ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Holstein Cattle ◽  
Nucleotide Polymorphisms ◽  
Genomic Relationship ◽  
Wide Range ◽  
High Heritability ◽  
Prediction Reliability

A single-nucleotide polymorphisms-based genomic relationship matrix (GSNP) discriminate less identity by state from identity by descent (IBD) alleles compared with a multi-locus haplotype-based relationship matrix (GHAP), which can better capture IBD alleles and recent relationships. We aimed to compare the prediction reliability and prediction bias of genomic best linear unbiased prediction (GBLUP) using either GSNP or GHAP in Holstein cattle. Therefore, a total of 57 traits with a wide range of heritability values were analyzed. Classical validation tests were done using a validation dataset comprised of 50k genotype records of 561–669 proven bulls born in 2010–2011 with an official estimated breeding value (EBV) in 2016 and a training set of 5314–19 678 bulls born before 2010, depending on the trait. The method for building the genomic relationship matrix (G) had significant, but small effect on observed reliability (r2GEBV) (p < 0.0001) and bias (p < 0.0001). A significant interaction between G and the level of trait heritability on r2GEBV and bias was also observed (p < 0.0001). The small gains in r2GEBV and small reductions in the bias by using GHAPBLUP were increased when predicting moderate to high-heritability traits compared with low-heritability traits.

468: Polymorphic CA Repeats in IGF-I Gene is a Common Genetic Modifier in the Etiology of Prostate Cancer and Benign Prostatic Hyperplasia

2004 ◽  
Vol 171 (4S) ◽  
pp. 125-125
Author(s):  
Lizhong Wang ◽  
Kazunari Sato ◽  
Norihiko Tsuchiya ◽  
Chikara Ohyama ◽  
Shigeru Satoh ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Benign Prostatic Hyperplasia ◽  
Genetic Modifier ◽  
Prostatic Hyperplasia ◽  
Igf I ◽  
I Gene

REALIZATION OF PARENTAL INDICES OF COW PRODUCTIVITY IN DIFFERENT MILKING BREEDS AT BREEDING FARM "AGROFIRMA "PAKHMA"

2020 ◽  
Keyword(s):  
Milk Yield ◽  
Cattle Breed ◽  
Holstein Cattle ◽  
Milk Productivity ◽  
Cattle Breeds ◽  
Significant Difference ◽  
Production Indices ◽  
High Level ◽  
Beta Lactoglobulin ◽  
Percentage Protein

Combination of genotypes of main types’ genetic markers causes milk productivity in cattle. The article studies correlation between kappa casein genotypes (C3N3), beta-lactoglobulin (LGB), their complexes and milk production indices in cows bred under equal conditions at a breeding farm. The calculation of parental milk yield and fat indices between the three breeds showed a significant difference (P>0,999) of PCI of Ayrshire and Holstein cattle breed milk yield - 3395 kg, PCI of fat - 0,22%; between Holstein and Yaroslavl cattle breeds - 3200 kg, PCI offat - 0,16%. A significant difference of realization indices of protein between all three breeds was not stated. The highest realization ofparental milk yield index was stated - between Ayrshire and Yaroslavl cattle breeds- 113%, Holstein cattle breed - 88%. As for the fat and protein indices, all three cattle breeds showed a high realization of PCI from 98% to 109%. However, Holstein cattle breed showed the highest percentage: protein - 101%, fat - 109%. A significant difference of PCI realization of milk productivity in CSN3 and LGB genotypes was not stated. It was also stated that there is a tendency of high level parental indices realization when there is a higher number of B-allele variants in genotypes of cows.

scholarly journals Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingyi Wang ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Gene Effects ◽  
Isogenic Lines ◽  
Trait Locus ◽  
Grain Yield And Quality ◽  
Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

scholarly journals Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1153-1164 ◽  
Author(s):  
Bala R. Thumma ◽  
Bronwyn A. Matheson ◽  
Deqiang Zhang ◽  
Christian Meeske ◽  
Roger Meder ◽  
...  
Keyword(s):  
Quantitative Traits ◽  
Association Studies ◽  
Allelic Expression ◽  
Cellulose Content ◽  
Nucleotide Polymorphisms ◽  
Cis Acting ◽  
Functional Polymorphisms ◽  
Functional Variants ◽  
Regulatory Polymorphism ◽  
Trait Locus

Populations with low linkage disequilibrium (LD) offer unique opportunities to study functional variants influencing quantitative traits. We exploited the low LD in forest trees to identify functional polymorphisms in a Eucalyptus nitens COBRA-like gene (EniCOBL4A), whose Arabidopsis homolog has been implicated in cellulose deposition. Linkage analysis in a full-sib family revealed that EniCOBL4A is the most strongly associated marker in a quantitative trait locus (QTL) region for cellulose content. Analysis of LD by genotyping 11 common single-nucleotide polymorphisms (SNPs) and a simple sequence repeat (SSR) in an association population revealed that LD declines within the length of the gene. Using association studies we fine mapped the effect of the gene to SNP7, a synonymous SNP in exon 5, which occurs between two small haplotype blocks. We observed patterns of allelic expression imbalance (AEI) and differential binding of nuclear proteins to the SNP7 region that indicate that SNP7 is a cis-acting regulatory polymorphism affecting allelic expression. We also observed AEI in SNP7 heterozygotes in a full-sib family that is linked to heritable allele-specific methylation near SNP7. This study demonstrates the potential to reveal functional polymorphisms underlying quantitative traits in low LD populations.

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