119 Genetic Highlights for Reproduction and Health Traits in Russian Black-and-White and Holstein Animals Selected for Production of High-Quality Embryos

2018 ◽  
Vol 30 (1) ◽  
pp. 199
Author(s):  
A. A. Sermyagin ◽  
A. F. Conte ◽  
V. V. Volkova ◽  
O. S. Romanenkova ◽  
A. A. Kharzhau ◽  
...  

The aim of genetic improvement in cattle breeding is to create animals, which are characterised by high economic efficiency while maintaining the high breeding values for health and reproduction traits. In Russia dairy cattle industry the integrated approaches based on application of genomic methods for cows’ fertility and health traits along with milk production are being developed. However, their efficiency depends largely on the ability for multiple replicating outstanding individuals by embryo transfer. Therefore, the target of our research was to develop a strategy for the integrated genetic improvements of fertility and udder health traits towards the production of embryos with high estimated breeding values (EBV). We analysed the culling factors of more than 23,400 Black-and-White and Holstein cows of the Moscow region cattle population. Using the genotyping procedure by Illumina Bovine SNP50 BeadChip (Illumina Inc., San Diego, CA, USA), the regional training group consisted of 401 proven bulls and 60 pre-selected cows was formed. After the quality check based on Plink 1.90, we selected 39,631 single nucleotide polymorphisms for the analysis. The GBLUP methodology was used to calculate genomic EBV (GEBV). The cows were additionally tested by PCR or PCR-RFLP (restricted fragment length polymorphism) for LoF mutations in the genes FANCI, APAF1, SMC2, GART, ITGB2, SLC35A3, and APOB, associated with fertility haplotypes HH0, HH1, HH34, HH4, HHB, HHC, and HCD, respectively. The evaluation of genetic variances and EBV for days open (DO), breeding per conception (BC), calving ease (CE), somatic cell score (SCS), milk yield (MY), fat yield (FY), and protein yield (PY) was carried out using the BLUPF90 family of programs. Cows’ culling rate for reproductive traits was 21% and for udder diseases was 8%. The genetic correlations, rg, between SCS and cows’ fertility traits were rg = 0.132 for BC, rg = 0.067 for DO, and rg = –0.056 for CE that can be used as an indicator for the monitoring reproductive disorders at the different stages of lactation. The frequencies of fertility haplotypes’ carriers among the potential donor dams were 6.6, 1.1, 8.8, 0.0, 1.1, 0.0, and 4.4% for HH0, HH1, HH3, HH4, HHB, HHC, and HCD, respectively. Based on EBV and carrier status for LoF mutations, we selected 46 dams and 28 sires to produce embryos with high GEBV for MY (+633, ..., +884 kg), FY (+26 kg), PY (+18 kg), and SCS (106 points) and higher as population average GEBV for fertility and udder health traits. Genome-wide association study analysis by the reliability of Bonferroni correction test (P < 1.2 × 10−6) showed the presence of quantitative trait loci on BTA1, BTA5, BTA9, BTA11, BTA12, BTA27, and BTX. Our results will be used to construct Russian fitness index for dairy cattle and for implementing embryo production technology into the Russian breeding system. Research supported by the Russian Science Foundation within Project no. 15-16-00020.

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Thierry Tribout ◽  
Pascal Croiseau ◽  
Rachel Lefebvre ◽  
Anne Barbat ◽  
Mekki Boussaha ◽  
...  

Abstract Background Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important traits. However, in general this approach does not allow to validate the effects of candidate mutations or determine if they are truly causative for the trait(s) in question. To address these questions, we applied a two-step, within-breed GWAS approach on 15 traits (5 linked with milk production, 2 with udder health, and 8 with udder morphology) in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cattle. We detected the most-promising candidate variants (CV) using imputed WGS of 2515 MON, 2203 NOR, and 6321 HOL bulls, and validated their effects in three younger populations of 23,926 MON, 9400 NOR, and 51,977 HOL cows. Results Bull sequence-based GWAS detected 84 QTL: 13, 10, and 30 for milk production traits; 3, 0, and 2 for somatic cell score (SCS); and 8, 2 and 16 for udder morphology traits, in MON, NOR, and HOL respectively. Five genomic regions with effects on milk production traits were shared among the three breeds whereas six (2 for production and 4 for udder morphology and health traits) had effects in two breeds. In 80 of these QTL, 855 CV were highlighted based on the significance of their effects and functional annotation. The subsequent GWAS on MON, NOR, and HOL cows validated 8, 9, and 23 QTL for production traits; 0, 0, and 1 for SCS; and 4, 1, and 8 for udder morphology traits, respectively. In 47 of the 54 confirmed QTL, the CV identified in bulls had more significant effects than single nucleotide polymorphisms (SNPs) from the standard 50K chip. The best CV for each validated QTL was located in a gene that was functionally related to production (36 QTL) or udder (9 QTL) traits. Conclusions Using this two-step GWAS approach, we identified and validated 54 QTL that included CV mostly located within functional candidate genes and explained up to 6.3% (udder traits) and 37% (production traits) of the genetic variance of economically important dairy traits. These CV are now included in the chip used to evaluate French dairy cattle and can be integrated into routine genomic evaluation.


1999 ◽  
Vol 24 ◽  
pp. 153-158
Author(s):  
R. Wassmuth ◽  
D. Boelling ◽  
J. Jensen

AbstractDisease incidence in dairy cattle is to be reduced for animal welfare and economical reasons. This should be achieved not only by improvement of management but preferably also by genetic means. This study looks at the possibility of decreasing disease incidence in first lactation cows by increasing food intake. The latter is not measured on the cows directly but on young bulls during their performance test. Data consisted of 2203 Danish Red, 4527 Danish Black and White and 1022 Danish Jersey potential AI-bulls and 56 494 Danish Red, 264107 Danish Black and White and 57 661 Danish Jersey first lactation cows. Measures of food intake were provided by two Danish performance test stations. Information on incidence of mastitis, retained placenta, metritis, sole ulcer and ketosis as well as calving interval and energy corrected milk yield of first lactation cows was based on data extracted from the national data base in Denmark. Genetic (co)variances were estimated using restricted maximum likelihood. Heritability estimates of disease incidence and calving interval were low, ranging from <0.01 to 0.13 depending on breed. Heritability estimates of energy corrected milk yield were in the range of 0.28 to 0.33. In all breeds, an unfavourable genetic relationship between milk yield and disease incidence was found, while genetic correlations between food intake and ketosis were favourable, ranging between -0.03 and -0.25. Fertility disorders had an inconsistent correlation with food intake traits across breeds. Food intake of bulls could be included in the selection process in order to avoid nutrition-related disorders like ketosis.


2001 ◽  
Vol 2001 ◽  
pp. 219-219
Author(s):  
H. Farhangfar ◽  
P. Rowlinson ◽  
M.B. Willis

Traditionally, in most dairy cattle breeding programmes genetic evaluation of dairy sires and cows has been primarily based on 305-day lactation yield. To provide 305-day lactation yields many partial lactations have to be extended by adjustment factors resulting in overestimation or underestimation of 305-day yields which in turn leads to biased prediction of breeding values. Over the past decade there has been a considerable interest in using monthly test day records instead of 305-day lactation yield to predict breeding values of dairy cattle as early as possible and also to increase genetic gain through reducing generation interval. The main objective of present research was to estimate the genetic correlations between 305-day and monthly test day milk yields in Iranian Holstein dairy heifers.


Author(s):  
Sarah Vosgerau ◽  
Nina Krattenmacher ◽  
Clemens Falker-Gieske ◽  
Anita Seidel ◽  
Jens Tetens ◽  
...  

Abstract  Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorphisms (SNPs), analysis of the genomic relationship revealed substructures reflecting breed origin and different breeding goals of the contributing breeding associations. A genome-wide association study confirmed a known quantitative trait locus (QTL) for withers height on equine chromosome (ECA) 3 close to LCORL and identified a further significant peak on ECA 1. Using a single-step approach with a combined relationship matrix, the estimated heritability for withers height was 0.31 (SE = 0.08) and the corresponding genomic breeding values ranged from − 2.94 to 2.96 cm. A mean reliability of 0.38 was realized for these breeding values. The analyses of withers height showed that compiling a reference population across breeds is a suitable strategy for German Warmblood horses. The single-step method is an appealing approach for practical genomic prediction in horses, because not many genotypes are available yet and animals without genotypes can by this way directly contribute to the estimation system.


2016 ◽  
Author(s):  
W. D. Hill ◽  
G. Davies ◽  
S. E Harris ◽  
S. P. Hagenaars ◽  
D. C. Liewald ◽  
...  

AbstractDifferences in general cognitive function have been shown to be partly heritable and to show genetic correlations with a several psychiatric and physical disease states. However, to date few single nucleotide polymorphisms (SNPs) have demonstrated genome-wide significance, hampering efforts aimed at determining which genetic variants are most important for cognitive function and which regions drive the genetic associations between cognitive function and disease states. Here, we combine multiple large genome-wide association study (GWAS) data sets, from the CHARGE cognitive consortium and UK Biobank, to partition the genome into 52 functional annotations and an additional 10 annotations describing tissue-specific histone marks. Using stratified linkage disequilibrium score regression we show that, in two measures of cognitive function, SNPs associated with cognitive function cluster in regions of the genome that are under evolutionary negative selective pressure. These conserved regions contained ~2.6% of the SNPs from each GWAS but accounted for ~ 40% of the SNP-based heritability. The results suggest that the search for causal variants associated with cognitive function, and those variants that exert a pleiotropic effect between cognitive function and health, will be facilitated by examining these enriched regions.


Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 86 ◽  
Author(s):  
Lijun Shi ◽  
Bo Han ◽  
Lin Liu ◽  
Xiaoqing Lv ◽  
Zhu Ma ◽  
...  

In our previous genome-wide association study (GWAS) on milk fatty acids (FAs) in Chinese Holstein, we discovered 83 genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk FAs. Two of them were close to lipase family member K (LIPK) and lipase family member J (LIPJ), respectively. Hence, this study is a follow-up to verify whether the LIPK and LIPJ have significant genetic effects on milk FAs in dairy cattle. By re-sequencing the entire exons, and 3 kb of 5′ and 3′ flanking regions, two and seven SNPs were identified in LIPK and LIPJ, respectively, including a novel SNP, ss158213049726. With the Haploview 4.1 software, we found that five of the SNPs in LIPJ formed a haplotype block (D′ = 0.96 ~ 1.00). Single-locus association analyses revealed that each SNP in LIPK and LIPJ was significantly associated with at least one milk FA (p = < 1.00×10-4 ~ 4.88×10-2), and the haplotype-based association analyses showed significant genetic effects on nine milk FAs (p = < 1.00×10-4 ~ 3.98×10-2). Out of these SNPs, the missense mutation in LIPK gene, rs42774527, could change the protein secondary structure and function predicted by SOPMA, SIFT, and PROVEAN softwares. With the Genomatix software, we predicted that two SNPs, rs110322221 in LIPK and rs211373799 in LIPJ, altered the transcription factors binding sites (TFBSs), indicating their potential regulation on promoter activity of the genes. Furthermore, we found that both LIPK and LIPJ had relatively high expressions in the mammary gland. In conclusion, our research is the first to demonstrate that LIPK and LIPJ genes have significant associations with milk FAs, and the identified SNPs might be served as genetic markers to optimize breeding programs for milk FAs in dairy cattle. This research deserves in-depth verification.


2021 ◽  
Author(s):  
Muktar Ahmed ◽  
Ville-Petteri Mäkinen ◽  
Anwar Mulugeta ◽  
Jisu Shin ◽  
Terry Boyle ◽  
...  

Abstract Hormone-related cancers, including cancers of the breast, prostate, ovaries, uterine, and thyroid, globally contribute to the majority of cancer incidence. We hypothesize that hormone-sensitive cancers share common genetic risk factors that have rarely been investigated by previous genomic studies of site-specific cancers. To test this hypothesis, we analysed five hormone-sensitive cancers in the UK Biobank as a single disease. We observed that a significant proportion of variance in disease liability was explained by the genome-wide single nucleotide polymorphisms (SNPs), i.e., SNP-based heritability on the liability scale was estimated as 10.06% (SE 0.70%) for the disease. Moreover, we found 55 genome-wide significant SNPs for the disease, using a genome-wide association study. Our finding suggests that heritable genetic factors may be a key driver in the mechanism of carcinogenesis shared by hormone-sensitive cancers.


1994 ◽  
Vol 42 (4) ◽  
pp. 371-378
Author(s):  
A.F. Groen ◽  
I. Hellinga ◽  
J.K. Oldenbroek

Direct selection for decreased disease incidence is difficult given low hsuperscript 2s and the absence of disease recording. Genetic correlations between diseases and type traits indicate possibilities for indirect selection; however, correlations often include experimentally instead of routinely scored type traits. The aim of this study was to estimate genetic correlations of clinical mastitis and feet and legs problems with milk yield and routinely scored type traits in Dutch Black and White [DBW; Dutch Black Pied] cows. From 1983 to 1991, the incidence of diseases was recorded at 44 farms with DBW dairy cattle. Records on 3617 cows sired by 224 bulls were analysed. Heritabilities for milk yield, type traits and diseases were obtained using an equal design multivariate Restricted Maximum Likelihood procedure considering all observations on a continuous scale. A bivariate threshold procedure was used to estimate hsuperscript 2s of diseases and genetic correlations of diseases with milk yield and type traits. Genetic correlations of clinical mastitis and feet and legs problems with milk yield were 0.16 and 0.26 respectively, and hsuperscript 2s for diseases were low 0.01-0.11. Unexpected positive relations between udder type traits and clinical mastitis were found (0.09-0.26), and possible reasons are discussed. Genetic correlations between type traits for feet and legs and problems of the feet and legs were negative -0.01 and -0.24 respectively. Final score for feet and legs could be used as a selection criterion to select to reduce the incidence of feet and legs problems.


2018 ◽  
Vol 51 ◽  
pp. 78-83
Author(s):  
T. A. Kruglyak

The grades of genealogy relationship of bulls with the head of bloodlines are not equivalent in each genealogical formation and are stipulated by the number of animals (branching) in bloodline, their diversity, distance from the head of bloodlines and system of selection. Thus, the coefficients of kinship of bulls, descendants of which have 5 and more ranks in genealogy: 1427381 Chief (n = 79), 1650414 Valiant (n = 10) and Elevation 1491007 (n = 64) with the ancestors of these bloodlines were 5,67; 8,81 and 8,37% respectively. Slight higher coefficients of genealogical kinship of bulls with successors of Chief bloodlines – Blackstar 1929410 – by 2,28 (7,35%) and Belwood 2103297– by 1,67% (6,37%), due to the use of the last ones in the pedigrees of these bulls on the maternal side. Significantly higher coefficientsof genealogical kinship of bulls of Starbuck 352790 bloodlines (n = 112) were with the ancestor and successors of this bloodline. Thus, the coefficient of kinship of bulls of Starbuck bloodline with their ancestor was 13,4% and with successors Aerostar 383622 – 16,9%, Mtoto 6001001962 – 9,0%, Storm 6820564– 10,9% and Shottle 598172 – 9,8%. It was found that the highest coefficient of genealogical kinship was at the bulls of new lines and related groups Marshal 2290977 – 30,5; Toystory 60372887 – 18,5; Buckeye 130588960 – 14,8; Goldwyn 10705608 – 19,1; Shottle 598172 – 25,1%. This is because the offspring were at 1-2 generations from their founders. The high interline genealogical kinship of bulls was revealed. Thus, the coefficient of genealogical kinship of bulls of all the bloodlines with progenitor of Starbuck 352790 bloodlines was 0,96-13,4 and with his son Aerostar 383622 – 2,9-16,9%. Average degrees of kinship of bulls of all the population with these leaders of the breed were also quite high (8,16 and 11,42% respectively). This shows the great saturation of pedigree of all the Holstein bulls bygenes of Starbuck 352790, Aerostar 383622 and Elevation 1491007, which complicates scheduling the breeding selection even at crossing bloodlines because ancestors of the same bulls of several lines are in pedigree of animals of each bloodline. This explains increasing inbred cows in the latest generation of Ukrainian Black-and-White Dairy cattle to 71,3-91,3%. Perhaps for restraining growth of the number of inbred cows, US experts prolong duration of hereditary qualities transmissionof a founder in generations by creating so-called "inbred" lines. To do this, for carefully selected mothers of bulls with high levels of economic useful traits (yield, fat and protein contents) of some line are selected bull-leaders of the same line with similar breeding values (homogeneous selection). Using inbreeding of different degrees from remote (V-V) and moderate degrees (III-IV, IV-IV) to close one (II-II, II-III, III-III), inbred animals are obtained and bred "in itself" again (integrated inbreeding). Probability of obtaining larger number of animals with hereditary traits of ancestor’s performance increases. So, 30 (8,77%) of 342 bulls used in Ukraine, are obtained in this way and bulls of only this line used as fathers in 4 ranks of their pedigree. Use of moderate and remote levels of inbreeding on ancestorsof lines maintains high genealogical kinship of animals at their distance in generation and accumulation of valuable traits in populations which are inherent for ancestorsof lines. Share of inbred bulls in all the lines is quite high – 80,7%. On average, 15 bulls were obtained as a result of the close degree of inbreeding in the population (II-II, II-III). The number of moderate levels of inbreeding (II-IV, III-IV, IV-IV and IV-V) at obtaining these bulls was 244 and remote one (V-V and above) – 195. In addition, 116 fathers and 59 mothers received as a result of various degrees of inbreedingwere foundin the pedigrees of the bulls. Among them 15 animals (8,57%) were as a result of close degree of inbreeding, 127 (72,6%) – moderate and 33 (18,8%) – remote; it also forms the genealogical relationship between bulls of various lines. Thus, the rate of genealogical kinship characterizes the intensity of using bull-leaders, ancestors of bloodlines and their successors for breeding stock, from both paternal and maternal sides of genealogy and genealogical relations between some bloodlines, it is important to consider while forming further genealogical structure of the breed and breeding selection as at breeding herds, so at production ones of domestic dairy cattle.


2017 ◽  
Vol 53 ◽  
pp. 115-119
Author(s):  
A. V. Dymchuk ◽  
O. I. Lyubynskyy

The studies of the dynamics results of body weight, absolute and daily average, relative increases averaging bulls of Ukrainian black-and-white and Ukrainian red-and-white dairy cattle. Researches are conducted in the conditions of POSP «Napadivske» Kalyinivka district of the Vinnytsya area after materials of primary pedigree account. In an economy use the whole-year of the same type feeding. In the structure of ration 40% make the concentrated sterns and also high-quality silage and soilage. Average daily increases of bulls for period of age to realization for a slaughter made over 1000 grammes. The dynamics of growth of living mass, absolute, average daily and relative increases of bulls, is analysed Ukrainian black-and-white and Ukrainian red-and-white dairy cattle. Living mass and weight gain researches of age to 12-monthly age with an interval in 3 months after the generally accepted methods. Materials of researches are worked out the methods of mathematical statistics with the use of programmatic package of Statistica 8.0. Living mass of bulls of the second group at birth made 36,3 kg, that anymore on 0,8 kg by comparison to new-born bulls of the first group. In all next periods living mass of animals of the second group was greater as compared to the animals of the same age of the first. In 3 months advantage made 1,7 kg, in 6 months – 4,6 kg (P>0,95), in 9 months – 8,8 kg (P>0,95), in 12 months – 12,5 kg (P>0,99). Difference of absolute increases of bulls of the second group above the bulls of the same age of the first of age to to 3-monthly age made 0,8 kg in behalf of animals of the second group. In a period 3-6 months a difference is after this index between the first and second groups made 2,9 kg in behalf of the last. In periods 6-9 and reliable advantage of animals of the second group is 9-12 months set above the bulls of the same age of the first on 4,1 kg (P>0,95) and 3,7 kg (P>0,95) accordingly. In a period of age to 18-monthly age absolute increases of bulls of the second group were greater by comparison to bulls first on 12,5 kg (R>0,99). Average daily increases of bulls of the second group of age to 3-monthly age made 763,0 grammes, that anymore on 8,9 grammes by comparison to bulls of the first group. In periods 3-6 months the average daily increases of animals of the second group prevailed the bulls of the same age of the first on 32,6 grammes. In a period 6-9 months the average daily increases of animals of the second group were made by 1045,9 grammes, that for certain anymore on 45,9 grammes (P>0,95) by comparison to the bulls of the same age of the first. Maximal increases of bulls were in a period 9-12 months and made 1210,4 grammes in the animals of the second group and 1168,9 grammes – for the bulls of the same age of the first, that for certain anymore on 41,5 grammes (P>0,95). In a period of age to 12-monthly age the average daily increases of bulls of the second group were made by 970,6 grammes, that was for certain anymore on 31,8 grammes (R>0,99) by comparison to the bulls of the same age of the first group. Relative increases of bulls of both groups were high. From birth to 3-monthly age greater increases had bulls of the first group – 97,8%, and in periods 3-6, 6-9 and 9-12 months greater were increases of bulls of the same age of the second group – 56,4; 40,1 and 32,4% accordingly. For all probed periods of reliable advantage it is not discovered between the compared groups. It is set researches, that at the identical terms of feeding and maintenance more rapid bulls grow Ukrainian red-and-white dairy cattle. In all age-old periods they prevailed the bulls of the same age of the Ukrainian black-and-white dairy cattle, in a that number, beginning from 9-monthly age, advantage was reliable (P>0,95–0,99). Average daily increases of bulls of two breeds were the least in a period of age to to 3-monthly age – 754,1-763,0 grammes, and most in a period 9-12 months – 1168,9–1210,4 grammes.


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