Genomics And Holstein Association And Cdcb Pdf Flow Chart

genomics and holstein association and cdcb pdf flow chart

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Print Send Add Share. Notes Abstract: The overall goal was to identify genes containing single nucleotide polymorphisms SNP explaining some of the genetic variation in fertility in Holstein cows.

It describes whether the reference population used for evaluation was composed of a single or multiple breeds. Breed base representation BBR was introduced in Most crossbreds have not been included in genomic evaluations because marker effects are computed separately within breeds.

Candidate Genes Associated with Fertility and Embryonic Development in Dairy Cattle

Print Send Add Share. Notes Abstract: The overall goal was to identify genes containing single nucleotide polymorphisms SNP explaining some of the genetic variation in fertility in Holstein cows. Identification of such SNP could lead to improvement of genomic estimates of fertility.

In addition, genes in which these SNP reside represent targets for physiological intervention to improve fertility. A group of 69 SNP previously associated with genetic merit for fertility and production was tested for association with genetic and phenotypic measures of fertility in an independent population of 2, cows selected for high or low genetic merit for daughter pregnancy rate DPR.

After imputation, inclusion of 39 genes containing SNP associated with DPR in the national genetic evaluation system increased reliability of the genetic estimate for DPR by 0. Subsequent studies indicated that the SNP associated with DPR affects mitochondrial function, body weight changes after calving, follicle growth and oocyte quality. Finally, experiments were performed to test whether WBP1 was important for development of the embryo to the blastocyst stage.

This gene was selected because a SNP in the coding region of WBP1 had earlier been related to embryonic development to the blastocyst stage. Knocking down mRNA for WBP1 reduced the percent of embryos developing to the blastocyst stage and reduced numbers of trophectoderm cells.

Taken together, these experiments represent successful examples of the candidate gene approach for gene discovery. Several SNP were identified related to fertility. A previously unknown role for COQ9 in oocyte and follicle function was described and a new gene participating in embryonic development, WBP1, was discovered.

General Note: Includes vita. Bibliography: Includes bibliographical references. Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. Thesis: Thesis Ph. Peter J.

Hansen, for his incredible guidance, and dedication and for mentoring me on what it takes to become a scientist. He challenged me every step of the way, and by doing so, motivated me to giv e my best. His knowledge, expertise and advice have been an inspiration for me, not only for my career as a scientist, but also to become a better person every day. I am being grateful to him fo r taking a chance on me and giving me the oppor tunity to be part of his group It was working with him where I gain ed the knowledge and tools to be successful in my future career, and I will always treasure that I would also like to thank my committee me mbers, Dr.

Geoffrey Dahl, Dr. Maureen Keller Wood, Dr. Jeremy Block, and e specially Dr. Alvaro Magalhaes and Lander Veterinary Clinic Turlock, California , for their assistance w ith obtaining samples and data. Thanks are also extended to Dr. Robert McKenna and Justin Kurian from the Department of Biochemistry and Molecular Biology for their assistance and input on protein modelling I am grateful also to the Department of Animal Sciences for providing me with the resources for my research and to the Animal Molecular and Cellular Biology Graduate P rogram for the award of a fellowship that provided me funding to complete my PhD.

Special thanks to Stephany and Venancio for their support and sincere friendship I t hank my family for everything To my grandma Ramona, for her kindness and support, and for always e ncourag ing me to pursue my dreams. T o my two brothers Mario and Roberto, for their love ; it has been great knowing that no matter what I can always count with you. I also thank my extended family aunts and cousins for their support. Finally I want to tha nk my mom, Marta.

Her unconditional love and support throughout my entire life shaped me to who I am today. Thank you for showing me that no dream is too big if you really want it and work hard for it I never could have done it without you. Hansen Major: Animal Molecular and Cellular Biology The overall goal was to identify genes containing single nucleotide polymorphisms SNP explaining some of the genetic variation in fertility in Holstein cows. In addit ion, genes in which these SNP reside represent targets for physiological intervention to improve fertility.

A group of 6 9 SNP previously associated with genetic merit for fertility and production was tested for association with genetic and phenotypic measu res of fertility in an independent population of 2 cows selected for high or low genetic merit for daughter pregnancy rate DPR. After imputation, inclus ion of 39 genes containing SNP associated with DPR in the national genetic evaluation system increased reliability of the genetic estimate for DPR by 0. Subsequent studies indicated that the SNP associated with DPR affects mitochondrial function body weight changes after calving, follicle growth and oocyte quality.

Knocking down mRNA for WBP1 reduced the percent of embryos developing to th e blastocyst stage and reduced numbers of trophectoderm cells. Several SNP were i dentified related to fertility. A previously unknown role f or COQ9 in oocyte and follicle function was described and a new gene participating in embryonic development, WBP1 was discovered. Physiological Events Leading to Pregnancy in the Lactating Dairy Cow There are two characteristics that define genetic regulation of reproduction.

First, reproductive traits are polygenic, i. The physiological basis for these two characteristics can be understood by considering the events a cow must undergo to successfully establish and maintain a pregnancy after calving. Doi ng so involves interplay among metabolic, endocrine and immune systems, each of which is controlled by many gene systems, and each system can be modified by the environment of the cow.

One of the first events that a cow must achieve after parturition is removal of pathogenic microorga nisms from the reproductive tract.

Initiation of milk production requires high expenditures of energy. Initially, the cow cannot eat sufficiently to provide that energy and the resultant negative energy balance requires mobilization of body reserves to meet the energy demands of lactation [2] Cows in deep negative PAGE 20 20 energy balance experience a delay in resumption of ovarian cyclicity [21, 22] and reduction of overall pregnancy rate [23] Negative energy balance is associated with reductions in circulating glucose, leptin, insul in, and IGF1 concentrations [24] Insulin and IGF1 have synergistic effects with FSH to regulate aromatase activity in granulosa cells [25] as well as increasing sensitivity to FSH and LH in the ovary [26] Low concentrations of IGF1, such as those present during negative energy balance, compromise steroidogenic capacity of ovarian follicles [27] resulting in a reduction of follicle growth, which can in turn affect resumption of ovulation.

Moreover, lactation itself causes a reduction in steroid hormone co ncentrations in the blood as a consequence of higher metabolism of these hormones in the liver [28] which affects target organs of these hormones brain, pituitary, and reproductive tract. A prerequisite for pregnancy in the postpartum cow is resumption of ovarian cyclicity.

First wave follicles develop under l ow concentrations of progesterone [33] ; and it has been shown that cows that develop the ovulatory follicle under low proges terone concentrations have reduced fertility [34] After resumption of estrous cycles, the cow must be bred by natural or AI at a time coincident with ovulation. This is made more difficult in lactating dairy cows because they experience reduced expressio n of estrus in terms of intensity and length e.

The net result is reduced pregnancy rates in lactating dairy cows under heat stress conditions [58, 59] T ypes of Mutations Responsible for Genetic Variation in Reproduction Genetic variation is the basis of biological diversity in a population.

In the bovine genome, the total sequence length is 2,,, bp UMD 3. Genetic mutations ultimately affect the proteome of the organism either by affecti ng the structural properties of a protein or by modifying the amount of protein in specific tissues. The following section will describe how the physical location of a mutation relative to the coding and regulatory regions of specific genes can cause varia tion in phenotype.

Given the degeneracy of the genetic code, not all SNP necessarily change the encoded am ino acid. For example, a change in a codon from GAA to GAG would not change the amino acid because both codons specify glutamic acid. Such mutations are called synonymous because the mutation does not change the amino acid sequence of the protein. Such mutations are called non synonymous because the amino acid sequence is altered.

A non synonymous SNP can be either a missen se or nonsense mutation. Missense SNP are those that result in a change in the codon and amino acid sequence in the protein. Nonsense mutations, on the other hand, generate a stop codon and result in a truncated version of a protein [62] One example of a missense mutation affecting reproduction is a SNP in BMP15 that results in production of a defective protein and premature ovarian failure in human [63, 64] In sheep, a missense mutation in GDF9 is associated with litter size, where the animals carrying the homozygous genotype for the minor allele have increased litter size probably as a result of a structural change in the protein that affects its binding capacity [65] Sonstegard et al.

The nonsense mutation causes a stop codon in exon 3 of CWC15 that reduces the size of the protein from to 54 amino acids. During evolution, synonymous mutations usually accumulate more rapidly than non synonymous ones because there is little alteration in fitness of the organism [67] When a gene is subject to natural selection, the ratio of non synonymous mutations to synonymous mutations increases bec ause the altered amino acid sequence provides superior fitness.

Even within a gene, there are regions in which the frequency of non synonymous mutations is tolerated more than in other regions [68] An example of accumulation of nonsynonymous and synonymou s mutations can be found in a study by Wang et al. Wang et al. Synonymous mutations are usually considered to be non functional and are referred to as silent SNP.

However, there is evidence that they can have effects on rates of protein translation because there is an optimal codo n for any given amino acid, which can skew tRNA usage and change the translation rate [70] An example occurs for the transcription factor NKX2 5 in human s S ynonymous mutations in the homeodomain and transactivation domain of the protein reduced transcriptional activities of NKX2 5 which is associated with congenital heart disease [71] Insertions and Deletions tion or deletion of bases in the DNA sequence.

Indels in the coding region that are less than three nucleotides or not a multiple of three will cause a frameshift mutation that shifts the grouping of bases into codons [72] In cattle, for example, a single nucleotide deletion in ARMC3 causes an alteration in the reading frame and induces premature translation termination, creating a non functional protein which is shortened by amino acids; animals carrying this mutation have disturbed spermatogenesis an d produce immotile spermatozoa [73] Another example of an indel affecting rep roduction is a kb deletion o n chromosome 12 including four genes which is embryo lethal in Nordic Red cattle.

Sequence variation in this region could alter transcription factor identification and binding and thereby influence gene expression [76, 77] A mutation in the upstream region of the FSHB transcription start site has been significantly associated with serum FSH concentrations and testes volume in men [78] A SNP in the promoter region of LEP in Holsteins is associated with leptin concentrations during the lactation period [79] SNP in the Intronic Region of a Gene Mutations in introns can affect RNA splicing, which is the process of removing introns from pre messenger RNA, and ligat ion of exons to produce mature mRNA.

An example of this type of mutation occurs for human CD44 which affect s splicing by modifying the consensus sequence of the splicing site on the pre mRNA of CD44 and which decreas es CD44 mRNA and CD44 expression; this reduction of CD44 expression seems to inhibit anti tumor immunity and favor breast cancer development [80] In cattle, an intronic SNP in CD46 causes a partial retention of intronic sequence within CD46 mRNA after splicing, and leads to a production of an aberrant CD46 isoform, which is associated with mastitis infection by Streptococcus in Holsteins [81] Copy Number Variation Copy number variations are DNA segments that are present at a variable copy number in comparison with a reference genome [82] They can be classified as short and long repeats, and can provoke large effects on gene regulation, structure and dosage.

Long repeats, also called segmental duplications, usually range 1 5 kb in size and only occur a few times in the genome. The proposed mechanism for segmental PAGE 27 27 duplication is an error in homologous recombination during meiosis. Such errors are p articularly likely between sequence stretches of high homology; the repeats can misalign and crossover resulting in genetic rearrangement [83, 84] Short repeated segments of DNA, which range from 2 15 bp in size, are products of duplications, inversions a nd deletions [84] Most of the work on copy number variations has been focused on disease risk.

The genetic component of a trait can be further subdivided in three subcomponents: the additive variance, which is contribution of one or more individual genes to a phenotype; the dominance genetic variance where the contribution of one allele masks the contribution of the alternate allele at that locus, and lastly the variance associated wi th the interaction between genes, termed epistasis [94] Genetic selection is usually based on utilizing the additive genetic variance.

The breeding value of an individual is the sum of the average effects of individual alleles of genes affecting a trait e xpressed as a deviation from the population mean.

The ability of an animal to influence the genetic composition of its offspring is half of the breeding value. Such a term is often referred to as PTA. The degree to which the PTA reflects the true transmitt ing ability is referred to as reliability.

The reliability depends on the heritability of the trait proportion of variance PAGE 29 29 due to genetics and the amount of information that contributes to the calculation of PTA ce as well as that of their relatives [95] Most reproductive traits are controlled by many genes, each of which has a small effect.

Moreover, a few markers, such as those on chromosome 14, explain a large portion of the genetic variation up to 40 additive genetic SD. The lo w heritability characteristic of reproductive traits is indicative that only a small proportion of phenotypic variance is due to additive actions of individual genes and that reliability estimates of breeding values are prone to be low. It does not, howeve r, mean that reproductive traits are not under genetic control.

Indeed, as will be discussed later, many specific genes have been identified that contain mutations that are associated with reproductive function. Furthermore, clear differences in fertility have been found between genetic lines of animals. In Holstein, for example, cows with higher genetic merit for fertility had fewer services per conception, and shorter intervals from calving to conception compared with cows with low genetic merit for ferti lity [97] In crossbred sheep, females with higher breeding values for fertility had shorter anestrous period than sheep with low breeding values for fertility [98] PAGE 30 30 In the United States, three main female fertility traits are used in official genetic eval uations of dairy cattle: DPR, CCR and HCR DPR is defined as the percent of cows eligible for breeding that become pregnant in each 21 day period i.

Conceptually, DPR is the product of estrous detection rate the percent of cow s in estrus that are detected in estrus and pregnancy rate per insemination the percent of inseminated cows that become pregnant.

Practically, DPR is calculated from days open, which is the inte rval from calving to conception. Further, t he reproductive traits are related. During the last 15 years, breeding values for DPR have improved, in part as a result of including fertility traits into economic ind ic es such as net merit and by inclusion of genomic information for breeding value calculations Figure 1 2.

Fertility ind ic es vary from country to country. In Ireland, the economic breeding index, which would be similar to n et merit in the United States, include s two fertility sub in d ic es: calving interval and survival of the cow during the lactation [] In the PAGE 31 31 Netherlands, the fertility index combines interval from calving to first insemination, non return rate at 56 days after insemination, calving interval, interval between firs t and last insemination and conception rate.

In New Zealand, where cows are bred during a defined breeding season, the fertility index comprises PM21, which is the percent of cows presented for mating during the first 21 days of the mating period, CR42 whi ch is from calving to conception, and calving interval [] Fertility traits among countries are correlated. Tenghe et al. There was an improvement in accuracy of prediction of fertility of 0. The advantage of using endocrine measurements is that they red to classical PAGE 32 32 traits which are more likely to be influenced by the farm management system.


For two centuries, Jersey cattle were exported globally, adapting to varying climates and production systems, yet the founding population remained genetically isolated on the Island of Jersey. The Island of Jersey formally allowed the importation of pure Jersey cattle in This study characterized the genetic variation of 49 popular bulls from the Island of Jersey born from to and compared them to 47 non-Island Jersey bulls and cows, primarily from the United States In addition, 21 Guernsey cattle derived from the Island of Guernsey and 71 Holstein cattle served as reference populations for genetic comparison. When compared to Holstein and Guernsey, all Jersey clustered together by breed. The Jersey breed demonstrated increased inbreeding in comparison to Holstein or Guernsey with slightly higher estimates of inbreeding coefficients and identity-by-descent. The Island and United States Jersey have relatively similar, yet statistically different inbreeding estimates despite vastly different population sizes and gene flow. Signatures of selection within Island Jersey were identified using genome-wide homozygosity association and marker-based F ST that provided population informative single-nucleotide polymorphism SNPs.

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Jodi Wright-Sec. Genetic Advancement Committee met in January to review genetic progress of the breed and analyze the current and forecasted changes in milk pricing. The new TPI formula, approved by the board of directors, will be implemented with the April genetic evaluations. Key points are: 1. All traits are then combined into a Health Trait Index for an overall economic value.

Stina Nagel. Alta News. With more traits, more breeds, more features, more options, and more sorting abilities, the all-new Alta Bull Search app is a more streamlined approach to bull searching. Chrissy Meyer. A genetic base change is an adjustment of predicted transmitting abilities PTAs for all animals in a given breed.

Material Information

Unlike any other country, Direct Genomic Values DGV have been published in Canada for genotyped animals as part of its genomic evaluation system. Ten years later, as of the December release, DGV will no longer be published or included in any outgoing data files associated with Canadian genetic evaluations. Some breeders have expressed their disagreement with this decision and misunderstanding continues to be propagated. This article provides further clarification regarding the decision to no longer publish DGV. The information in Figure 1 was regularly used as part of this educational campaign. This estimate of its genetic potential is simply based on a formula that averages the genetic evaluation of its recorded parents. As a heifer calf ages and becomes a cow after first calving, her own performance data contributes to her genetic evaluation, labelled as an EBV Estimated Breeding Value.

Answer ALL the questions. Start the answers to each question at the top of a NEW page. Number the answers correctly according to the numbering system used in this question paper. D ulation of similar animals which can interbreed A population of organisms which breed to produce fertile offspring A community of organisms which can interbreed. Link to this page:.

Мгновение спустя появились еще двое - тучный мужчина и рыжеволосая женщина. Они также подошли к Танкадо. - Неудачный выбор места, - прокомментировал Смит.  - Халохот думал, что поблизости никого. Халохот какое-то время наблюдал за происходящим, потом скрылся за деревьями, по-видимому, выжидая. - Сейчас произойдет передача, - предупредил Смит.  - В первый раз мы этого не заметили.

 Интуиция? - с вызовом проговорил .


Anne P.


CDCB Dairy Industry webinar, November VanRaden Holstein Association USA, Genetic Advancement Committee Meeting, January Cole, John, The future of genomic evaluations of Holstein cattle, DOWNLOAD Powell, Rex, Trends in international flow of Holstein genes[poster presentation], DOWNLOAD.

Crescent L.


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