Estimating variance components and breeding values for number of oocytes and number of embryos in dairy cattle using a single-step genomic evaluation.

Reproductive technologies such as multiple ovulation and embryo transfer (MOET) and ovum pick-up (OPU) accelerate genetic improvement in dairy breeding schemes. To enhance the efficiency of embryo production, breeding values for traits such as number of oocytes (NoO) and number of MOET embryos (NoM) can help in selection of donors with high MOET or OPU efficiency. The aim of this study was therefore to estimate variance components and (genomic) breeding values for NoO and NoM based on Dutch Holstein data. Furthermore, a 10-fold cross-validation was carried out to assess the accuracy of pedigree and genomic breeding values for NoO and NoM. For NoO, 40,734 OPU sessions between 1993 and 2015 were analyzed. These OPU sessions originated from 2,543 donors, from which 1,144 were genotyped. For NoM, 35,695 sessions between 1994 and 2015 were analyzed. These MOET sessions originated from 13,868 donors, from which 3,716 were genotyped. Analyses were done using only pedigree information and using a single-step genomic BLUP (ssGBLUP) approach combining genomic information and pedigree information. Heritabilities were very similar based on pedigree information or based on ssGBLUP [i.e., 0.32 (standard error = 0.03) for NoO and 0.21 (standard error = 0.01) for NoM with pedigree, 0.31 (standard error = 0.03) for NoO, and 0.22 (standard error = 0.01) for NoM with ssGBLUP]. For animals without their own information as mimicked in the cross-validation, the accuracy of pedigree-based breeding values was 0.46 for NoO and NoM. The accuracies of genomic breeding values from ssGBLUP were 0.54 for NoO and 0.52 for NoM. These results show that including genomic information increases the accuracies. These moderate accuracies in combination with a large genetic variance show good opportunities for selection of potential bull dams.

Reproductive technologies and genomic selection in dairy cattle.

Genomic tools are now available for most livestock species and are used routinely for genomic selection (GS) in cattle. One of the most important developments resulting from the introduction of genomic testing for dairy cattle is the application of reasonably priced low-density single nucleotide polymorphism technology in the selection of females. In this context, combining genome testing and reproductive biotechnologies in young heifers enables new strategies to generate replacement and elite females in a given period of time. Moreover, multiple markers have been detected in biopsies of preimplantation stage embryos, thus paving the way to develop new strategies based on preimplantation diagnosis and the genetic screening of embryos. Based on recent advances in GS, the present review focuses on new possibilities inherent in reproductive technologies used for commercial purposes and in genetic schemes, possible side effects and beneficial impacts on reproductive efficiency. A particular focus is on the different steps allowing embryo genotyping, including embryo micromanipulation, DNA production and quality assessment.

Cysteamine supplementation during in vitro maturation of slaughterhouse- and opu-derived bovine oocytes improves embryonic development without affecting cryotolerance, pregnancy rate, and calf characteristics.

Optimization of ovum pick up (OPU) followed by in vitro embryo production (IVP) is strongly driven by the needs of both beef and dairy cattle breeders to enhance genetic improvement. The rapidly growing use of genomic selection in cattle has increased the interest in using OPU-IVP technology to increase the number of embryos and offspring per donor, thus allowing enhanced selection intensity for the next generation. The aim of this study was to optimize embryo production through supplementation of cysteamine during in vitro maturation (IVM) and in vitro culture (IVC) of both slaughterhouse- and OPU-derived oocytes. The effects on embryo production and on embryo cryotolerance, post-transfer embryo survival, and calf characteristics, including gestation length, birth weight, perinatal mortality, and sex ratio were studied. In study 1, immature slaughterhouse-derived cumulus-oocyte complexes (COCs) were matured in IVM medium supplemented with or without 0.1 mM cysteamine, fertilized and cultured for 7 days in 0.5 ml SOFaaBSA. In study 2, cysteamine was present during both IVM (0.1 mM) and IVC (0.01, 0.05, 0.1 mM) from Days 1 to 4. In study 3, OPU-derived COCs were matured in medium supplemented with or without 0.1 mM cysteamine in a 2 × 2 factorial design (OPU week and cysteamine treatment). Embryos were evaluated for stage and grade on Day 7 and, depending on the number of transferable embryos and recipients available, the embryos were transferred either fresh or frozen-thawed at a later date. The presence of cysteamine during IVM significantly increased the embryo production rate with slaughterhouse-derived COCs (24.0% vs. 19.4%). The higher number of embryos at Day 7 was due to an increased number of blastocysts, whereas the distribution of embryos among different quality grades and cryotolerance was not affected. Embryo production rate was negatively affected when cysteamine was present during both the processes of IVM and IVC during Days 1 to 4 of culture (13.2%-19.3% vs. 26.4%). The presence of cysteamine during IVM of OPU-derived COCs also significantly increased the embryo production rate (34.4% vs. 23.4%). The higher number of embryos was again totally due to an increased number of blastocysts, whereas cryotolerance was not affected. The relative increase in embryo production rate was higher with OPU-derived oocytes compared with slaughterhouse-derived COCs (47% vs. 24%). This improvement resulted in a mean of 1.73 transferable embryos per OPU session compared with 1.06 in the absence of cysteamine. The presence of cysteamine did not affect pregnancy rate, gestation length, birth weight, perinatal mortality, and sex of calves born from either fresh or frozen-thawed embryos. This study reported that cysteamine supplementation during IVM greatly improved the efficiency and affectivity of an OPU-IVP program.

Bovine OPU-derived oocytes can be matured in vitro for 16-28 h with similar developmental capacity.

The aim of this study was to determine the optimal maturation culture period of ovum pick up (OPU)-derived cumulus oocytes complexes (COCs) in relation to their developmental capacity. Embryo production, embryo cryotolerance, post-transfer embryonic survival and calf characteristics such as gestation length, birthweight and sex ratio were investigated. This retrospective study covers the analyses of ovum pick up -in vitro production and calving results from a commercial programme that took place between March 1994 and September 2004. Donors were both heifers (of which approximately 90% pregnant) and cows (of which approximately 10% pregnant). Embryo production analyses were based on 7800 OPU sessions conducted from January 1995 until January 1999. Analyses of calving rate were based on 13 468 embryo transfers performed during January 1995 until May 2002. Analyses on calf characteristics were based on 2162 calves born between March 1994 and September 2004. The in vitro maturation culture period ranged from 16 to 28 h. The mean production rate of transferable embryos was 16.5% (1.2 embryos per OPU session). Length of maturation culture period did not affect the production of transferable embryos. Mean calving rate was 40.9% and 38.7% for fresh and frozen/thawed embryos, respectively. Calving rate was not affected by the maturation culture period. Mean birthweight, gestation length and proportion of male calves were 46 kg, 281.9 days and 52.8%, respectively. Maturation culture period did not affect these variables. In conclusion, this study shows that the in vitro maturation culture period within the range of 16-28 h does not affect in vitro embryo production, embryo cryotolerance, post-transfer embryonic survival and calf characteristics, suggesting that all COC batches collected by OPU on the same day, can be fertilized in one IVF session without a significant loss in the production from oocyte to calf.

Whole-genome association study for milk protein composition in dairy cattle.

Our objective was to perform a genome-wide association study for content in bovine milk of α(S1)-casein (α(S1)-CN), α(S2)-casein (α(S2)-CN), ß-casein (ß-CN), κ-casein (κ-CN), α-lactalbumin (α-LA), ß-lactoglobulin (ß-LG), casein index, protein percentage, and protein yield using a 50K single nucleotide polymorphism (SNP) chip. In total, 1,713 Dutch Holstein-Friesian cows were genotyped for 50,228 SNP and a 2-step association study was performed. The first step involved a general linear model and the second step used a mixed model accounting for all family relationships. Associations with milk protein content and composition were detected on 20 bovine autosomes. The main genomic regions associated with milk protein composition or protein percentage were found on chromosomes 5, 6, 11, and 14. The number of chromosomal regions showing significant (false discovery rate <0.01) effects ranged from 3 for ß-CN and 3 for ß-LG to 12 for α(S2)-CN. A genomic region on Bos taurus autosome (BTA) 6 was significantly associated with all 6 major milk proteins, and a genomic region on BTA 11 was significantly associated with the 4 caseins and ß-LG. In addition, regions were detected that only showed a significant effect on one of the milk protein fractions: regions on BTA 13 and 22 with effects on α(S1)-CN; regions on BTA 1, 9, 10, 17, 19, and 28 with effects on α(S2)-CN; a region on BTA 6 with an effect on ß-CN; regions on BTA 13 and 21 with effects on κ-CN; regions on BTA 1, 5, 9, 16, 17, and 26 with effects on α-LA; and a region on BTA 24 with an effect on ß-LG. The proportion of genetic variance explained by the SNP showing the strongest association in each of these genomic regions ranged from <1% for α(S1)-CN on BTA 22 to almost 100% for casein index on BTA 11. Variation associated with regions on BTA 6, 11, and 14 could in large part but not completely be explained by known protein variants of ß-CN (BTA 6), κ-CN (BTA 6), and ß-LG (BTA 11) or DGAT1 variants (BTA 14). Our results indicate 3 regions with major effects on milk protein composition, in addition to several regions with smaller effects involved in the regulation of milk protein composition.

Genetic parameters for oocyte number and embryo production within a bovine ovum pick-up-in vitro production embryo-production program.

Genetic factors influencing the outcome of bovine ovum pick-up-in vitro production (OPU-IVP) and its relation to female fertility were investigated. For the first time, genetic parameters were estimated for the number of cumulus-oocyte complexes (Ncoc), quality of cumulus-oocyte complexes (Qcoc), number and proportion of cleaved embryos at Day 4 (Ncleav(D4), Pcleav(D4)), and number and proportion of total and transferable embryos at Day 7 of culture (Nemb(D7), Pemb(D7) and NTemb(D7), PTemb(D7), respectively). Data were recorded by CRV (formally Holland Genetics) from the OPU-IVP program from January 1995 to March 2006. Data were collected from 1508 Holstein female donors, both cows and pregnant virgin heifers, with a total of 18,702 OPU sessions. Data were analyzed with repeated-measure sire models with permanent environment effect using ASREML (Holstein Friesian). Estimates of heritability were 0.25 for Ncoc, 0.09 for Qcoc, 0.19 for Ncleav(D4), 0.21 for Nemb(D7), 0.16 for NTemb(D7), 0.07 for Pcleav(D4), 0.12 for Pemb(D7), and 0.10 for PTemb(D7). Genetic correlation between Ncoc and Qcoc was close to zero, whereas genetic correlations between Ncoc and the number of embryos were positive and moderate to high for Nemb(D7) (0.47), NTemb(D7) (0.52), and Ncleav(D4) (0.85). Genetic correlations between Ncoc and percentages of embryos (Pcleav(D4), Pemb(D7), and PTemb(D7)) were all close to zero. Phenotypic correlations were in line with genetic correlations. Genetic and phenotypic correlations between Qcoc and all other traits were not significant except for the phenotypic correlations between Qcoc and number of embryos, which were negative and low to moderate for Nemb(D7) (-0.20), NTemb(D7) (-0.24), and Ncleav(D4) (-0.43). Results suggest that cumulus-oocyte complex (COC) quality, based on cumulus investment, is independent from the total number of COCs collected via OPU and that in general, a higher number of COCs will lead to a higher number of embryos produced. The correlation between the estimated breeding values for Ncoc and PTemb(D7) of sires in this study and the sires breeding index for female-fertility based on the Dutch cattle population was close to zero. This study revealed OPU-IVP traits (Nemb(D7), NTemb(D7), and Ncoc) that could be of potential value for selection. Introduction of such traits in breeding programs would enhance the number of offspring from superior donors as well as improve the cost efficiency of OPU-IVP programs.

Genome-wide scan for bovine milk-fat composition. I. Quantitative trait loci for short- and medium-chain fatty acids.

A genome-wide scan was performed to identify quantitative trait loci (QTL) for short- and medium-chain fatty acids (expressed in wt/wt %). Milk samples were available from 1,905 cows from 398 commercial herds in the Netherlands, and milk-fat composition was measured by gas chromatography. DNA was available from 7 of the paternal half-sib families: 849 cows and their 7 sires. A genetic map was constructed comprising 1,341 SNP and 2,829 cM, with an average information content of 0.83. Multimarker interval mapping was used in an across-family regression on corrected phenotypes for the 7 half-sib families. Four QTL were found: on Bos taurus autosome (BTA) 6, a QTL was identified for C6:0 and C8:0; on BTA14, a QTL was identified for fat percentage, all odd-chain fatty acids, and C14:0, C16:0, C16:1, and their unsaturation indices; on BTA19, a QTL affected C14:0; and on BTA26, a QTL was identified for the monounsaturated fatty acids and their unsaturation indices. The QTL explained 3 to 19% of phenotypic variance. Furthermore, 49 traits with suggestive evidence for linkage were found on 21 chromosomes. Additional analyses revealed that the QTL on BTA14 was most likely caused by a mutation in DGAT1, whereas the QTL on BTA26 was most likely caused by a mutation in the SCD1 gene. Quantitative trait loci that affect specific fatty acids might increase the understanding of physiological processes regarding fat synthesis and the position of the causal genes.

What affects fertility of sexed bull semen more, low sperm dosage or the sorting process?

Until now it has been unclear to what extent the reduced fertility with sexed semen in the dairy industry is caused by too few sperm per AI dose, or by the effect of flow cytometric sorting, which is the established procedure for sexing semen. Therefore, we evaluated the effects of low sperm numbers per dose with and without sorting on non-return rates after 56 days (NRR 56); in addition, we evaluated the effects of bulls, in order to further optimize use of sexed semen. Based on results of using sexed semen from seven Holstein bulls, an overall numerical decline of 13.6% in NRR 56 was observed (P<0.05). About two-thirds of this decline (8.6%) was due to the low dose (P<0.05), and a third (5.0%) due to the process of sorting (P<0.05). The effect of low dosage and sorting differed among bulls. We observed a sex ratio of 91.6% females for sexed semen from the first 131 calves born. Currently the best way to increase fertility of sexed semen is by closely monitoring fertility so that the highest fertility bulls are used, and by improving farm animal management. However, to make substantial progress, more in depth studies are needed on the sexing technology, especially on aspects such as sorting procedures and sperm dosage.

Breeding value estimation for fat percentage using dense markers on Bos taurus autosome 14.

Prediction of breeding values using whole-genome dense marker maps for genomic selection has become feasible with the advances in DNA chip technology and the discovery of thousands of single nucleotide polymorphisms in genome-sequencing projects. The objective of this study was to compare the accuracy of predicted breeding values from genomic selection (GS), selection without genetic marker information (BLUP), and gene-assisted selection (GEN) on real dairy cattle data for 1 chromosome. Estimated breeding values of 1,300 bulls for fat percentage, based on daughter performance records, were obtained from the national genetic evaluation and used as phenotypic data. All bulls were genotyped for 32 genetic markers on chromosome 14, of which 1 marker was the causative mutation in a gene with a large effect on fat percentage. In GS, the data were analyzed with a multiple quantitative trait loci (QTL) model with haplotype effects for each marker bracket and a polygenic effect. Identical-by-descent probabilities based on linkage and linkage disequilibrium information were used to model the covariances between haplotypes. A Bayesian method using Gibbs sampling was used to predict the presence of a putative QTL and the effects of the haplotypes in each marker bracket. In BLUP, the haplotype effects were removed from the model, whereas in GEN, the haplotype effects were replaced by the effect of the genotype at the known causative mutation. The breeding values from the national genetic evaluation were treated as true breeding values because of their high accuracy and were used to compute the accuracy of prediction for GS, BLUP, and GEN. The allele substitution effect for the causative mutation, obtained from GEN, was 0.35% fat. The accuracy of the predicted breeding values for GS (0.75) was as high as for GEN (0.75) and higher than for BLUP (0.51). When some markers close to the QTL were omitted from the model, the accuracy of prediction was only slightly lower, around 0.72. The removal of all markers within 8 cM from the QTL reduced the accuracy to 0.64, which was still much higher than BLUP. It is concluded that, when applied to 1 chromosome and if genetic markers close to the QTL are available, the presented model for GS is as accurate as GEN.

Carbon-activated gas filtration during in vitro culture increased pregnancy rate following transfer of in vitro-produced bovine embryos.

Many environmental conditions for in vitro embryo production (IVP) systems for cattle have been relatively standardised, e.g. media composition, temperature, pH, water quality, and atmospheric composition. However, little attention has been paid to the quality of ambient laboratory air and the gas environment in incubators. Although a few studies have examined the effects of chemical air contamination on IVP of human embryos, there are no published accounts for domestic animal embryos. Therefore, this study investigated the effects of an intra-incubator carbon-activated air filtration system (CODA) during in vitro culture (IVC) on embryonic development and subsequent pregnancy rate of bovine embryos. Immature cumulus-oocyte-complexes (COCs) were obtained twice-weekly by ultrasonic-guided transvaginal oocyte aspiration. The COCs were matured in TCM199/FCS/LH/FSH, fertilized with frozen-thawed Percoll-separated semen, and subsequently cultured for 7 day in SOFaaBSA. Day 7 embryos were transferred either fresh or frozen/thawed. The experimental design was a 2 x 2 factorial; presumptive zygotes were placed either in a conventional CO(2)-O(2)-N(2) incubator (Control group) or in an identical CO(2)-O(2)-N(2) incubator with a CODA intra-incubator air purification unit (CODA group) for IVC. The embryo production rate at Day 7 was not affected by the CODA air purification unit (23.4 and 24.7% morulae and blastocysts per oocyte for control and CODA, respectively) nor was there any significant effect on embryo stage or quality. However, the pregnancy rate was improved (P=0.043) for both fresh (46.3% versus 41.0%) and frozen/thawed embryos (40.8% versus 35.6%). In conclusion, atmospheric purification by the CODA intra-incubator air purification unit significantly increased pregnancy rate following transfer of in vitro-produced bovine embryos.

Effects of insemination-ovulation interval on fertilization rates and embryo characteristics in dairy cattle.

The objective of this study was to examine effects of the interval between insemination and ovulation on fertilization and embryo characteristics (quality scored as good, fair, poor and degenerate; morphology; number of cell cycles and accessory sperm number) in dairy cattle. Time of ovulation was assessed by ultrasonography (every 4h). Cows were artificially inseminated once between 36h before ovulation and 12h after ovulation. In total 122 oocytes/embryos were recovered 7d after ovulation. Insemination-ovulation interval (12h-intervals) affected fertilization and the percentages of good embryos. Fertilization rates were higher when AI was performed between 36-24 and 24-12h before ovulation (85% and 82%) compared to AI after ovulation (56%). AI between 24 and 12h before ovulation resulted in higher percentages of good embryos (68%) compared to AI after ovulation (6%). Insemination-ovulation interval had no effect on number of accessory sperm cells and number of cell cycles when corrected for embryo quality. This study showed that the insemination-ovulation interval with a high probability of fertilization is quite long (from 36 to 12h before ovulation). However, the insemination-ovulation interval in which this fertilized oocyte has a high probability of developing into a good embryo is shorter (24-12h before ovulation).

Follicular dynamics around the recruitment of the first follicular wave in the cow.

The present study aimed to test the generally accepted view that a follicular wave starts with follicles newly recruited from the population smaller than 3 mm, which later compete for dominance. According to this view, subordinate follicles are expected to be too atretic to join the next follicular wave. Ten cows were ovariectomized shortly prior to the LH surge, thus around the start of the first follicular wave of the cycle. Per cow, on average, 14.4 follicles of >/=3 mm were dissected. Follicular health was determined on the basis of four parameters: 1) judgment of the degree of atresia by stereomicroscope, 2) incidence of apoptotic nuclei among the granulosa cells, 3) estradiol and progesterone concentrations, and 4) insulin-like growth factor-I (IGF-I) binding proteins (IGFBPs)-2, -4, and -5 concentrations in the follicular fluid. In addition to the preovulatory follicle, 3.1 other follicles, mainly sized 3-4.5 mm, were found to be healthy based on the proportion of apoptotic nuclei, and concentrations of estradiol/progesterone, and IGFBPs. The ability of these follicles to respond with growth on the preovulatory and periovulatory FSH surges was supported by a comparison to the follicular population of four cows 31-68 h after the LH surge. The present results point to an alteration of the view on the follicular wave. The larger follicles during the first days of the follicular wave are, in general, derived from follicles that also joined the previous wave. A portion of these growing follicles are estradiol active and compete for dominance. Other growing follicles lack estradiol production and are probably derived from rather atretic follicles. The first newly recruited follicles do not reach the size of 3 mm before 31 h after the preovulatory FSH surge. At that time, the larger follicles are already competing for dominance.

Factors affecting oocyte quality and quantity in commercial application of embryo technologies in the cattle breeding industry.

With the introduction of multiple ovulation, embryo recovery and transfer techniques (MOET) plus embryo freeze-thaw methods in the early 1980s, the breeding industry has the tools in hand to increase the number of calves from donors of high genetic merit. In the early 1990s, the introduction of ovum pick-up followed by in vitro embryo production (OPU-IVP) opened up even greater possibilities. Using these technologies, we challenge biological mechanisms in reproduction. Where normally one oocyte per estrous cycle will develop to ovulation, now numerous other oocytes that otherwise would have degenerated are expected to develop into an embryo. Completion of oocyte growth and pre-maturation in vivo before final maturation both appear to be essential phases in order to obtain competence to develop into an embryo and finally a healthy offspring. In order to increase oocyte quality and quantity in embryo production technologies, current procedures focus primarily on improving the homogeneity of the population of oocytes with regard to growth and state of pre-maturation at the start of a treatment. In the case of MOET, dominant follicle removal (DFR) before superovulation treatment improves the number of viable embryos per session from 3.9 to 5.4 in cows but not in heifers and a prolonged period of follicle development obtained by preventing release of the endogenous LH surge increases the number of ova but not the number of viable embryos per session. In the case of OPU-IVP, the frequency of OPU clearly affects quantity and quality of the collected oocytes and FSH stimulation prior to OPU every 2 weeks resulted in 3.3 embryos per session. Analysis of 7,800 OPU sessions demonstrated that the oocyte yield is dependent on the team, in particular, the technician manipulating the ovaries. It is concluded that an increased understanding of the processes of oocyte growth, pre- and final maturation will help to improve the efficiency of embryo technologies. However, somewhere we will meet the limits dictated by nature.

Effects of different reproduction techniques: AI MOET or IVP, on health and welfare of bovine offspring.

Since the introduction of in vitro production (IVP) of bovine and sheep pre-implantation embryos, increased birth weights and other deviations of IVP calves and lambs compared with AI or MOET offspring have been reported. Study 1 of the present paper, a comparison between AI, MOET and IVP (co-culture/serum) calves with respect to calf and calving characteristics in large-scale field conditions, confirms these reports. In addition, it is shown that MOET calves tend towards higher birth weights and have significantly longer gestations and more difficult calvings than AI calves. It is presently unknown if the effect of IVP is also observed later in life. In this paper, data on reproduction characteristics of bovine IVP co-culture/serum offspring are presented. Semen production--and non return data of one year old IVP bulls and superovulation-, AI- and OPU/IVP results of one year old IVP heifers are compared with those of one year old AI and MOET animals producing semen or embryos in the same time period. So far, there are no indications that the use of IVP is reflected in deviate reproduction characteristics of bovine IVP offspring. It has been suggested that use of co-culture cells and serum during in vitro culture of bovine (and sheep) embryos may partially explain the increased birth weights and other deviations of bovine and sheep IVP offspring. Deletion of these factors in semi-defined culture media, e.g. Synthetic Oviductal Fluid (SOF), could result in more normal offspring. Study 2 investigates this hypothesis in both field conditions (Study 2a, comparing AI, IVP co-culture/serum and IVP SOF calves) and in semi-standardized conditions (Study 2b, comparing MOET, IVP co-culture/serum and IVP SOF calves at one herd). In Study 2a, although IVP SOF calves showed (non-significant) shorter gestations, easier calvings and lower percentages of perinatal mortality and congenital malformations than IVP co-culture calves, birth weights were not decreased. In Study 2b however, the difference between IVP co-culture and IVP SOF calves in birth weight and ease of calving was significant (P < 0.05), IVP SOF calves resembling MOET calves more. IVP calves differed significantly from MOET calves with respect to several physiological parameters, such as blood oxygen saturation level, heart beat frequency and some measures of the heart. In addition, in Study 2b, recipients receiving an IVP SOF embryo showed a more regular return to estrus than those receiving an IVP co-culture embryo. From Study 2 it can be concluded that using a semi-defined medium for in vitro culture (SOF) may improve characteristics of IVP calves born.

Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing.

Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of several hundred loci as spots in a 2-D pattern. The majority of the loci resolved are polymorphic. Using linkage analysis in a large CEPH family, this study reports the mapping of 34 loci detected by the minisatellite core probe 33.6. By multipoint linkage analysis, regional chromosome positions of the 33.6 loci could be deduced, showing no evidence of clustering. In the analysis of spot patterns, use was made of a computerized image analysis system specifically designed for 2-D DNA typing. Since experimental variations between different separation patterns were automatically corrected for with this program, rapid and reliable scorings could be obtained. The results presented demonstrate the availability of reliable genetic information throughout the 2-D separation pattern. Adding the use of semiautomated computerized pattern analysis, this study further substantiates the applicability of 2-D DNA typing in genome scanning, not only in theoretical but also in practical terms. Moreover, it can be anticipated that this method will have a specific advantage in studies that scan for trinucleotide repeat expansions and somatic instability, where the repeat sequences detected by appropriate core probes are of particular interest.

Comprehensive and accurate mutation scanning of the CFTR gene by two-dimensional DNA electrophoresis.

The large number of possible disease-causing mutations in the 27 exons of the cystic fibrosis transmembrane conductance regulator (CFTR) gene has severely limited direct diagnosis of cystic fibrosis (CF) patients and carriers by mutation detection. Here we show that in principle testing for mutations in the CFTR gene can be both substantially facilitated and made virtually complete, by two-dimensional DNA electrophoretic separation of polymerase chain reaction (PCR) amplified exons on the basis of size and basepair sequence in denaturing gradient gels. Under a single optimized set of conditions we were able to obtain a pattern of spots representing all 27 exons of the CFTR gene and to readily detect 17 out of 17 identified sequence variations in 9 different exons in DNA from 11 CF patients and carriers. Our results demonstrate the potential of 2-dimensional DNA electrophoresis for comprehensive mutation analysis of the CFTR gene. The approach serves as a model for comprehensive diagnosis of the many other large disease genes for which a variety of mutations have also which been reported.

Two-dimensional DNA typing of human pedigrees: spot pattern characterization and segregation.

By two-dimensional (2-D) genome typing, i.e., electrophoretic separation of restriction enzyme-digested genomic DNA on the basis of both size and sequence in denaturing gradient gels followed by hybridization analysis, several hundred alleles (spots) can be analyzed in parallel, using a micro- or minisatellite core probe. We studied the segregation of 213 and 214 spots detected by microsatellite core probe (CAC)n and minisatellite core probe 33.6, respectively, in two three-generation human pedigrees. Reproducibility of the spot patterns was such that particular spot variants could be scored in both pedigrees. Between 73 and 74% of the spots scored were variant and were transmitted in a Mendelian manner. Very little cosegregation among the 2-D spots themselves was observed, suggesting a random distribution over the genome. Several pairs of spots that appeared to contain both alleles from single loci were identified. The few spots detected by both probes (overlapping spots) showed different segregation patterns, indicating that each probe detects independent sets of genetically informative loci. These results provide a firm basis for using 2-D DNA typing to identify disease loci and for constructing a 2-D spot genetic linkage map of the human genome.

Two-dimensional DNA typing as a genetic marker system in humans.

By two-dimensional (2-D) DNA typing several hundred genomic loci can be analysed simultaneously in a two-dimensional pattern as spots detected by micro- or minisatellite core probes. Many of these loci display DNA sequence polymorphisms, and we have examined whether it is possible to extract genetic information from the rather complex but potentially very informative 2-D DNA typing patterns. To do so, the segregation of 9 spots detected by the microsatellite core probe (CAC)n was followed in a large CEPH pedigree, and by linkage analysis it was possible to obtain chromosomal assignments of the corresponding (CAC)n loci in all cases except one. Furthermore, a regional, physical localization of these loci emerged from analysis of the existing genetic and physical localization data of DNA markers flanking the (CAC)n loci. We have hereby obtained evidence that the spots detected by the microsatellite core probe (CAC)n segregate in a Mendelian manner and that it is possible to reliably score the segregation of single spots within a family. These results indicate that the large amount of potential information inherent in 2-D DNA typing may be used as a genetic marker system; an important prerequisite for its application as a genome scanning method, e.g. in detection of genomic alterations in cancer and in mapping of genetic traits.

Two-dimensional DNA electrophoresis in mutation detection.

Accurate detection of gene mutations is important in many areas of biology and medicine. In fundamental studies of mutagenesis it is often necessary to assess all possible mutations, either spontaneous or induced by genotoxic agents, in a particular gene or gene sequence to explain a given cellular or physiological endpoint. In molecular medicine comprehensive detection of all possible mutations in a disease gene is required before clinical genetic testing becomes feasible. Of the many mutation detection methods currently available none is capable of scanning for all possible mutations in a cost-effective manner. Here we show that by two-dimensional DNA electrophoretic separation, on the basis of both size and base pair sequence, in principle all mutations in a given gene can be detected. This is illustrated by some data on 2-D electrophoresis of 10 exons of the cystic fibrosis gene.