Biomedical subjects

P M VanRaden

Publications and source records attributed to P M VanRaden.

At least 19 recordsLinked to original sources

PubMed2026

Accounting for voluntary waiting period changes in US dairy herds: Adjusting daughter pregnancy rate and introducing first-service to conception.

The genetic evaluation of female fertility traits in dairy cattle in the United States has progressed over the past 2 decades, with 4 additional traits integrated into the national evaluation system since the introduction of daughter pregnancy rate (DPR) in 2004. However, concerns have arisen in the dairy sector, with reports of producers extending the voluntary waiting period (VWP), which is the time of initial breeding after calving, due to more persistent lactation yields. Since its inception, DPR calculations in the US evaluation have assumed a fixed 50-d VWP, which may not reflect modern reproductive strategies. Furthermore, producers may determine that some of their cows should have their VWP extended while others may follow the standard time. A re-evaluation of the current female fertility evaluation is necessary to ensure traits align with current management practices. Therefore, this study explores the addition of a potential new trait, First Service to Conception (FSC), along with a revised DPR formula that permits more flexibility with VWP. About 32 million records from the National Cooperator Database, covering 5 major dairy breeds (2003-2023), were used for this study. Data for cows calving before 2003 were unavailable because insemination records were not recorded prior. The findings suggest FSC enhances female fertility evaluations, providing a more comprehensive reproductive assessment independent of VWP. Another approach was an adjustment to the DPR calculation (DPRadj) to account for herd VWP on a herd-year and lactation group basis. The mean DPR value was 45.06%, while DPRadj increased the mean value to 52.58%. The mean FSC was 62.64 d. In an analysis using first lactation cows for cow traits and heifers for heifer traits, genetic correlations of FSC with other fertility traits were 0.97 with Cow Conception Rate (CCR) and DPR, 0.98 with DPRadj, 0.40 with Heifer Conception Rate (HCR), and 0.32 with Early First Calving (EFC). Predicted transmitting abilities (PTA) were calculated to assess the implications of adding FSC to, or replacing DPR with DPRadj within the CDCB multi-trait evaluation index, Net Merit $ (NM$). The highest correlation among the top 10% of bulls occurred when replacing DPR with DPRadj (0.99). Adding FSC to the original model reduced the latter correlation to 0.88, which indicates slight re-ranking of top bulls. Among animals with PTA reliability above 50%, the lowest correlation was between the original index and the index replacing DPR with FSC (0.95). This work advances genetic evaluation in dairy cattle, improving reproductive efficiency and productivity.

daughter pregnancy rate↗

PubMed2006

Effects of nonadditive genetic interactions, inbreeding, and recessive defects on embryo and fetal loss by seventy days.

Lethal recessive genes that cause early embryo loss are difficult to detect. Nonreturn rate at 70 d after first insemination (NR) was evaluated as a trait of the embryo using 1,739,055 first-service records from 1,251 Holstein bulls represented as both service sires and sires of cows. Effects modeled included herd-year-season, parity of cow, sire of cow, service bull, interaction of service bull with sire of cow, and regression on inbreeding of embryo. Variances of service bull and sire of cow were estimated using REML and estimated effects were removed from the data. Interaction variance was estimated from the residuals using the tilde-hat approximation to REML. An additive relationship matrix was used for sire of cow and a dominance relationship matrix for the interaction term. Service bull effects were assumed constant across time and unrelated. For each 10% increase in inbreeding, NR percentage declined by an estimated 1%. A regression of this size could be explained by > 20% of animals carrying defects that cause early embryo loss. Of the total variance, service bull contributed 0.36%; sire of cow, 0.24% (heritability of 1.0%); and interaction, 0.18% (dominance variance of 2.8%). Numbers of records exceeded 500 for 50 bull pair subclasses. Predicted interactions that included effects of inbreeding ranged from - 3.6% to +2.9%, compared with the mean NR of 56%. The largest negative interactions were not caused by known recessive defects. Complex vertebral malformation generally causes loss of pregnancies later in gestation, and few current bulls carry the gene for deficiency of uridine monophosphate synthase. Further study of the families with largest negative interactions could uncover new recessive defects.

Abortion, Veterinary↗

PubMed2006

Genetic evaluation and best prediction of lactation persistency.

Cows with high persistency tend to produce less milk than expected at the beginning of lactation and more than expected at the end. Best prediction of persistency was calculated as a function of a trait-specific standard lactation curve and a linear regression of test-day deviations on days in milk. Regression coefficients were deviations from a balance point to make yield and persistency phenotypically uncorrelated. The objectives of this study were to calculate (co)variance components and breeding values for best predictions of persistency of milk (PM), fat (PF), protein (PP), and SCS (PSCS) in Holstein cows. Data included 8,682,138 lactations from 4,375,938 cows calving since 1997, and 39,354 sires were evaluated. Sire estimated breeding values (EBV) for PM, PF, and PP were similar and ranged from -0.70 to 0.75 for PM; EBV for PSCS ranged from -0.37 to 0.28. Regressions of sire EBV on birth year were near zero (<0.003) but positive for PM, PF, and PP, and negative for PSCS. Genetic correlations of PM, PF, and PP with PSCS were moderate and favorable, indicating that increasing SCS decreases yield traits, as expected. Genetic correlations among yield and persistency were low to moderate and ranged from -0.09 (PSCS) to 0.18 (PF). This definition of persistency may be more useful than those used in test-day models, which are often correlated with yield. Routine genetic evaluations for persistency are feasible and may allow for improved predictions of yield traits. As calving intervals increase, persistency may have greater value.

Animals↗

PubMed2006

Productive life including all lactations and longer lactations with diminishing credits.

Alternative measures of productive life (PL) were compared, and life expectancy factors were updated to replace estimates from 1993. Alternatives were proposed with extra credits for lactations longer than 10 mo and beyond 84 mo of age and for each calving so that an extremely long lactation would not receive more credits than multiple shorter lactations with dry periods between. Maximum credits per lactation of 10 mo (original PL), 12 mo, and unlimited were compared. The unlimited credits option either included or excluded a calf value equal to 2 mo of production and had credits given for all days either uniformly or based on lactation curves (diminishing credits). Standard lactation curves (first, second, and greater lactations) were estimated based on the test-day yields of Holstein cows remaining in lactation from a set of 903,579 lactation records. For the diminishing credits alternative, credit for a given day of a parity was derived using the predicted yield of the day proportional to the average daily yield of the first 305 d of second parity. Daily yields were deviations from a baseline of 13.62 kg. Heritabilities and genetic correlations were estimated by multitrait REML for alternative measures of PL, for longevity censored at various ages, and for yield traits and SCS in first parity. Data for REML analysis included records from 1,098,329 Holsteins born from 1994 through 1997 from 5,109 sires, and a relationship matrix among sires was included in the model. Lactations beyond 84 mo added little information. Heritability of PL was 0.073 with 10 mo, 0.069 with 12 mo, 0.068 and 0.067 with unlimited (uniform) lactation credits (with and without calf credits, respectively), and 0.070 with unlimited diminishing credits. Corresponding correlations among predicted transmitting abilities for PL and protein yield were 0.07, 0.06, 0.12, 0.23, and 0.09, all much lower than the 0.46 estimated in 1993. Heritability of PL with diminishing credits improved from 0.017 to 0.070 when censoring age increased from 36 to 96 mo. There was no further increase in heritability beyond 96 mo. Genetic correlation with the final PL was 0.87 when PL was censored at 36 mo, but the estimate increased steadily with the censoring age. The PL with diminishing credits, which was favorable in both economic and genetic aspects, was desirable in crediting cows for complete lactations.

Aging↗

PubMed2004

Use of early lactation days open records for genetic evaluation of cow fertility.

National genetic evaluations for cow fertility were introduced by the USDA in February, 2003. These evaluations, reported as daughter pregnancy rate, are based on days open. One requirement of the evaluation system is that lactations be at least 250 d in milk (DIM) to be included for analysis. The objective of this research was to develop a predictor of days open, usable in genetic evaluation, to allow for earlier predicted transmitting abilities (PTA), especially for young bulls. The final prediction equation included an overall intercept, the effects of lactation and calving ease score, the linear and quadratic effects of age at calving, and a regression on days open based on last breeding. Data used for estimation were breeding records from 4 dairy records processing centers for the years 1995 through 1998. Genetic correlations were > or =0.91 by d 130, and phenotypic means of predicted days open were in agreement with means for final days open, indicating that the predictions were phenotypically unbiased. Comparison of mean PTA based on actual and predicted days open indicated no bias in PTA, and correlations between PTA were > or =0.92 by d 130. The earlier use of data increased reliability by about 5% for sires between the ages of 4 and 5 yr. The USDA began using predicted days open for records that are at least 130 DIM in national evaluations starting November, 2003.

Aging↗

PubMed2004

Development of a national genetic evaluation for cow fertility.

A national fertility evaluation was developed based on pregnancy rate, which measures the percentage of nonpregnant cows becoming pregnant within each 21-d opportunity period. Data for evaluation are days open, which are calculated as date pregnant minus previous calving date. Date pregnant is determined from last reported breeding or from subsequent calving minus expected gestation length. Success or failure of last breeding can be confirmed by veterinary diagnosis or a report that the cow was sold because of infertility. Data are adjusted for parity and calving season within geographic region and time period and evaluated. Fertility records are considered complete at 250 d in milk, and lower and upper limits of 50 and 250 d are applied to days open. For calculation of genetic evaluations, days open are converted to pregnancy rate by the linear formula pregnancy rate = 0.25 (233 - days open). Evaluations are expressed as predicted transmitting ability for daughter pregnancy rate, and calculation is done with an animal model. Genetic correlations among several fertility measures and other evaluated traits were estimated from 3 large data sets. Correlation with days open was less for nonreturn rate than for days to first breeding, probably because nonreturn rate had lower heritability. Cow fertility was negatively correlated with yield but is a major component of longevity. Thus, recent selection for longevity may have slowed the long-term decline in fertility. Direct selection for fertility could halt or reverse the decline.

Agriculture↗

PubMed2004

Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle.

We report putative quantitative trait loci affecting female fertility and milk production traits using the merged data from two research groups that conducted independent genome scans in Dairy Bull DNA Repository grandsire families to identify quantitative trait loci (QTL) affecting economically important traits. Six families used by both groups had been genotyped for 367 microsatellite markers covering 2713.5 cM of the cattle genome (90%), with an average spacing of 7.4 cM. Phenotypic traits included PTA for pregnancy rate and daughter deviations for milk, protein and fat yields, protein and fat percentages, somatic cell score, and productive life. Analysis of the merged dataset identified putative quantitative trait loci that were not detected in the separate studies, and the pregnancy rate PTA estimates that recently became available allowed detection of pregnancy rate QTL for the first time. Sixty-one putative significant marker effects were identified within families, and 13 were identified across families. Highly significant effects were found on chromosome 3 affecting fat percentage and protein yield, on chromosome 6 affecting protein and fat percentages, on chromosome 14 affecting fat percentage, on chromosome 18 affecting pregnancy rate, and on chromosome 20 affecting protein percentage. Within-family analysis detected putative QTL associated with pregnancy rate on six chromosomes, with the effect on chromosome 18 being the most significant statistically. These findings may help identify the most useful markers available for QTL detection and, eventually, for marker-assisted selection for improvement of these economically important traits.

Animals↗

PubMed2004

Invited review: selection on net merit to improve lifetime profit.

Genetic selection has made dairy cows more profit-able producers of milk. Genetic evaluations began with 2 traits measured on a few cows but now include many traits measured on millions of cows. Selection indexes from USDA included yield traits beginning in 1971, productive life and somatic cell score beginning in 1994, conformation traits in 2000, and cow fertility and calving ease in 2003. This latest revision of net merit should result in 2% more progress, worth 5 million dollars/yr nationally, with improved cow health and fitness, but slightly less progress for yield. Fertility and longevity evaluations have similar reliability because cows can have several fertility records, each with lower heritability, compared with one longevity record with higher heritability. Lifetime profit can be estimated more accurately if less heritable traits are evaluated and included instead of ignored. Milk volume has a positive value for fluid use, but a negative value for cheese production. Thus, multiple selection indexes are needed for different markets and production systems. Breeding programs should estimate future rather than current costs and prices. Many other nations have derived selection indexes similar to US net merit.

Animals↗

PubMed2004

Body condition scores and dairy form evaluations as indicators of days open in US Holsteins.

The objectives of this study were to estimate genetic correlations among body condition score (BCS), dairy form, milk yield, and days open in US Holsteins and investigate the potential of using BCS or dairy form evaluations as early indicators of days open. Dairy form and BCS obtained from the Holstein Association USA, Inc., were merged with mature equivalents (ME) for milk yields and days open data from AIPL-USDA. Cows were required to be classified between 24 and 60 mo of age, before 335 d in milk (DIM) and have ME milk of at least 4537 kg. A minimum of 20 daughters per sire and 10 cows per herd-classification visit (HV) or herd-year-season of calving (HYS) were required. The final data set included 159,700 records. Heritabilities and correlations among dairy form, BCS, milk yield, and days open were estimated with multiple trait sire models. Fixed effects included age at classification for dairy form and BCS, age at calving for milk yield, HV for dairy form and BCS, HYS for milk yield and days open, DIM within lactation group for dairy form and BCS and lactation group for milk yield and days open. Correlations among dairy form, BCS, and days open were generated with and without a ME milk covariable. Correlations between ME milk and days open were generated with and without covariables for dairy form or BCS. Random effects included sire and error. The genetic correlation estimates of days open with dairy form, BCS, and ME milk were 0.48, -0.30, and 0.38, respectively. The genetic correlation estimate between days open and dairy form was 0.38 after adjustment for ME milk, whereas the genetic correlation between days open and BCS was -0.24 after adjustment for ME milk. Combining dairy form evaluations with days open evaluations for 19 recently proven bulls resulted in an average increase of 0.06 for reliability of days open evaluations. The addition of BCS evaluations did not increase reliability when dairy form observations were available.

Aging↗

PubMed2003

Economic merit of crossbred and purebred US dairy cattle.

Heterosis and breed differences were estimated for milk yield traits, somatic cell score (SCS), and productive life (PL), a measure of longevity. Yield trait data were from 10,442 crossbreds and 140,421 purebreds born since 1990 in 572 herds. Productive life data were from 41,131 crossbred cows and 726,344 purebreds born from 1960 through 1991. The model for test-day yields and SCS included effects of herd-year-season, age, lactation stage, regression on sire's predicted transmitting ability, additive breed effects, heterosis, and recombination. The model for PL included herd-year-season, breed effects, and general heterosis. All effects were assumed to be additive, but estimates of heterosis were converted to a percentage of the parent breed average for reporting. Estimates of general heterosis were 3.4% for milk yield, 4.4% for fat yield, and 4.1% for protein yield. A coefficient of general recombination was derived for multiple-breed crosses, but recombination effects were not well estimated and small gains, not losses, were observed for yield traits in later generations. Heterosis for SCS was not significant. Estimated heterosis for PL was 1.2% of mean productive life and remained constant across the range of birth years. Protein yield of Brown Swiss x Holstein crossbreds (0.94 kg/d) equaled protein yield of purebred Holsteins. Fat yields of Jersey x Holstein and Brown Swiss x Holstein crossbreds (1.14 and 1.13 kg/d, respectively) slightly exceeded that of Holsteins (1.12 kg/d). With cheese yield pricing and with all traits considered, profit from these crosses exceeded that of Holsteins for matings at breed bases. For elite matings, Holsteins were favored because the range of evaluations is smaller and genetic progress is slower in breeds other than Holstein, in part because fewer bulls are sampled. A combined national evaluation of data for all breeds and crossbreds may be desirable but would require an extensive programming effort. Animals should receive credit for heterosis when considered as mates for another breed.

Aging↗

PubMed2003

Technical note: detection and adjustment of abnormal test-day yields.

A method to detect and to adjust or exclude abnormally low or high milk, fat, and protein yields on test-day (TD) was developed. Predicted TD yield is calculated based on preceding and subsequent (if available) TD yields. Observed TD yields that are < 60% or > 150% of predicted TD yield are defined as abnormal. Most abnormal yields are adjusted to this floor or ceiling, but some are excluded. Yields of < 4.5 kg that are identified as from a cow that was sick or that are less than half the mean of adjacent tests are excluded as are yields of > 59 kg above predicted yield. Lactation yields are calculated from the restricted TD yields. When this procedure was applied to 2002 data, 1.8% of milk, 2.4% of fat, and 1.6% of protein yields on TD were below the acceptance range and 0.1% of milk and protein and 0.8% of fat were above. Predicted TD yield was calculated as preceding TD yield plus preceding test interval multiplied by daily yield change (slope) based on days in milk (DIM), DIM2, previous normal TD yield, and interaction between DIM and previous TD yield. To accommodate changes in slope at peak yield, separate coefficients were estimated for < 50 and > or = 50 DIM. Herd mean was used when only one TD was recorded for a cow (or when two were recorded and the second was designated as abnormal based on the first) and to determine an acceptable range for component percentages. Predicted TD yield for first TD was based on subsequent rather than previous normal TD. To test the adjustments, lactation records with one abnormal TD yield or more were matched with subsequent lactation records. Correlation between consecutive lactations increased from 0.692 to 0.693 for milk (561,063 lactation pairs), from 0.653 to 0.660 for fat (951,387 lactation pairs), and from 0.686 to 0.694 for protein (488,653 lactation pairs). Outlier adjustment improved the correlation between consecutive lactation yields and is applied routinely to TD records of cows for calvings since 1997.

Animals↗

PubMed2002

International dairy bull evaluations expressed on national, subglobal, and global scales.

Genetic evaluations on a global scale were calculated for Holstein bulls using the May 2001 International Bull Evaluation Service (Interbull) evaluations expressed on each of 27 national scales. National scale data were weighted by the country's proportion of total daughters from all bulls (population size) to represent market share. Correlations between Interbull evaluations on national scales and evaluations on a global scale ranged from 0.961 to 0.998 (mean of 0.988). Number of top 100 bulls for protein yield that were in common between national and global scales ranged from 54 to 94 and was related significantly to mean genetic correlation between a country and the other 26 countries. Weighting of evaluations on national scales by population size, inverse of population size weight, or equal weight produced practically the same group of top bulls and correlations among the three global scales were 0.999. Thus, the method for combining Interbull evaluations expressed on national scales had only minor impact and was much less important than use of all data. Subglobal scales were established by a clustering technique that gave two to five groups. For grazing countries or other atypical systems, a subglobal scale may provide better guidance, although a scale representing three grazing countries did not provide the expected improvement over a global scale in the relationship with the three country scales. If conditions in non-participating countries are generally represented by participating countries, most needs are met by a global scale.

Animals↗

PubMed2001

Evaluation of sire predicted transmitting abilities for evidence of X-chromosomal inheritance in north american sire families.

This study tested for differences between genetic merits of sons and daughters of sires and for evidence of segregating quantitative trait loci on the X chromosomes of North American Holsteins. Son PTA adjusted for sire PTA was used as the dependent variable to test for biases and for genes that were passed from sire to daughter but not to son. The test of variability across sires of sons merely indicated an unaccounted source of variation, for which genes on X chromosomes might be responsible. Critical values for this test and power were determined by simulation for a variety of populations and traits differing in heritability, size of the X chromosome effect, and allelic frequency. Simulated genes on the X chromosome were detected with high power at intermediate frequencies of the favorable allele. The power of the test increased as the size of the effect increased and as genetic variance attributed to autosomes decreased. The test was then applied to recently evaluated data from US and Canadian Holstein populations. Genetic evaluations for >17,000 bulls from the US and >9000 from Canada were included. Results suggested that little extra variation was present for some traits formally evaluated in North America, but that genes on the X chromosome were unlikely to be the cause.

Animals↗

PubMed1999

A genome scan for QTL influencing milk production and health traits in dairy cattle.

A genome scan was conducted in the North American Holstein-Friesian population for quantitative trait loci (QTL) affecting production and health traits using the granddaughter design. Resource families consisted of 1,068 sons of eight elite sires. Genome coverage was estimated to be 2,551 cM (85%) for 174 genotyped markers. Each marker was tested for effects on milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score, and productive herd life using analysis of variance. Joint analysis of all families identified marker effects on 11 chromosomes that exceeded the genomewide, suggestive, or nominal significance threshold for QTL effects. Large marker effects on fat percentage were found on chromosomes 3 and 14, and multimarker regression analysis was used to refine the position of these QTL. Half-sibling families from Israeli Holstein dairy herds were used in a daughter design to confirm the presence of the QTL for fat percentage on chromosome 14. The QTL identified in this study may be useful for marker-assisted selection and for selection of a refined set of candidate genes affecting these traits.

Animals↗

PubMed1999

Standardization and conversion of marker polymorphism measures.

Large scale gene mapping efforts in domestic animals have generated and mapped a large number of genetic markers that are useful for mapping quantitative trait and disease loci and for DNA diagnostic purposes such as parentage testing. Marker polymorphism is an important criterion for selecting genetic markers in planning experiment for mapping quantitative trait loci or for DNA diagnostic purposes. Current formulations of marker polymorphism measures are functions of marker allele frequencies. In this study, two measures of marker polymorphism that are available from gene mapping studies and do not require allele frequencies were proposed and analyzed: the observed polymorphic information content (PIC) and the observed family information content (FIC). The observed FIC was more stable than the observed PIC because the observed FIC is unaffected by the variation in the frequency of heterozygous parents. However, both FIC and PIC are dependent on the gene mapping design. The effective number of alleles is recommended as a tool to standardize marker polymorphism measures so that polymorphism of different markers can be compared on an equal basis, and to obtain a new polymorphism measure (such an exclusion probability) from an existing measure (such as FIC). The usage of the effective number of alleles to standardize FIC, PIC and exclusion probabilities is illustrated using genetic markers in a published linkage map.

Animals↗

PubMed1999

Comparison of test interval and best prediction methods for estimation of lactation yield from monthly, a.m.-p.m., and trimonthly testing.

A method with best prediction properties that condenses information from all test days into measures of lactation yield and persistency has been proposed as a possible replacement for the test interval method and projection factors. The proposed method uses previously established correlations between individual test days and includes inversion of a matrix for each lactation. Milk weights that were representative of monthly, a.m.-p.m., and trimonthly test plans were examined to compare the accuracy of best prediction and test interval methods for estimating lactation yield. Individual milk weights or daily yields of 658 Canadian cows in 17 herds were selected to correspond to test intervals for 100,000 US cows. For a.m.-p.m. testing, the initial milk weight that was credited was selected randomly from the a.m. or p.m. milking and was alternated thereafter. Trimonthly credits were from one of the first three designated test day weights, selected randomly, and each third designated test weight thereafter. Correlations between 305-d actual lactation yield and lactation estimates by the test interval method were 0.97, 0.96, and 0.93 for monthly, a.m.-p.m., and trimonthly testing, respectively. Corresponding correlations for the best prediction method were 0.97, 0.97, and 0.93. Standard deviations of differences between estimated and 305-d actual yields for monthly, a.m.-p.m., and trimonthly testing were 373, 400, and 546 kg, respectively, for best prediction regressed on herd mean, which was a reduction in estimation error of 4, 6, and 10% over the test interval method. The advantage of best prediction was moderate if two milk weights were recorded monthly and was larger if testing was less frequent. Advantages also were found for fat and protein yields estimated by multitrait best prediction for records with reduced component sampling.

Animals↗

PubMed1999

Selection and mating considering expected inbreeding of future progeny.

Animals most related or least related to current members of their breed were revealed by calculating the expected inbreeding of their future progeny. A sample of potential mates was chosen by randomly selecting 600 females from a recent birth year (1995). Relationships among the sample were computed by the tabular method. Relationships of other animals to the sample population were computed quickly from the relationships of their parents or ancestors. To-Mar Blackstar-ET and Round Oak Rag Apple Elevation were most related to the Holstein breed with expected inbreeding of 7.9 and 7.7%, respectively. Corresponding Jersey bulls were Highland Magic Duncan and Soldierboy Boomer Sooner of CJF with expected inbreeding of 10.9 and 9.5%, respectively. The highest expected inbreeding was 11.1% for Selwood Bettys Commander, 8.6% for Forest Lawn Simon Jetway, 10.1% for Dutch Mill Telestars Fayette, and 7.4% for Korncrest Pacesetter for Ayrshire, Brown Swiss, Guernsey, and Milking Shorthorn breeds, respectively. Regression on inbreeding in the genetic evaluation model removed effects of past inbreeding. Future inbreeding effects could be included for each potential mating or by adjusting breeding values for average inbreeding expected with random mating. The correlation between Holstein breeding values unadjusted and adjusted for inbreeding was 0.9976. The estimated genetic trend was 6% lower with future inbreeding included.

Animals↗

PubMed1998

Designs of reference families for the construction of genetic linkage maps.

The reference family panel is the foundation of a gene mapping program because it affects the cost and quality of the genetic linkage maps, and should be designed to yield reliable linkage detection and locus ordering at minimal gene mapping cost. A map cost function was defined as the number of genotypes required per marker per unit of genome coverage and was used to obtain optimal designs with respect to linkage detection. An ordering reliability function was defined as the likelihood ratio of the most likely order to the second most likely order of genetic markers and was used to find optimal designs with respect to locus ordering. Optimum levels of recombination frequency were found to be in the neighborhood of 0.11-0.15 for linkage detection and were in the region of 0.05-0.20 for locus ordering. Therefore, recombination frequencies optimal for linkage detection are also optimal for locus ordering. Based on the optimal detection levels, sample size (number of offspring) and map cost requirements were derived for six representative designs, assuming gender-specific linkage maps and two alleles with equal frequency for each marker. The sample size required for linkage detection ranged from 168 to 432 offspring for full-sib designs and ranged from 350 to 600 offspring for half-sib designs depending on the family size and the target LOD score, with corresponding minimal map costs of 10-20 genotypes per marker per centiMorgan map coverage. Locus ordering generally requires more genotypes than linkage detection. For full-sib designs, meioses from both genders should be used for locus ordering even when the maps are gender-specific. For half-sib designs, additional families may be needed for locus ordering. Sample size for ordering closely linked loci as required by positional cloning were provided. Effects of family size, grandparents, and marker polymorphism on design efficiency were analyzed.

Chromosome Mapping↗