Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century

The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long-targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker-assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new-found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.

Intrauterine position and adjacent fetal sex affects fetal and placental growth throughout gestation, but not embryonic viability, in pigs selected for component traits of litter size

Intrauterine position and sex of adjacent fetuses in litter bearing species have been implicated in physiological and behavioral differences of offspring. The effects of uterine position and sex status of flanking fetuses with crowded uterine conditions on fetal and placental growth rate was tested. Gilts were unilaterally hysterectomized-ovariectomized at 160 d of age and mated at approximately 280 d of age, with fetal harvest at 45, 65, 85, or 105 d of gestation. Uterine position relative to the cervix, fetal status (alive, dead, sex), fetal weight, and placental weight were recorded at harvest. Each fetus was coded as adjacent to 0, 1, or 2 opposite sex fetuses and analyzed using an ANOVA fitting contemporary group, line, and flanking fetal sex code as fixed effects with sire as a random effect. The fraction of live fetuses in each classification (0, 1, 2) was 26.4%, 50.1%, and 23.4%, respectively, indicating no effect on fetal survival. Fetal weight was affected by flanking sex status between 65 d (P <  0.05) and 105 d (P <  0.001), with means at 105 d of 800.0 ± 20.3, 748.5 ± 17.8, and 672.7 ± 25.2 g, respectively for flanking sex status codes 0, 1, 2. Placental weight was similarly affected (P <  0.01) by flanking sex code, but only at 105 d. It is concluded that fetal growth and placental development in pigs is influenced by sex status of adjacent fetuses. This could be a potential source of variation in behavioral and reproductive differences later in life.

Litter-of-origin trait effects on gilt development

The preweaning litter environment of gilts can affect subsequent development. In a recent experiment designed to test the effects of diet on gilt development, litter-of-origin traits including individual birth weights, immunocrits (a measure of colostrum intake), sow parity, number weaned, and individual weaning weights were collected for approximately 1,200 gilts that were progeny of approximately 300 sows. Subsequently, BW, LM area, and backfat were measured at 100 d of age and at 28-d intervals until slaughter (260 d of age). From 160 d of age to slaughter, gilts were observed daily for estrus. At slaughter, the reproductive tract and 1 mammary gland were recovered. The reproductive tract was classified as cyclic or prepubertal; the number of corpora lutea was counted. Uterine horn lengths and ovarian dimensions were measured. Uterus and ovary samples from every 10th gilt were prepared for histological evaluation of uterine gland development and follicle counts, respectively. Mammary gland tissue protein and fat were assayed. Day of the estrous cycle at slaughter was calculated using the first day of the most recent standing estrus (d 0) recorded previous to slaughter. Each gilt development trait was analyzed for association with each litter-of-origin trait, after adjusting for dietary treatment effects. Uterine length, ovarian dimensions, mammary gland protein and fat, and uterine gland development were also adjusted for day of the estrous cycle at slaughter. All litter-of-origin traits were associated ( < 0.05) with growth traits. Top-down (backward elimination) multiple regression analysis indicated that BW and LM accretion in gilts was positively associated with immunocrit ( < 0.01), birth weight ( < 0.01), preweaning growth rate ( < 0.01), and parity ( < 0.01). Backfat accretion was positively associated with preweaning growth rate ( < 0.01), number weaned ( < 0.05), and parity ( < 0.05). Age at puberty was associated with birth weight (positive; < 0.01) and preweaning growth rate (negative; < 0.01). Total uterine length was positively associated with only birth weights ( < 0.05). Mammary gland protein was negatively associated with preweaning growth ( < 0.01). Mammary gland fat was positively associated with birth weight and number of piglets weaned ( > 0.05). These results indicate that colostrum consumption, birth weights, preweaning growth rate, number weaned, and parity are associated with gilt development traits during later life.

Plasma concentrations of acyl-ghrelin are associated with average daily gain and feeding behavior in grow-finish pigs

The objectives of this study were to determine the effect of sex, sire line, and litter size on concentrations of acyl-ghrelin and total ghrelin in plasma of grow-finish pigs and to understand the relationship of plasma concentrations of ghrelin with feeding behavior, average daily gain (ADG), and back fat in grow-finish swine. Yorkshire-Landrace crossbred dams were inseminated with semen from Yorkshire, Landrace, or Duroc sires. Within 24 h of birth, pigs were cross-fostered into litter sizes of normal (N; >12 pigs/litter) or small (S; ≤ 9 pigs/litter). At 8 wk of age, pigs (n = 240) were blocked by sire breed, sex, and litter size and assigned to pens (n = 6) containing commercial feeders modified with a system to monitor feeding behavior. Total time eating, number of daily meals, and duration of meals were recorded for each individual pig. Body weight was recorded every 4 wk. Back fat and loin eye area were recorded at the conclusion of the 12-wk feeding study. A blood sample was collected at week 7 of the study to quantify concentrations of acyl- and total ghrelin in plasma. Pigs from small litters weighed more (P < 0.05) and tended (P = 0.07) to be fatter than pigs from normal litters. Postnatal litter size did not affect ADG, feeding behavior, or concentrations of ghrelin in plasma during the grow-finish phase. Barrows spent more time eating (P < 0.001) than gilts, but the number of meals and concentrations of ghrelin did not differ with sex of the pig. Pigs from Duroc and Yorkshire sires had lesser (P < 0.0001) concentrations of acyl-ghrelin than pigs from Landrace sires, but plasma concentrations of total ghrelin were not affected by sire breed. Concentrations of acyl-ghrelin were positively correlated with the number of meals and negatively correlated with meal length and ADG (P < 0.05). A larger number of short-duration meals may indicate that pigs with greater concentrations of acyl-ghrelin consumed less total feed, which likely explains why they were leaner and grew more slowly. Acyl-ghrelin is involved in regulating feeding behavior in pigs, and measuring acyl-ghrelin is important when trying to understand the role of this hormone in swine physiology.

Selection for uterine capacity improves lifetime productivity of sows

Selection for 11 generations for uterine capacity (UC) increased litter size in gilts by 1.6 more fully formed pigs at birth compared to an unselected control line (CO) despite averaging one less ovulation. The objective of the present study was to quantify line by parity interactions and characterize litter performance traits of sows in each line at later parities. Gilts farrowed in contemporary groups of 19 litters and were maintained through four parities if successfully mated in that contemporary group. A total of 243 litters and 2639 piglets were analyzed. Fixed effects of farrowing group, line, parity (1-4), and two-way interactions involving line were fitted. Sire (n=57) of the sow within farrowing group and line was fitted as a random effect. No significant line by parity interactions were observed. Parity effects were detected (P<0.01) for individual piglet birth weight, pre-weaning gain, and weaning weight. Parity effects were also detected (P<0.05) for total number born, average and total litter birth weight, and average and total litter weaning weight. Selection line differences for litter traits were detected (P<0.05) for number stillborn piglets and approached significance (P=0.06) for number of piglets weaned. Retention of sows in the herd was greater (P<0.05) with an average of 2.33 parities for the UC line females compared to 1.87 parities for the CO line. This resulted in favorable cumulative lifetime productivity of the UC line for total number of piglets born, number of piglets born alive, litter birth weight, number of piglets weaned and litter weaning weight.

The relationship of plasma urea nitrogen with growth traits and age at first estrus in gilts

Gilts that reach puberty at an earlier age with more backfat have greater lifetime productivity. Increased growth rates generally promote earlier age at first estrus; however, an association of age at first estrus with discrete measures of body fatness remains controversial. We tested the hypothesis that metabolic state as determined by concentrations of plasma urea nitrogen (PUN), which reflect lean tissue growth, were correlated with age at first estrus. Blood samples were collected from gilts (n = 337) at 102, 123, and 145 d of age during development. Concentrations of albumin, creatinine, glucose, and PUN were determined. Body weight and backfat thickness were determined at each time point. From 130 to 240 d of age, gilts were monitored for first pubertal estrus. Concentrations of creatinine increased whereas concentrations of glucose decreased with increasing age (P < 0.0001). Concentrations of albumin and PUN remained relatively stable throughout development. Average daily BW gain (r = 0.22) and change in backfat thickness (r = 0.29) had a positive phenotypic correlation (P < 0.0001) with PUN at 145 d of age. Concentrations of PUN at 102 and 123 d of age were not phenotypically correlated with pubertal age, but there was a moderately negative phenotypic correlation (r = -0.22; P < 0.0001) of PUN at 145 d of age with age at first estrus along with a negative genetic correlation (r = -0.42). The relationship of PUN with age at first estrus shifted from liner to quadratic with advancing age. These data demonstrate that near the age at which gilts are selected for entry into the breeding unit, those with greater PUN have increased BW and backfat thickness and display pubertal estrus earlier but that PUN does not account for additional variation in age at first estrus beyond growth rate or backfat. It is concluded that PUN can be used to select gilts with increased efficiency of nutrient use without negatively impacting pubertal development.

Boar sperm quality in lines of pigs selected for either ovulation rate or uterine capacity

Selection for 11 generations in swine for ovulation rate (OR) or uterine capacity (UC) resulted in significant changes in component traits of litter size. Our objective was to conserve the unique germplasm for the future and to characterize sperm quality as a correlated response to the selection criterion imposed compared with an unselected control line (CO). Boars representing genetic diversity available in all 3 lines were produced in 2 farrowing seasons. Season 1 was born in September 2005 and was sampled for semen characteristics in October 2006. Season 2 was born in March 2006 and was sampled for semen characteristics in February and March 2007. Each boar (n = 60) was collected twice. The sperm-rich fraction was obtained, and volume and concentration of sperm cells were measured to estimate total sperm production. Each ejaculate was extended 1:3 (vol/vol) with Androhep Plus (Minitube, Verona, WI) and was packed for shipping to the National Animal Germplasm Program laboratory for processing into frozen straws. Semen quality was measured by computer-assisted semen analysis at 3 semen processing points: fresh (FR), 24 h after extender added (E), and postthaw (PT). A mixed model ANOVA was applied to the data. Fixed effects of farrowing season, line, and 2-way interactions were fitted. The random effect of boar (n = 60) within farrowing season and line was used to test line differences. Sperm concentration was not different (P = 0.18) among the lines (0.594 × 10(9), 0.691 × 10(9), and 0.676 × 10(9) cells/mL for CO, OR, and UC lines, respectively). However, significance (P = 0.04) was detected for the volume of the sperm-rich fraction, greatest for OR (86.4 mL), intermediate for UC (75.5 mL), and least for CO (70.2 mL). Line differences were thus detected (P = 0.02) for total sperm production per ejaculate, greatest for OR (54.9 × 10(9)), intermediate for UC (48.7 × 10(9)), and least for CO (40.5 × 10(9)). A larger percentage of progressively motile sperm and greater estimates of sperm velocity only at processing point E (P < 0.01) were detected in favor of CO. Estimates of motility, velocity, and other parameters of sperm movement measured on E processing points were positively correlated with the same estimates obtained PT, but the magnitude was low to moderate (r range -0.03 to 0.23). Thus, selection for component traits of female reproduction had a favorable effect on total sperm production of boars.

Contributions of the maternal uterine environment and piglet genotype on weaning survivability potential: I. Development of neonatal piglets after reciprocal embryo transfers between Meishan and White crossbred gilts

In commercial pigs, the greatest susceptibility for pre-weaning mortality occurs in low birth-weight piglets. Despite their overall decreased birth weight, Meishan (MS) piglets have decreased pre-weaning mortality rates compared with contemporary Western breeds. The objective of the current study was to determine the contributions of the maternal uterine environment, piglet genotype, and their interaction on the development of neonatal piglets pertaining to pre-weaning survivability using reciprocal embryo transfer between MS and White crossbred (WC) pigs. Twenty-five successful pregnancies were produced from 2 farrowing seasons, generating litters of maternal uterine environment (MUE) by piglet genotype (PigG) combinations; MS × MS (n = 4 litters), MS × WC (n = 7 litters), WC × MS (n = 7 litters), and WC × WC (n = 7 litters). At approximately 24 h of age (Day 1), piglets (n = 173) were weighed and a blood sample was taken. Hematocrit, hemoglobin, glucose, plasma urea nitrogen, albumin, NEFA, lactate, and cortisol were measured in all blood samples. Representative piglets (n = 46) from each litter were harvested and body measurements (i.e., organ weights, tissue glycogen content, and body composition) were determined. Piglet data were analyzed by ANOVA using MIXED model procedures. Both MUE (P < 0.001) and PigG (P < 0.01) affected piglet BW, illustrating that piglets gestated in WC gilts were heavier than piglets gestated in MS gilts, and WC piglets were heavier than MS piglets. Serum albumin concentrations were increased (P < 0.05) in MS piglets compared with WC piglets, indicating greater liver maturity. Significant MUE × PigG interactions were observed for hematocrit and hemoglobin, in which the greatest concentrations were observed in MS piglets gestated in MS and WC gilts, and the lowest concentrations were observed in WC piglets gestated in WC gilts, demonstrating increased oxygen-carrying capability. The percentage of fat and nitrogen, as well as the GE of the body, were greater (P < 0.05) in MS piglets, indicating greater energy stores. Liver, bicep femoris, and LM glycogen concentrations were greater (P < 0.01) in WC piglets compared with MS piglets, demonstrating increased glycogen catabolism in MS piglets. This study demonstrated limited interactions between the maternal uterine environment and piglet genotype on weaning survivability potential, suggesting that the MS piglet is a viable model for pre-weaning survivability.

148 PIGLET GROWTH AND BLOOD COMPONENTS DURING LACTATION FOLLOWING RECIPROCAL EMBRYO TRANSFER BETWEEN MEISHAN AND WHITE CROSSBRED GILTS

Sow productivity has a significant economic impact on the swine industry and is influenced by several factors, including preweaning piglet mortality. In Western breeds, low birth weight piglets exhibit the greatest susceptibility to preweaning mortality. In contrast, Meishan (MS) piglets have decreased birth weights but lower preweaning mortality rates, suggesting that birth weight is not the sole component of preweaning survival. The objective of the current study was to determine the contributions of the maternal and piglet breed and their interactions on piglet growth and blood components pertaining to survivability during lactation following reciprocal embryo transfer between MS and White crossbred (WC) gilts. Twenty-five successful pregnancies were produced by embryo transfer in 2 farrowing seasons that represented all maternal and piglet breed combinations; MS × MS (n = 4 litters), MS × WC (n = 7 litters), WC × MS (n = 7 litters), and WC × WC (n = 7 litters). At Day 1, 10, and weaning (average weaning age = 18 days), piglets (n = 147, 97, and 94, respectively at Day 1, 10, and weaning) were weighed and blood samples were taken. Hematocrit, hemoglobin, glucose, nitrogen, nonesterified fatty acids, albumin, and cortisol were measured in all blood samples. All data were analysed for ANOVA using mixed model procedures. Piglet weights were greater (P < 0.001) throughout lactation in piglets from WC dams regardless of piglet breed. As a result, average daily gains from Days 1 to 10 and weaning were greater (P < 0.05) in piglets from WC dams. There were significant (P < 0.001) maternal × piglet × day interactions for hematocrit and hemoglobin levels in which levels were greatest at Day 1 in MS piglets from WC dams and at Day 10 in MS piglets from MS dams but decreased in WC piglets from WC dams at Day 1. Glucose was greater (P < 0.05) at Day 1 in piglets from WC dams regardless of piglet breed but was greater (P < 0.05) at weaning in WC piglets regardless of maternal breed. Nitrogen was similar at Day 1 for all maternal and piglet breed combinations, but at Day 10 and weaning, nitrogen levels were greater (P < 0.001) in MS piglets regardless of maternal breed. Nonesterified fatty acid was greater throughout lactation in piglets from MS dams irrespective of piglet breed. Albumin was greater (P < 0.05) in MS piglets throughout lactation regardless of maternal breed. Cortisol was not different between the maternal and piglet breed combinations throughout lactation, but cortisol was greater (P < 0.001) at Day 1 compared with Day 10 and weaning. This study demonstrated that piglet growth during lactation was influenced more by maternal breed in favor of WC dams, which supports previous crossbreeding studies. However, blood components pertaining to survivability displayed complex interactions between the piglet and maternal breed, which may signify possible mechanisms for improved preweaning survivability of MS pigs.

Functional genomic approaches for the study of fetal/placental development in swine with special emphasis on imprinted genes

This chapter describes the application of functional genomic approaches to the study of imprinted genes in swine. While there are varied definitions of "functional genomics", in general they focus on the application of DNA microarrays, single nucleotide polymorphism (SNP) arrays, and other high coverage genomic analyses, and their combination with downstream methods of gene modification such as silencing RNA (siRNA) and viral and non-viral transfection. Between the initial data acquisition and the actual genetic manipulation of the system lies bioinformatics, where massive amounts of data are analyzed to extract meaningful information. This area is in constant flux with an increased emphasis on detection of affected pathways and processes rather than generation of simple affected gene lists. We will expand on each of these points and describe how we have used these technologies for the study of imprinted genes in swine. First we will introduce the biological question to provide context for the discussion of the functional genomic approaches and the types of information they generate.

Development of the pig placenta

Placental insufficiency results in fetal loss, low birth weight, stillbirth, preweaning mortality and poor growth. Placental development begins at conceptus elongation, which is a primary factor controlling the size of the placenta. After elongation, the allantois develops outward from the embryo to establish the allantochorion, which defines the size of the functional placenta. During implantation, chorionic trophoblasts adhere to endometrial epithelial cells. Placental structures known as areolae develop at the openings of the endometrial glands and take up endometrial gland secreted products (histotrophe). Between day 30 and 35 of gestation, the adhered trophoblast-endometrial epithelial bilayer undergoes microscopic folding. Fetal and maternal capillaries develop adjacent to the bilayer and blood flows are arranged in a cross-countercurrent manner. Except for nutrients secreted by the glands, nutrient exchange takes place between these capillaries within these folds. By day 85, the folds deepen and become more complex, increasing surface area. The epithelial bilayer thins and capillaries indent the plane of each layer (but do not penetrate), reducing distance between capillaries. The folded bilayer is surrounded by endometrial stroma on the maternal side and placental stroma on the fetal side. The fetal-placental stroma is partially composed of glycosaminoglycans, the most abundant being hyaluronan and heparan sulfate. Changes in both hyaluronoglucosaminidase and heparanase during placental development suggest that these enzymes play a role in placental development. In addition to structural modifications, various nutrient specific transport mechanisms exist. These mechanisms are likely to be as important to transport of specific nutrients as placental size or structure.

Conceptus development during blastocyst elongation in lines of pigs selected for increased uterine capacity or ovulation rate

Lines of pigs selected for increased uterine capacity have improved conceptus survival, whereas pigs selected for increased ovulation rate have decreased conceptus survival relative to an unselected control line. The objective of this study was to evaluate conceptus development during blastocyst elongation as a potential contributing factor to differences in conceptus survival rate among these pig lines. Conceptuses were recovered from pregnant control, uterine capacity, and ovulation rate line gilts at d 10 and 12 of gestation. At d 10 of gestation, conceptus morphologic diversity was assessed by comparing within-litter average conceptus diameter and the standard deviation of conceptus diameters. At d 12 of gestation, conceptus morphologic diversity was assessed by comparing blastocyst populations obtained from individual gilts. Real-time PCR analyses for transcripts involved in steroidogenesis, cellular differentiation, and immune responsiveness were performed on spherical, ovoid, and filamentous conceptuses recovered from these selection lines. Uterine flushings were also assayed for total protein and estradiol-17beta at d 10 and 12 of gestation. Morphological data were analyzed using ANOVA with the fixed effects of line, farrowing season, and their interactions. Conceptus mortality, uterine flushing, and real-time PCR data were analyzed using ANOVA with the fixed effects of line, day or blastocyst morphology, farrowing season, and their interactions. Conceptus mortality, measured as the ratio of conceptus recovery to ovulation rate, was not different between the lines on d 10 and 12 of gestation. There were no significant line effects for conceptus morphologic diversity at d 10 and 12 of gestation. Expression of transcripts associated with steroidogenesis (steroidogenic acute regulatory protein, cytochrome P450 side chain cleavage, and aromatase), cellular differentiation (cytokeratin-18 and vimentin), and immune responsiveness (interleukin-1beta) in spherical, ovoid, and filamentous conceptuses was not different between the lines. Furthermore, protein and estradiol-17beta in uterine flushings at d 10 and 12 of gestation were not different between the selection lines. These findings indicate limited, if any, deviations between these lines of pigs in conceptus development during blastocyst elongation and suggest that mechanisms involved in generating line differences in survival rate likely are manifested later in gestation.

Development of cell lines from the sheep used to construct the CHORI-243 Ovine BAC library

Two cell lines, designated MARC.OVSM, and MARC.OKF, were initiated from the aorta and kidney, respectively, obtained from the Texel ram used to make the CHORI-243 Ovine BAC library. These cell lines have been submitted to the NIA Aging Cell Repository at the Coriell Cell Respositories, Camden, NJ, USA, and will be made publicly available.

Differences in placental structure during gestation associated with large and small pig fetuses

The efficiency of nutrient transport from the pregnant female pig to the developing fetus depends on the size and function of the placenta. It has been reported that maternal and fetal blood vessels are arranged in a cross-countercurrent arrangement within placental microscopic folds. Thus, the blood supplies are in close apposition to each other within these microscopic folds, and maternal and fetal blood flows in approximately opposite directions perpendicular to the plane of the placenta. This arrangement indicates that the width of the microscopic folds influences placental efficiency. The objective of this study was to determine whether differences in pig placental microscopic fold development are associated with differences in fetal size or are influenced by selection for ovulation rate or uterine capacity. Gilts from a randomly selected control line, a line selected for ovulation rate, and a line selected for uterine capacity were slaughtered, and uterine wall samples were collected within the placentas associated with the largest and smallest fetuses in each litter on d 45, 65, 85, and 105 of gestation. The uterine wall samples were processed for histology and analyzed using computer-assisted morphometry. Average width of the placental folds and average width of the placental stroma above the folds were measured. To measure fold complexity, the length of the epithelial bilayer for a given length of placenta was also measured. The width of the folded bilayer increased significantly from d 65 to 105 and was greater in placentas associated with small fetuses compared with large fetuses on d 105 of gestation. In contrast, the width of the placental stroma above the folded bilayer decreased with gestation and decreased more rapidly in placenta associated with the smallest compared with the largest fetus. These results indicate that the width of the microscopic folds of the placental trophoblast/endometrial epithelial bilayer is increased in placenta associated with small fetuses, which we hypothesize will increase the surface area for interaction between maternal and fetal blood supplies, thus improving placental efficiency in response to reduced placental size.

Number of fetuses and conceptus growth throughout gestation in lines of pigs selected for ovulation rate or uterine capacity

Selection for 11 generations in swine for ovulation rate (OR) or uterine capacity (UC) resulted in 19.6% greater prenatal survival at term in UC compared with OR. Our objective was to characterize the number of fetuses throughout gestation in each line, including an unselected control (CO) line. Five hundred ninety-three gilts produced over 4 farrowing seasons were subjected to unilateral-hysterectomy-ovariectomy at 160 d of age and mated within line at 280 d of age. Gilts were assigned within sire family to be slaughtered (+/- 2 d) at d 25, 45, 65, 85, or 105 of gestation. Ovulation rate and number of live and dead fetuses were recorded for each pregnant gilt (n = 402). Fetal and placental weights were also recorded. Ovulation rate of OR line gilts (18.0 +/- 0.3 ova) exceeded (P < 0.001) CO and UC lines (15.0 +/- 0.3 and 14.0 +/- 0.3 ova, respectively). Line and gestational age interacted to affect number of live fetuses (P < 0.001). Least squares means for CO were 10.1, 8.3, 7.2, 6.7, and 7.3 live fetuses for d 25, 45, 65, 85, and 105, respectively (average SE = 0.46 fetuses). Corresponding means for OR were 13.4, 8.3, 7.9, 6.5, and 6.7 live fetuses, respectively (average SE = 0.44 fetuses). Means for UC were 10.2, 9.0, 8.5, 7.5, and 8.0 live fetuses, respectively (average SE = 0.47 fetuses). In each line, number of live fetuses at d 25 was approximately 72% of ovulation rate. Mortality to d 45 was greatest in OR, intermediate in CO, and least in UC. Reductions in live fetuses continued to occur from d 45 to 105, but line differences at d 45 were essentially maintained to d 105. Number of live fetuses in gilts at d 114 was estimated from each of the survival curves and predicted values of 7.0, 5.9, and 7.8 per uterine horn for CO, OR, and UC lines, respectively. Selection for uterine capacity improved fetal survival primarily during the time period between d 25 and 45. Relative growth rate coefficients throughout gestation for placental tissue indicated a change in rank of the line means, implicating a relative later growth pattern of placental tissue in the UC line.

Single nucleotide polymorphisms for pig identification and parentage exclusion

Single nucleotide polymorphisms (SNPs) have become an important type of marker for commercial diagnostic and parentage genotyping applications as automated genotyping systems have been developed that yield accurate genotypes. Unfortunately, allele frequencies for public SNP markers in commercial pig populations have not been available. To fulfil this need, SNP markers previously mapped in the USMARC swine reference population were tested in a panel of 155 boars that were representative of US purebred Duroc, Hampshire, Landrace and Yorkshire populations. Multiplex assay groups of 5-7 SNP assays/group were designed and genotypes were determined using Sequenom's massarray system. Of 80 SNPs that were evaluated, 60 SNPs with minor allele frequencies >0.15 were selected for the final panel of markers. Overall identity power across breeds was 4.6 x 10(-23), but within-breed values ranged from 4.3 x 10(-14) (Hampshire) to 2.6 x 10(-22) (Yorkshire). Parentage exclusion probability with only one sampled parent was 0.9974 (all data) and ranged from 0.9594 (Hampshire) to 0.9963 (Yorkshire) within breeds. Sire exclusion probability when the dam's genotype was known was 0.99998 (all data) and ranged from 0.99868 (Hampshire) to 0.99997 (Yorkshire) within breeds. Power of exclusion was compared between the 60 SNP and 10 microsatellite markers. The parental exclusion probabilities for SNP and microsatellite marker panels were similar, but the SNP panel was much more sensitive for individual identification. This panel of SNP markers is theoretically sufficient for individual identification of any pig in the world and is publicly available.

Changes in fetal organ weights during gestation after selection for ovulation rate and uterine capacity in swine1,2

We hypothesized that the ability of the fetus to alter nutrient shunting and organ growth might be associated with uterine capacity. White crossbred gilts from a randomly selected control line, a line selected for ovulation rate, and a line selected for uterine capacity (UC) were unilaterally hysterectomized-ovariectomized at 160 d of age, mated at estrus, and slaughtered at 45, 65, 85, and 105 d of gestation (9 to 18 gilts for each line x day combination). Analysis of the data revealed that heart weights and fetal weights were decreased in the ovulation rate line. No significant differences were obtained in fetal, placental, or fetal organ weights between the control and UC lines. Allometric growth of organs was assessed by examination of the slopes of the relationships between fetal weights and fetal organ weights after natural log transformation. Only the relative growth of the liver differed between selection lines and was greater (P = 0.01) in the UC compared with the control line during early pregnancy (d 45 and 65). Allometric growth of the fetal brain, liver, and heart differed with day of gestation. A brain-sparing effect was greater (P < 0.01) on d 85 and 105 compared with d 45 and 65. By contrast, a heart-sparing effect was present during early gestation and disappeared in later gestation. Fetal liver weights were hypersensitive to differences in fetal weights on d 45, possibly associated with placental effects on fetal liver weight. Fetal spleen weights were proportional to fetal weights throughout gestation. These results indicate that selection for ovulation rate decreased total fetal and fetal heart weights, and that selection for UC altered the relationship between total fetal and fetal liver weights during early gestation. Results further indicate significant changes in allometric growth of organs during gestation.

Evaluation of associations between prion haplotypes and growth, carcass, and meat quality traits in a Dorset × Romanov sheep population1,2

There is concern about potential antagonistic correlated responses due to intensive selection for scrapie-resistant haplotypes of the prion (PRNP) gene in sheep. The objective of the present research was to test for associations of PRNP haplotypes for codons 136, 154, and 171 with growth, carcass, and meat quality traits in an F2 Dorset x Romanov population (n = 415) segregating the 2 callipyge alleles. Haplotypes of the 3 PRNP codons were determined for each sheep, and breed of origin of each gamete was predicted by genotyping 6 microsatellite markers flanking the PRNP locus. Twenty-five growth, carcass, and meat quality traits were evaluated. Data were analyzed using a basic model consisting of fixed effects of year, sex, and callipyge genotype, the random effect of sire, and 7 covariates corresponding to the probability that a lamb inherited a specific PRNP haplotype of either Dorset or Romanov origin. A fixed effect of litter size was added to the model for growth traits. The model for carcass traits contained the linear and quadratic effects of chilled carcass weight and the interactions among callipyge genotype and linear and quadratic terms. For meat quality traits, the model contained chilled carcass weight as a covariate and the interaction between callipyge genotype and chilled carcass weight. A contrast between the resistant ARR haplotype and the average effect of other PRNP haplotypes was tested to investigate the effects of potential selection for ARR within each breed of origin (Dorset, ARR vs. ARQ, VRQ, and AHQ; Romanov, ARR vs. ARQ and VRQ). There was limited evidence that selecting for scrapie resistance would cause correlated responses due to linkage disequilibrium. Associations of only 3 traits with PRNP haplotypes were detected in either breed of origin. In Romanov, the ARR haplotype was associated with longer carcasses (P < 0.013), narrower rumps (P = 0.038), and less marbling (P = 0.022) than the average of ARQ and VRQ haplotypes. No significant contrasts were detected for Dorset. This study is the first to account for breed of origin while investigating haplotype associations in an F2 population. This study provided limited evidence of associations between PRNP haplotypes and growth, carcass, and meat quality traits.

Evaluation of the ovine callipyge locus: IV. Genotypic effects on reproductive traits1,2

A resource population of ewes derived from Dorset and Romanov grandparents was generated over 5 yr to provide genotypic and phenotypic data to estimate effects of each callipyge genotype on component traits of reproduction. Effects on ovulation rate were estimated from data recorded by examination of ovaries from serially slaughtered ewe lambs (n = 174) born in 1994 and 1995. Productivity and longevity through 5 yr of age were recorded on a total of 265 F2 ewes produced in 1996 through 1998. Number of lambs born, birth weights, and weaning weights of lambs were calculated for each ewe. Weaning weight was recorded for each lamb and adjusted for age to 56 and 32 d for dam- and nursery-reared lambs, respectively. Longevity was determined as a binary trait based on the presence or absence of the ewe in the breeding flock at 5 yr of age. Ewes generated 937 records for breeding weight and 925 records for conception rate, which was determined on ewes exposed and still present at the start of each lambing season. Seven hundred seventeen records were analyzed for traits based on the number of ewes lambing. Genotypes for the causative callipyge mutation were determined using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assay. Each ewe was classified into 1 of 4 genotypes; NMatNPat, NMatCPat, CMatNPat, or CMatCPat, where N represents wild type and C represents the mutant allele. The mean ovulation rate of the ewe lambs genotyped NMatNPat was greater (P < 0.02) than that exhibited by NMatCPat; however, the estimated difference of 0.25 ovum in the ewe lambs did not affect the number born. The live weight of NMatCPat ewes at breeding was 2.5 kg less than that of other genotypes (P < 0.01). The callipyge genotype class did not significantly affect conception rates, fecundity, maternal ability, or ewe longevity. Maintaining a ewe flock to produce homozygous mutant rams for use in terminal sire mating systems presents no unusual problems from a reproduction standpoint.

256 LINES OF PIGS SELECTED FOR COMPONENT TRAITS OF LITTER SIZE EXHIBIT DIFFERENTIAL GENE REGULATION AT THE ONSET OF EMBRYO (TROPHECTODERM) ELONGATION

Significant embryonic (<18%) loss occurs in the pig as the pre-implantation embryo undergoes a dramatic morphological change from ovoid (8-10 mm) at gestational Day 11 to a long, thin filament (<150 mm) by Day 12. Lines of pigs selected for increased uterine capacity have improved embryonic survival, whereas pigs selected for increased ovulation rate have decreased embryo survival. Alterations in the expression of genes that play key roles in embryo elongation and maternal recognition of pregnancy may reflect differences in embryo survival observed in these lines of pigs. The objective of the current study was to evaluate the expression level of transcripts involved in developmentally important processes, such as steroidogenesis, cellular differentiation, cell-cell interaction, and immune modulation, at the onset of porcine embryo elongation (gestational Day 11) in control animals and lines selected for increased ovulation rate or uterine capacity. Total RNA was isolated from Day 11 ovoid embryos, and gene expression was measured via real-time PCR. Data were analyzed for analysis of variance using GLM procedures. Expression of steroidogenic acute regulatory protein mRNA was decreased (P = 0.02) in embryos from the ovulation rate and uterine capacity lines compared with controls. Similarly, expression of cytochrome P450scc and aromatase mRNA were decreased (P < 0.003) in embryos from the ovulation rate and uterine capacity lines, compared with the control line. Interestingly, 17�-hydroxylase mRNA expression was decreased (P = 0.0004) only in embryos from the ovulation rate line compared with the control and uterine capacity lines. In contrast, expression of cytokeratin-8 and -18 mRNA were increased (P < 0.02) in embryos from the uterine capacity and ovulation rate lines, compared with controls. Expression of galectin 1 mRNA was increased (P = 0.02) in embryos from the uterine capacity line, compared with the ovulation rate line. Expression of interleukin-1 receptor type 1 mRNA was increased (P = 0.03) in embryos from the uterine capacity line, compared with both the control and the uterine capacity lines. Constitutive expression of 17�-hydroxysteroid dehydrogenase, stratifin, and interleukin-1� mRNA were observed in embryos from all lines. These results demonstrate altered gene expression in embryos from pigs selected for increased uterine capacity and ovulation rate compared with controls, and may contribute to differences observed in embryo survival between these lines of pigs.

Evaluation of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds of sheep: V. Reproduction of F1 ewes in spring mating seasons1,2

Objectives were to estimate effects of sire breed (Dorset, Finnsheep, Romanov, Texel, and Montadale), dam breed [Composite III (CIII) and northwestern whiteface (WF)], mating season (March and May), and their interactions on reproductive traits of mature F1 ewes in spring mating seasons. A total of 1,099 F1 ewes produced 1,754 litters of 2,995 lambs from exposures to Suffolk rams during March and May mating seasons in 1995 through 1999. Fertility rate and ewe longevity were measured. Number born and litter birth weight were recorded, and number and weight at weaning and 20 wk of age were analyzed separately for dam- and nursery-reared litter mates. Total productivity from 4 to 6 yr of age for each ewe entering the breeding flock was calculated as the sum of 20-wk weights for dam-reared lambs and separately for nursery-reared lambs. Interactions of sire breed x mating season, ewe age x mating season, and ewe age x dam breed were often significant. Interactive effects of sire breed and mating season on fertility rate (P < 0.001) were primarily due to differences in magnitude. Fertility rates of sire breeds for March and May matings, respectively, were 92 and 89% for Romanov, 91 and 72% for Finnsheep, 90 and 52% for Texel, 88 and 52% for Montadale, and 83 and 62% for Dorset. Sire breed x mating season also affected number born (P < 0.03); March and May values were 2.12 and 2.05 for Romanov, 2.00 and 1.94 for Finnsheep, 1.39 and 1.41 for Texel, 1.37 and 1.51 for Montadale, and 1.37 and 1.55 for Dorset, respectively. Interaction of sire breed x dam breed on fertility rate (P < 0.01) was due to change in rank as well as magnitude. Romanov- and Dorset-sired ewes out of CIII dams had greater fertility rates than Romanov- and Dorset-sired ewes out of WF dams. The opposite situation existed for ewes by Finnsheep, Texel, and Montadale sires. Differences between dam breeds (CIII and WF) in total productivity of dam-reared lambs were not detected, whereas ewes exposed in March (78 kg) were more productive (P < 0.01) than those exposed in May (68 kg). Means of sire breeds for total productivity of dam-reared lambs were 47, 65, 70, 70, and 111 kg for Texel, Montadale, Dorset, Finnsheep, and Romanov, respectively (P < 0.001). Superior reproduction of Romanov sired ewes was primarily due to greater fertility rate and prolificacy at each mating season and ewe age. Use of Romanov-crossbred ewes would increase fertility during spring mating, an important constraint of the sheep industry.

Allelic variation in the secreted folate binding protein gene is associated with uterine capacity in swine1

Previous comparisons between the cDNA and gene sequences for secreted folate binding protein (sFBP) indicated a 12-bp insertion/deletion (ins/del) polymorphism in exon 1 and a SNP that altered (Ser-Arg) the protein AA sequence. The effect of the Ser-Arg SNP on reproductive traits was examined in three groups of Meishan-White European breed crossbred gilts. The gilts for all three groups were unilaterally hysterectomized-ovariectomized (UHO) at 100 d of age. Group 1 gilts (n = 77) were mated at estrus, slaughtered at d 105 of pregnancy, and a blood sample was collected from each fetus to determine fetal hematocrit. The number of corpora lutea and fetuses and the fetal and placental weights were recorded. Group 2 gilts (n = 46) were mated, the remaining uterine horn was flushed with 20 mL of saline on d 11 of pregnancy, conceptuses were counted, and flushings were measured for total sFBP. Gilts were allowed an estrous cycle to recover, mated again at estrus, slaughtered at 105 d of gestation, and the data as described for Group 1 were collected. Groups 1 and 2 gilts were genotyped for the Ser-Arg SNP. In Group 3, gilts (n = 70) and boars (n = 30) were genotyped for the Ser-Arg SNP before mating, and like genotypes were mated. Gilts were then treated as described for Group 2. The effect of the 12-bp ins/del on reproductive traits was examined in 407 white crossbred UHO gilts from a randomly selected control line and from lines selected for ovulation rate (OR) and uterine capacity (UC). Gilts were mated and slaughtered at 105 d of age, and the numbers of corpora lutea and live fetuses, and fetal and placental weights and fetal hematocrits were recorded. The 12-bp ins/del also was evaluated in 131 intact gilts from the OR selected line. These gilts were mated at approximately 250 d of age and farrowed. The numbers of fully formed and live piglets were recorded. A significant effect (P < 0.05) of the Ser-Arg SNP was detected on the number of embryos present on d 11 of pregnancy and on UC. The sFBP 12-bp ins/del was associated with UC (P < 0.01) and the number of CL (P < 0.05) in UHO gilts, but not with litter size in intact gilts from the OR line. Results suggest that the 12-bp ins/del polymorphism could be exploited to increase litter size in swine, provided that the negative effect of the polymorphism on OR is overcome.

Allelic variation in the erythropoietin receptor gene is associated with uterine capacity and litter size in swine

A single nucleotide polymorphism (SNP; C vs. T) that creates an extra GATA-1 site (T allele) in intron 4 of the swine erythropoietin receptor (EPOR) gene was discovered and a genotyping assay for this SNP was developed. A total of 402 gilts from lines selected either at random (control), for ovulation rate (OR) or for uterine capacity (UC) for 11 generations were unilaterally hysterectomized-ovariectomized (UHO) at 160 days of age, mated at approximately 250 days of age and slaughtered at 105 days of pregnancy. Blood samples and spleens were collected from each foetus and the numbers of corpora lutea (CL) and live foetuses, the weights of each foetus and placenta, and each foetal haematocrit were recorded. In addition, intact gilts from the OR line or from a Yorkshire, Landrace, Duroc, crossbred line (BX) were mated and farrowed. At farrowing, the numbers of fully formed and live piglets were recorded for each litter. Genomic DNA was isolated for both the UHO and intact gilts, from foetuses from the UHO gilts that were heterozygous for the EPOR SNP, and from the boars from the BX line and were then used to determine EPOR SNP genotypes. Only CC and CT gilts were observed in the control, OR and UC selected lines. Presence of the EPOR T allele was associated (P < 0.05) with increased UC in these gilts. The number of heterozygous and homozygous foetuses did not differ within UHO litters, or did EPOR genotype influence foetal haematocrit. In intact gilts from the OR line, litter size was significantly associated (P < 0.05) with EPOR SNP genotype. Finally, results from intact gilts of the BX line, in which both the gilt and the boar genotypes were known, allowed an analysis to determine the effect of the gilt and/or the foetal genotype on litter size. This analysis indicated that the predicted foetal genotype (with gilt genotype as covariate) was associated with litter size (an increase of 2.6 +/- 1.0 piglets born alive predicted for homozygous T litters compared with homozygous C litters, P < 0.01) whereas the effect of the gilt genotype (adjusted for foetal genotype) on litter size was not significant. These results indicate that the EPOR SNP is associated with UC and litter size in two distinct populations and could be useful in increasing litter size in swine that are not limited in OR.

Evaluation of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds of sheep: II. Reproduction of F1 ewes in fall mating seasons

Objectives were to estimate effects of sire breed (Dorset, Finnsheep, Romanov, Texel, and Montadale), dam breed (Composite III and northwestern whiteface), mating season (August, October, and December), ewe age (1, 2, and 3 yr), and their interactions on reproductive traits of F1 ewes. A total of 1,799 F1 ewes produced 3,849 litters from 4,804 exposures to Suffolk rams during 35-d mating seasons over 3 yr. Ewes were weighed at breeding. Conception rate and ewe longevity (present or absent at 42 mo of age) were determined. Number born and litter birth weight were recorded, and number and weight at weaning and 20 wk of age were analyzed separately for dam- and nursery-reared litter mates. Total productivity through 3 yr of age for each ewe entering the breeding flock was calculated as the sum of 20-wk weights for dam- or nursery-reared lambs. Interactions of sire breed x mating season, sire breed x ewe age, and mating season x ewe age were generally significant, whereas interactions of sire breed, mating season, and ewe age x dam breed were seldom detected. Interactions of sire breed x mating season were often due to changes in rank as well as magnitude, indicating the importance of matching sire breed to a specific mating season. The number born to Dorset-, Texel-, and Montadale-sired ewes was not affected by dam breed; however, Finnsheep-sired ewes out of northwestern whiteface dams were more prolific than Finnsheep-sired ewes out of Composite III dams, and the opposite situation existed for Romanov-sired ewes. Least squares means of sire breeds (P < 0.001) for total productivity of dam-reared lambs were 98.5, 103.5, 106.9, 124.6, and 154.9 kg/ewe entering the breeding flock for Texel, Dorset, Montadale, Finnsheep, and Romanov, respectively. Superior reproduction of Romanov-sired ewes was due to greater conception rate and prolificacy for each mating season and ewe age, as well as greater ewe longevity. Total productivity of F1 ewes by Composite III dams (125.6 kg) was greater (P < 0.001) than for ewes born to northwestern whiteface dams (109.7 kg), and the effect of mating season increased (P < 0.001) from August to October to December. Litter weight at 20 wk of age of 2- and 3-yr-old ewes was similar but greater (P < 0.001) than for 1-yr-old ewes. Experimental results provide comprehensive information about the appropriate use of these breeds in crossbreeding systems to meet specific production-marketing objectives.

Evaluation of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds of sheep: IV. Survival, growth, and carcass traits of F1 lambs1,2

The objectives of this study were to estimate effects of sire breed (Dorset, Finnsheep, Romanov, Texel, and Montadale), and dam breed (Composite III and Northwestern whiteface) on survival, growth, carcass, and composition traits of F1 lambs. Effects of mating season (August, October, and December) were estimated for survival and growth traits. Data were collected on 4,320 F1 lambs sired by 102 purebred rams over 3 yr. Birth weight was recorded on all lambs, and subsequent BW were adjusted to 56 (weaning), 70, and 140 d of age (n = 3,713, 3,654, and 3,579 observations, respectively). Survival of dam-reared progeny (n = 4,065) to weaning was recorded. Each year, wethers from October matings were slaughtered in three groups at 25, 29, and 33 wk of age to obtain carcass data (n = 546). In addition to standard carcass traits, resistive impedance measurements were recorded on the warm carcass to predict lean mass. Dam breed (P = 0.37) did not influence lamb survival to weaning, but sire breed (P < 0.05) was important. Romanov-sired lambs excelled in survival rate to weaning (94.1%), followed by Finn-sheep (93.0%), Texel (90.7%), Dorset (90.0%), and Montadale (89.1%) sired progeny. Lower (P < 0.01) postweaning growth rate was observed for Texel (267 g/d) and Finnsheep (272 g/d) sired progeny than for Dorset (285 g/d), Montadale (282 g/d), and Romanov (278 g/d) sired progeny. Sire breed and dam breed were generally significant for most carcass traits. Breed differences in distribution of carcass fat and carcass shape were detected; however, carcass composition was similar for all sire breeds when compared at a constant carcass weight. When evaluated at a constant 12th-rib fat depth, carcasses of lambs from Finnsheep, Romanov, and Texel sires produced 1 to 1.5 kg less (P < 0.001) predicted lean mass per lamb than carcasses of lambs from Dorset and Montadale sires. These experimental results provide information about the direct breed effects for survival, growth, and carcass traits of these breeds and their potential use in crossbreeding systems.

Evaluation of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds of sheep: III. Wool characteristics of F1 ewes12

An experiment was designed to evaluate the effects of five sire breeds (Dorset, Finnsheep, Romanov, Texel, and Montadale), two dam breeds (Composite III [CIII] and northwestern whiteface [WF]), and three shearing seasons (December, February, and April, corresponding to August, October, and December breeding seasons) and their interactions on wool and other characteristics of F1 ewes. Fleeces were collected and characterized from six 2-yr-old F1 ewes representing each of the 90 sire breed x dam breed x shearing season x year (three) subclasses. Characteristics measured objectively were grease and clean fleece weights, clean yield, mean fiber diameter and SD, and mean staple length and SD. Visual assessments of fleece color were also made. Data collected on the F1 ewes were analyzed using a mixed model analysis of variance procedure. The model included fixed effects of year of birth, sire breed, dam breed, shearing season, six two-way interactions, and the three-way interaction of sire breed x dam breed x shearing season. The random effect of individual sire within year of birth x sire breed was also fitted. Texel- and Montadale-sired ewes produced more clean wool (P < 0.05) (approximately 0.24 kg) than Dorset-, Finnsheep-, and Romanov-sired ewes. Texel-sired ewes produced the coarsest wool (28.7 microm) (P < 0.05), whereas Romanov-sired ewes produced the finest (24.9 microm) and longest (9.12 cm) fleeces (P < 0.05). Ewes from WF dams produced more and finer wool (0.15 kg and 2.7 microm) than ewes from CIII dams (P < 0.001). Ewes shorn in December produced more, coarser, and longer wool (P < 0.05) than those shorn in February and April. This trend in wool production is opposite to that in conception rate (reported previously). Romanov-sired ewes produced the lowest percentage of white fleeces (62.6%), whereas Dorset-sired ewes produced the most (P < 0.001) white fleeces (96.3%). Estimates of heritability were calculated for grease and clean fleece weights (0.36), percentage of clean yield (0.31), average fiber diameter and SD (0.86 and 0.42, respectively), and average staple length and SD (0.49 and 0.00, respectively). Although necessary for a thorough evaluation of these 10 types of crossbred ewes, it is estimated that wool income would only constitute a small portion (1 to 5%) of overall income from sheep of this type.

An integrated comparative map of the porcine X chromosome

The objectives of this study were to assign both microsatellite and gene-based markers on porcine chromosome X to two radiation hybrid (RH) panels and to develop a more extensive integrated map of SSC-X. Thirty-five microsatellite and 20 gene-based markers were assigned to T43RH, and 16 previously unreported microsatellite and 15 gene-based markers were added to IMpRH map. Of these, 30 microsatellite and 12 gene-based markers were common to both RH maps. Twenty-two gene-based markers were submitted to BLASTN analysis for identification of orthologues of genes on HSA-X. Single nucleotide polymorphisms (SNPs) were detected for 12 gene-based markers, and nine of these were placed on the genetic map. A total of 92 known loci are present on at least one porcine chromosome X map. Thirty-seven loci are present on all three maps; 31 loci are found on only one map. Location of 33 gene-based markers on the comprehensive map translates into an integrated comparative map that supports conservation of gene order between SSC-X and HSA-X. This integrated map will be valuable for selection of candidate genes for porcine quantitative trait loci (QTLs) that map to SSC-X.

Single nucleotide polymorphism (SNP) discovery in porcine expressed genes

High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs.

Comparative mapping of BTA15 and HSA11 including a region containing a QTL for meat tenderness

The starting point of the present study was the reported identification of a chromosomal region on bovine Chromosome (Chr) 15 (BTA15) carrying loci affecting meat tenderness. A comparative linkage map of BTA15 and human Chr 11 (HSA11) was constructed to identify potential positional candidate genes and to provide a resource of genetic markers to support marker-assisted selection (MAS). Relative rearrangements between the bovine and human genomes for these chromosomes are the most complex observed in comparative mapping between the two species, with nine alternating blocks of conserved synteny between HSA11 and bovine Chrs 15 and 29. The results of this study were the addition of nine genes to the HSA11/BTA15 comparative linkage map, and development of five microsatellite markers within the quantitative trait locus (QTL) interval. One gene with known effects on muscle development (MYOD1) was mapped to the interval. A second gene (CALCA) involved in regulation of calcium levels, a key factor in postmortem tenderization, also mapped within the interval. Refinement of the comparative map and QTL position will reduce the interval on the human transcription map to be scanned in search of candidates, reducing the effort and resources required to identify the allelic variation responsible for the genetic effect.

Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle

An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this powerful approach in cattle research, four normalized cDNA libraries were produced and arrayed for high-throughput sequencing. The libraries were made with RNA pooled from multiple tissues to increase efficiency of normalization and maximize the number of independent genes for which sequence data were obtained. Target tissues included those with highest likelihood to have impact on production parameters of animal health, growth, reproductive efficiency, and carcass merit. Success of normalization and inter- and intralibrary redundancy were assessed by collecting 6000-23,000 sequences from each of the libraries (68,520 total sequences deposited in GenBank). Sequence comparison and assembly of these sequences was performed in combination with 56,500 other bovine EST sequences present in the GenBank dbEST database to construct a cattle Gene Index (available from The Institute for Genomic Research at http://www.tigr.org/tdb/tgi.shtml). The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the Web site. Analysis of individual library sequence data indicates that the pooled-tissue approach was highly effective in preparing libraries for efficient deep sequencing.

Comparative mapping of the ovine clpg locus

We used a comparative mapping approach to identify segments of conserved synteny between human Chromosome 14 (HSA14), bovine Chromosome 21 (BTA21), and the portion of ovine Chromosome 18 (OAR18) that contains the clpg locus. A bovine radiation hybrid map of the region was constructed with available Type II genetic markers and seven candidate genes to establish the comparative interval between BTA21 and HSA14. We developed polymorphic microsatellite and SNP markers associated with five candidate genes and placed them on the ovine and/or bovine genetic maps by multipoint linkage analysis. Three additional genes were mapped by virtue of their physical linkage to genetically mapped makers. Development of integrated linkage and physical maps facilitates the selection of positional candidate genes from the gene rich human map. The physically linked candidate genes PREF-1 and MEG3 map to the interval containing the clpg locus. Comparative biology suggests imprinting of MEG3 and/or the influences of PREF-1 on cellular differentiation, should be examined for their role in the parent-of-origin dependent influence of mutant clpg alleles on sheep muscle characteristics.

Evaluation of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds of sheep: I. Effects of ram breed on productivity of ewes of two crossbred populations

Effects of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds for performance as sires were estimated in the initial phase of a comprehensive evaluation of these breeds as contributors to sheep crossbreeding systems. Objectives were to evaluate the effects of ram breed, ewe breed, season of mating, and two-way interactions. Rams from the five breeds were single-sire-mated with ewes from two breed types to produce lambs over a 3-yr period. Ewes were assigned to one of three distinct 35-d mating seasons initiated each year in August, October, and December. A different sample of six rams per breed was used each year across all three seasons, and each ram was penned with ewes of both breeds. Traits evaluated and number of ewe records were conception rate and litter weaning weight per ewe exposed (n = 3,261) and number born, litter birth weight, average birth weight, number weaned, and litter weaning weight per ewe lambing (n = 2,751). Ram breed and ewe breed interacted (P < .01) for conception rate and litter weaning weight per ewe exposed, implicating mating preferences, particularly of Romanov rams. In mixed groups of ewes exposed to Romanov rams, conception rate was 12.7% lower and litter weight weaned was 8.4 kg lower in the ewe breed presumably less preferred for mating by the rams. On a per ewe exposed basis, Romanov-sired litters produced either the largest or the smallest values for litter weaning weight, depending on the breed of ewe. Effects of ram breed on number born and litter birth weight interacted (P < .05) with season of mating. The largest litters within each ram breed were associated with the October mating season. Montadale and Romanov rams sired larger and heavier litters from August matings than from December matings, whereas the opposite was true for Dorset-sired litters. Texel- and Finnsheep-sired litters were similar in size and weight from August and December matings. Breed of ram differences affected per ewe lambing productivity measurements (P < .01). Differences between ram breeds for ewe productivity were noted, with increased number born and improved survival of crossbred progeny to weaning for Romanov-sired litters. These results may have implications for using these ram breeds as sires in different crossbreeding systems. Structured mating systems or the creation of new composite populations involving these breeds could be used to match the resources, environment, and market of specific production situations.

Genomic organization and genetic mapping of the bovine PREF-1 gene

As a potential regulator of nutrient partitioning in beef cattle, we have cloned and genetically mapped the bovine PREF-1 gene. A full-length PREF-1 cDNA was isolated by iterative purification from a mixed-tissue cDNA library to which adipose contributed mRNA. Analysis of partial cDNAs from this library revealed that the 3'-terminal exon of the bovine PREF-1 mRNA is spliced in a manner analogous to its murine ortholog. However, we have also detected a PREF-1 splice form apparently unique to cattle. Aside from this alternative selection of a splice donor in the bovine fifth exon, the exon/intron junctions of the bovine PREF-1 gene recapitulate those observed for mice. The sequences proximal to the bovine PREF-1 transcription start site are homologous to the mouse PREF-1 promoter. Importantly, the sequence experimentally identified as critical to PREF-1 "suppression in adipocyte differentiation" is conserved in the bovine gene. The bovine PREF-1 gene was mapped to the telomeric end of BTA 21 by virtue of a physically linked microsatellite with seven alleles and 285 informative meiosis.

Evaluation of the ovine callipyge locus: III. genotypic effects on meat quality traits

A resource flock of 362 F2 lambs provided phenotypic and genotypic data to estimate effects of callipyge (CLPG) genotypes (NN, NC, CN, and CC) on meat quality traits. The mutant allele is represented as C, the normal allele(s) as N, and the paternal allele of a genotype is given first. Lambs of each genotype born in 1994 and 1995 were serially slaughtered in six groups at 3-wk intervals starting at 23 wk of age. Warner-Bratzler shear force and subjective evaluation of marbling were collected during both years from longissimus. Calpastatin activity was measured on longissimus from the 1994 group, and ELISA quantification of calpastatin protein was obtained from the 1995 group. Significant additive and paternal polar overdominance effects on meat quality traits were detected. This is in contrast to previous research that detected only polar overdominance effects on slaughter and carcass traits in this population. The magnitude of genotypic effects on shear force differed significantly between years; however, additive (P < .01), paternal polar overdominance (P < .001), and maternal dominance (P < .01) effects adjusted for variation in carcass weight were detected within each year. Shear force data adjusted to the mean slaughter age or carcass weight indicated that the means and variances of CN and CC genotypes were greater than values of NC and NN. Shear force values were greatest for CN and were intermediate for CC. The difference in shear force (adjusted for variation in slaughter age) between homozygous genotypes (additive effect) was supported by calpastatin activity data with 2-df F-tests of 3.66 (P < .05) and 11.84 (P < .001) at d 0 and 7 postmortem, respectively. Corresponding values for the paternal polar overdominance effects on calpastatin activity were 53.80 (P < .001) and 87.43 (P < .001). Calpastatin ELISA data (d 0, adjusted for slaughter age) exhibited a paternal polar overdominance effect exclusively with a 2-df F-test of 57.63 (P < .001). Additive and paternal polar overdominance effects on marbling adjusted for slaughter age had F-tests of 6.41 (P < .01) and 93.29 (P < .001), respectively. Consequences of increased longissimus shear force must be addressed if the advantages of CN lambs for dressing percentage and carcass composition are to be realized. Further research is needed to establish whether selection targeted at changing the background genome can mitigate the negative effects of the C allele on meat tenderness.

Evaluation of the ovine callipyge locus: II. Genotypic effects on growth, slaughter, and carcass traits

A resource flock of 362 F2 lambs provided phenotypic and genotypic data to estimate effects of callipyge (CLPG) genotypes on growth, slaughter, and carcass traits. Lambs were serially slaughtered in six groups at 3-wk intervals starting at 23 wk of age to allow comparisons at different end points. Probabilities of CLPG genotypes were calculated at a position 86 cM from the most centromeric marker of chromosome 18. A contrast of CLPG genotypic effects, based on the paternal polar overdominance model, was used to evaluate callipyge and normal phenotypes. Relationships of traits with slaughter age, carcass weight, or 12th-rib fat depth for callipyge and normal phenotypic groups were estimated by regression. Callipyge and normal lambs did not differ for growth traits measured from birth to slaughter. Callipyge lambs produced 55.9% of live weight as chilled carcass weight compared with 51.7% for normal lambs at the same mean live weight of 48.32 kg. Lighter pelt, kidney-pelvic fat, and liver weights contributed to this advantage of callipyge lambs for dressing percentage (P < .001). Estimated accretion rates of carcass protein at the mean slaughter age were 12.5 and 10.2 g/d for callipyge and normal carcasses, respectively. Corresponding values for carcass fat were 35.2 and 42.1 g/d. Compositional differences in favor of callipyge carcasses were detected at constant values of slaughter age, carcass weight, and 12th-rib fat depth. Callipyge carcasses had 2.56 kg greater fat-free lean and 1.39 kg less fat than normal carcasses at the same mean age of 214.9 d (P < .001). The majority of these differences were established before the initial group was slaughtered and were maintained as age increased. Callipyge carcasses consisted of 24.3% fat and 71.3% fat-free lean, compared with 31.5 and 64.0% for normal carcasses at 25.6 kg of carcass weight. When evaluated at .49 cm of 12th-rib fat depth, callipyge lambs were 15.4 d older and produced 4.1 kg heavier carcasses with 4.3% less fat (P < .001). Effects of CLPG genotypic groups on carcass composition were greater than virtually all reported breed substitution effects. Use of the CLPG mutant allele in structured mating systems can dramatically increase production of lean lamb.

Evaluation of the ovine callipyge locus: I. Relative chromosomal position and gene action

Genotypic and phenotypic data were collected to estimate chromosomal position of the callipyge (CLPG) gene and to test gene action. Nine Dorset rams of extreme muscling phenotype and 114 Romanov ewes composed the grandparent generation of a resource flock of 362 F2 lambs segregating at the CLPG locus. The parent generation consisted of eight F1 sires and 138 F1 dams. The F2 lambs were serially slaughtered in six groups at 3-wk intervals starting at 23 wk of age to allow comparisons at different end points. A linkage group of 25 marker loci (mean of 708 informative meioses per marker) spanning 87.2 cM was developed and improved the previous known coverage and precision of marker order and interval distance from available maps of ovine chromosome 18. Probabilities of each CLPG genotype were calculated at 1-cM intervals (0 to 107 cM). Statistical models included effects of year, sex, sire, regressions on genotypic probabilities, and genotype-specific linear and quadratic regressions on appropriate covariates. Orthogonal contrasts of CLPG genotypic effects evaluated additive, maternal dominance, and paternally derived polar overdominance models of gene action. The most parsimonious model did not include the additive and maternal dominance genetic contrasts. From analyses of four key traits, a consensus for position of CLPG was obtained at 86 cM relative to the most centromeric marker. An F-test with 3 df representing polar overdominance was maximum at position 86 cM (F = 407.4; P < .00001) with leg score as the dependent variable. These results are consistent with assignment of the CLPG locus to the telomeric region of chromosome 18 and support the polar overdominance model of gene action proposed by Cockett et al. (1996). Furthermore, recombinant individuals with definitive phenotypes confined the position of CLPG to a 3.9-cM interval, facilitating positional cloning experiments.

A second-generation linkage map of the sheep genome

A genetic map of Ovis aries (haploid n = 27) was developed with 519 markers (504 microsatellites) spanning approximately 3063 cM in 26 autosomal linkage groups and 127 cM (female specific) of the X Chromosome (Chr). Genotypic data were merged from the IMF flock (Crawford et al., Genetics 140, 703, 1995) and the USDA mapping flock. Seventy-three percent (370/504) of the microsatellite markers on the map are common to the USDA-ARS MARC cattle linkage map, with 27 of the common markers derived from sheep. The number of common markers per homologous linkage group ranges from 5 to 22 and spans a total of 2866 cM (sex average) in sheep and 2817 cM in cattle. Marker order within a linkage group was consistent between the two species with limited exceptions. The reported translocation between the telomeric end of bovine Chr 9 (BTA 9) and BTA 14 to form ovine Chr 9 is represented by a 15-cM region containing 5 common markers. The significant genomic conservation of marker order will allow use of linkage maps in both species to facilitate the search for quantitative trait loci (QTLs) in cattle and sheep.

Microsatellite evolution: testing the ascertainment bias hypothesis

Previous studies suggest the median allele length of microsatellites is longest in the species from which the markers were derived, suggesting that an ascertainment bias was operating. We have examined whether the size distribution of microsatellite alleles between sheep and cattle is source dependent using a set of 472 microsatellites that can be amplified in both species. For those markers that were polymorphic in both species we report a significantly greater number of markers (P < 0.001) with longer median allele sizes in sheep, regardless of microsatellite origin. This finding suggests that any ascertainment bias operating during microsatellite selection is only a minor contributor to the variation observed.

Extensive genomic conservation of cattle microsatellite heterozygosity in sheep

We report the evaluation of 1036 bovine microsatellite primer pairs for their suitability as linkage markers in sheep. Approximately 58% (605/1036) of bovine primer pairs amplified a locus in sheep. Sixty-seven per cent (409/605) of amplified loci were detected as polymorphic. Marker heterozygosity, allele number and range of allele sizes were significantly lower in sheep than cattle sampled in this study. However, median fragment size was similar. These data suggest that high-resolution comparative linkage maps between closely related species can be constructed relatively efficiently.

Divergent selection for heat loss in mice: II. Correlated responses in feed intake, body mass, body composition, and number born through fifteen generations

Divergent selection for heat loss (kcal.kg-.75.d-1), measured in 9- to 11-wk-old male mice, was conducted for 15 generations. Selection for high (MH) and low (ML) heat loss and unselected control (MC) occurred in each of three replicates for a total of nine unique lines. Feed intake in males was measured during Generations 9 through 15. Body mass at commencement of mating in females and at time of measurement of heat loss in males was recorded. Body fat percentage at 12 wk for animals of Generations 6, 10, and 14 was predicted as a function of electrical conductivity and body mass. Litter size was recorded for all generations, and components of litter size were evaluated at Generation 11 in one replicate and Generation 12 in the other two replicates. Feed intake changed in the same direction as heat loss for the MH and ML selections; at Generation 15, the difference between MH and ML (P < .002) was 20.6% of the MC mean. Body mass did not change with selection for heat loss. Differences in body fat percentage were not significant in earlier generations, but at Generation 14, MH and ML were significantly (P < .01) different with MH mice having the lowest fat percentage; MC was intermediate. Selection had a significant (MH vs ML; P < .01) effect on litter size, causing an increase in MH and a decrease in ML. This difference was explained by a difference (P < .01) in ovulation rate. There was no asymmetry of response in feed intake, fatness, litter size, or number of ovulations.