标记辅助导入中不同背景选择方法的比较

模拟比较了随机选择、标记值选择及BLUP选择3种背景选择方法在标记辅助导入(利用标记辅助将供体群中的一个有利QTL等位基因导入到受体群中)的选择效果。前景选择是借助与目标基因连锁的两侧标记对目标基因进行间接选择。研究结果表明,在背景选择中,利用标记值选择能使受体基因组很快得到恢复,2个世代的回交就能恢复90%以上,4个世代的回交就能完全恢复。利用BLUP选择虽然不能使受体基因组迅速全部恢复,但能使特定的背景性状得到最大的遗传进展。     

The influence of selection and epistasis on inbreeding depression estimates

Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coefficients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coefficients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coefficient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was difficult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.     

Energy expenditure for chewing in sheep fed timothy or sudangrass hay at the same intake level

In order to investigate the energy expended in chewing during eating and rumination in sheep fed timothy or sudangrass hay at the same intake level, the energy expenditure of the head was measured using the arterial-venous difference technique and that of the whole body was measured using an open-circuit, indirect respiration calorimeter. There was no difference in the per-chew energy expenditure between timothy hay and sudangrass hay during eating and rumination, but for both types of hay there was a difference in energy expenditure between eating (0.25 J per chew per kilogram body weight) and rumination (0.18 J per chew per kilogram body weight). There was no effect of time period after feeding on the energy expended in one chew during eating and rumination. On average, for a given type of hay, the energy expended in chewing during eating + rumination accounted for 4.9% of the daily energy expenditure of the whole body.     

The joint regulation of genetic gain and inbreeding under mate selection

SUMMARY: Stochastic simulation was used to evaluate a range of selection strategies with respect to both additive genetic response and inbreeding. Strategies involving selection on BLUP ebvs or individual phenotype, followed by random mating, were compared with mate selection strategies which used portfolio analysis to give joint consideration to genetic merit and inbreeding. An adapted Mean Of Total Absolute Deviations (MOTAD) method was used in a mate selection model to define optimal matings with regard to aggregate genetic merit and inbreeding for a base population h(2) of 0.2. Compared with random mating following selection on BLUP ebvs, inbreeding levels after 10 years of selection were able to be reduced under BLUP plus mate selection from ～.23 to as little as .11. Additive genetic gain was either little compromised or increased. The results suggest that information linking expected levels of genetic merit and inbreeding can be used to find the preferred selection strategy. ZUSAMMENFASSUNG: Gemeinsame Kontrolle von Zuchtfortschritt und Inzucht bei Partnerselektion Es wurde stochastische Simulation zur Auswertung einer Reihe von Selektionsstrategien hinsichtlich Zuchtwertzuwachs und Inzucht verwendet. Strategien mit Selektion auf der Basis von BLUP ebvs oder individuellem Ph?notyp mit nachfolgender Zufallspaarung wurden mit Partnerselektionsstrategien verglichen, die Portfolioanalyse zur gemeinsamen Beachtung von Zuchtwert und Inzucht verwendeten. Eine Methode adaptierter MITTELWERTE TOTALER ABSOLUTER ABWEICHUNGEN (MOTAD) Methode wurde beim Partnerselektionsmodell zur Definition optimaler Paarungen in Hinblick auf Gesamtzuchtwert und Inzucht bei einer Populationsheritabilit?t von 0,2 verwendet. Verglichen mit Zufallspaarung nach Selektion auf BLUP ebvs waren die Inzuchtgrade nach 10 Selektionsjahren von 0,23 auf 0,11 reduziert und additiver Zuchtfortschritt war dabei wenig beeintr?chtigt oder nahm sogar zu. Die Ergebnisse weisen darauf hin, da? Information, die Zuchtwert und Inzucht verbindet, zur Identifikation erwünschter Selektionsstrategien führen kann.     

The use of mathematical programming to control inbreeding in selection schemes

Selection on the best estimate of the breeding value of individuals should, in large populations, provide the maximal response in breeding value. However, many breeders deal with the selection of small numbers of animals from relatively small populations and therefore there is a trend for inbreeding to rise because of genetic drift. Moreover, as the evaluation of candidates is traditionally based on methodologies including information from relatives [selection indices, best linear unbiased predictor (BLUP)] more individuals are selected from the best families and so closely related individuals will generate most of the offspring. This effect is more important for traits with low heritability as phenotype gives little information on the breeding value of the individuals and more weight is given to relatives’ data. The need for controlling inbreeding refers not only to a better use of the genetic variability available and to a reduced inbreeding depression in the selected trait, but also to a reduced depression of fitness-related traits, which may be the most serious drawback at present due to the increase in inbreeding in domestic populations (M euwissen and W oolliams 1994). In recent years considerable work has been carried out on the design of strategies to maintain genetic diversity in selection programmes. These strategies are aimed at simultaneously optimizing genetic gain and inbreeding, either by reducing the rate of inbreeding (or variance of response) while keeping genetic gains at a predetermined level, or by increasing selection response under a restriction on inbreeding (or on variance of response). Following T oro and P& eacute ; rez -E nciso (1990) the different strategies can be classified according to the factor on which they act: (i) the selection criterion used; (ii) the mating system imposed; (iii) the number of selected individuals and their contribution to the next generation. The first group of strategies proposes the use of a suboptimal selection criterion that reduces the weight given to family information or the use of an upward-biased heritability in BLUP evaluation (T oro and P& eacute ; rez -E nciso 1990; see G rundy et al. 1998a for the latest development of this idea). The second group of strategies proposes action on the mating system including factorial mating designs, minimum co-ancestry mating (using linear programming) or compensatory mating (see review by C aballero et al. 1996). The third group of strategies includes the ones considered in the present work. The first possibility is to modify the contribution of the selected individuals of generation t to the selected individuals of generation t + 1, by practising some form of within-family selection with respect to BLUP values. Two strategies of this type were considered: modified within-family selection (MWFS) and restricted co-ancestry selection (RCS). The second possibility is to modify the contribution of the selected individuals of generation t to the evaluated individuals of generation t + 1 (instead of to the selected individuals) by a strategy called weighted selection (T oro and N ieto 1984). Three strategies were considered in this case: weighted selection (WS), restricted co-ancestry weighted selection (RCWS) and pair weighted selection (PWS). More specifically, the aim of the present paper is to show how these five strategies can be implemented using mathematical programming techniques. A small example comparing all of these strategies with standard truncation selection (TS) is also given for illustration.     

Comparison of four direct algorithms for computing inbreeding coefficients

One widely used measure in genetic analyses of livestock species is the inbreeding coefficient. Computation costs of inbreeding coefficients are of importance for large populations. Very recently, a ‘direct’ method for computing inbreeding coefficients was modified using a relatively efficient method to construct lists of ancestors in which the integrity of chronological order within each ancestral path is kept. Using simulated data, the computational efficiency of the recently modified algorithm was investigated by comparing it with three other algorithms – the original direct algorithm, its previously modified algorithm and another direct algorithm. The recently modified algorithm became considerably faster than the original algorithm and its previous modification when the number of generations increased, and it was fast relative to the other direct algorithm when the average number of generations and family size were not large. When only animals born in the most recent year were evaluated with the knowledge of inbreeding coefficients for their ancestors, the recently modified algorithm outperformed the other algorithms, indicating its possible advantage in updating situations.     

Role of selection and inbreeding on the incidence of cutaneous malignant melanoma in Sinclair swine

Summary This paper reports the quantitative analysis of the historical database of a herd of Sinclair swine affected by cutaneous malignant melanoma. The herd was under partial and non-systematic selection for melanoma susceptibility (animals having at least one tumour during the first 6 weeks of life). Weighted selection differentials for the number of tumours at birth and the number of tumours at 6 weeks were generally positive and between −0.43 and 4.76 tumours for the number of tumours at 6 weeks. Estimates of the heritability for number of tumours at birth and at 6 weeks using 1934 animals were 0.27 (±0.03) and 0.25 (±0.03), respectively. The estimate of the genetic correlation between these two traits was 0.95 (±0.03). Genetic trends were positive for the number of tumours at birth and at 6 weeks. In spite of positive selection differentials and a moderate heritability, there was a negative phenotypic trend in the number of tumours. Natural selection might be acting in a direction opposite to artificial selection in the Sinclair herd. The slopes of the regression of the number of tumours at birth, at 6 weeks, and melanoma susceptibility on individual inbreeding coefficients were non-significant, indicating no evidence of dominance. The number of live-born pigs was lower in litters from parents susceptible to the disease (p < 0.01).     

Comparison of in vitro development of embryos collected from the same gilts at first and third estrus

In vitro development of embryos collected from the same gilts mated at first and third estrus was compared. Embryos from one to eight cells were collected from gilts 36 to 48 h after detection of estrus. Embryos were cultured for 8 d in Whitten's medium in a humidified atmosphere of 5% CO2 in air at 37 degrees C and were observed daily. No differences were detected among percentages of one- to eight-cell embryos developing into morulae from gilts in first or third estrus (P greater than .05). Similar percentages of one- to two-cell embryos from gilts mated at first and third estrus developed into blastocysts (45.8 and 55.2%, respectively), expanded blastocysts (10.4 and 24.1%, respectively) and hatching blastocysts (4.2 and 3.4%, respectively; P greater than .05). Fewer three- to eight-cell embryos from gilts in first estrus than from gilts in third estrus developed into blastocysts (63.4 and 91.1%) and expanded blastocysts (14.6 and 55.6%; P less than .01). Similar percentages of embryos with abnormal morphology were observed among morulae developing from one- to eight-cell embryos collected from gilts mated at first and third estrus (14.9 and 9.9%, respectively; P greater than .05). In contrast, more morphologically abnormal embryos were observed among blastocysts developing from gilts mated at first estrus than at third estrus (31.2% and 14.0%, respectively; P less than .05). The results suggest that the reduced in vitro development of embryos collected from gilts mated at first estrus may be due to an aberration in blastocoel formation and expansion.     

闭锁群体BLUP选择下遗传方差和近交系数的变化

采用计算机随机模拟方法模拟了在一个闭锁群体内连续对单个性状进行 1 5个世代选择的情况。选择过程中世代不重叠 ,每个世代的种畜根据动物模型最佳线性无偏预测 (BLUP)法估计的育种值进行选留 ,并在此基础上系统地比较了不同群体规模、公母比例和性状遗传力对群体遗传方差和近交系数变化的影响。结果表明 ,扩大育种群规模、增加公畜比例以及对低遗传力性状进行选择时 ,群体遗传方差降低的速度和近交系数上升的速度会更慢 ,在长期选择时可望获得更大的持续进展和适宜的近交增量     

Comparison of three methods of differentiating bovine mycoplasma.

Growth inhibition (GI) by specific antisera, direct fluorescent antibody technique (FAT), and fatty-acid profile analysis by gas-liquid chromatography (GLC) were compared as methods for identifying 13 strains of bovine mycoplasma. By the FAT, there were 8 bilateral and 13 unilateral cross reactions. In the GI study, there were 4 bilateral and 7 unilateral cross reactions. In both FAT and GI studies, there were fluorescence and inhibition, respectively, with 13 homologous antisera. Analysis by GLC revealed the 13 mycoplasmas could be placed into 4 distinct chromatographic groupings. The GLC profiles of 2 organisms were sufficiently unique that they could be used for specific identification.     

Growth patterns of Angus, Hereford and shorthorn cattle. I. Comparison of inbred and noninbred lines, changes in patterns over time and effects of level of inbreeding and reproductive performance

Mature weight (A) and rate of maturing (K) were estimated for 283 Angus, 140 Hereford and 280 Shorthorn cows utilizing the asymptotic regression equation Yt=A(1-Be-Kt). The Yt was weight of the individual at age t; and B was an estimate related to early life weight changes and provided for a Y-intercept (A-B). Each breed consisted of four inbred and two noninbred lines. Regression of estimated growth curve parameters on levels of inbreeding of the individuals and of their dams and effects of early reproductive performance (EREPRO) were studied as sources of variation in addition to line differences and trends in line values over years. Considered jointly with inbreeding of the dam and with EREPRO, inbreeding of the individual was negatively related (P less than .01) to estimates of A in the three breeds and unrelated (P greater than .10) to estimates of K. Each 1% increase in inbreeding of the individual was associated with about 2 kg decrease in estimated mature weight. An increase in inbreeding of the dam of an individual was negatively related to estimates of K in Angus (P less than .01) and Shorthorns (P less than .05). Inbreeding of dams was positively related to estimates of A in the three breeds, but only in Shorthorns could the relationship be declared significant. Estimates of A were about 46 kg heavier and estimates of K about .010 less for each year an individual failed to produce a calf during her first three opportunities. In general, A values declined in all three breeds during the study. Significant changes were observed in all Hereford analyses and after inbreeding was included in the Angus analysis, while inclusion of inbreeding in the Shorthorn analysis caused the change to become unimportant. The K values increased in all three breeds during the study; however, the change could be declared significant only in Herefords.     

Comparison of four methods of calf confinement. I. Physiology

Holstein bull calves were blocked by birth order and randomly assigned to one of three treatments in trial I: stall (N = 7), pen (N = 7) and hutch (N = 7), and to one of four treatments in trial II: stall (N = 6), pen (N = 5), hutch (N = 6) and yard (N = 8). Stalls were elevated, .56 X 1.2 m, with wooden slatted floors. Stalled calves were tethered from the front with a collar and .5-m chain. Pens were elevated, 1.2 X 1.5 m, with wooden slatted floors and were located in the same open-front building as the stalls. Hutches were 1.2 X 1.2 X 2.4 m long and open on one end. Hutch calves were restrained with a dog collar and 2.4-m chain. Yard calves were housed as a group in a 3.6 X 7.9 m, outdoor enclosure, of which one-half was a covered, three-sided structure. Calves were placed on treatment between 12 to 24 h of age, bottle-fed 1.9 liters colostrum twice daily for 2 d and then bucket-fed 1.9 liters milk replacer twice daily, with continuous access to hay and grain. Jugular blood samples taken at 6 wk were analyzed for blood cell counts, blood chemistry profile (13 items), triiodothyronine (T3), thyroxine (T4), basal cortisol and adrenal response (cortisol) to exogenous adrenocorticotrophic hormone (ACTH). Average daily gain from 0 to 42 d was highly variable and was not significantly different for different treatments.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparison of four methods of calf confinement. II. Behavior

Holstein bull calves (N = 46) were blocked by birth order and randomly assigned to be individually reared in stalls, pens or hutches (trials I and II) or as a group in a 3.6 X 7.9 m yard (trial II only). Treatments differed by the degree of restraint and social isolation imposed, with stalls the most restrictive and yard the least. Stalls and pens had wooden slatted floors; hutches and yard were on ground. Calves were placed on treatment within 24 h of birth and remained on treatment 6.5 wk. Total time standing or lying per 24 h in situ at 5 wk was not affected by treatment (P greater than .05), but hutch calves changed position between standing and lying more often than others (P less than .05), in order to remain in sun or shade. At 6.5 wk, calves (N = 24) in trial II were individually open-field tested for 20 min in the presence of alien calves. Stall and pen calves performed more actions utilized in locomotion and defense and engaged in more social behavior than hutch or yard calves (P less than .05). Only stall and pen calves stumbled and fell, but observations were insufficient to allow statistical analysis of these incidents. Treatment effects were found with respect to vocalizations: stall and pen calves emitted more "baaocks," while yard calves emitted more "moos." Results of this study and of a companion physiological study of the calves suggest that the intensification of drives induced by chronic suppression of their release may be accompanied by physiological responses associated with chronic stress.     

Maximizing genetic gain over multiple generations with quantitative trait locus selection and control of inbreeding

Stochastic computer simulation was used to investigate the potential extra genetic gains obtained from gene-assisted selection (GAS) by combining 1) optimization of genetic contributions for maximizing gain, while restricting the rate of inbreeding with 2) optimization of the relative emphasis given to the QTL over generations. The genetic model assumed implied a mixed inheritance model in which a single quantitative trait locus (i.e., QTL) is segregating together with polygenes. When compared with standard GAS (i.e., fixed contributions and equal emphasis on the QTL and polygenic EBV), combined optimization of contributions of selection candidates and weights on the QTL across generations allowed substantial increases in gain at a fixed rate of inbreeding and avoided the conflict between short- and long-term responses in GAS schemes. Most of the increase of gain was produced by optimization of selection candidates' contributions. Optimization of the relative emphasis given to the QTL over generations had, however, a greater effect on avoiding the long-term loss usually observed in GAS schemes. Optimized contribution schemes led to lower gametic phase disequilibrium between the QTL and polygenes and to higher selection intensities both on the QTL and polygenes than with standard truncation selection with fixed contributions of selection candidates.     

Effects of data structure and selection on estimated inbreeding depression in experimental Tribolium castaneum lines

SUMMARY: Inbreeding depression was estimated for four experimental Tribolium castaneum lines. Each line, containing approximately 7000 animals, was selected for 16 generations either randomly (control), on pupae weight (PWT), on family size (FST) or on an index containing both PWT and FST. The inbreeding trend was 0.9, 0.5, 0.5 and 0.4 % inbreeding per generation in PWT-selected, FST-selected, index-selected, and control line, respectively. The model used to estimate the inbreeding depression included a linear regression on individual inbreeding coefficients, and random additive genetic effects. Using all the performance and pedigree data, estimated inbreeding depressions in the control line were -0.13 (SE = 0.16; #) and -8.50 (SE = 2.66; μg) per 1 % inbreeding for FST and PWT, respectively. Using only performance data of the latest generation in the control line, the estimated inbreeding depressions changed considerably: -0.17 (SE = 0.82) and -37.4 (SE= 11.9) for FST and PWT, respectively. Estimated inbreeding depression for FST in the FST-selected line was - 0.40 (SE = 0.31). Inbreeding depression for PWT in the PWT-selected line was 21.6 (SE = 25.8). This study indicates that estimating inbreeding depression might best be based on the performance data of animals with an equal and sufficiently-large number of ancestral generations known. ZUSAMMENFASSUNG: Wirkung von Datenstruktur und Selektion auf gesch?tzte Inzuchtdepression in experimentellen Triboleum castaneum Linien Jede der vier experimentellen Linien, aus je etwa 7000 Individuen, wurde durch 16 Generationen selektiert, zuf?llig die Kontrolle, auf Puppengewicht (PWT), Familiengr??e (FST), oder auf einen beide Merkmale kombinierenden Index. Inzucntzuw?chse in diesen vier Linien waren 0.4, 0.9, 0.5 und 0.5% je Generation. Das Modell zur Sch?tzung der Inzuchtdepression beinhaltete eine lineare Regression auf individuelle Inzuchtkoeffizienten und zuf?llige additive-genetische Wirkungen. Aus allen Daten, Leistung und Pedigree, ergaben sich -0.13 (SE = 0.16; #) und - 8.5 (SE = 2.66; mg) je 1% Inzucht für FST und PWT, Daten der letzten Generation ergaben deutlich andere Werte: -0.17 (SE = 0.82) und -37.4 (SE = 11.9) für FST und PWT. Inzuchtdepressionen für FST bzw. PWT in den jeweils hierfür selektierten Linien waren -0.40 (SE = 0.31) und 21.6 (SE = 25.8). Es wird gefolgert, da? Sch?tzungen auf Leistungen von hinreichend gro?er Zahl von Vorfahrengenerationen beruhen sollten.     

Alternative methods of selection for litter size in mice: II. Response to thirteen generations of selection

Selection was conducted on an index of components of litter size (I = 1.21 x ovulation rate + 9.05 x ova success; ovulation rate measured by number of corpora lutea and ova success measured as number of pups born + number of corpora lutea), on uterine capacity (measured as number of pups born to unilaterally ovariectomized dams) and on litter size concurrent with an unselected control for 13 generations. Selection criteria (IX = index, UT = uterine capacity, LS = litter size and LC = control) were applied in each of three replicates. In an evaluation after five generations, IX and LS each exceeded LC by about .5 pups, with no response in UT. After 13 generations, mean ovulation rate, ova success and litter size (measured as number of fetuses at 17 d gestation in intact females) were, for IX, 14.25, .84, 11.95; for LS, 14.15, .82, 11.64; for UT, 12.61, .86, 10.77; and for LC, 12.27, .82, 9.98. The regression of number born (litter size in IX, LS and LC; uterine capacity with only a functional left uterine horn in UT) on cumulative selection differential across 13 generations was .12 +/- .01, .09 +/- .02 and .08 +/- .02 for IX, LS and UT, respectively. The regression of breeding value for litter size on each selection criterion, estimated as response in the generation-13 evaluation divided by cumulative selection differential, was .11 +/- .02, .08 +/- .01 and .05 +/- .03 for IX, LS and UT, respectively. Regression of response in number born on generation number was .17 +/- .01, .15 +/- .04 and .10 +/- .02 for IX, LS and UT, respectively. Selection in IX was promising relative to LS, and selection in UT changed number born.