Quantitative trait loci for litter size and prenatal loss in a White Duroc × Chinese Erhualian resource population

To detect quantitative trait loci (QTL) for litter size related traits, the total number of born piglets (TNB), the number of born alive piglets (NBA), the number of stillborn piglets (NSB) and the number of mummies (NM) at the first parity were recorded in 299 F₂ sows in a White Duroc × Chinese Erhualian intercross resource population. A whole genome scan was performed with 183 microsatellites distributed across 19 porcine chromosomes in the resource population, and the QTL analysis was performed with a least-squares method. A 5% genome-wide significant QTL was detected at 88 cM on pig chromosome (SSC) 15 for NBA, which also showed suggestive effect on TNB. In addition, four suggestive QTL were detected on SSC 6, 7, 8 and 15 for TNB, NBA or NSB. Two of the five QTL detected showed accordance with previous reports. No QTL was found for NM.     

Identification and reciprocal introgression of a QTL affecting body mass in mice

The aim of this study was to examine the effects of a QTL in different genetic backgrounds. A QTL affecting body mass on chromosome 6 was identified in an F₂ cross between two lines of mice that have been divergently selected for this trait. The effect of the QTL on mass increased between 6 and 10 weeks of age and was not sex-specific. Body composition analysis showed effects on fat-free dry body mass and fat mass. To examine the effect of this QTL in different genetic backgrounds, the high body mass sixth chromosome was introgressed into the low body mass genetic background and vice versa by repeated marker-assisted backcrossing. After three generations of backcrossing, new F₂ populations were established within each of the introgression lines by crossing individuals that were heterozygous across the sixth chromosome. The estimated additive effect of the QTL on 10-week body mass was similar in both genetic backgrounds and in the original F₂ population (i.e., ~0.4 phenotypic standard deviations); no evidence of epistatic interaction with the genetic background was found. The 95% confidence interval for the location of the QTL was refined to a region of approximately 7 cM between D6Mit268 and D6Mit123.     

Genetic parameters for canalisation analysis of litter size and litter weight traits at birth in mice

The aim of this research was to explore the genetic parameters associated with environmental variability for litter size (LS), litter weight (LW) and mean individual birth weight (IW) in mice before canalisation. The analyses were conducted on an experimental mice population designed to reduce environmental variability for LS. The analysed database included 1976 records for LW and IW and 4129 records for LS. The total number of individuals included in the analysed pedigree was 3997. Heritabilities estimated for the traits under an initial exploratory approach varied from 0.099 to 0.101 for LS, from 0.112 to 0.148 for LW and from 0.028 to 0.033 for IW. The means of the posterior distribution of the heritability under a Bayesian approach were the following: 0.10 (LS), 0.13 (LW) and 0.03 (IW). In general, the heritabilities estimated under the initial exploratory approach for the environmental variability of the analysed traits were low. Genetic correlations estimated between the trait and its variability reached values of -0.929 (LS), -0.815 (LW) and 0.969 (IW). The results presented here for the first time in mice may suggest a genetic basis for variability of the evaluated traits, thus opening the possibility to be implemented in selection schemes.     

An epistatic genetic basis for fluctuating asymmetry of mandible size in mice

The genetic basis of fluctuating asymmetry (FA), or nondirectional variation in the subtle differences between left and right sides of bilateral characters, continues to be of considerable theoretical interest. FA generally has been thought to arise from random noise during development and therefore to have a largely or entirely environmental origin. Whereas additive genetic variation for FA generally has been small and often insignificant, a number of investigators have hypothesized that interactions between loci, or epistasis, significantly influence FA. We tested this hypothesis by conducting a whole-genome scan to detect any epistasis in FA of centroid size in the mandibles of more than 400 mice from an F2 intercross population formed from crossing the Large (LG/J) and Small (SM/J) inbred strains. Genotypic deviations were imputed at each site 2 cM apart on all 19 autosomes, and these and centroid size asymmetry values were used in canonical correlation analyses for each of the 171 possible pairs of 19 autosomes to identify the most probable sites for epistasis. Epistasis for centroid size asymmetry was abundant, occurring far more often than was expected by chance alone (there were 30 separate instances of epistasis at the 0.001 significance level, when only two were expected by chance alone). The contributions of epistasis from 30 pairwise combinations of loci tended to suppress the additive and dominance genetic variance, but greatly increased the epistatic genetic variance for FA in centroid size given the intermediate allele frequencies of an F2 intercross population.     

Genetic components of litter size variability in sheep

Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved.     

基于单片段代换系的水稻穗长QTL加性及其上位性效应

穗长是影响水稻(Oryza sativa)产量的重要因子之一, 研究水稻穗长QTL间的上位性效应对于发掘水稻产量潜力具有重要意义。该研究以16个单片段代换系(single segment substitution lines, SSSLs)和15个双片段聚合系(double segment pyramiding lines, DSPLs)为材料研究了水稻穗长QTL的加性及上位性效应。以P<0.01为阈值, 共检测到6个穗长QTL和9对基因互作座位。其中2个(Pl-2和Pl-10)是尚未报道的穗长QTL。穗长QTL互作后, 一些互作对的上位性效应与单个QTL的作用方式及效应大小各不相同, 预示着基因聚合后会产生不同的互作效应。该研究结果对于通过分子聚合育种手段改良穗长具有重要意义。     

Food resource allocation patterns in lactating females in a long-term selection experiment for litter size in mice

Resource allocation patterns, as quantified by residual food intake (RFI), and the consequences for offspring development were investigated during lactation in 96 females of a mouse line selected for 104 generations for high litter size at birth (S-line) and in 87 females of a non-selected control line (C-line). Litters of 45 C-line dams (Cs) and 48 S-line dams (Ss) were standardised (s) at birth; other dams (ns) supported total number of pups born (Cns and Sns, respectively). RFI during lactation was significantly lower in Sns-dams than in C-line dams and Sns-dams. After weaning Sns-dams seemed to be able to restore the negative resource situation. Sns-pups were about 25% less mature than Cns-pups at all times. Maturity was similar for Cs- and Ss-pups from 2 d in lactation on, and about 18% and 53% higher than Cns- and Sns-pups. The pre-weaning mortality rate was significantly higher in Sns-litters (35.6 ± 2.76) than in Cns-litters (4.95 ± 2.23). The results suggest that S-line dams allocated considerably more resources to maintenance of offspring than C-line dams. This was insufficient to provide the offspring with an adequate amount of resources, resulting in reduced pup development and increased pre-weaning mortality rates.     

The evolution of genetic architectures underlying quantitative traits

In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in quantitative trait loci mapping have begun to elucidate the genetic architectures underlying vast numbers of phenotypes across diverse taxa, producing observations that sometimes contrast with Fisher''s blueprint. Despite these considerable empirical efforts to map the genetic determinants of traits, it remains poorly understood how the genetic architecture of a trait should evolve, or how it depends on the selection pressures on the trait. Here, we develop a simple, population-genetic model for the evolution of genetic architectures. Our model predicts that traits under moderate selection should be encoded by many loci with highly variable effects, whereas traits under either weak or strong selection should be encoded by relatively few loci. We compare these theoretical predictions with qualitative trends in the genetics of human traits, and with systematic data on the genetics of gene expression levels in yeast. Our analysis provides an evolutionary explanation for broad empirical patterns in the genetic basis for traits, and it introduces a single framework that unifies the diversity of observed genetic architectures, ranging from Mendelian to Fisherian.     

基于单片段代换系的水稻穗长QTL加性及其上位性效应

穗长是影响水稻（Oryza sativa）产量的重要因子之一,研究水稻穗长QTL间的上位性效应对于发掘水稻产量潜力具有重要意义。该研究以16个单片段代换系（single segment substitution lines,SSSLs）和15个双片段聚合系（double segment pyramiding lines,DSPLs）为材料研究了水稻穗长QTL的加性及上位性效应。以P〈0.01为阈值,共检测到6个穗长QTL和9对基因互作座位。其中2个（Pl-2和Pl-10）是尚未报道的穗长QTL。穗长QTL互作后,一些互作对的上位性效应与单个QTL的作用方式及效应大小各不相同,预示着基因聚合后会产生不同的互作效应。该研究结果对于通过分子聚合育种手段改良穗长具有重要意义。     

Genetic and phenotypic parameters of age at first mating, litter size and animal size in Finnish mink

Mink skin size in Finland, as well as in other countries, has increased considerably during last decade. However, there are signs that selection for large body size has a negative impact on litter size (LS) and also for survival of kits. Therefore, it is important to study the genetic relationships among fertility traits and animal size (AS). The variance components for age at first mating (AFM) and first three parity LS and AS were estimated using multi-trait restricted maximum likelihood animal model. Data included 82 945 animals born during 1990 to 2004, originating from nine farms. Heritability estimates for the fertility traits were from 0.10 to 0.15. For AS, heritability was estimated to be 0.18. Genetic correlation between AS and all fertility traits was estimated to be negative (varying from -0.004 to -0.38). It is important to recognize this antagonistic relationship and include the reproductive traits into breeding goals to maintain good reproductive performance when selecting for increased body size and hence larger pelts in fur animals. Genetic correlations between the traits should be accounted in breeding value evaluations by using a multi-trait model. Including AFM into breeding value estimation would also improve the accuracy of breeding value estimation for fertility, because females missing the first LS still have record on AFM.     

Epistasis plays an important role as genetic basis of heterosis in rice

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Genetic determinism for within-litter birth weight variation and its relationship with litter weight and litter size in the Ripollesa ewe breed

Birth weight plays a central role in lamb survival and growth, and the knowledge of its genetic determinism has become essential in worldwide selection programmes. Within this context, within-litter birth weight variation (BWV) has been suggested as an attractive trait to homogenise litters in prolific species, although it has not been analysed in sheep. The objective of this study was to ascertain whether maternal additive genetic variance exists for BWV in Ripollesa ewes, and to study its genetic, permanent environmental and residual relationships with litter weight (LW) and litter size (LS) at birth. Data were recorded in the Ripollesa experimental flock of the Universitat Autònoma of Barcelona, between 1986 and 2005, and included 1 662 litters from 380 ewes, with 712 records of BWV and 1 530 records of LW. Traits were analysed with a multivariate animal model solved through Bayesian methodologies, and with a threshold characterisation of LS. Additionally, the effect of BWV on lamb survival was studied. Additive genetic variance was observed for BWV (h² = 0.061), as well as for LW (h² = 0.200) and LS (h² = 0.141). Nevertheless, genetic correlations among those traits were not substantial (BWV and LW = 0.151; BWV and LS = − 0.219; LW and LS = − 0.320) and suffered from a high degree of uncertainly, with the null correlation included within the highest posterior interval at 95%. Within-litter birth weight variation and LS showed a negative and large permanent environmental correlation ( − 0.872), and LW and LS were negatively correlated due to residual ( − 0.762) and permanent environmental ( − 0.449) random sources of variation. Within-litter birth weight variation influenced lamb mortality during the first 7 days of life (P < 0.05), increasing and decreasing survivability in heavier and lighter littermates, respectively. Nevertheless, stillbirths and lambs died after the 1st week of life were not affected by BWV (P>0.05). The low heritability found indicates that slow genetic progress may be expected from selecting for BWV. Close to zero genetic correlations suggest that this selection will probably not affect LS and LW, although some significant permanent and residual correlations must be taken into account. Further studies are needed to understand better the genetic architecture among these three reproductive traits.     

Proteomic analysis of reproduction proteins involved in litter size from porcine placenta

A gel-free and label-free quantitative proteomic approach based on a spectral counting strategy was performed to discover prolificacy-related proteins. Soluble proteins of porcine placenta from small litter size group (SLSG) and large litter size group (LLSG) were extracted and subsequently applied to in-solution tryptic digestion followed by liquid chromatography–tandem mass spectrometry analysis. Six and thirteen proteins were highly expressed in SLSG and LLSG, respectively. Of the dominantly expressed proteins, we chose prolificacy-related proteins such as puromycin-sensitive aminopeptidase (PSA) and retinol-binding protein 4 (RBP4). Western blot analysis confirmed that the processed form (70 kDa) of PSA was more expressed and RBP4 (23 kDa) was dominantly expressed in LLSG. These results indicate that PSA and RBP4 are representative proteins involved in porcine fertility traits, and this finding may help to increase litter size of pigs.     

A genome‐wide linkage analysis for reproductive traits in F2 Large White × Meishan cross gilts

Female reproductive performance traits in pigs have low heritabilities thus limiting improvement through traditional selective breeding programmes. However, there is substantial genetic variation found between pig breeds with the Chinese Meishan being one of the most prolific pig breeds known. In this study, three cohorts of Large White × Meishan F₂ cross‐bred pigs were analysed to identify quantitative trait loci (QTL) with effects on reproductive traits, including ovulation rate, teat number, litter size, total born alive and prenatal survival. A total of 307 individuals were genotyped for 174 genetic markers across the genome. The genome‐wide analysis of the trait‐recorded F₂ gilts in their first parity/litter revealed one QTL for teat number significant at the genome level and a total of 12 QTL, which are significant at the chromosome‐wide level, for: litter size (three QTL), total born alive (two QTL), ovulation rate (four QTL), prenatal survival (one QTL) and teat number (two QTL). Further support for eight of these QTL is provided by results from other studies. Four of these 12 QTL were mapped for the first time in this study: on SSC15 for ovulation rate and on SSC18 for teat number, ovulation rate and litter size.     

Gene interactions from maternal effects

Theoretical analyses have demonstrated a potential role for epistasis in many of the most important processes in evolution. These analyses generally assume that an individual's genes map directly to its phenotype and epistasis results from interactions among loci that contribute to the same biochemical or developmental pathways (termed physiological, or within-genotype, epistasis). For many characters, particularly those expressed early in life, an individual's phenotype may also be affected by genes expressed by its parents. The presence of these parental effects allows for interactions between the genes present in the parental and offspring genomes. When the phenotypic effect of a locus in the offspring depends on the alleles possessed by its parents, genotype-by-genotype, or among-genotype, epistasis occurs. The among-genotype epistasis resulting from parental effects may contribute to ruggedness of adaptive landscapes because early mortality often accounts for much of the variance in fitness in populations. To demonstrate how parent-offspring interactions can result in among-genotype epistasis, I use a two-locus model, with one maternal effect locus and one direct effect locus, each with two alleles. Dynamical equations are presented for the two-locus model and are directly contrasted with the dynamical equations derived for a model for physiological epistasis. The relationship between the evolutionary dynamics resulting from these two forms of epistasis is discussed. Three scenarios are presented to illustrate systems in which maternal-offspring, genotype-by-genotype epistasis may occur. The implications of maternal-offspring epistasis for quantitative-trait-loci studies are also discussed.     

EPISTASIS AS A SOURCE OF INCREASED ADDITIVE GENETIC VARIANCE AT POPULATION BOTTLENECKS

The role of epistasis in evolution and speciation has remained controversial. We use a new parameterization of physiological epistasis to examine the effects of epistasis on levels of additive genetic variance during a population bottleneck. We found that all forms of epistasis increase average additive genetic variance in finite populations derived from initial populations with intermediate allele frequencies. Average additive variance continues to increase over many generations, especially at larger population sizes (N = 32 to 64). Additive-by-additive epistasis is the most potent source of additive genetic variance in this situation, whereas dominance-by-dominance epistasis contributes smaller amounts of additive genetic variance. With additive-by-dominance epistasis, additive genetic variance decreases at a relatively high rate immediately after a population bottleneck, rebounding to higher levels after several generations. Empirical examples of epistasis for murine adult body weight based on measured genotypes are provided illustrating the varying effects of epistasis on additive genetic variance during population bottlenecks.     

水稻苗期耐旱性基因位点及其互作的分析

随着全球水资源的日益贫乏和旱灾的日趋严重,水稻耐旱性的研究越来越重要,对籼稻窄叶青8号（ZYQ8）和粳稻京系17（JX17）以及由它们构建的加倍单倍体（DH）群体,参照国际水稻研究所的耐旱鉴定方法,在苗期进行断水,调查期耐旱性,利用该群体的分子连锁图谱进行数量性状座位（QTL）区间作图分析,共检测到2个耐旱的QTL（qDT-5和qDT-12),分别位于第5染色体的GA41-GA257之间的和第12染色体的RG457-Y12817R之间,这两个QTL的加性效应均来自ZYQ8的等位基因,用Epistat软件检测到2个单位点,即GA257和Y12817R,与区间作图分析的结果一致,Epistat还检测到与GA257互作的3个位点（RG541、G318和G192,分别位于第1、4和8染色体上）和与Y12817R互作的1个位点（CT234,位于第3染色体上）。     

Genetic parameters for litter size in sheep: natural versus hormone-induced oestrus

The litter size in Suffolk and Texel-sheep was analysed using REML and Bayesian methods. Litters born after hormonal induced oestrus and after natural oestrus were treated as different traits in order to estimate the genetic correlation between the traits. Explanatory variables were the age of the ewe at lambing, period of lambing, a year*flock-effect, a permanent environmental effect associated with the ewe, and the additive genetic effect. The heritability estimates for litter size ranged from 0.06 to 0.13 using REML in bi-variate linear models. Transformation of the estimates to the underlying scale resulted in heritability estimates from 0.12 to 0.17. Posterior means of the heritability of litter size in the Bayesian approach with bi-variate threshold models varied from 0.05 to 0.18. REML estimates of the genetic correlations between the two types of litter size ranged from 0.57 to 0.64 in the Suffolk and from 0.75 to 0.81 in the Texel. The posterior means of the genetic correlation (Bayesian analysis) were 0.40 and 0.44 for the Suffolk and 0.56 and 0.75 for the Texel in the sire and animal model respectively. A bivariate threshold model seems appropriate for the genetic evaluation of prolificacy in the breeds concerned.     

Selection for fertility in mice using different methods of litter size manipulation

Summary A short-term selection experiment for increasing the first-day litter size (LS1) and 28-day litter weight (LW28) was conducted with three populations of mice over 8 generations. Different methods of litter size manipulation were used for the populations — in S the litter size was standardized to 8 (4 , 4 ) on the first day, in LA it was adjusted to the average size of all litters born on the same day and NL had the natural litter size. To eliminate temporary environmental effects, a control population was kept in each case. The selection results per generation were, for LS 1 b=0.30 (S, NL) and 0.20 (LA), and for LW28 b=5.62 g (S), 5.26 g (NL), and 4.32 g (LA). The heritability obtained was between 0.18 and 0.13 for LS 1 and from 0.42 to 0.12 for LW28. The populations differed in the correlated responses for body weight parameters (litter weight gain). The implantation rate increased in populations S and NL (b=0.19, 0.37), but not in population LA. Postnatal mortality went down (b=-0.07) and the dam's milk production rose (b=1.11 g) only in population LA. The estimated partial regression coefficient linking body weight at mating (BWM) for the dam and the daughter's litter size showed an effect on the litter size.