Genetic analysis of low survival rate of pups in RR/Sgn inbred mice

Newborn offspring of the inbred mouse RR/Sgn strain have a low survival rate prior to weaning. We hypothesized that this is a consequence of an inferior nurturing ability of RR/Sgn mothers and that RR/Sgn mothers have a tendency to lose their pups. We performed quantitative trait locus (QTL) mapping for inferior nurturing ability and tendency to lose pups in RR/Sgn mothers. The number of pups was adjusted to 6 per dam on the day of delivery, and the number of surviving pups and their total weight (litter weight) were scored at 12 days after birth. Nurturing ability was evaluated by litter weight, and tendency to lose pups was evaluated by scoring whether or not the mothers lost their pups. For litter weight, we identified one significant QTL on chromosome 4 and three suggestive QTLs on chromosomes 7, 9 and 17. The RR/Sgn allele was associated with lower litter weight at all loci. For the tendency to lose pups, we identified three suggestive QTLs on chromosomes 4, 9 and 16. The RR/Sgn allele was associated with an increased tendency to lose pups at all loci. These results supported our hypothesis that the low survival rate phenotype was attributable, at least in part, to a phenotype whereby mothers display inferior nurturing ability and a tendency to lose pups. Thus, it suggests that these two traits share genetic basis.     

Quantitative trait locus analysis of plasma cholesterol levels and body weight by controlling the effects of the Apoa2 allele in mice

Colleagues and I previously performed quantitative trait locus (QTL) analysis on plasma total-cholesterol (T-CHO) levels in C57BL/6J (B6) x RR F2 mice. We identified only one significant QTL (Cq6) on chromosome 1 in a region containing the Apoa2 gene locus, a convincing candidate gene for Cq6. Because Cq6 was a highly significant QTL, we considered that the detection of other potential QTLs might be hindered. In the present study, QTL analysis was performed in B6.KK-Apoa2b N(8) x RR F2 mice [B6.KK-Apoa2b N(8) is a partial congenic strain carrying the Apoa2b allele from the KK strain, and RR also has the Apoa2b allele] by controlling of the effects of the Apoa2 allele, for identifying additional QTLs. Although no significant QTLs were identified, 2 suggestive QTLs were found on chromosomes 2 and 3 in place of the effects of the Apoa2 allele. A significant body weight QTL was identified on chromosome 3 (Bwq7, peak LOD score 5.2); its effect on body weight was not significant in previously analyzed B6 x RR F2 mice. Suggestive body weight QTL that had been identified in B6 x RR F2 mice on chromosome 4 (LOD score 3.8) was not identified in B6.KK-Apoa2b N(8) x RR F2 mice. Thus, contrary to expectation, the genetic control of body weight was also altered significantly by controlling of the effects of the Apoa2 allele. The QTL mapping strategy by controlling of the effects of a major QTL facilitated the identification of additional QTLs.     

Identification of quantitative trait loci affecting female reproductive traits in a multigeneration Meishan-White composite swine population.

A multigeneration crossbred Meishan-White composite resource population was used to identify quantitative trait loci (QTL) for age at first estrus (AP) and the components of litter size: ovulation rate (OR; number of ova released in an estrous period) and uterine capacity (UC). The population was established by reciprocally mating Meishan (ME) and White composite (WC) pigs. Resultant F1 females were mated to either ME or WC boars to produce backcross progeny (BC) of either 3/4 WC 1/4 ME or 1/4 WC 3/4 ME. To produce the next generation (F3), 3/4 WC 1/4 ME animals were mated to 1/4 WC 3/4 ME animals yielding half-blood (1/2 WC 1/2 ME) progeny. A final generation (F4) was produced by inter se mating F3 animals. Measurements for AP and OR were recorded on 101 BC, 389 F3, and 110 F4 gilts, and UC data were from 101 BC and 110 F4 first parity litters. A genomic scan was conducted with markers (n = 157) spaced approximately 20 cM apart. All parental, F1, BC, and F4 animals but only 84 F3 animals were genotyped and included in this study. The QTL analysis fitted a QTL at 1-cM intervals throughout the genome, and QTL effects were tested using approximate genome-wide significance levels. For OR, a significant (E[false positive] < .05) QTL was detected on chromosome 8, suggestive (E[false positive] < 1.0) QTL were detected on chromosomes 3 and 10, and two additional regions were detected that may possess a QTL (E[false positive] < 2.0) on chromosomes 9 and 15. Two regions possessed suggestive evidence for QTL affecting AP on chromosomes 1 and 10, and one suggestive region on chromosome 8 was identified for UC. Further analyses of other populations of swine are necessary to determine the extent of allelic variation at the identified QTL.     

Further mapping and characterization of Naq1, a quantitative trait locus responsible for maternal inferior nurturing ability in RR mice

Females of the inbred mouse RR strain have a limited ability to nurture their offspring, and frequently the young die during rearing. We previously identified a significant quantitative trait locus (QTL) responsible for the inferior nurturing ability on chromosome 5 (Naq1), on the basis of litter weight of six pups at days 7, 12, and 21 after parturition. Here, we carried out further mapping of Naq1 to define the confidence interval precisely. At the same time, we analyzed new quantitative trait variables, litter weight gain between days 7 and 12 (WG1), and that between days 12 and 21 (WG2), to characterize further the physiology of inferior nurturing ability. Consequently, a peak LOD score for the Naq1 was identified on D5Mit218 (72 cM), which was located approximately 2 cM distal to our previous expectation, as a significant QTL for WG1 (LOD 5.5), but not for WG2 (LOD 0.9). Because the growth of pups depends purely on milk obtained from the dam up to day 12 after birth, it seems possible to assume that the inferior nurturing ability in RR mice is related to defects in maternal nutritional support (that is, lactation) rather than to defects in pup growth. Naq1 is a novel QTL as far as the QTL results of relevant female reproductive traits in cattle and pigs are concerned.     

水稻饲料营养含量的QTL定位分析

应用85个SSR标记,对普通野生稻与粳稻台中65为亲本建立的F₂群体进行基因检测,构建了覆盖水稻基因组12条染色体的SSR分子标记连锁图,采用Mapmaker/QTL1.0统计软件对决定水稻饲用营养价值的粗蛋白、粗纤维、粗脂肪、粗灰分、硅酸和可溶性糖含量的基因座位进行了定位分析。结果定位了影响粗蛋白含量的3个QTLs,影响粗脂肪含量的1个QTL,影响可溶性糖含量的3个QTLs,影响硅酸含量的2个QTLs,这9个QTLs分别位于第1,2,4,7,8,9,10和11染色体上。其中主效QTL4个,分别是影响粗脂肪含量的qCEE-1(贡献率56.8%),影响可溶性糖含量的qCWSC-4(贡献率23.1%)和qCWSC-7(贡献率25.0%),影响硅酸含量的qCS-9(贡献率15.9%),其余5个为微效QTL。没有检测到影响粗纤维含量和粗灰分含量的QTL。     

Apolipoprotein gene polymorphisms as cause of cholesterol QTLs in mice

Quantitative trait locus (QTL) analyses of plasma cholesterol levels were carried out in three sets of F(2) mice that were formed in a 'round-robin' manner from C57BL/6J, KK (-A(y)), and RR strains. Six QTLs were identified on chromosomes 1 (Cq1, Cq2, and Cq6), 3 (Cq3), and 9 (Cq4 and Cq5); of these, Cq2 colocalized with Cq6, and Cq4 colocalized with Cq5. The major candidate gene for Cq2 and Cq6 is Apoa2, and that for Cq4 and Cq5 is Apoa4. The adequacy of polymorphisms in candidate genes as cause of QTLs was investigated in this study. For Apoa2, three different alleles (Apoa2(a), Apoa2(b), and Apoa2(c)) are known. Since there was no significant physiologic difference between Apoa2(a) and Apoa2(c) alleles, previous hypothesis that Apoa2(b) was different from Apoa2(a) and Apoa2(c) in the ability to increase cholesterol levels was further supported. Presumably, G-to-A substitution at nucleotide 84 and/or C-to-T substitution at nucleotide 182 are crucial to make the Apoa2(b) unique. On the other hand, for Apoa4, the most striking polymorphism was the number of Glu-Gln-Ala/Val-Gln repeats in carboxyl end; however, this might not be responsible for QTLs. Instead, a silent mutation, C-to-T substitution at nucleotide 771, was shown to be completely correlated with the occurrence of QTLs in a total of six F(2) intercrosses. Provisionally, but reasonably, these base substitutions are qualified as primary causes that constitute QTL effect. The potential strategy for identifying genes and base substitutions underlying QTLs is discussed.     

非传染病因素对母猪死胎与木乃伊胎发生的Logistic回归分析

目的:探讨除疾病以外对母猪死胎,木乃伊胎的影响因素。方法,用Logistic回归分析对胎次,配种月份、产仔月份、产活仔数、总产仔数、木乃伊胎率和死胎率进行回归分析。结果表明,在死胎的回归分析中,产活仔数、木乃伊胎率和总产仔数3个因素被选入多因素Logistic回归模型中,其OR值分别为:36.266、0.030和0.002。在木乃伊胎进行回归分析中,分娩月份、产活仔数、死胎率和总产仔数4个因素被选入多因素Logistic回归模型中,其OR值分别为:1.092,0.404,0.227,2.561。结论:死胎的发生与环境温度、胎次无回归关系,木乃伊胎与分娩时环境温度或临近分娩时的环境温度有正回归关系,死胎和木乃伊胎都与产活仔数有负回归关系,与总产仔数有正回归关系,互相进入对方的回归方程。     

Quantitative trait loci that control plasma lipid levels in an F2 intercross between C57BL/6J and DDD.Cg-A(y) inbred mouse strains

The objectives of this study were to characterize plasma lipid phenotypes and dissect the genetic basis of plasma lipid levels in an obese DDD.Cg-A(y) mouse strain. Plasma triglyceride (TG) levels were significantly higher in the DDD.Cg-A(y) strain than in the B6.Cg-A(y) strain. In contrast, plasma total-cholesterol (CHO) levels did not substantially differ between the two strains. As a rule, the A(y) allele significantly increased TG levels, but did not increase CHO levels. Quantitative trait locus (QTL) analyses for plasma TG and CHO levels were performed in two types of F(2) female mice [F(2)A(y) (F(2) mice carrying the A(y) allele) and F(2) non- A(y) mice (F(2) mice without the A(y) allele)] produced by crossing C57BL/6J females and DDD.Cg-A(y) males. Single QTL scan identified one significant QTL for TG levels on chromosome 1, and two significant QTLs for CHO levels on chromosomes 1 and 8. When the marker nearest to the QTL on chromosome 1 was used as covariates, four additional significant QTLs for CHO levels were identified on chromosomes 5, 6, and 17 (two loci). In contrast, consideration of the agouti locus genotype as covariates did not detect additional QTLs. DDD.Cg-A(y) showed a low CHO level, although it had Apoa2(b), which was a CHO-increasing allele at the Apoa2 locus. This may have been partly due to the presence of multiple QTLs, which were associated with decreased CHO levels, on chromosome 8.     

Bone mineral density QTL at sexual maturity and end of lay

1. An F₂ cross of a broiler male line and a White Leghorn layer line was used to identify quantitative trait loci (QTL) for bone density at the onset of lay and at the end of the laying period. A total of 686 measures of humeral bone density were available for analysis.

2. There was no evidence for epistasis.

3. Genome-wide significant QTL for bone density at the onset of lay were identified on chromosomes 1 (311?cM) and 8 (2?cM) and on chromosomes 1 (311?cM), 3 (57?cM) and 8 (2?cM) with a covariate for the number of yellow follicles (a proxy for the concentration of circulating oestrogen).

4. Evidence for only 4 chromosome-wide suggestive QTL were detected at the end of lay (72 weeks).

5. Analysis of the combined data confirmed two genome-wide suggestive QTL on chromosome 1 (137 and 266?cM) and on chromosomes 8 (2?cM) and 9 (10?cM) in analyses with or without the covariate.

6. Positive QTL alleles came from the broiler line with the exception of 2 suggestive QTL at the onset of lay on chromosomes 3 and 5 in an analysis with the covariate.

7. In general, QTL acted additively, except that dominant effects were identified for three suggestive QTL at the onset of lay on chromosomes 3 (57 and 187?cM) and 5 (9?cM).

8. The significant QTL in this study were at similar locations to QTL identified in a range of crosses in other publications, suggesting that they are prime candidates for the search for genes and mutations that could be used as selection criteria to improve bone strength and decrease fractures in commercial laying hens.     

大白母猪妊娠天数影响因素分析及遗传参数估计

【目的】分析胎次、配种季节和与配公猪3个固定效应对大白母猪妊娠天数的影响,估计妊娠天数的遗传参数并探索其与总产仔数、产活仔数、初生窝重、死胎数、木乃伊数的关系。【方法】收集2 138头大白母猪妊娠天数、总产仔数、产活仔数、初生窝重、死胎数及木乃伊数6种生产表型,共包含4个胎次(1～4)的4 261条记录。利用一般线性模型分析试验猪群的固定效应对妊娠天数的影响,并采用多性状重复力模型估计妊娠天数与其他繁殖性状的遗传参数(遗传力、重复力、遗传相关、表型相关)。【结果】大白母猪平均妊娠天数为116.08 d,经t检验分析与114 d差异显著(P<0.05)。胎次对妊娠天数有显著影响,且第1胎妊娠期显著短于第2胎(P<0.05);配种季节对妊娠天数有极显著影响(P<0.01),春季配种的母猪妊娠天数最短,秋季配种的母猪妊娠天数最长,相差0.73 d(P<0.05);与不同公猪个体配种后母猪的妊娠天数之间有显著差异(P<0.05),差异最大达3.05 d。妊娠天数遗传力为0.1603,与总产仔数、产活仔数、初生窝重、死胎数及木乃伊数之间均呈现负表型和负遗传相关。【结...     

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.     

Long-term responses, changes in genetic variances and inbreeding depression from 122 generations of selection on increased litter size in mice

Data on mice selected for litter size over 122 generations have been analysed in order to reveal the effect of long‐term selection on responses and changes in variances over a long selection period. Originally, three lines were established from the same base population, namely an H line selected for large litter size, an L line selected for small litter size and a K line without selection. In generation 122, the mean number of pups born alive (NBA) was 22 for the H line and 11 for the K line. Phenotypic response to selection is reduced over generations, but crossing of plateaued lines increased responses and realized heritabilities. Both realized heritabilities and heritabilities from residual maximal likelihood (REML) analyses were, in general, calculated from generation (?1)–44 (period 1), 45–70 (period 2) and 71–122 (period 3) separately. Realized heritabilities were in general smaller than heritabilities estimated from mixed model analysis. An overall estimate of heritability for NBA was found to be 0.19 (±0.01) by REML analysis. Additive variance is constant over all periods in the high line and the control line, but is reduced over periods in the low line. The reduction of additive variance in the low line could probably be explained by changes in gene frequencies. In all lines, environmental variances increased over periods. Inbreeding reduced the mean litter size by 0.72 (±0.10) pups per 10% increase in inbreeding, with substantial variance between periods and lines.     

Mapping QTL for fat area ratios and serum leptin concentrations in a Duroc purebred population

The reduction of extra subcutaneous, intermuscular and abdominal fat is important to increase the carcass lean percentage of pigs. Image analyses of fat area ratios were effective for estimation of separated fat in pig carcasses. Serum concentrations of leptin are useful as physiological predictors of fat accumulation in pigs. The objectives of the present study were to perform a quantitative trait locus (QTL) analysis for fat area ratios and serum leptin concentrations in a Duroc purebred population. Pigs (n = 226 to 538) were measured for fat area ratios of carcass cross‐sections at the fifth to sixth thoracic vertebrae, half body length and last thoracic vertebra using an image analysis system, and serum leptin concentration. In total, animals were genotyped for 129 markers and used for QTL analysis. For fat area ratios, four significant and 12 suggestive QTLs were detected on chromosomes 1, 6, 7, 8, 9, 12 and 13. Significant QTLs were detected on the same region of chromosome 6, which was located near a leptin receptor gene. For serum leptin concentrations, two significant and two suggestive QTLs were detected on chromosomes 6, 9, and 16, and the QTLs on chromosome 6 were also in the same region for fat area ratios.     

Identification of quantitative trait loci affecting corpora lutea and number of teats in a Meishan x Duroc F2 resource population

Understanding of the genetic control of female reproductive performance in pigs would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing 3 to 5 more viable piglets per litter than Western breeds. This difference in prolificacy is attributed to the Meishan's superior prenatal survival. Our study utilized a 3-generation resource population, in which the founder grandparental animals were purebred Meishan and Duroc pigs, in a genome scan for QTL. Grandparent, F1, and F2 animals were genotyped for 180 microsatellite markers. Reproductive traits, including number of corpora lutea (number of animals = 234), number of fetuses per animal (n = 226), number of teats (n = 801), and total number born (n = 288), were recorded for F2 females. Genome-wide significance level thresholds of 1, 5, and 10% were calculated using a permutation approach. We identified 9 QTL for 3 traits at a 10% genome-wise significance level. Parametric interval mapping analysis indicated evidence of a 1% genome-wise significant QTL for corpora lutea on SSC 3. Nonparametric interval mapping for number of teats found 4 significant QTL on chromosomes SSC3 (P < 0.01), SSC7 (P < 0.01), SSC8 (P < 0.01), and SSC12 (P < 0.05). Partial imprinting of a QTL affecting teat number (P < 0.10) was detected on SSC8. Using the likelihood-ratio test for a categorical trait, 2 QTL for pin nipples were detected on SSC2 and SSC16 (P < 0.01). Fine mapping of the QTL regions will be required for their application to introgression programs and gene cloning.     

Quantitative trait loci that control body weight and obesity in an F2 intercross between C57BL/6J and DDD.Cg-Ay mice

I have developed a congenic mouse strain for the A(y) allele at the agouti locus in an inbred DDD/Sgn strain, DDD.Cg-A(y). DDD.Cg-A(y) females are extremely obese and significantly heavier than B6.Cg-A(y) females. The objectives of this study were to determine the genetic basis of obesity in DDD.Cg-A(y) mice, and to determine whether or not their high body weight was due to the presence of DDD background-specific modifiers. I performed quantitative trait locus (QTL) analyses for body weight and body mass index in two types of F(2) mice [F2 A(y) (F(2) mice carrying the A(y) allele) and F(2) non-A(y) (F2 mice without the A(y) allele)] produced by crossing C57BL/6J females and DDD.Cg-A(y) males. The results of the QTL analysis of F(2) A(y) mice were very similar to those obtained for F(2) non-A(y) mice. It was unlikely that the high body weight of DDD.Cg-A(y) mice was due to the presence of specific modifiers. When both F(2) datasets were merged and analyzed, four significant body weight QTLs were identified on chromosomes 6, 9, and 17 (2 loci) and four significant obesity QTLs were identified on chromosomes 1, 6, 9, and 17. Although the presence of DDD background-specific modifiers was not confirmed, a multifactorial basis of obesity in DDD.Cg-A(y) females was thus revealed.     

Stillbirth in the pig in relation to genetic merit for farrowing survival

The objectives of this study were to analyze the incidence of different categories of stillborn piglets in relation to genetic merit for farrowing survival of sows and litters and to analyze relationships of total number of piglets born per litter, average BW of the litter, and within-litter variation in BW with genetic merit for farrowing survival of sows and litters. Records of 336 purebred litters, produced by 307 first-to eighth-parity sows, were collected on a nucleus farm in Brouennes, France. Breeding values for farrowing survival were estimated for sows (EBVfs_maternal) and litters (EBVfs_direct) using a large data set from which information obtained in the current study was excluded. For each litter, BW, number of stillborn piglets (classified as nonfresh stillborn, prepartum stillborn, intrapartum stillborn, and postpartum stillborn), and number of live-born piglets were recorded. Birth weights of stillborn piglets were lower than BW of live-born piglets (P < 0.0001), except for prepartum stillbirths. The total number of stillborn piglets per litter and the number of stillborn piglets in each category decreased with increasing EBVfs_maternal (P < 0.01). An increase in EBVfs_direct was also associated with a decrease in the total number of stillborn piglets per litter (P < 0.01). This decrease was due to a decrease in the number of nonfresh, prepartum, and postpartum stillborn piglets but not to a decrease in the number of intrapartum stillborn piglets. Probabilities of stillbirth in relation to EBVfs_maternal were higher than probabilities of stillbirth in relation to EBVfs_direct. Total number of piglets born decreased with increasing EBVfs_direct (P = 0.0003), but was not related to EBVfs_maternal. Average BW of the litter (P < 0.0001) and within-litter variation in BW (P = 0.05) decreased with increasing EBVfs_maternal but were not related to EBVfs_direct. Selection for the maternal genetic component of farrowing survival seems a better strategy than selection for the direct genetic component. Selection for the maternal genetic component of farrowing survival reduces stillbirth in all categories and does not affect litter size.     

Impacts of an endophyte-infected fescue seed diet on traits of mouse lines divergently selected for response to that same diet

In previous work, mouse lines were selected for eight generations for resistance (R) or susceptibility (S) to endophyte-infected fescue toxicosis using depression in postweaning gain caused by a toxin-containing diet as the selection criterion. Characterizing biological changes associated with resistance or susceptibility in those mice might suggest genetic or therapeutic approaches to alleviate fescue toxicosis in cattle. The first objective of the current experiment was to determine whether the toxin-containing diet depressed reproduction and mature size more severely in S than in R mice. The second was to investigate line and diet effects on hepatic glutathione-S-epoxytransferase (GST) and uridine diphosphate glucuronosyl-transferase (UDPGT) activities and to relate enzyme activities to reproduction within line by diet groups. Twenty-eight pairs per line (S or R) x diet (toxin-containing [+] or toxin-absent [-]) group cohabitated for 36 wk. The + diet depressed the number of pups born and weaned and litter weight weaned (P < .01) within the first two litters produced. Diet effects were greatest early in the experiment. Percentage changes in reproduction caused by the + diet for R and S pairs, respectively, were -13 and -28 for total pups born, -10 and -25 for total pups weaned, -13 and -14 for total litters produced, and -30 and -42 for total litter weight weaned. The S line mice were heavier than R line mice on both diets, but the + diet had a larger depressing effect on mature size of S line than of R line males (line x diet interaction, P = .09) and females (interaction not significant). Averaged across diets, GST activity was higher in R than in S dams (P = .05) at 44 wk of age but was not affected by diet or line x diet. Activity of GST was correlated with number of pups born (-.50), number of litters produced (-.44), and survival percentage (.40) within the R- group; in the R+ group, GST activity was correlated only with survival percentage (.37). In the S- and S+ groups, GST activity was not correlated with any reproductive trait. Line, diet, and their interaction did not affect UDPGT activity, and UDPGT activity was not correlated with any reproductive trait in any line x diet group. Selected lines differed in response to a toxin-containing diet as measured by its effect on reproduction and mature size. The R and S mice also differed in GST activity, but GST activity was correlated with reproductive traits only in R-line mice.     

Genome-wide association study of swine farrowing traits. Part II: Bayesian analysis of marker data

Reproductive efficiency has a great impact on the economic success of pork (sus scrofa) production. Number born alive (NBA) and average piglet birth weight (ABW) contribute greatly to reproductive efficiency. To better understand the underlying genetics of birth traits, a genome-wide association study (GWAS) was undertaken. Samples of DNA were collected and tested using the Illumina PorcineSNP60 BeadChip from 1,152 first parity gilts. Traits included total number born (TNB), NBA, number born dead (NBD), number stillborn (NSB), number of mummies (MUM), total litter birth weight (LBW), and ABW. A total of 41,151 SNP were tested using a Bayesian approach. Beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on the SSCX, SNP were assigned to groups of 5 consecutive SNP by chromosome-position order and analyzed again using a Bayesian approach. From that analysis, 5-SNP groups were selected having no overlap with another 5-SNP groups and no overlap across chromosomes. These selected 5-SNP non-overlapping groups were defined as QTL. Of the available 8,814 QTL, 124 were found to be statistically significant (P < 0.01). Multiple testing was considered using the probability of false positives. Eleven QTL were found for TNB, 3 on SSC1, 3 on SSC4, 1 on SSC13, 1 on SSC14, 2 on SSC15, and 1 on SSC17. Statistical testing for NBA identified 14 QTL, 4 on SSC1, 1 on SSC4, 1 on SSC6, 1 on SSC10, 1on SSC13, 3 on SSC15, and 3 on SSC17. A single NBD QTL was found on SSC11. No QTL were identified for NSB or MUM. Thirty-three QTL were found for LBW, 3 on SSC1, 1 on SSC2, 1 on SSC3, 5 on SSC4, 2 on SSC5, 5 on SSC6, 3 on SSC7, 2 on SSC9, 1 on SSC10, 2 on SSC14, 6 on SSC15, and 2 on SSC17. A total of 65 QTL were found for ABW, 9 on SSC1, 3 on SSC2, 9 on SSC5, 5 on SSC6, 1 on SSC7, 2 on SSC8, 2 on SSC9, 3 on SSC10, 1 on SSC11, 3 on SSC12, 2 on SSC13, 8 on SSC14, 8 on SSC15, 1 on SSC17, and 8 on SSC18. Several candidate genes have been identified that overlap QTL locations among TNB, NBA, NBD, and ABW. These QTL when combined with information on genes found in the same regions should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.     

Quantitative trait loci for leg weakness traits in a Landrace purebred population

Leg weakness in pigs is a serious problem in the pig industry. We performed a whole genome quantitative trait locus (QTL) analysis to find QTLs affecting leg weakness traits in the Landrace population. Half-sib progeny ( n  = 522) with five sires were measured for leg weakness traits. Whole genome QTL mapping was performed using a half-sib regression-based method using 190 microsatellite markers. No experiment-wide significant QTLs affecting leg weakness traits were detected. However, at the 5% chromosome-wide level, QTLs affecting leg weakness traits were detected on chromosomes 1, 3, 10 and 11 with QTL effects ranging from 0.07 to 0.11 of the phenotypic variance. At the 1% chromosome-wide level, QTLs affecting rear feet score and total leg score were detected on chromosomes 2 and 3 with QTL effects of 0.11 and 0.13 of the phenotypic variance, respectively. On chromosome 3 and 10, some QTLs found in this study were located at nearby positions. The present study is one of the first reports of QTLs affecting fitness related traits such as leg weakness traits, that segregate within the Landrace population. The study also provides useful information for studying QTLs in purebred populations.     

Genetic variation of farrowing kinetics traits and their relationships with litter size and perinatal mortality in French Large White sows

Genetic parameters of litter traits and their relationships with farrowing kinetics traits were estimated in a Large White population to examine the impact of selection for litter size on perinatal mortality and one of its main determinants, farrowing kinetics. Data were collected on 2,947 farrowings from 1,267 sows between 1996 and 2004. Litter traits included the number born in total (NBT), number born alive (NBA), and the number (NSB) and proportion (PSB) of stillborn piglets. Four farrowing kinetics traits were considered: farrowing duration (FD), birth interval (BI = FD/NBT), heterogeneity of birth intervals (SDNB = SD of the number of piglets born each one-half hour), and birth assistance (BA) during the farrowing process. Genetic parameters were estimated using restricted maximum likelihood methodology. All traits were analyzed using a mixed linear animal model including year x month and parity as fixed effects; the additive genetic value of each animal and the sow permanent environment were treated as random effects. To normalize their distribution, kinetics traits were Box-Cox-transformed. Low heritability estimates were obtained for litter size and mortality traits, which was in agreement with literature results (i.e., 0.10 +/- 0.02, 0.08 +/- 0.02, 0.19 +/- 0.02, and 0.14 +/- 0.02 for NBT, NBA, NSB, and PSB, respectively). Heritability values were also low for kinetics traits: 0.10 +/- 0.02, 0.08 +/- 0.02, 0.01 +/- 0.01, and 0.05 +/- 0.03 for FD, BI, SDNB, and BA, respectively. The genetic correlation between NBT and NBA was strongly positive (ra = 0.90). On both phenotypic and genetic scales, NBT was positively associated with stillbirth (ra = 0.45 +/- 0.11, rp = 0.38 for NSB; ra = 0.46 +/- 0.13, rp = 0.17 for PSB). Conversely, NBA had low correlations with SB and PSB. Number born in total was moderately correlated to FD (ra = 0.34 +/- 0.15) and BI (ra = -0.37 +/- 0.15). A stronger relationship was found between NBA and BI (ra = -0.49 +/- 0.13), whereas the relationship with FD was lower (ra = 0.16 +/- 0.17). Moreover, FD was strongly correlated with stillbirth (ra = 0.42 +/- 0.12 with NSB), whereas BI was nearly independent of stillbirth. Contrary to selection on NBT, selection on NBA appears to be a good way to limit the negative side effects on stillbirth. Moreover, selection on NBA would lead to a small increase in FD and a faster and more regular birth process than would be obtained by selecting on NBT.