Evaluation of SNPs in the chicken HMGA2 gene as markers for body weight gain

A QTL affecting body weight in chickens has been mapped to GGA1, between the markers GCT0006 and MCW0106. The gene HMGA2, which was previously identified as a candidate gene for determining body height in humans and mice, is also conspicuously close to the MCW0106 marker in chickens. Subsequently, 14 SNP markers of HMGA2 were genotyped in CAU chicken resource populations, and the associations between body weight and those SNP markers that displayed polymorphisms were analysed. Three SNPs (rs13849241, rs15231472 and rs13849381) were found to be significantly correlated with body weight in chickens (P < 0.05). Furthermore, haplotypes constructed based on these three SNPs were also discovered to be associated with body weight in chickens at the ages of 6, 7, 9 and 12 weeks. These results suggest that the chicken HMGA2 gene is indeed involved in body weight gain.     

Identification of quantitative trait loci for shank length and growth at different development stages in chicken

Shank length affects chicken leg health and longer shanks are a source of leg problems in heavy-bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F₂ chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t , while developmental QTL affected shank growth from time t− 1 to time t . Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2–3, 4–5, 5–6, 10–11 and 11–12. A static QTL and a developmental QTL ( SQSL1 and DQSL2 ) were identified at GGA2 (between ADL0190 and ADL0152 ). SQSL1 explained 2.87–5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.     

Quantitative trait loci associated with body weight and abdominal fat traits on chicken chromosomes 3, 5 and 7

Body weight and abdominal fat traits in meat-type chickens are complex and economically important factors. Our objective was to identify quantitative trait loci (QTL) responsible for body weight and abdominal fat traits in broiler chickens. The Northeast Agricultural University Resource Population (NEAURP) is a cross between broiler sires and Baier layer dams. We measured body weight and abdominal fat traits in the F(2) population. A total of 362 F(2) individuals derived from four F(1) families and their parents and F(0) birds were genotyped using 29 fluorescent microsatellite markers located on chromosomes 3, 5 and 7. Linkage maps for the three chromosomes were constructed and interval mapping was performed to identify putative QTLs. Nine QTL for body weight were identified at the 5% genome-wide level, while 15 QTL were identified at the 5% chromosome-wide level. Phenotypic variance explained by these QTL varied from 2.95 to 6.03%. In particular, a QTL region spanning 31 cM, associated with body weight at 1 to 12 weeks of age and carcass weight at 12 weeks of age, was first identified on chromosome 5. Three QTLs for the abdominal fat traits were identified at the 5% chromosome-wide level. These QTLs explained 3.42 to 3.59% of the phenotypic variance. This information will help direct prospective fine mapping studies and can facilitate the identification of underlying genes and causal mutations for body weight and abdominal fat traits.     

Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome

Pulmonary hypertension syndrome (PHS), also referred to as ascites syndrome, is a growth-related disorder of chickens frequently observed in fast-growing broilers with insufficient pulmonary vascular capacity at low temperature and/or at high altitude. A cross between two genetically different broiler dam lines that originated from the White Plymouth Rock breed was used to produce a three-generation population. This population was used for the detection and localization of quantitative trait loci (QTL) affecting PHS-related traits. Ten full-sib families consisting of 456 G2 birds were typed with 420 microsatellite markers covering 24 autosomal chromosomes. Phenotypic observations were collected on 4202 G3 birds and a full-sib across family regression interval mapping approach was used to identify QTL. There was statistical evidence for QTL on chicken chromosome 2 (GGA2), GGA4 and GGA6. Suggestive QTL were found on chromosomes 5, 8, 10, 27 and 28. The most significant QTL were located on GGA2 for right and total ventricular weight as percentage of body weight (%RV and %TV respectively). A related trait, the ratio of right ventricular weight as percentage to total ventricular weight (RATIO), reached the suggestive threshold on this chromosome. All three QTL effects identified on GGA2 had their maximum test statistic in the region flanked by markers MCW0185 and MCW0245 (335-421 cM).     

Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens

Two growth-selected lines in chickens have been developed from a single founder population by divergent selection for body weight at 56 days of age. After more than 40 generations of selection they show a nine-fold difference in body weight at selection age and large differences in growth rate, appetite, fat deposition and metabolic characteristics. We have generated a large intercross between these lines comprising more than 800 F2 birds. QTL mapping revealed 13 loci affecting growth. The most striking observation was that the allele in the high weight line in all cases was associated with enhanced growth, but each locus explained only a small proportion of the phenotypic variance using a standard QTL model (1.3-3.1%). This result is in sharp contrast to our previous study where we reported that the two-fold difference in adult body size between the red junglefowl and White Leghorn domestic chickens is explained by a small number of QTLs with large additive effects. Furthermore, no QTLs for anorexia or antibody response were detected despite large differences for these traits between the founder lines. The result is an excellent example where a large phenotypic difference between populations occurs in the apparent absence of any single locus with large phenotypic effects. The study underscores the need for powerful experimental designs in genetic studies of multifactorial traits. No QTL at all would have reached genome-wide significance using a less powerful design (e.g. approx. 200 F2 individuals) regardless of the nine-fold phenotypic difference between the founder lines for the selected trait.     

Quantitative trait loci affecting body weight and fatness from a mouse line selected for extreme high growth.

Quantitative trait loci (QTL) influencing body weight were mapped by linkage analysis in crosses between a high body weight selected line (DU6) and a control line (DUKs). The two mouse lines differ in body weight by 106% and in abdominal fat weight by 100% at 42 days. They were generated from the same base population and maintained as outbred colonies. Determination of line-specific allele frequencies at microsatellite markers spanning the genome indicated significant changes between the lines on 15 autosomes and the X chromosome. To confirm these effects, a QTL analysis was performed using structured F2 pedigrees derived from crosses of a single male from DU6 with a female from DUKs. QTL significant at the genome-wide level were mapped for body weight on chromosome 11; for abdominal fat weight on chromosomes 4, 11, and 13; for abdominal fat percentage on chromosomes 3 and 4; and for the weights of liver on chromosomes 4 and 11, of kidney on chromosomes 2 and 9, and of spleen on chromosome 11. The strong effect on body weight of the QTL on chromosome 11 was confirmed in three independent pedigrees. The effect was additive and independent of sex, accounting for 21-35% of the phenotypic variance of body weight within the corresponding F2 populations. The test for multiple QTL on chromosome 11 with combined data from all pedigrees indicated the segregation of two loci separated by 36 cM influencing body weight.     

Quantitative trait loci affecting fatness in the chicken

An F2 chicken population of 442 individuals from 30 families, obtained by crossing a broiler line with a layer line, was used for detecting and mapping Quantitative Trait Loci (QTL) affecting abdominal fat weight, skin fat weight and fat distribution. Within-family regression analyses using 102 microsatellite markers in 27 linkage groups were carried out with genome-wide significance thresholds. The QTL for abdominal fat weight were found on chromosomes 3, 7, 15 and 28; abdominal fat weight adjusted for carcass weight on chromosomes 1, 5, 7 and 28; skin and subcutaneous fat on chromosomes 3, 7 and 13; skin fat weight adjusted for carcass weight on chromosomes 3 and 28; and skin fat weight adjusted for abdominal fat weight on chromosomes 5, 7 and 15. Interactions of the QTL with sex or family were unimportant and, for each trait, there was no evidence for imprinting or of multiple QTL on any chromosome. Significant dominance effects were obtained for all but one of the significant locations for QTL affecting the weight of abdominal fat, none for skin fat and one of the three QTL affecting fat distribution. The magnitude of each QTL ranged from 3.0 to 5.2% of the residual phenotypic variation or 0.2-0.8 phenotypic standard deviations. The largest additive QTL (on chromosome 7) accounted for more than 20% of the mean weight of abdominal fat. Significant positive and negative QTL were identified from both lines.     

Genetic mapping of quantitative trait loci affecting body weight, egg character and egg production in F2 intercross chickens

Phenotypic measurements of chicken egg character and production traits are restricted to mature females only. Marker assisted selection of immature chickens using quantitative trait loci (QTL) has the potential to accelerate the genetic improvement of these traits in the chicken population. The QTL for 12 traits (i.e. body weight (BW), six for egg character, three for egg shell colour and two for egg production) of chickens were identified. An F2 population comprising 265 female chickens obtained by crossing White Leghorn and Rhode Island Red breeds and genotyped for 123 microsatellite markers was used for detecting QTL. Ninety-six markers were mapped on 25 autosomal linkage groups, and 13 markers were mapped on one Z chromosomal linkage group. Eight previous unmapped markers were assigned to their respective chromosomes in this study. Significant QTL were detected for BW on chromosomes 4 and 27, egg weight on chromosome 4, the short length of egg on chromosome 4, and redness of egg shell colour (using the L*a*b* colour system) on chromosome 11. A significant QTL on the Z chromosome was linked with age at first egg. Significant QTL could account for 6-19% of the phenotypic variance in the F2 population.     

Identification of quantitative trait loci associated with egg quality, egg production, and body weight in an F2 resource population of chickens

Egg production and egg quality are complex sex-limited traits that may benefit from the implementation of marker-assisted selection. The primary objective of the current study was to identify quantitative trait loci (QTL) associated with egg traits, egg production, and body weight in a chicken resource population. Layer (White Leghorn hens) and broiler (Cobb-Cobb roosters) lines were crossed to generate an F2 population of 508 hens over seven hatches. Phenotypes for 29 traits (weekly body weight from hatch to 6 weeks, egg traits including egg, albumen, yolk, and shell weight, shell thickness, shell puncture score, percentage of shell, and egg shell colour at 35 and 55 weeks of age, as well as egg production between 16 and 55 weeks of age) were measured in hens of the resource population. Genotypes of 120 microsatellite markers on 28 autosomal groups were determined, and interval mapping was conducted to identify putative QTL. Eleven QTL tests representing two regions on chromosomes 2 and 4 surpassed the 5% genome-wise significance threshold. These QTL influenced egg colour, egg and albumen weight, percent shell, body weight, and egg production. The chromosome 4 QTL region is consistent with multiple QTL studies that define chromosome 4 as a critical region significantly associated with a variety of traits across multiple resource populations. An additional 64 QTL tests surpassed the 5% chromosome-wise significance threshold.     

Mapping quantitative trait loci regulating chicken body composition traits

Genome scans were conducted on an F₂ resource population derived from intercross of the White Plymouth Rock with the Silkies Fowl to detect QTL affecting chicken body composition traits. The population was genotyped with 129 microsatellite markers and phenotyped for 12 body composition traits on 238 F₂ individuals from 15 full-sib families. In total, 21 genome-wide QTL were found to be responsible for 11 traits, including two newly studied traits of proventriculus weight and shank girth. Three QTL were genome-wide significant: at 499 c m on GGA1 (explained 3.6% of phenotypic variance, P  < 0.01) and 51 c m on GGA5 (explained 3.3% of phenotypic variance, P  < 0.05) for the shank & claw weight and 502 c m on GGA1 (explained 1.4% of phenotypic variance, P  < 0.05) for wing weight. The QTL on GGA1 seemed to have pleiotropic effects, also affecting gizzard weight at 490 c m , shank girth at 489 c m and intestine length at 481 c m . It is suggested that further efforts be made to understand the possible pleiotropic effects of the QTL on GGA1 and that on GGA5 for two shank-related traits.     

A chicken linkage map based on microsatellite markers genotyped on a Japanese Large Game and White Leghorn cross

A detailed linkage map is necessary for efficient detection of quantitative trait loci (QTL) in chicken resource populations. In this study, microsatellite markers isolated from a (CA)n-enriched library (designated as ABR Markers) were mapped using a population developed from a cross between Japanese Game and White Leghorn chickens. In total, 296 markers including 193 ABR, 43 MCW, 31 ADL, 22 LEI, 3 HUJ, 2 GCT, 1 UMA and 1 ROS were mapped by linkage to chicken chromosomes 1-14, 17-21, 23, 24, 26-28 and Z. In addition, five markers were assigned to the map based on the chicken draft genomic sequence, bringing the total number of markers on the map to 301. The resulting linkage map will contribute to QTL mapping in chicken.     

Genome-wide association study of body weight in chicken F2 resource population

Chicken body weight is an economically important trait and great genetic progress has been accomplished in genetic selective for body weight. To identify genes and chromosome regions associated with body weight, we performed a genome-wide association study using the chicken 60 k SNP panel in a chicken F2 resource population derived from the cross between Silky Fowl and White Plymouth Rock. A total of 26 SNP effects involving 9 different SNP markers reached 5% Bonferroni genome-wide significance. A chicken chromosome 4 (GGA4) region approximately 8.6 Mb in length (71.6-80.2 Mb) had a large number of significant SNP effects for late growth during weeks 7-12. The LIM domain-binding factor 2 (LDB2) gene in this region had the strongest association with body weight for weeks 7-12 and with average daily gain for weeks 6-12. This GGA4 region was previously reported to contain body weight QTL. GGA1 and GGA18 had three SNP effects on body weight with genome-wide significance. Some of the SNP effects with the significance of "suggestive linkage" overlapped with previously reported results.     

A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population

We performed a genome-wide QTL scan for production traits in a line cross between Duroc and Pietrain breeds of pigs, which included 585 F(2) progeny produced from 31 full-sib families genotyped with 106 informative microsatellites. A linkage map covering all 18 autosomes and spanning 1987 Kosambi cM was constructed. Thirty-five phenotypic traits including body weight, growth, carcass composition and meat quality traits were analysed using least square regression interval mapping. Twenty-four QTL exceeded the genome-wide significance threshold, while 47 QTL reached the suggestive threshold. These QTL were located at 28 genomic regions on 16 autosomal chromosomes and QTL in 11 regions were significant at the genome-wide level. A QTL affecting pH value in loin was detected on SSC1 between marker-interval S0312-S0113 with strong statistical support (P < 3.0 x 10(-14)); this QTL was also associated with meat colour and conductivity. QTL for carcass composition and average daily gain was also found on SSC1, suggesting multiple QTL. Seventeen genomic segments had only a single QTL that reached at least suggestive significance. Forty QTL exhibited additive inheritance whereas 31 QTL showed (over-) dominance effects. Two QTL for trait backfat thickness were detected on SSC2; a significant paternal effect was found for a QTL in the IGF2 region while another QTL in the middle of SSC2 showed Mendelian expression.     

Mapping quantitative trait loci for egg production traits in an F2 intercross of Oh-Shamo and White Leghorn chickens

We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F₂ hens derived from an intercross between the Oh‐Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main‐effect QTL for AFE on chromosome 1 and four main‐effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome‐wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26–34 weeks of hen age) and the remaining one was discovered at the late stage (54–58 weeks). The alleles at the two EPR QTL derived from the Oh‐Shamo breed unexpectedly increased the trait values, irrespective of the Oh‐Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh‐Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main‐effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4–8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.     

Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population

We searched for quantitative trait loci (QTL) underlying fitness-related traits in a free-living pedigree of 588 Soay sheep in which a genetic map using 251 markers with an average spacing of 15 cM had been established previously. Traits examined included birth date and weight, considered both as maternal and offspring traits, foreleg length, hindleg length, and body weight measured on animals in August and jaw length and metacarpal length measured on cleaned skeletal material. In some cases the data were split to consider different age classes separately, yielding a total of 15 traits studied. Genetic and environmental components of phenotypic variance were estimated for each trait and, for those traits showing nonzero heritability (N= 12), a QTL search was conducted by comparing a polygenic model with a model including a putative QTL. Support for a QTL at genome-wide significance was found on chromosome 11 for jaw length; suggestive QTL were found on chromosomes 2 and 5 (for birth date as a trait of the lamb), 8 (birth weight as a trait of the lamb), and 15 (adult hindleg length). We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general.     

Quantitative trait Loci for glomerulosclerosis, kidney weight and body weight in the focal glomerulosclerosis mouse model.

In 183 male progeny derived from a backcross between the FGS/Kist strain, a new mouse model for focal glomerulosclerosis (FGS) in humans, and the standard normal strain, C57BL/6J, we performed a genome-wide scan for quantitative trait loci (QTLs) affecting the glomerulosclerosis index (GSI) based on histological observation as well as kidney and body weights. Two QTLs for GSI (Gsi1-2) located on chromosomes (Chrs) 8 and 10, a kidney weight QTL (Kdw1) on Chr 19, and a body weight QTL (Bdw1) on Chr 13 were detected at the genome-wide 5% or less level. The allele derived from FGS/Kist increased GSI at Gsi1, but decreased it at Gsi2. The mice homozygous for the FGS/Kist allele decreased body and kidney weights. The identified QTLs accounted for 5-8% of the phenotypic variance.     

不同发育时期小麦粒重性状QTL的动态分析

利用6044×01-35构建的重组自交系(RIL)群体为试验材料,对小麦粒重性状进行发育动态QTL分析。结果表明,在小麦花后子粒灌浆的7个不同时期,两个试验点共检测到16个与粒重性状相关的QTL。其中开花后20d检测到的单穗粒重QTL位于2A染色体上,解释率达12%,遗传效应超过10;两环境下控制千粒重QTL在7个时期均被检测到。花后的各个时期均能在Xgwm448-Xgpw7399标记区间定位到千粒重QTL。其中花后10d检测到1个千粒重QTL,位于2A染色体的Xgwm448-Xgpw7399标记区间,解释较大的表型变异,达到18%。Qtl8、Qtl13和Qtl14均定位在Xgwm448-Xgpw7399标记区间的同一位置,共同解释11%的表型变异。花后20d和花后25d均检测到1个QTL,位于2A染色体的Xgwm372-Xgwm95标记区间的不同位点,均能解释4%的表型变异。花后40d检测到1个QTL,位于1D染色体的Xwmc93-Xgpw2224标记区间,解释1%的表型变异。从连锁群的位置上看,控制千粒重的QTL主要集中在2A染色体的Xgwm448-Xgpw7399标记区间,这是一个控制千粒重QTL的富集区域,以期进行精细定位和图位克隆。     

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Gestation length and maternal ability are important to improve the sow reproduction efficiency and their offspring survival. To map quantitative trait loci (QTL) for gestation length and maternal ability related traits including piglet survival rate and average body weight of piglets at weaning, more than 200 F2 sows from a White Duroc × Erhualian resource population were phenotyped. A genome-wide scan was performed with 194 microsatellite markers covering the whole pig genome. QTL analysis was carried out using a composite regression interval mapping method via QTL express. The results showed that total number of born piglets was significantly correlated with gestation length (r = -0.13, P < 0.05). Three QTL were detected on pig chromosome (SSC)2, 8 and 12 for gestation length. The QTL on SSC2 achieved the 5% genome-wide significant level and the QTL on SSC8 was consistent with previous reports. Four suggestive QTL were identified for maternal ability related traits including 1 QTL for survival rate of piglets at weaning on SSC8, 3 QTL for average body weight of piglet at weaning on SSC3, 11 and 13.     

Quantitative trait loci for body weight in the intercross between SM/J and A/J mice.

We performed a genome-wide quantitative trait locus (QTL) analysis of body weight at 10 weeks of age in a population of 321 intercross offspring from SM/J and A/J mice, progenitor strains of SMXA recombinant inbred strains. Interval mapping revealed two significant QTLs, Bwq3 (body weight QTL3) and Bwq4, on Chromosomes (Chrs) 8 and 18 respectively, and five suggestive QTLs on Chrs 2, 6, 7, 15 and 19. Bwq3 and Bwq4 explained 6% of the phenotypic variance. The SM/J alleles at both QTLs increased body weight, though the SM/J mouse was smaller than the A/J mouse. On the other hand, four of the five suggestive QTLs detected had male-specific effects on body weight and the remainder was female-specific. These suggestive QTLs explained 5-6% of the phenotypic variance and all the SM/J alleles decreased body weight.     

Mapping and exclusion mapping of genomic imprinting effects in mouse F2 families

Parent-of-origin effects were mapped by multimarker regression analysis in a cross between a high body weight selected line (DU6) and a control line (DUKs). The difference between F(2) progeny being heterozygous Qq and qQ (first allele is paternally derived) for grandpaternal Q and grandmaternal q alleles was genome-wide significant for the traits liver weight and spleen weight with a paternal imprinting effect at 1 cM on proximal chromosome 11. Suggestive imprinting effects (chromosome-wide error probability less than 0.05) were found for the traits body weight, liver weight, and kidney weight, and were located on chromosome 14 at 25 cM, 23 cM, and 32 cM, respectively. A genome-wide significant quantitative trait locus (QTL) for spleen weight at 26 cM slightly failed the suggestive significance level for imprinting. The effect was consistently maternal for all these traits on chromosome 14. Further suggestive imprinting effects were found for abdominal fat percentage on chromosome 3, for spleen weight on chromosome 5, and for liver weight on chromosome X. Our results are supported by a likely imprinting in a human genome region with homology to mouse chromosome 14 and agree well with the known imprinting of proximal chromosome 11 in the mouse.