F2 Intercross Research Articles

A breeding strategy to identify modifiers of high genetic risk for methamphetamine intake.

Trace amine-associated receptor 1 (Taar1) impacts methamphetamine (MA) intake. A mutant allele (Taar1m1J ) derived from the DBA/2J mouse strain codes for a non-functional receptor, and Taar1m1J/m1J mice consume more MA than mice possessing the reference Taar1+ allele. To study the impact of this mutation in a genetically diverse population, heterogeneous stock-collaborative cross (HS-CC) mice, the product of an eight-way cross of standard and wild-derived strains, were tested for MA intake. HS-CC had low MA intake, so an HS-CC by DBA/2J strain F2 intercross was created to transfer the mutant allele onto the diverse background, and used for selective breeding. To study residual variation in MA intake existing in Taar1m1J/m1J mice, selective breeding for higher (MAH) vs lower (MAL) MA intake was initiated from Taar1m1J/m1J F2 individuals; a control line of Taar1+/+ individuals (MAC) was retained. The lines were also examined for MA-induced locomotor and thermal responses, and fluid and tastant consumption. Taar1m1J/m1J F2 mice consumed significantly more MA than Taar1+/+ F2 mice. Response to selection was significant by generation 2 and there were corresponding differences in fluid consumed. Fluid consumption was not different in non-MA drinking studies. Taar1m1J/m1J genotype (MAL or MAH vs MAC mice) was associated with heighted MA locomotor and reduced hypothermic responses. MAL mice exhibited greater sensitization than MAH mice, but the selected lines did not consistently differ for thermal or tastant phenotypes. Residual variation among high-risk Taar1m1J/m1J mice appears to involve mechanisms associated with neuroadaptation to MA, but not sensitivity to hypothermic effects of MA.

Ablation of Iah1, a candidate gene for diet-induced fatty liver, does not affect liver lipid accumulation in mice.

Nonalcoholic fatty liver disease (NAFLD) is a pathological condition caused by excess triglyceride deposition in the liver. The SMXA-5 severe fatty liver mouse model has been established from the SM/J and A/J strains. To explore the genetic factors involved in fatty liver development in SMXA-5 mice, we had previously performed quantitative trait locus (QTL) analysis, using (SM/J×SMXA-5)F2 intercross mice, and identified Fl1sa on chromosome 12 (centromere-53.06 Mb) as a significant QTL for fatty liver. Furthermore, isoamyl acetate-hydrolyzing esterase 1 homolog (Iah1) was selected as the most likely candidate gene for Fl1sa. Iah1 gene expression in fatty liver-resistant A/J-12SM mice was significantly higher than in fatty liver-susceptible A/J mice. These data indicated that the Iah1 gene might be associated with fatty liver development. However, the function of murine Iah1 remains unknown. Therefore, in this study, we created Iah1 knockout (KO) mice with two different backgrounds [C57BL/6N (B6) and A/J-12SM (A12)] to investigate the relationship between Iah1 and liver lipid accumulation. Liver triglyceride accumulation in Iah1-KO mice of B6 or A12 background did not differ from their respective Iah1-wild type mice under a high-fat diet. These results indicated that loss of Iah1 did not contribute to fatty liver. On the other hands, adipose tissue dysfunction causes lipid accumulation in ectopic tissues (liver, skeletal muscle, and pancreas). To investigate the effect of Iah1 deficiency on white adipose tissue, we performed DNA microarray analysis of epididymal fat in Iah1-KO mice of A12 background. This result showed that Iah1 deficiency might decrease adipokines Sfrp4 and Metrnl gene expression in epididymal fat. This study demonstrated that Iah1 deficiency did not cause liver lipid accumulation and that Iah1 was not a suitable candidate gene for Fl1sa.

RNA-Seq Analysis of Genetic and Transcriptome Network Effects of Dual-Trait Selection for Ethanol Preference and Withdrawal Using SOT and NOT Genetic Models.

BackgroundGenetic factors significantly affect alcohol consumption and vulnerability to withdrawal. Furthermore, some genetic models showing predisposition to severe withdrawal are also predisposed to low ethanol (EtOH) consumption and vice versa, even when tested independently in naïve animals.MethodsBeginning with a C57BL/6J × DBA/2J F2 intercross founder population, animals were simultaneously selectively bred for both high alcohol consumption and low acute withdrawal (SOT line), or vice versa (NOT line). Using randomly chosen fourth selected generation (S4) mice (N = 18‐22/sex/line), RNA‐Seq was employed to assess genome‐wide gene expression in ventral striatum. The MegaMUGA array was used to detect genome‐wide genotypic differences. Differential gene expression and the weighted gene co‐expression network analysis were implemented as described elsewhere (Genes Brain Behav 16, 2017, 462).ResultsThe new selection of the SOT and NOT lines was similar to that reported previously (Alcohol Clin Exp Res 38, 2014, 2915). One thousand eight hundred and sixteen transcripts were detected as differentially expressed between the lines. For genes more highly expressed in the SOT line, there was enrichment in genes associated with cell adhesion, synapse organization, and postsynaptic membrane. The genes with a cell adhesion annotation included 23 protocadherins, Mpdz and Dlg2. Genes with a postsynaptic membrane annotation included Gabrb3, Gphn, Grid1, Grin2b, Grin2c, and Grm3. The genes more highly expressed in the NOT line were enriched in a network module (red) with annotations associated with mitochondrial function. Several of these genes were module hub nodes, and these included Nedd8, Guk1, Elof1, Ndufa8, and Atp6v1f. ConclusionsMarked effects of selection on gene expression were detected. The NOT line was characterized by higher expression of hub nodes associated with mitochondrial function. Genes more highly expressed in the SOT aligned with previous findings, for example, Colville and colleagues (Genes Brain Behav 16, 2017, 462) that both high EtOH preference and consumption are associated with effects on cell adhesion and glutamate synaptic plasticity.

A quantitative trait locus on chromosome 2 was identified that accounts for a substantial proportion of phenotypic variance of the yellow plumage color in chicken

Chicken plumage color is an important economical trait in poultry breeding, as triple-yellow indigenous broilers are preferred over western commercial broilers in the Chinese market. However, the studies on the pigmentation of plumage coloration are relatively rare at present. Here, we performed a genome-wide mapping study on an F2 intercross, whose 2 founders were one hybrid commercial line “High Quality chicken Line A” that originated from the Anak red chicken and one indigenous line “Huiyang Beard” chicken that is a classical “triple-yellow” Chinese indigenous breed. Moreover, we used an automatic colorimeter that can quantitatively assess the colorations in L∗, a∗, and b∗ values. One major quantitative trait locus (QTL) on chromosome 2 was thus identified by both genome-wide association and linkage analyses, which could explain 10 to 20% of the total phenotypic variance of the b∗ measurements of the back plumage color. Using linkage analysis, 2 additional QTL on chromosome 1 and 20 were also found to be significantly associated with the plumage coloration in this cross. With additional samples from Anak red and Huiyang Beard chickens as well as pooled resequencing data from the 2 founders of this cross, we then further narrowed down the QTL regions and identified several candidate genes, such as CABLES1, CHST11, BCL2L1, and CHD22. As the effects of QTL found in this study were substantial, quantitatively measuring the coloration rather than the descriptive measurements provides stronger statistical power for the analyses. In addition, this major QTL on chromosome 2 that was associated with feather pigmentation at the genome-wide level will facilitate the future chicken breeding for yellow plumage color. In conclusions, we mapped 3 associated QTL on chromosome 1, 2, and 20. The candidate genes identified in this study shed light in the genetic basis of yellow plumage color in chicken.

Mouse genome-wide association and systems genetics identifies Lhfp as a regulator of bone mass

Bone mineral density (BMD) is a strong predictor of osteoporotic fracture. It is also one of the most heritable disease-associated quantitative traits. As a result, there has been considerable effort focused on dissecting its genetic basis. Here, we performed a genome-wide association study (GWAS) in a panel of inbred strains to identify associations influencing BMD. This analysis identified a significant (P = 3.1 x 10−12) BMD locus on Chromosome 3@52.5 Mbp that replicated in two separate inbred strain panels and overlapped a BMD quantitative trait locus (QTL) previously identified in a F2 intercross. The association mapped to a 300 Kbp region containing four genes; Gm2447, Gm20750, Cog6, and Lhfp. Further analysis found that Lipoma HMGIC Fusion Partner (Lhfp) was highly expressed in bone and osteoblasts. Furthermore, its expression was regulated by a local expression QTL (eQTL), which overlapped the BMD association. A co-expression network analysis revealed that Lhfp was strongly connected to genes involved in osteoblast differentiation. To directly evaluate its role in bone, Lhfp deficient mice (Lhfp-/-) were created using CRISPR/Cas9. Consistent with genetic and network predictions, bone marrow stromal cells (BMSCs) from Lhfp-/- mice displayed increased osteogenic differentiation. Lhfp-/- mice also had elevated BMD due to increased cortical bone mass. Lastly, we identified SNPs in human LHFP that were associated (P = 1.2 x 10−5) with heel BMD. In conclusion, we used GWAS and systems genetics to identify Lhfp as a regulator of osteoblast activity and bone mass.

An Animal Model of Cutaneous Cyst Development Enables the Identification of Three Quantitative Trait Loci, Including the Homologue of a Human Locus (TRICY1)

Using inbred BN and LE/Stm rats susceptible and resistant, respectively, to chemically induced cutaneous cyst development we were able to further unveil the genetic architecture of inherited multiple cyst formation. N-methyl-N-nitrosourea-treated (BN x LE) F2 intercross rats proved to develop differential numbers of cutaneous cysts, demonstrating epidermal, trichilemmal and verrucous keratinization types. Male rats developed significantly more cysts per animal than females. QTL interval mapping yielded three loci on rat chromosomes 1, 8 and 11 (Ccd1, Ccd2, Ccd3) linked to cutaneous cyst formation. Ccd2 proved to be homologous to the human TRICY1 region which could further be narrowed down by genome comparison in both species. It contains 11 genes with evidence of expression in human keratinocytes.

QTL fine mapping for intramuscular fat and fatty acid composition using high-density SNP chip array on SSC12 in Korean native pig × Yorkshire F2 population

Intramuscular fat (IMF) and fatty acid composition are characteristics that are used as important indicators of evaluating high quality pork and contribute to the economic benefits of the pig farming industry. In this study, quantitative trait loci (QTL) fine mapping of chromosome 12 was performed in a population of F2 intercross between Yorkshire (YS) and Korean native pigs (KNPs) by adopting combined linkage and linkage disequilibrium method using high-density SNP chips. QTLs for IMF (H3GA0034813 to H3GA0034965) and oleic acid (C18:1) (ASGA0054380 to ALGA0066299) were located at 120 cM (54.112–57.610 kb) and 85 cM (36.097–38.601 kb), respectively, within chromosome 12 (Sscrofa11.1 genomic reference). In addition, 31 candidate genes present within the IMF QTL region and 28 candidate genes existing within C18:1 QTL region were chosen. In order to understand the function of these candidate genes at the molecular level, these candidate genes were functionally categorized by studying gene ontology and analyzing network and pathway. Among the 59 candidate genes within the region of IMF QTL and C18:1 QTL, five (MYH1, MYH2, MYH4, ACACA, and RPS6KB1) directly interacting candidate genes were found. Furthermore, the RPS6KB1 gene was assumed to be an important candidate gene that is involved in leptin and insulin signaling pathway and participates in controlling adipogenic differentiation, fat deposition, and fatty acid composition, which is related to obesity of pigs.

Genetic Predisposition to Hepatocarcinogenesis in Inbred and Outbred Mouse Lines Selected for High or Low Inflammatory Response.

AIRmax and AIRmin mouse strains phenotypically selected for high and low acute inflammatory responsiveness (AIR) are, respectively, susceptible or resistant to developing hepatocellular carcinoma (HCC) induced by the chemical carcinogens urethane and diethylnitrosamine (DEN). Early production of TNF-α, IL-1β, and IL-6 in the liver after DEN treatment correlated with tumor development in AIRmax mice. Transcriptome analysis of livers from untreated AIRmax and AIRmin mice showed specific gene expression profiles in each line, which might play a role in their differential susceptibility to HCC. Linkage analysis with SNP markers in F2 (AIRmax×AIRmin) intercross mice revealed two quantitative trait loci (QTL) in chromosomes 2 and 9, which are significantly associated with the number and progression of urethane-induced liver tumors. An independent linkage analysis with an intercross population from A/J and C57BL/6J inbred mice mapped regions in chromosomes 1 and 7 associated with the progression of urethane-induced liver tumors, evidencing the heterogeneity of HCC genetic control.

Effects of quantitative trait loci determining testicular weight in DDD/Sgn inbred mice are strongly influenced by circulating testosterone levels.

ObjectiveTesticular growth and development are strongly influenced by androgen. Although both testis weight and plasma testosterone level are inherited traits, the interrelationship between them is not fully established. Males of DDD/Sgn (DDD) mice are known to have extremely heavy testes and very high plasma testosterone level among inbred mouse strains. We dissected the genetic basis of testis weight and analyzed the potential influence of plasma testosterone level in DDD mice.MethodsQuantitative trait loci (QTL) mapping of testis weight was performed with or without considering the influence of plasma testosterone level in reciprocal F2 intercross populations between DDD and C57BL/6J (B6) mice, thereby assessing the influence of testosterone on the effect of testis weight QTL. Candidate genes for testis weight QTL were investigated by next-generation sequencing analysis.ResultsFour significant QTL were identified on chromosomes 1, 8, 14, and 17. The DDD-derived allele was associated with increased testis weight. The F2 mice were then divided into two groups according to the plasma testosterone level (F2 mice with relatively “low” and “high” testosterone levels), and QTL scans were again performed. Although QTL on chromosome 1 was shared in both F2 mice, QTL on chromosomes 8 and 17 were identified specifically in F2 mice with relatively high testosterone levels. By whole-exome sequencing analysis, we identified one DDD-specific missense mutation Pro29Ser in alpha tubulin acetyltransferase 1 (Atat1).ConclusionMost of the testis weight QTL expressed stronger phenotypic effect when they were placed on circumstance with high testosterone level. High testosterone influenced the QTL by enhancing the effect of DDD-derived allele and diminishing the effects of B6-derived allele. Since Pro29Ser was not identified in other inbred mouse strains, and since Pro29 in Atat1 has been strongly conserved among mammalian species, Atat1 is a plausible candidate for testis weight QTL on chromosome 17.

Genome-wide association study identifies variants in the CAPN9 gene associated with umbilical hernia in pigs.

Pig umbilical hernia (UH) affects pig welfare and brings considerable economic loss to the pig industry. To date, the molecular mechanisms underlying pig UH are still poorly understood. To identify potential loci for susceptibility to this disease, we performed a genome-wide association study in an Erhualian×Shaziling F2 intercross population. A total of 45 animals were genotyped using Illumina Porcine SNP60 BeadChips. We observed a SNP (rs80993347) located in the calpain-9 (CAPN9) gene on Sus scrofa chromosome 14 that was significantly associated with UH (P=1.97×10-10 ). Then, we identified a synonymous mutation rs321865883 (g.20164T>C) in exon 10 of the CAPN9 gene that distinguished two affected individuals (CC) from their normal full-sibs (TC). Finally, quantitative polymerase chain reaction was explored to investigate the mRNA expression profile of the CAPN9 gene in 12 tissues in Yorkshire pigs at different developmental stages (3, 90 and 180days). CAPN9 showed high expression levels in the gastrointestinal tract at these three growth stages. The results of this study indicate that the CAPN9 gene might be implicated in UH. Further studies are required to establish a role of CAPN9 in pig UH.

A deletion in the Ctns gene causes renal tubular dysfunction and cystine accumulation in LEA/Tohm rats

The Long-Evans Agouti (LEA/Tohm) rat has recently been established as a new rat model of type 2 diabetes. The onset of diabetes mellitus was observed only in male LEA/Tohm rats; however, urinary glucose appeared before the onset of diabetes. To clarify the genetic basis of urinary glucose, we performed genetic linkage analysis using (BN × LEA) F2 intercross progeny. A recessively acting locus responsible for urinary glucose excretion (ugl) was mapped to a 7.9 Mb region of chromosome 10, which contains the cystinosin (Ctns) gene. The Ctns gene encodes the cystine transporter, which transports cystine out of the lysosome and is responsible for nephropathic cystinosis in humans. Sequence analysis identified a 13-bp deletion in the Ctns gene, leading to a truncated and loss-of-function protein, which cause cystine accumulation in various tissues. We also developed a novel congenic rat strain harboring the Ctnsugl mutation on the F344 genetic background. Phenotypic analysis of F344-Ctnsugl rats indicated that the incidence of urinary glucose was 100% in both males and females at around 40 weeks of age, and marked cystine accumulation was observed in the tissues, as well as remarkable renal lesions and cystine crystals in the lysosomes of the renal cortex. Furthermore, treatment with cysteamine depleted the cystine contents in F344-Ctnsugl rat embryonic fibroblasts. These results indicated that the F344-Ctnsugl rat provides a novel rat model of cystinosis, which allows not only a better understanding of the pathogenesis and pathophysiology of cystinosis but will also contribute to the development of new therapies.

Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p

BackgroundThe size and type of ears are important conformation characteristics that distinguish pig breeds. A significant quantitative trait locus (QTL) for ear size has been identified on SSC5 (SSC for Sus scrofa chromosome) but the underlying causative gene and mutation remain unknown. Thus, our aim was to identify the gene responsible for enlarged ears in pig.ResultsFirst, we narrowed down the QTL region on SSC5 to a 137.85-kb interval that harbors only the methionine sulfoxide reductase B3 (MSRB3) gene. Then, we identified a 38.7-kb copy number variation (CNV) that affects the last two exons of MSRB3 and could be the candidate causative mutation for this QTL. This CNV showed complete concordance with genotype at the QTL of the founder animals in a white Duroc × Erhualian F2 intercross and was found only in pigs from six Chinese indigenous breeds with large ears and from the Landrace breed with half-floppy ears. Moreover, it accounted for the significant association with ear size on SSC5 across the five pig populations tested. eQTL mapping revealed that this CNV was significantly associated with the expression of the microRNA (miRNA) miR-584-5p, which interacts with MSRB3, one of its target genes. In vivo and in vitro experiments confirmed that miR-584-5p inhibits the translation of MSRB3 mRNA. Taken together, these results led us to conclude that presence of the 38.7-kb CNV in the genome of some pig breeds affects ear size by altering the expression of miR-584-5p, which consequently hinders the expression of one of its target genes (e.g. MSRB3).ConclusionsOur findings shed insight into the underlying mechanism of development of external ears in mammals and contribute to a better understanding of how the presence of CNV can regulate gene expression.

Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail

The L strain of Japanese quail exhibits a plumage phenotype that is light yellowish in colour. In this study, we identified a nonsense mutation in the premelanosome protein (PMEL) gene showing complete concordance with the yellowish plumage within a pedigree as well as across strains by genetic linkage analysis of an F2 intercross population using approximately 2,000 single nucleotide polymorphisms (SNPs) that were detected by double digest restriction site-associated DNA sequencing (ddRAD-seq). The yellowish plumage was inherited in an autosomal recessive manner, and the causative mutation was located within an 810-kb genomic region of the LGE22C19W28_E50C23 linkage group (LGE22). This region contained the PMEL gene that is required for the normal melanosome morphogenesis and eumelanin deposition. A nonsense mutation that leads to a marked truncation of the deduced protein was found in PMEL of the mutant. The gene expression level of PMEL decreased substantially in the mutant. Genotypes at the site of the nonsense mutation were fully concordant with plumage colour phenotypes in 196 F2 offspring. The nonsense mutation was not found in several quail strains with non-yellowish plumage. Thus, the yellowish plumage may be caused by the reduced eumelanin content in feathers because of the loss of PMEL function.

Marker-assisted pyramiding of two major, broad-spectrum bacterial blight resistance genes, Xa21 and Xa33 into an elite maintainer line of rice, DRR17B.

Bacterial blight (BB) disease reduces the yield of rice varieties and hybrids considerably in many tropical rice growing countries like India. The present study highlights the development of durable BB resistance into the background of an elite maintainer of rice, DRR17B, by incorporating two major dominant genes, Xa21 and Xa33 through marker-assisted backcross breeding (MABB). Through two sets of backcrosses, the two BB resistance genes were transferred separately to DRR17B. In this process, at each stage of backcrossing, foreground selection was carried out for the target resistance genes and for non-fertility restorer alleles concerning the major fertility restorer genes Rf3 and Rf4, using gene-specific PCR-based markers, while background selection was done using a set of 61 and 64 parental polymorphic SSR markers respectively. Backcross derived lines possessing either Xa21 or Xa33 along with maximum genome recovery of DRR17B were identified at BC3F1 generation and selfed to develop BC3F2s. Plants harboring Xa21 or Xa33 in homozygous condition were identified among BC3F2s and were intercrossed with each other to combine both the genes. The intercross F1 plants (ICF1) were selfed and the intercross F2(ICF2) plants possessing both Xa21 and Xa33 in homozygous condition were identified with the help of markers. They were then advanced further by selfing until ICF4 generation. Selected ICF4 lines were evaluated for their resistance against BB with eight virulent isolates and for key agro-morphological traits. Six promising two-gene pyramiding lines of DRR17B with high level of BB resistance and agro-morphological attributes similar or superior to DRR17B with complete maintenance ability have been identified. These lines with elevated level of durable resistance may be handy tool for BB resistance breeding.

Joint linkage and linkage disequilibrium mapping reveals association of BRMS1L with total teat number in a large intercross between Landrace and Korean native pigs

Previously, we reported a quantitative trait locus (QTL) that affects total teat number (TTN) on pig chromosome 7 (SSC7) in a large F2 intercross population between Landrace and Korean native pigs. The aim of this study was to refine the QTL associated with TTN and to identify positional candidate gene(s) within the refined genomic region. TTN was recorded in 1105 F2 progeny. All experimental animals were genotyped using 980 informative single nucleotide polymorphism (SNP) markers located on SSC7. A haplotype-based linkage and association analysis using the PHASEBOOK programme was applied to refine the QTL region. Additionally, linear mixed-effect models were used to assess the effect of a positional candidate gene on TTN and other economically important traits [i.e., thoracic vertebrae number (THO), carcass body length (CBL) and weight (CW), back fat thickness (BFT) and intramuscular fat content (IMF) in loin muscles]. Joint linkage and association analysis refined the critical region to a 4.50 Mb region that included a novel positional candidate gene, BRMS1L that encodes the breast cancer metastasis-suppressor 1-like protein, which could possibly be implicated in normal mammary gland development. Significant association of an SNP marker (g. −1087 G > A) in the 5′-flanking region of BRMS1L with TTN (P = 1.10 × 10−8), THO (P = 5.80 × 10−4), and CBL (P = 0.038) was observed. Based on these data, we propose BRMS1L as a positional candidate gene for TTN in pigs. After validation of the association in other independent populations, these results could be useful in optimizing breeding programmes that improve TTN and other economically important traits in swine.

Modifier locus mapping of a transgenic F2 mouse population identifies CCDC115 as a novel aggressive prostate cancer modifier gene in humans

BackgroundIt is well known that development of prostate cancer (PC) can be attributed to somatic mutations of the genome, acquired within proto-oncogenes or tumor-suppressor genes. What is less well understood is how germline variation contributes to disease aggressiveness in PC patients. To map germline modifiers of aggressive neuroendocrine PC, we generated a genetically diverse F2 intercross population using the transgenic TRAMP mouse model and the wild-derived WSB/EiJ (WSB) strain. The relevance of germline modifiers of aggressive PC identified in these mice was extensively correlated in human PC datasets and functionally validated in cell lines.ResultsAggressive PC traits were quantified in a population of 30 week old (TRAMP x WSB) F2 mice (n = 307). Correlation of germline genotype with aggressive disease phenotype revealed seven modifier loci that were significantly associated with aggressive disease. RNA-seq were analyzed using cis-eQTL and trait correlation analyses to identify candidate genes within each of these loci. Analysis of 92 (TRAMP x WSB) F2 prostates revealed 25 candidate genes that harbored both a significant cis-eQTL and mRNA expression correlations with an aggressive PC trait. We further delineated these candidate genes based on their clinical relevance, by interrogating human PC GWAS and PC tumor gene expression datasets. We identified four genes (CCDC115, DNAJC10, RNF149, and STYXL1), which encompassed all of the following characteristics: 1) one or more germline variants associated with aggressive PC traits; 2) differential mRNA levels associated with aggressive PC traits; and 3) differential mRNA expression between normal and tumor tissue. Functional validation studies of these four genes using the human LNCaP prostate adenocarcinoma cell line revealed ectopic overexpression of CCDC115 can significantly impede cell growth in vitro and tumor growth in vivo. Furthermore, CCDC115 human prostate tumor expression was associated with better survival outcomes.ConclusionWe have demonstrated how modifier locus mapping in mouse models of PC, coupled with in silico analyses of human PC datasets, can reveal novel germline modifier genes of aggressive PC. We have also characterized CCDC115 as being associated with less aggressive PC in humans, placing it as a potential prognostic marker of aggressive PC.

Identification of Two Additional Genomic Loci Responsible for experimentally induced testicular teratoma 2 and 3 (ett2 and ett3).

Experimental testicular teratomas (ETTs) can be induced in 129/Sv mouse by E12.5 fetal testes transplant into adult testes. Previously, we conducted linkage analysis to explore candidate genes possibly involved in ETT development using F2 intercross fetuses derived from F1[LTXBJ × 129/Sv- + /Ter (+ /+)] hybrids. By linkage analysis on Chr 18 and Chr 19, we identified the genomic locus for experimental testicular teratoma 1 (ett1) on Chr 18. In the present study, we conducted additional mapping and linkage analysis on teratoma susceptibility and genome composition on Chr 1-17. The results revealed two new candidate loci, experimental testicular teratoma 2 (ett2) and experimental testicular teratoma 3 (ett3), on Chr 3 and 7. Interestingly, the rates of ETT generation were increased in the case of ett2 and ett3 regions replaced with LTXBJ strain. To determine whether a polymorphic gene was present, we performed exome analysis of 129/Sv- + /Ter (+ /+) and LTXBJ. This revealed the presence of SNPs in all three loci, ett1 to ett3. ett1 contains polymorphic Mc4r; ett2 contains polymorphic Polr3c, Cd160, and Pdzk1; and ett3 contains polymorphic Prmt3. We found additional loci responsible for ETT formation, namely, ett2 and ett3, and identified candidate genes in these regions by exome analysis.

SNP- and pedigree-based estimation of genetic parameters for back fat thickness traits in an F2 intercross between Landrace and Jeju native black pigs

SNP- and pedigree-based estimation of genetic parameters for back fat thickness traits in an F2 intercross between Landrace and Jeju native black pigs

Quantitative Trait Loci Associated with Egg Traits in F2 Intercross between Golden Montazah and White Leghorn Chickens

Quantitative trait loci (QTL) affecting age at first egg (AFE), weight at first egg (WFE), 120-days of egg number (EN), egg weight (EW), Hugh unit (HU) and egg shell strength (ESS) were identified in F2 intercross population produced by crossing males of Golden Montazah (M) with females of White Leghorn (L). Phenotypic data for egg traits of 4131 hens were analyzed using multi-traits animal model. For QTL analysis, 1011 hens of F2 were genotyped using 45 genetic markers in nine autosomal linkage groups and Z chromosome and the mixed model including the fixed effects of hatch along with the additive and dominance effects of QTL as random effects was used. The total map length was 1949 cM and a total of 15 significant QTL were detected for egg traits and these QTL were distributed over four distinct regions on five chromosomes (2, 3, 4, 8 and Z). The QTL region on the Z chromosome was large and including QTL for AFW, EW, EN and ESS. The significant QTL were located on chromosomes 2, 4, 8 and Z for WFE at position of 322, 156, 61 and 102 cM; on the chromosomes 3 and Z for AFE at position of 189 and 128 cM, on the chromosomes 4 and Z sex chromosome for EW at position of 191 and 76 cM; on the chromosomes 4 and Z for EN at position of 55 and 89 cM; on the chromosomes 2, 4 and 8 for HU at position of 89, 222, and 18 cM; on Z sex chromosome for ESS at position of 97 cM, respectively. A total of four significant QTL were detected at 5 % chromosome-wise significance level, while a total of 11 significant QTL were detected at 1 % genomic-wise significance level and the total variances explained by QTL were 10.7, 12.2, 18.6, 12.2, 15.3 and 5 % for WFE, AFE, EW, EN, HU and ESS, respectively. The additive effects attributable to QTL explaining 5.4 to 53.0 % for WFE, 1.6 % for AFE, 4.4 to 8.2 % for EN, 3.0 to 6.5 % for EW, -0.6 and -6.2 % for Hu and -55.6 % for ESS of the total phenotypic variance of the F2 population, while the dominance effects attributable to QTL explained 0.3 to 10.5, 4.0, -1.1 to -18.0, -1.6, -3.9 to -5.3 for WFE, AFE, EN, EW and HU, respectively

Adiposity QTL Adip20 decomposes into at least four loci when dissected using congenic strains.

An average mouse in midlife weighs between 25 and 30 g, with about a gram of tissue in the largest adipose depot (gonadal), and the weight of this depot differs between inbred strains. Specifically, C57BL/6ByJ mice have heavier gonadal depots on average than do 129P3/J mice. To understand the genetic contributions to this trait, we mapped several quantitative trait loci (QTLs) for gonadal depot weight in an F2 intercross population. Our goal here was to fine-map one of these QTLs, Adip20 (formerly Adip5), on mouse chromosome 9. To that end, we analyzed the weight of the gonadal adipose depot from newly created congenic strains. Results from the sequential comparison method indicated at least four rather than one QTL; two of the QTLs were less than 0.5 Mb apart, with opposing directions of allelic effect. Different types of evidence (missense and regulatory genetic variation, human adiposity/body mass index orthologues, and differential gene expression) implicated numerous candidate genes from the four QTL regions. These results highlight the value of mouse congenic strains and the value of this sequential method to dissect challenging genetic architecture.