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Strategies to assess structural variation in the chicken genome and its associations with biodiversity and biological performance.

A primary goal in the assessment of structural variation in the avian genome is to understand the relationship of this variation with biodiversity and with biological performance. To develop such knowledge, certain essential tools are needed. One set of tools includes the laboratory techniques used to assess molecular genetic variation. The current time is a transitional one for this field, in that the recently sequenced chicken genome will add significantly to the portfolio of existing methods used to identify molecular markers. To most efficiently discover marker-trait associations, the experimental mapping populations must be appropriately designed and the relevant statistical analyses applied. This paper reviews methods for assessment of molecular markers in poultry and their use in the characterization of avian biodiversity and in studies to identify marker associations with biological traits, including important considerations of population structure and statistical analysis.

Animals↗

A refined radiation hybrid map of the telomeric region of bovine chromosome 18q25-q26 compared with human chromosome 19q13.

Genome-wide scans have mapped economically important quantitative trait loci (QTL) for mastitis susceptibility in dairy cattle at the telomeric end of bovine chromosome 18 (BTA18). In order to increase the density of markers in this chromosomal region and to improve breakpoint resolution in the human-bovine comparative map, this study describes the chromosomal assignment of seven newly developed gene-associated markers and five microsatellites and eight previously mapped sequence tagged site markers near these QTL. The orientation of KCNJ14, BAX, CD37, NKG7, LIM2, PRKCG, TNNT1, MGC2705, RPL28, EPN1, ZNF582, ZIM2, STK13, ZNF132 and SLC27A5 on the 3000-rad radiation hybrid (RH) map of BTA18 is homologous to the organization found on the corresponding 10 Mbp of human chromosome 19q (HSA19q). The resulting bovine RH map with a length of 20.9 cR spans over about 11 cM on the bovine linkage map. The location of KCNJ14 and SLC27A5 flanking the RH map on BTA18q25-26 has been confirmed by fluorescence in situ hybridization. The data of this refined human-bovine comparative map should improve selection of candidate genes for mastitis susceptibility in dairy cattle.

Animals↗

A directed search for quantitative trait loci on chromosomes 4 and 7 in pigs.

Improvements in the porcine genetic map and availability of resource families to study performance traits in pigs have made it possible to re-examine previous findings that linked certain traits to genes or chromosomal regions. Previous studies suggested that chromosomes 4 and 7 may be associated with growth and performance traits. To confirm these previous results, an interval mapping-regression approach was used to determine whether quantitative trait loci (QTL) exist in the Iowa State University reference/resource families. Traits measured were birth weight; body weight at 21 d; weaning weight (weight at 42 d); average daily gain; backfat at the first, 10th, lumbar, and last ribs and average backfat thickness; loin eye area; meat color; marbling; and firmness. The total number of F2 pigs used ranged from 241 to 330 and came from five Chinese x American resource families. Five markers (S0001, SW871, S0175, S0214, and SW445) were genotyped and mapped on chromosome 4, and so were 10 markers (S0064, tumor necrosis factor alpha [TNFalpha], S0102, S0078, S0158, S0066, SW304, SW1083, S0101, and S0212) on chromosome 7. Data were analyzed for each family (breed cross) separately and were also pooled. Experiment-wise thresholds were used to determine significance. Suggestive evidence of QTL on chromosomes 4 and 7 was observed for several traits in pooled and individual family analyses. Suggestive evidence of a QTL with a relatively large effect for average daily gain was detected on chromosome 4 in the pooled analysis. Significant (P < .05) evidence for QTL was seen on chromosome 7 for 10th-rib, last-rib, and average backfat thickness in the pooled data set in a region of the chromosome that was near TNFalpha. These results verify in part that chromosomes 4 and 7 contain QTL for growth and carcass traits.

Animals↗

Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton.

In order to construct a saturated genetic map and facilitate marker-assisted selection (MAS) breeding, it is necessary to enhance the current reservoir of known molecular markers in Gossypium. Microsatellites or simple sequence repeats (SSRs) occur in expressed sequence tags (EST) in plants. Many ESTs are publicly available now and represent a good tool in developing EST-SSRs. From 13,505 ESTs developed from our two cotton fiber/ovule cDNA libraries constructed for Upland cotton, 966 (7.15%) contained one or more SSRs and from them, 489 EST-SSR primer pairs were developed. Among the EST-SSRs, 59.1% are trinucleotides, followed by dinucleotides (30%), tetranucleotides (6.4%), pentanucleotides (1.8%), and hexanucleotides (2.7%). AT/TA (18.4%) is the most frequent repeat, followed by CTT/GAA (5.3%), AG/TC (5.1%), AGA/TCT (4.9%), AGT/TCA (4.5%), and AAG/TTC (4.5%). One hundred and thirty EST-SSR loci were produced from 114 informative EST-SSR primer pairs, which generated polymorphism between our two mapping parents. Of these, 123 were integrated on our allotetraploid cotton genetic map, based on the cross [(TM-1xHai7124)TM-1]. EST-SSR markers were distributed over 20 chromosomes and 6 linkage groups in the map. These EST-SSR markers can be used in genetic mapping, identification of quantitative trait loci (QTLs), and comparative genomics studies of cotton.

Base Sequence↗

A QTL on rat chromosome 7 modulates prepulse inhibition, a neuro-behavioral trait of ADHD, in a Lewis x SHR intercross.

BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is a complex neuropsychiatric disorder with a substantial genetic component. The Spontaneously Hypertensive Rats (SHR), considered as a good animal model of ADHD, also show less anxiety-like behaviors than Lewis (LEW) rats. The use of these inbred rat strains led us to the mapping of two quantitative trait loci (QTL), named Ofil1 (on chromosome 4) and Ofil2 (on chromosome 7), related to locomotion in the central and aversive area of an open field. Herein, we examined whether LEW and SHR rats differ in the acoustic startle reflex, a test used to study the neurobiology of anxiety, and in the prepulse inhibition of the startle response, which is known to be impaired in ADHD patients. The effect of the two aforementioned loci on these behavioral responses was also studied. METHODS: For this latter purpose, rats deriving from an F2 intercross between the LEW and SHR strains were selected according to their genotype at markers flanking the QTLs and bred to obtain lines of rats homozygous LEW/LEW or SHR/SHR for each of the two loci, thus generating 4 genotypic combinations. RESULTS: The SHR rats displayed decreased startle and prepulse inhibition levels when compared to LEW rats. Ofil2 affected prepulse inhibition in female rats only. CONCLUSION: The results suggest that the LEW and SHR strains are appropriate for studying mechanisms of sensorimotor gating and indicate that the locus Ofil2 on rat chromosome 7 contain genes controlling prepulse inhibition, a neuro-behavioral trait of ADHD.

Journal Article↗

Molecular genetic analysis of QTLs for ferulic acid content in dried straw of rice (Oryza sativa L.).

Phenolic acids are secondary metabolic organic compounds produced by plants and often are mentioned as allelochemicals. This study was conducted to determine the genetic basis controlling the ferulic acid content of rice straw in a recombinant inbred (RI) population derived from a cross between a japonica variety, Asominori, with a higher content of ferulic acid, and an indica variety, IR24, with a lower content, using 289 RFLP markers. Continuous distributions and transgressive segregations of ferulic acid content were observed in the RI population, which showed that ferulic acid content in rice straw was quantitatively inherited. Single marker analysis and composite interval mapping identified three quantitative trait loci (QTLs) for ferulic acid content with LOD values of 2.03 (chromosome 3), 3.16 (chromosome 6), and 3.06 (chromosome 7); all three had increased additive effects (13.5, 18.3, and 18.1 microg g(-1)) from the Asominori parent and accounted for 5.5, 16.9, and 12.8% of total phenotypic variation, respectively. This is the first report on the identification of QTLs associated with ferulic acid and their chromosomal localization on the molecular map of rice. The tightly linked molecular markers that flank the QTLs might be useful in breeding and selection of varieties with higher phenolic acid content.

Chromatography, Gas↗

QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines.

The genetic mechanism underlying six palatability properties of cooked rice and three physico-chemical traits was dissected in 66 BC(3)F(2) chromosome segment substitution lines (CSSLs), using a complete linkage map in three successive years. The CSSLs showed transgressive segregation for all traits studied. Significant correlation was detected among most palatability traits. A total of 25 QTLs for the nine traits were identified on nine chromosomes, and many QTLs affecting different quality traits were mapped in the same regions. Six QTLs--qLT-8 for luster, qTD-6 and qTD-8 for tenderness, qIVOE-6 and qIVOE-8 for integrated value of organoleptic evaluation, and qAC-8 for amylose content--were repeatedly detected across the 3 years. Phenotypic values were significantly different between the recurrent parent, cultivar Asominori, and the CSSLs harboring any of the six QTL alleles across the three environments, indicating that these six QTLs were non-environment-specific and could be used for marker-assisted selection in rice quality improvement.

Chromosome Mapping↗

Mapping a gene for familial situs abnormalities to human chromosome Xq24-q27.1.

Ambiguous abdominal situs, asplenia/polysplenia and severe cardiac malformations characterize heterotaxy in humans. These anomalies result from the inability of the developing embryo to establish normal left-right asymmetry. We have studied an interesting family in which the heterotaxy phenotype segregates as an X-linked recessive trait. In order to map the heterotaxy locus (HTX), we have analysed 39 family members using highly-polymorphic microsatellite markers from the X chromosome. One of these markers, DXS994, shows no recombination with the disease locus in 20 informative meioses. Linkage analysis results in a maximum lod score of 6.37. Current genetic and physical mapping data assign the order of loci in Xq24-q27.1 as cen-DXS1001-(DXS994, HTX)-DXS984-tel. These results establish the first mapping assignment of situs abnormalities in humans.

Child↗

Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid.

The genetic basis of heterosis of an elite rice hybrid was investigated by using an "immortalized F(2)" population produced by randomly permutated intermating of 240 recombinant inbred lines from a cross between the parents of Shanyou 63, the most widely cultivated hybrid in China. Measurements of heterosis for crosses in the immortalized F(2) population were obtained from replicated field trials over 2 years by inter-planting the hybrids with the parental recombinant inbred lines. The analyses were conducted making use of a linkage map comprising 231 segregating molecular marker loci covering the entire rice genome. Heterotic effects were detected at 33 loci for the four traits with modified composite interval mapping. The heterotic loci showed little overlap with quantitative trait loci for trait performance, suggesting that heterosis and trait performance may be conditioned by different sets of loci. Large numbers of digenic interactions were resolved by using two-way ANOVA and confirmed by randomization tests. All kinds of genetic effects, including partial-, full-, and overdominance at single-locus level and all three forms of digenic interactions (additive by additive, additive by dominance, and dominance by dominance), contributed to heterosis in the immortalized F(2) population, indicating that these genetic components were not mutually exclusive in the genetic basis of heterosis. Heterotic effects at the single-locus level, in combination with the marginal advantages of double heterozygotes caused by dominance by dominance interaction at the two-locus level could adequately explain the genetic basis of heterosis in Shanyou 63. These results may help reconcile the century-long debate concerning the genetic basis of heterosis.

Analysis of Variance↗

Phylogenetic analysis and trait evolution in Australian lineages of drywood termites (Isoptera, Kalotermitidae).

A phylogenetic analysis of Australian drywood termites (Isoptera, Kalotermitidae) based on partial sequence from the cytochrome oxidase II (COII) and cytochrome b genes is presented. In addition to providing new information on the evolutionary relationships among 25 species from seven genera, we evaluate the relative likelihoods of alternative topological hypotheses, including those derived from morphology-based classifications. We also test the applicability of a molecular clock for estimating the age of the Kalotermitidae and infer the evolution of species-specific variation for habitat type and soldier caste phragmosis by mapping this information onto the independently derived phylogeny. Maximum-likelihood analysis of both nucleotide and protein sequences from a multigene data set jointly support a single topology, which is shown to be the best estimate of the true phylogeny among the alternatives tested. Our results support the monophyly of all genera but question the discrimination between Procryptotermes and Cryptotermes. A basal dichotomy among generic groups suggests two principle lines of divergence within the family. Intergeneric relationships show mixed congruence to previous proposals, resulting in one morphology-based classification being rejected. A molecular clock hypothesis is not supported due to significant among-lineage rate heterogeneity in the COII gene. Patterns revealed through trait mapping suggest that the most recently diverged taxa tend to occupy the driest habitats and that these same taxa reflect a defensive transition away from large mandibulate soldiers toward small phragmotic soldiers. The association between habitat and defensibility supports the hypothesis that these two characters have been tightly linked throughout the social diversification of termites.

Animals↗

Populus: arabidopsis for forestry. Do we need a model tree?

Trees are used to produce a variety of wood-based products including timber, pulp and paper. More recently, their use as a source of renewable energy has also been highlighted, as has their value for carbon mitigation within the Kyoto Protocol. Relative to food crops, the domestication of trees has only just begun; the long generation time and complex nature of juvenile and mature growth forms are contributory factors. To accelerate domestication, and to understand further some of the unique processes that occur in woody plants such as dormancy and secondary wood formation, a 'model' tree is needed. Here it is argued that Populus is rapidly becoming accepted as the 'model' woody plant and that such a 'model' tree is necessary to complement the genetic resource being developed in arabidopsis. The genus Populus (poplars, cottonwoods and aspens) contains approx. 30 species of woody plant, all found in the Northern hemisphere and exhibiting some of the fastest growth rates observed in temperate trees. Populus is fulfilling the 'model' role for a number of reasons. First, and most important, is the very recent commitment to sequence the Populus genome, a project initiated in February 2002. This will be the first woody plant to be sequenced. Other reasons include the relatively small genome size (450-550 Mbp) of Populus, the large number of molecular genetic maps and the ease of genetic transformation. Populus may also be propagated vegetatively, making mapping populations immortal and facilitating the production of large amounts of clonal material for experimentation. Hybridization occurs routinely and, in these respects, Populus has many similarities to arabidopsis. However, Populus also differs from arabidopsis in many respects, including being dioecious, which makes selfing and back-cross manipulations impossible. The long time-to-flower is also a limitation, whilst physiological and biochemical experiments are more readily conducted in Populus compared with the small-statured arabidopsis. Recent advances in the development of large expressed sequence tagged collections, microarray analysis and the free distribution of mapping pedigrees for quantitative trait loci analysis secure Populus as the ideal subject for further exploitation by a wide range of scientists including breeders, physiologists, biochemists and molecular biologists. In addition, and in contrast to other model plants, the genus Populus also has genuine commercial value as a tree for timber, plywood, pulp and paper.

Arabidopsis↗

Regulatory polymorphisms underlying complex disease traits.

There is growing evidence that genetic variation plays an important role in the determination of individual susceptibility to complex disease traits. In contrast to coding sequence polymorphisms, where the consequences of non-synonymous variation may be resolved at the level of the protein phenotype, defining specific functional regulatory polymorphisms has proved problematic. This has arisen for a number of reasons, including difficulties with fine mapping due to linkage disequilibrium, together with a paucity of experimental tools to resolve the effects of non-coding sequence variation on gene expression. Recent studies have shown that variation in gene expression is heritable and can be mapped as a quantitative trait. Allele-specific effects on gene expression appear relatively common, typically of modest magnitude and context specific. The role of regulatory polymorphisms in determining susceptibility to a number of complex disease traits is discussed, including variation at the VNTR of INS, encoding insulin, in type 1 diabetes and polymorphism of CTLA4, encoding cytotoxic T lymphocyte antigen, in autoimmune disease. Examples where regulatory polymorphisms have been found to play a role in mongenic traits such as factor VII deficiency are discussed, and contrasted with those polymorphisms associated with ischaemic heart disease at the same gene locus. Molecular mechanisms operating in an allele-specific manner at the level of transcription are illustrated, with examples including the role of Duffy binding protein in malaria. The difficulty of resolving specific functional regulatory variants arising from linkage disequilibrium is demonstrated using a number of examples including polymorphism of CCR5, encoding CC chemokine receptor 5, and HIV-1 infection. The importance of understanding haplotypic structure to the design and interpretation of functional assays of putative regulatory variation is highlighted, together with discussion of the strategic use of experimental tools to resolve regulatory polymorphisms at a transcriptional level. A number of examples are discussed including work on the TNF locus which demonstrate biological and experimental context specificity. Regulatory variation may also operate at other levels of control of gene expression and the modulation of splicing at PTPRC, encoding protein tyrosine phosphatase receptor-type C, and of translational efficiency at F12, encoding factor XII, are discussed.

Autoimmune Diseases↗

Evidence for a female-specific effect of a chromosome 4 locus on anxiety-related behaviors and ethanol drinking in rats.

Previous studies using the inbred rat strains Lewis (LEW) and spontaneously hypertensive rats (SHR) led to the mapping of two quantitative trait loci, named Ofil1 (on chromosome 4 of the rat) and Ofil2 (on chromosome 7), for open-field inner locomotion, a behavioral index of anxiety. Studies using other strains showed that the region next to Ofil1 influences measures of not only anxiety but also ethanol consumption. In view of the high prevalence of psychiatric disorders such as anxiety and alcoholism, as well as the comorbidity between them, the present study was designed to better characterize the contribution of these two loci to complex emotional and consummatory responses. Rats deriving from an F2 intercross between the LEW and the SHR strains were selected according to their genotype at markers flanking the loci Ofil1 and Ofil2 and bred to obtain lines of rats homozygous LEW/LEW or SHR/SHR for each of the two loci, thus generating four genotypic combinations. These selected animals as well as purebred LEW and SHR rats of both sexes were submitted to a battery of tests including measures of locomotor activity, anxiety, sweet and bitter taste reinforcement and ethanol intake. Lewis rats displayed more anxiety-like behavior and less ethanol intake than SHR rats. Ofil1 (on chromosome 4) affected both the activity in the center of the open field and ethanol drinking in females only. These results suggest that Ofil1 contains either linked genes with independent influences on anxiety-related responses and ethanol drinking or a pleiotropic gene with simultaneous effects on both traits.

Alcohol Drinking↗

GrainGenes 2.0. an improved resource for the small-grains community.

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.

Breeding↗

Interacting quantitative trait loci control phenotypic variation in murine estradiol-regulated responses.

The steroid hormone estradiol (E2) elicits a spectrum of systemic and uterotropic responses in vivo. For example, E2 treatment of ovariectomized adult and sexually immature rodents leads to uterine leukocytic infiltration, cell proliferation, and organ growth. E2-regulated growth is also associated with a variety of normal and pathological phenotypes. Historically, the uterine growth response has been used as the key model to understand the molecular and biochemical mechanisms underlying E2-dependent growth. In this study, genome exclusion mapping identified two quantitative trait loci (QTL) in the mouse, Est2 and Est3 on chromosomes 5 and 11, respectively, that control the phenotypic variation in uterine wet weight. Both QTL are linked to a variety of E2-regulated genes, suggesting that they may represent loci within conserved gene complexes that play fundamental roles in mediating the effects of E2. Interaction and multiple trait analyses using the uterine leukocyte response and wet weight suggest that Est4, a QTL on chromosome 10, may encode an interacting factor that influences the quantitative variation in both responses. Our results show that E2-dependent responses can be genetically controlled and that a genetic basis may underlie the variation observed in many E2-dependent phenotypes.

Animals↗

Sex-specific and sex-independent quantitative trait loci for facets of the metabolic syndrome in WOKW rats.

WOKW rats develop a complete metabolic syndrome closely resembling human disease. Since genetic studies using male (WOKW x DA)F2 progeny showed that several independent genetic factors were involved, a polygenic basis for the syndrome in WOKW was assumed. However, because the metabolic syndrome in human clearly demonstrates sex differences, we have extended our study to include both male and female (WOKW x DA)F2 progeny in a genome-wide scan. Male- or female-specific quantitative trait loci (QTLs) were mapped for body weight, body mass index, adiposity index and serum insulin on chromosomes 1 and 5, serum triglycerides on chromosomes 4, 7, 11, and 16, serum total and high density lipoprotein cholesterol on chromosomes 3, 4, 5, 10, and 17, and serum leptin on chromosomes 8 and 16 as well as blood glucose and glucose tolerance (AUC) on chromosomes 3, 4 and 17. QTLs for both, males and females were only found for body weight on chromosome 1 and for serum total cholesterol on chromosome 3 and 10. These findings clearly demonstrate that there are sex-specific and sex-independent QTLs for facets of the metabolic syndrome in WOKW rats.

Animals↗

Molecular characterization and expression of porcine bone morphogenetic protein receptor-IB in the uterus of cyclic and pregnant gilts.

Previous gene mapping analyses revealed a quantitative trait locus for uterine capacity on chromosome 8. Comparison of porcine and human genetic maps suggests that the bone morphogenetic protein receptor IB (BMPR-IB) gene may be located near this region. The objectives of this study were to 1) clone the full coding region for BMPR-IB, 2) examine BMPR-IB gene expression by the endometrium and its cellular localization in cyclic and pregnant gilts, and 3) map the BMPR-IB gene. By iterative screening of an expressed sequence tag library, we obtained a 3559-base pair cDNA clone including the full coding region of BMPR-IB. Endometrial BMPR-IB mRNA expression of White composite gilts was determined by Northern blotting in Days 10, 13, and 15 cyclic and Days 10, 13, 15, 20, 30, and 40 pregnant gilts. In cyclic gilts, endometrial BMPR-IB mRNA expression was elevated on Days 13 and 15 (P < 0.01) compared with Day 10. Expression of BMPR-IB mRNA was localized in both luminal and glandular epithelium on Day 15. However, in pregnant gilts, BMPR-IB mRNA expression was not significantly different in the endometrium from Day 10 to Day 20, and it was significantly decreased on Days 30 and 40 (P = 0.011). The BMPR-IB gene was mapped to 108 cM on chromosome 8. These findings show that BMPR-IB mRNA expression is regulated differently in cyclic and pregnant gilts; this pattern of gene expression may be important for endometrial function during the luteal phase of the estrous cycle as compared with early pregnancy.

Amino Acid Sequence↗

Common quantitative trait loci for alcohol-related behaviors and central nervous system neurotensin measures: locomotor activation.

We have analyzed LSXSS recumbinant inbred for ethanol-induced activity using 2.0 g/kg ethanol and a new method we call ethanol activation slope. The ethanol activation slope provides a robust dose-response measure of ethanol activation, independent of both activity after saline and the inhibitory effects of ethanol on locomotor activity. These behavioral data were used in a quantitative trait locus analysis to map chromosomal loci involved in ethanol-induced locomotor activity. We tentatively identified seven loci that mediate the low-dose stimulatory effect of ethanol and six loci involved in locomotion after 2.0 g/kg ethanol. Only one of the loci are in common between the two behaviors. We also compared the behavioral quantitative trait locus to those previously identified that are involved in regulating central nervous system neurotensin levels and neurotensin receptor densities. Six chromosomal regions were identified that regulate at least one central nervous system neurotensin measure and an ethanol-induced locomotor behavior. The identification of loci controlling both central nervous system neurotensin levels or neurotensin receptor densities and ethanol-induced locomotor activity strengthens the proposal that neurotensin regulates, in part, ethanol-induced behaviors and central nervous system sensitivity to ethanol.

Alcoholism↗