Mapping functional chicken genes: an alternative approach

Sex identification by alternative polymerase chain reaction methods in falconiformes

A number of avian species are difficult to sex morphologically, especially as nestlings. Like other avian species, many species of Falconiformes are sexually monomorphic. Therefore, it is desirable that new methods based on DNA analysis are established in Falconiformes and other sexual monomorphic species. We identified sex in Falconiformes by two alternative methods. First, we used a sexing method based on the intronic length variation between CHD1W and CHD1Z using primers flanking the intron. In this method, two species of Falconidae could be identified for sexing. However, six species of Accipitridae could not, because they have few length variations. The second method used was based on differences in sequences between CHD1W and CHD1Z. From sequence analysis, a 3'-terminal mismatch primer on point mutation conserved among Falconiformes was designed, and identification of sex with the amplification refractory mutation system (ARMS) was performed. This method could identify sex in all species tested. In addition, because the 3'-terminal mismatch primer was designed on a point mutation conserved among Falconiformes, ARMS with these primers may identify sex in all Falconiformes. These are simple and rapid sexing methods, since only polymerase chain reaction (PCR) and agarose electrophoresis are required. In conclusion, sex identification by an alternative PCR approach based on intronic length variation and on differences in sequences between CHD1W and CHD1Z proved applicable to and useful for Falconiformes.

Mapping chicken genes using preferential amplification of specific alleles

To map the chicken genome, an international reference population was developed at our laboratory (East Lansing, MI) using an F2 backcross between inbred jungle fowl (JF) and inbred white leghorns (WL). To augment the number of type I genes on the East Lansing (E) map, segregation of the JF-specific allele was followed using preferential amplification of specific alleles (PASA) in polymerase chain reactions (PCR). Among 15 functional genes that were added to the E map, agrin and mannose-6-phosphate receptor genes were found to occur in conserved syntenic groups. Using this PCR-based approach, six conserved groups spanning more than 243 centimorgans (cM) in the chicken were syntenic with human and mouse.

Identification of rabbit immunoglobulin latent Ckappa1 allotype genes alters the concept of allelic inheritance

In the rabbit, expression of immunoglobulin Ckappa1 light chain genes is believed to be under allelic control. Conventionally, four nominal allotypic variants, b4, b5, b6 and b9 have been shown to be co-dominantly expressed at the Ckappa1 gene locus. Analogously, the heavy chain allotypes, VHa1, VHa2 and VHa3, found in the V region, are also believed to be inherited co-dominantly. However, after our earlier discovery of non-allelic or latent allotypes in the serum and on cell surfaces. we subsequently reported that cDNA sequences for latent b5 and b6 were identical to nominal b5 and b6, respectively (Ishaq et al., 1990). The latent b5 cDNAs were from two homozygous b4,b4 rabbits; the latent b6 cDNA was found in a heterozygous b4,b9 rabbit. The cDNA sequences had been obtained from lymph nodes and spleens of rabbits which had been infected with Trypanosoma brucei in order to induce latent allotypes more consistently. In this article, employing spleen DNA from three different T. brucei-infected rabbits, (one, heterozygous b4,b9; two others, homozygous, b4,b4), we initially detected two bands by Southern analysis after Hind III digestion using a 624 base pair Ckappa1 b4 probe derived from a b4,b4 rabbit. However, the probe was non-specific allotypically as it hybridized to b5, b6 and b9 Ckappa1 DNA. Therefore, in order to search for the latent genes, we used allotype-specific oligonucleotides for b5, b6 and b9 to probe DNAs from both normal and T. brucei-infected rabbits by Southern blotting. At the outset, employing a b4 oligonucleotide probe, we detected a single 5.8 Kb segment in two b4,b4 rabbit DNAs after Bg1 II digestion. The findings, using the 624 base pair Ckappa1 b4 probe and the b4 oligomer, agreed with earlier data reported by others. Subsequently, we tested kidney, liver and spleen DNAs from one of these and other rabbits for genomic latent b5, b6 and b9 using these specific oligomeric probes. For each latent allotype, Southern analysis revealed latent-allotype specific DNA segments in the genome. After cosmid cloning and sequencing, latent kappa1, b5, b6 and b9 genes were found to be identical in their coding regions with their nominal counterparts. The genes contained at the 5' end the PyPyXPyAG RNA splice acceptor site found in immunoglobulin and many eukaryotic genes. as well as the termination codon TAG, together with AATAAA and the T-rich sites responsible for cleavage-polyadenylation in the untranslated region downstream from the 3' end. Single cosmid clones representing the b5, b6 and b9 genes were mapped for restriction sites which resulted in identifying putative Jk and enhancer regions. The results thus indicate that latent allotype genes are potentially functional. The data provide evidence that allotypes are not strictly controlled by allelic genes but must be regulated by an hierarchical mechanism which provides for synthesis of allelic allotypes mainly (10-20 mg/ml) together with non-allelic allotypes at lower concentrations (2-20 microg/ml) following activation of the latent genes. These results lay to rest the belief that Ckappa1 latent allotypes are the products of scrambled genes or idiotypic mimicry. Importantly, we now have the possibility of investigating the factors leading to latent allotype gene expression, the Vk and Jk regions associated with the genes, and therefore whether antibody diversity is expanded. We do not know, nor do we imply, that latent allotypes are present in all rabbits. However, since the four conventional Ckappa1 allotypes are present in the genome of several of our tested rabbits, and are presumably functional. we are faced with the probability that rabbit allotypes under certain conditions may in fact behave as isotypes and not allotypes.

The CAR1 gene encoding a cellular receptor specific for subgroup B and D avian leukosis viruses maps to the chicken tvb locus

Host susceptibility to subgroup B, D, and E avian leukosis viruses (ALV) is determined by specific alleles of the chicken tvb locus. Recently, a chicken gene that encodes a cellular receptor, designated CAR1, specific for subgroups B and D ALV was cloned, and it was proposed that this gene was the s3 allele of tvb (J. Brojatsch, J. Naughton, M. M. Rolls, K. Zingler, and J. A. T. Young, Cell 87:845-855, 1996). We now report that in a backcross derived from an F1 (Jungle Fowl x White Leghorn [WL]) male mated with inbred WL females, the cloned ALV receptor gene cosegregated with two markers linked to tvb. The two markers used were a tvb(s1)-specific antigen recognized by the chicken R2 alloantiserum and restriction fragment length polymorphisms associated with the expressed sequence tag com152e. With all three markers, no crossovers were observed among 52 backcross progeny tested and LOD linkage scores of 15.7 were obtained. These data demonstrate that CAR1 is the subgroup B and D ALV susceptibility gene located at tvb(s3).

Genetic variability in white leghorns revealed by chicken liver expressed sequence tags

A total of 92 expressed sequence tags from chicken liver (CLEST) were searched for homology with known genes. Among the CLEST, 29% had no sequence similarities with known genes, 34% showed sequence similarity to rRNA, 9% to mitochondrial genes, 23% to known nuclear genes, and 5% to human expressed sequence tags. Among the nuclear CLEST (excluding rRNA), clones with sequence similarity to aldolase B were represented four times, whereas all the other clones represented unique genes. The presence of MspI and TaqI restriction fragment length polymorphisms (RFLP) associated with CLEST were analyzed by bulk Southern blotting in 16 strains of White Leghorn chickens derived from five different genetic bases. No RFLP were observed with rRNA CLEST and a single MspI RFLP was observed with mitochondrial CLEST. The nuclear CLEST with sequence similarity to known nuclear genes were grouped into two classes on the basis of their involvement in intermediary metabolism. Among the nine genes coding for metabolic enzymes, all but one were polymorphic at MspI and/or TaqI sites in at least one of the strains, whereas among the other genes six of nine were polymorphic. The average frequency of clones revealing RFLP per cDNA clone and restriction enzyme for the two classes were 0.7 and 0.3, respectively. The analysis indicated that in White Leghorns, RFLP markers in the vicinity of nuclear CLEST are relatively frequent. Further, RFLP in the vicinity of genes coding for metabolic enzymes were significantly more frequent than near genes coding for other proteins.

The chicken genome contains two functional nonallelic beta1,4-galactosyltransferase genes. Chromosomal assignment to syntenic regions tracks fate of the two gene lineages in the human genome

Two distinct but related groups of cDNA clones, CKbeta4GT-I and CKbeta4GT-II, have been isolated by screening a chicken hepatoma cDNA library with a bovine beta1,4-galactosyltransferase (beta4GT) cDNA clone. CKbeta4GT-I is predicted to encode a type II transmembrane glycoprotein of 41 kDa with one consensus site for N-linked glycosylation. CKbeta4GT-II is predicted to encode a type II transmembrane glycoprotein of 43 kDa with five potential N-linked glycosylation sites. At the amino acid level, the coding regions of CKbeta4GT-I and CKbeta4GT-II are 52% identical to each other and 62 and 49% identical, respectively, to bovine beta4GT. Despite this divergence in amino acid sequence, high levels of expression of each cDNA in Trichoplusia ni insect cells demonstrate that both CKbeta4GT-I and CKbeta4GT-II encode an alpha-lactalbumin-responsive, UDP-galactose:N-acetylglucosamine beta4-galactosyltransferase. An analysis of CKbeta4GT-I and CKbeta4GT-II genomic clones established that the intron positions within the coding region are conserved when compared with each other, and these positions are identical to the mouse and human beta4GT genes. Thus CKbeta4GT-I and CKbeta4GT-II are the result of the duplication of an ancestral gene and subsequent divergence. CKbeta4GT-I maps to chicken chromosome Z in a region of conserved synteny with the centromeric region of mouse chromosome 4 and human chromosome 9p, where beta4-galactosyltransferase (EC 2.4.1.38) had previously been mapped. Consequently, during the evolution of mammals, it is the CKbeta4GT-I gene lineage that has been recruited for the biosynthesis of lactose. CKbeta4GT-II maps to a region of chicken chromosome 8 that exhibits conserved synteny with human chromosome 1p. An inspection of the current human gene map of expressed sequence tags reveals that there is a gene noted to be highly similar to beta4GT located in this syntenic region on human chromosome 1p. Because both the CKbeta4GT-I and CKbeta4GT-II gene lineages are detectable in mammals, duplication of the ancestral beta4-galactosyltransferase gene occurred over 250 million years ago in an ancestral species common to both mammals and birds.

DNA marker technology: a revolution in animal genetics

The development of DNA-based markers has had a revolutionary impact on gene mapping and, more generally, on all of animal and plant genetics. With DNA-based markers, it is theoretically possible to exploit the entire diversity in DNA sequence that exists in any cross. For this reason, high resolution genetic maps are being developed at an unprecedented speed. The most commonly used DNA-based markers include those based on a cloned and (usually) sequenced DNA fragment and other, more random, assays for genetic polymorphism that can be grouped under the heading of fingerprint markers. The advantages and disadvantages of the various marker types are discussed, along with their application to the reference chicken genetic linkage maps and to the search for quantitative trait loci (QTL). The prospects for the use of DNA-based markers in marker-assisted selection are considered, along with likely future trends in poultry gene mapping. Further development of both physical and linkage genome maps of the chicken will allow animal scientists to more efficiently detect and characterize QTL and will provide them access to the wealth of genetic information that is being generated about the human genome and the genomes of model species, such as the mouse and Drosophila.

Map-based quantitative trait locus identification

Poultry gene mappers chose microsatellites as the main source of genetic markers for poultry genome mapping, similar to the marker type used for other farm animals, laboratory animals, and humans. Optimal strategies for applying DNA markers in poultry populations are discussed, including the number of markers to be used, genome representation, population structure, choice of markers, population size, statistical stringency for association between markers and quantitative trait loci (QTL), and biological verification of a linkage. It is shown that an efficient strategy should be based on a combination of a low stringent statistical test for the existence of linkage between a marker and QTL and an appropriate genetic test for the discrimination between true and false linkage. The source of the genetic variation to be used is discussed and, as an illustration, three types of resource populations are presented. The informativeness of different matings using various genotypes of the parents are considered and it appears that selection of markers based on the heterozygosity of the sire is the most efficient marker screening approach.

Comparative mapping of the chicken genome using the East Lansing reference population

The annotation of known genes on linkage maps provides an informative framework for synteny mapping. In comparative gene mapping, conserved synteny is broadly defined as groups of two or more linked markers that are also linked in two or more species. Although many anonymous markers have been placed on the chicken genome map, locating known genes will augment the number of conserved syntenic groups and consolidate linkage groups. In this report, 21 additional genes have been assigned to linkage groups or chromosomes; five syntenic groups were identified. Ultimately, conserved syntenic groups may help to pinpoint important quantitative trait loci.