Cost-effective development of highly polymorphic microsatellite in Japanese quail facilitated by next-generation sequencing

Next-generation sequencing technologies permit rapid and cost-effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild-derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3-4.1 and 0.11-0.53 respectively. Compared with the wild-derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (FST ) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.

Association between ovocalyxin-32 gene haplotypes and eggshell quality traits in an F2 intercross between two chicken lines divergently selected for eggshell strength

Broken and cracked eggshells contribute significantly to economic losses in the egg production industry. We previously identified ovocalyxin-32 as a potential gene influencing eggshell traits, by analysing an intercross between two parent lines developed from the same founder population by a two-way selection for eggshell strength with non-destructive deformation (DEF) conducted over 14 generations. We determined the nucleotide sequences of six ovocalyxin-32 exons in the parent individuals and analysed the association between ovocalyxin-32 and eggshell traits in the F2 individuals. We identified three haplotypes (W, M and S) of ovocalyxin-32 in the parent individuals. A mismatch amplification mutation assay was performed to distinguish six diplotype individuals (WW, MM, SS, WM, MS and WS) inthe F2 population. The egg weight (EW) of SS-diplotype individuals was significantly higher than that of WW-, WM- and WS-diplotypes. Short length of the egg (SLE) of SS-diplotype individuals was significantly higher than that of WW-, WM- and MS-diplotypes. Long length of the egg (LLE) of SS-diplotype individuals was significantly higher than that of WM and WS-diplotypes. DEF of WW-diplotype individuals was significantly higher than that ofSS-, WM, MS and WM-diplotypes. Haplotypic effect analyses showed significant differences between the W-haplotype and the S-haplotypes in the EW, SLE, LLE and DEF. The DEF of M-haplotype was significantly lower than that of W- and S-haplotypes. These results suggest that S- and M-haplotypes are critical for high quality of eggshells in the F2 population. In conclusion, ovocalyxin-32 is a useful marker of eggshell traits and can be used to develop strategies for improving eggshell traits in commercial layer houses.

62 COMPARATIVE PROTEOMIC ANALYSIS OF LIVER MITOCHONDRIA DERIVED FROM DECEASED NEWBORN CLONED CALVES AND ADULT CLONES BY TWO-DIMENSIONAL DIFFERENTIAL GEL ELECTROPHORESIS

Aberrant reprogramming of donor somatic cell nuclei may result in many severe problems in animal cloning. The inability to establish functional interactions between donor nucleus and recipient mitochondria is also likely responsible for developmental deficiency. However, an understanding of the expressed proteins in cattle is lacking. In the present study, alterations in mitochondrial protein levels between somatic cell nuclear transferred (SCNT) and control animals (mostly produced by AI) were investigated. Nuclear transfer was performed using donor cells prepared from cumulus cells (B1), ear skin, or skeletal muscle from adult Japanese Black cattle, and enucleated in vitro matured oocytes (Holstein or Japanese Black) as previously reported (Akagi et al. 2003). Liver samples were collected from postmortem SCNT calves (CB1-3; 0, 1, and 9 days postnatally) and adult SCNT cattle (CA1-4; 6, 6, 6, and 5 years of age) produced from the same cell line (B1) and preserved at –80°C. Mitochondrial fractions were prepared from the frozen–thawed liver samples by mechanical homogenization and differential centrifugation, and subjected to two-dimensional difference in gel electrophoresis (2D-DIGE) using CyDye™ dyes (Cy2, Cy3, Cy5; GE Healthcare) for specific labelling. Protein expression changes were confirmed by ImageMaster 2D Platinum software with a volume ratio greater than 2.0 (Student’s t-test; P < 0.05). The expression of 5 proteins were up-regulated in SCNT calves compared to control calves (n = 6; Day 250 fetus, 0, 4, 8, 8, and 8 days after birth; P < 0.05). Expressed protein patterning compared to control groups was different among SCNT calves. The protein spots of CB-1 showed great differences compared with other SCNT calves; 13 spots were up-regulated, and 18 spots were down-regulated. In adult SCNT cattle, the concentrations of 3 proteins were higher when compared to control cattle (n = 4; 2, 2, 6, and 8 years of age; P < 0.05). Protein expression was different among individual SCNT animals even if they were produced from the same donor cell source. For example, 9 spots were up-regulated and 7 spots were down-regulated in CA-1. In contrast, no differences were detected in 2 of the SCNT cattle (CA-3 and 4; P < 0.05). Novel proteins were not identified in any of the SCNT cattle or calves. In conclusion, alteration of mitochondrial protein expression levels were observed in non-viable neonatal SCNT calves and varied among SCNT individuals; suggesting that mitochondrial related gene expression may be implicated in early losses. Comparative proteomic analysis represents an important tool for further studies on SCNT animals. We thank Dr. C. A. Pinkert (Auburn Univ.) and Dr. Somfai (NARO) for their assistance. This work was supported by a grant from the NARO, Japan.

Genetic mapping of quantitative trait loci affecting growth and carcass traits in F2 intercross chickens

We constructed a chicken F(2) resource population to facilitate the genetic improvement of economically important traits, particularly growth and carcass traits. An F(2) population comprising 240 chickens obtained by crossing a Shamo (lean, lightweight Japanese native breed) male and White Plymouth Rock breed (fat, heavyweight broiler) females was measured for BW, carcass weight (CW), abdominal fat weight (AFW), breast muscle weight (BMW), and thigh muscle weight (TMW) and was used for genome-wide linkage and QTL analysis, using a total of 240 microsatellite markers. A total of 14 QTL were detected at a 5% chromosome-wide level, and 7 QTL were significant at a 5% experiment-wide level for the traits evaluated in the F(2) population. For growth traits, significant and suggestive QTL affecting BW (measured at 6 and 9 wk) and average daily gain were identified on similar regions of chromosomes 1 and 3. For carcass traits, the QTL effects on CW were detected on chromosomes 1 and 3, with the greatest F-ratio of 15.0 being obtained for CW on chromosome 3. Quantitative trait loci positions affecting BMW and TMW were not detected at the same loci as those detected for BMW percentage of CW and TMW percentage of CW. For AFW, QTL positions were detected at the same loci as those detected for AFW percentage of CW. The present study identified significant QTL affecting BW, CW, and AFW.

Migration and Proliferation of Primordial Germ Cells in the Early Chicken Embryo

In avian species, primordial germ cells (PGC) use the vascular system as a vehicle to transport them to the future gonadal region. The aim of this study was to elucidate the details of migration system and size of the PGC population in the early chicken embryo. We analyzed whole chicken embryos during stages X and 2 to 17 by immunohistochemical staining using specific antibody raised against chicken vasa homolog. At stage X, PGC were dense in the central zone of the area pellucida. Following the formation of the primitive streak, PGC moved anteriorly to the edge of the extraembryonic region. The size of the PGC population increased gradually during stages X (130.4 +/- 31.9) to 10 (439.3 +/- 93.6). At stage 10, PGC began to accumulate in the region anterior to the head, and then we could observe that PGC invaded into the vascular system in this region. At stage 11, the number of PGC decreased in the region anterior to the head (129.8 +/- 42.5 to 46.7 +/- 4.2) and increased in the blood vessels (194.0 +/- 41.6 to 285.0 +/- 7.5). No PGC could be recognized in the intermediate mesoderm, the future gonadal region, until stage 14, but they first appeared there at stage 15. The number of PGC recognized in the intermediate mesoderm increased from stage 15 to 17. Interestingly, the number of PGC between the left and right sides of this region was consistently and significantly different (P < 0.05) in females and males. The present study mainly clarified that chicken PGC continue to proliferate throughout early development, many PGC invaded into the vascular system from the region anterior to the head in stage 11, and PGC actively left the blood vessels and migrated to the intermediate mesoderm from stage 15.

90 GERM-LINE TRANSMISSION OF DONOR MITOCHONDRIAL DNA IN NUCLEAR TRANSFER-DERIVED COWS

In embryos derived by nuclear transfer (NT), fusion, or injection of donor cells with recipient oocytes caused mitochondrial heteroplasmy. Previous studies have reported varying patterns of mitochondrial DNA (mtDNA) transmission in cloned calves. Distribution of donor mtDNA found in offspring of NT-derived founders may also vary from donor–host embryo heteroplasmy to host embryo homoplasmy. Here we examined the transmission of mtDNA from NT cows to their progeny. NT cows were originally produced by fusion of enucleated oocytes with Jersey (J) or Holstein (H1) oviduct epithelial cells, or Holstein (H2) or Japanese Black (B) cumulus cells, as previously reported (Goto et al. 1999 Anim. Sci. J. 70, 243–245; Yonai et al. 2005 J. Dairy Sci. 88, 4097–4110; Akagi et al. 2003 Mol. Reprod. Dev. 66, 264–272). Transmission of donor cell mtDNA was analyzed by PCR-mediated single-strand conformation polymorphism (PCR-SSCP) analysis of the mitochondrial D-loop region. Eleven NT founder cows were analyzed, 4 (2 = J-NT, and 2 = H1-NT) of them were heteroplasmic whereas 7 (1 = J-NT, 1 = H1-NT, 2 = H2-NT, and 3 = B-NT) were homoplasmic for the host embryo mitochondria. The proportions of donor mtDNA detected in one J-NT cow was 7.7%, and those of other cow lineages were &lt;2%. Heteroplasmic NT cows delivered a total of 9 progeny. Four of the 9 progeny exhibited heteroplasmy with high percentages of donor cell mtDNA populations (52%, 37%, 17%, and 43%). The other 5 progeny were obtained from heteroplasmic NT cows, and all samples of the 10 progeny obtained from the homoplasmic NT cows did not harbor detectable donor cell mtDNA. A genetic bottleneck in the female germ-line will generally favor the transmission of a single mitochondrial population, leading to a return to homoplasmy. Thus, some of progeny maintained heteroplasmy with a higher ratio than that of their NT mothers, which may also reflect a segregation distortion caused by the proposed mitochondrial bottleneck. These results demonstrated that donor mtDNA in NT cows could be transmitted to progeny with varying efficiencies, in a lineage-specific fashion.

150 THE DISTRIBUTION PATTERN OF PRIMORDIAL GERM CELLS IN EARLY CHICK EMBRYOS

In all vertebrates, primordial germ cells (PGCs) appear during early stages of development in extragonadal sites, then they migrate to the gonad and give rise to ova or spermatozoa. Unlike in other species, however, in avian and reptile embryos, PGCs use the vascular system as a vehicle to transport them to the future gonadal region where they leave the blood vessels. The present study was carried out to know the details of this unique migration pathway and the proliferation of endogenous PGCs in chicken embryos. Whole of the chicken embryos during stages X [Roman numerals refer to the staging system of Eyal-Giladi and Kochav (1976 Dev. Biol. 49, 321–327) to 17 (Arabic numerals refer to the staging system of Hamburger and Hamilton (1951 J. Morphol. 88, 49-82))] or embryonic blood during stages 12 to 17 were immunohistochemical stained using specific antibody raised against chicken vasa homolog (CVH), which could be recognized as a marker for chicken PGCs. The distribution patterns and populations of PGCs in embryos were observed under a stereomicroscope. The numbers of PGCs were presented mean and standard deviation (mean � SD). Anti-CVH staining revealed the distribution and population of chicken PGCs in early chick embryos. PGCs existed mainly in the area pellucida and concentrated in the central zone at stage X. The mean number of PGCs per embryo at this stage was 130.4 � 31.9. With the formation of primitive streak, PGCs were carried anteriorly to the edge of the blastoderm. The PGCs scattered anteriorly began to concentrate to the anterior point of the head on the dorsal side of stage 10 embryos. The average number of PGCs per embryo at stage 10 was 439.3 � 93.6. The mean numbers of PGCs per embryo during stages X to 10 increased gradually as development progressed to stage 10. We found the entrance point of PGCs from anterior edge of the blastoderm to the vascular network during stages 10 to 11. In the blood, PGCs could be detected from all of the samples during stages 12 to 17. In contrast, no PGC was recognized in the future gonadal region before stage 14, and then they began to appear in the same region at stage 15. The mean numbers of PGCs that located in the future gonadal region during stages 15 to 17 increased intensively and were 97.3 � 57.3, 200.3 � 113.5, and 327.6 � 102.4, respectively. Interestingly, the numbers of PGCs within future gonadal region during stages 15 to 17 were consistently and significantly different (P &lt; 0.05) between the left and right side of the region. The results suggest that chicken PGCs move from extraembryonic area to the vascular network during stages 10 to 11, circulate in the blood stream, and finally, they begin to leave the blood vessels actively and migrate to the future gonadal region at stage 15.

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

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

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.

Quantitative trait loci analysis for growth and carcass traits in a Meishan x Duroc F2 resource population

We constructed a pig F2 resource population by crossing a Meishan sow and a Duroc boar to locate economically important trait loci. The F2 generation was composed of 865 animals (450 males and 415 females) from four F1 males and 24 F1 females and was genotyped for 180 informative microsatellite markers spanning 2,263.6 cM of the whole pig genome. Results of the genome scan showed evidence for significant quantitative trait loci (<1% genomewise error rate) affecting weight at 30 d and average daily gain on Sus scrofa chromosome (SSC) 6, carcass yield on SSC 7, backfat thickness on SSC 7 and SSC X, vertebra number on SSC 1 and SSC 7, loin muscle area on SSC 1 and SSC 7, moisture on SSC 13, intramuscular fat content on SSC 7, and testicular weight on SSC 3 and SSC X. Moreover, 5% genomewise significant QTL were found for birth weight on SSC 7, average daily gain on SSC 4, carcass length on SSC 6, SSC 7, and SSC X and lightness (L value) on SSC 3. We identified 38 QTL for 28 traits at the 5% genomewise level. Of the 38 QTL, 24 QTL for 17 traits were significant at the 1% genomewise level. Analysis of marker genotypes supported the breed of origin results and provided further evidence that a suggestive QTL for circumference of cannon bone also was segregating within the Meishan parent. We identified genomic regions related with growth and meat quality traits. Fine mapping will be required for their application in introgression programs and gene cloning.

Genetic relationships among Japanese native breeds of chicken based on microsatellite DNA polymorphisms

Genetic relationships among Japanese native breeds of chickens were studied on the basis of microsatellite DNA polymorphisms. DNA samples from 10 Japanese native breeds (Iwate-Jidori, Aizu-Jidori, Sadohige-Jidori, Siba-Tori, Onaga-Dori, Echigonankin, Hinai, Kinpa, Koeyoshi, and Tomaru) and one imported breed (White Leghorn) were analyzed using eight microsatellite markers that were isolated from a microsatellite DNA-enriched library of chickens (Takahashi et al. 1996). The PCR primers to detect (CA)n repeat length polymorphisms were synthesized based on the sequences of clones, and these markers were typed by PCR amplification and electrophoresis using a DNA sequencer. Since all eight microsatellite markers were polymorphic, genetic distance between the breeds could be calculated based on the frequencies of alleles of the microsatellites and phylogenetic relationships between the breeds could be estimated. Most Japanese native chickens were grouped into three groups that correspond to the origin breeds, Jidori, Shokoku, and Shamo. The results suggest that microsatellite DNA markers are a useful tool for studying the genetic relationships among chicken breeds.

An in vitro culture method for chick embryos obtained from the anterior portion of the magnum of oviduct

1. Chick embryos, obtained from the anterior portion of the magnum of the oviduct 60 to 80 min after the preceding egg had been laid, were cultured in vitro in small and large recipient eggshells until hatching. 2. Of 82 embryos cultured, 46.3% had survived to day 4 of incubation, and 19.5% survived to hatching. 3. The method for culturing embryos used in this experiment could facilitate research on the in vitro manipulation of early chick embryos.

Preservation of quail blastoderm cells in liquid nitrogen

1. Quail blastoderm cells isolated from the yolk were preserved in liquid nitrogen. 2. Frozen-thawed blastoderm cells of the quail were viable and survived in vitro. By injecting the frozen-thawed cells into chick embryos, quail-chick chimaeras were produced.

Developmental ability of twin embryos produced by microinjection treatment into chick blastoderm

Twins and triplets of chick embryos were produced by microinjection treatment of cell suspension into the blastoderm. One pair of the twin embryos had an ability to develop normally and survived up to Day 21 of incubation, but did not hatch. The other twins and triplets died within 7 days.

Production of quail-chick chimaeras by blastoderm cell transfer

1. Quail-chick chimaeras were produced by injecting dissociated quail blastoderm cells into chick embryos. 2. Quail blastoderms were removed from the yolk and the cells were dispersed by trypsin treatment or pipetting. The cell suspension (1 to 5 microliters) was injected into the subgerminal cavity of unincubated chick embryos. The chick embryos were then cultured in recipient eggshells. 3. Quail blastoderm cells injected into the chick embryos adhered to the chick embryonic cells. The rates of hatching were 8.6% (38 chicks from 441 eggs) and 40.3% (48 chicks from 119 eggs) when the volumes of the cell suspension injected were 3 to 5 microliters and 1 microliter, respectively. 4. Seven out of 86 hatched birds were clearly identified as being chimaeric because part of the feather colouring was of quail specificity. In addition to these chimaeric birds, there were 8 chimaeric embryos which died before hatching. The distribution patterns of the quail feathers were varied among the chimaeric birds and embryos. 5. This technique provides a basis for the investigation of chick embryo cryopreservation, genetic transformation and analysis of cell lineage of chickens.

Development in culture of the chick embryo from fertilized ovum to hatching

An experiment was carried out to investigate whether thick albumen is essential for the normal development of the chick embryo. Fertilized ova recovered from the oviducts of hens were cultured in vitro and transferred to recipient eggshells with (method A) or without (method B) replacement of the thick albumen by thin albumen. Embryos from freshly laid eggs were transferred to recipient eggshells with (method C) or without (method E) replacement of the thick albumen by thin albumen or with replacement of the thick albumen by thin albumen diluted with solution of salts (method D). Embryos were then incubated until hatching. The rates of hatching of the cultured embryos were 34.4%, 16.2%, 50.0%, 6.9-26.7%, and 47.5% for methods A, B, C, D, and E, respectively. Thus the rate of hatching of cultured fertilized ova was increased by replacement of the thick albumen by thin albumen at the blastoderm stage. Chicks obtained by method A reached maturity and produced viable offspring, and this technique provides an improved method for the culture of fertilized ova to hatching.

Duration of egg formation in hens selected for increased rate of lay under 23 h and 24 h light-dark cycles

1. The intervals from oviposition to the next ovulation and the times spent by the ovum in various parts of the oviduct were examined, in hens selected for increased rate of lay over 5 generations under a 23 h light-dark cycle (23HS line) and kept in a 22 h light-dark cycle, and in hens selected under a 24 h light-dark cycle (24HS line) and kept in a 24 h light-dark environment. 2. The intervals from oviposition to the next ovulation were 13 min and 25 min in the 23HS and 24HS lines respectively. Times from ovulation to entry of the ovum into the uterus were 4 h 44 min and 4 h 43 min in the 23HS and 24HS lines respectively, and times spent by the ovum in the uterus were 19 h and 19 h 24 min in the 23HS and 24HS lines respectively. 3. It is concluded that the reduced oviposition interval in the 23HS line compared to the 24HS line was caused by the reduction in the interval from oviposition to the next ovulation and the time spent by the ovum in the uterus.

Selection experiment for increased egg production under 23 H and 24 H light-dark cycles in the domestic fowl

A selection experiment was conducted for increased rate of lay under 23-h (23 HS line) and 24-h (24 HS line) light-dark cycles over 5 generations. In generation 5, rate of lay was higher in the 23 HS line than in the 24 HS line, and the proportion of hens with mean intra-sequence intervals of less than 24 h in the 23 HS line increased to 88% in the generation 5 from 15% in the base generation. The realised heritability for rate of lay was 0.25 plus/minus 0.04 in the 23 HS line and 0.15 plus/minus 0.05 in the 24 HS line. Egg weight and shell weight decreased in both lines, and the decrease in the proportion of shell was larger in the 23 HS line than in the 24 line. It is suggested that a regimen of 23 h light and dark may be an effective environment for selection to improve the laying performance of a population approaching a plateau for egg production.