Relationship between band sharing levels of DNA fingerprints and inbreeding coefficients and estimation of true inbreeding in turkey lines

Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds

Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.

Genetic variation in pure lines and crosses of large-bodied turkeys. 4. Body shape and carcass traits

An experimental line (F) of turkeys selected long-term for increased 16-wk BW was reciprocally crossed with a primary breeding sire line (C) from a major international turkey breeder to study the inheritance of carcass traits and body shape. The birds were weighed and killed at 16 wk of age, and various measurements of muscling, leg bones, and body shape were made. The BW of males were 16.0 and 15.1 kg, respectively, in the C and F lines. The respective BW for females were 12.2 and 11.2 kg. Additive genetic variation, as indicated by differences between the F and C line, was a more important source of variation for measurements of muscling than for measurements of leg bones. The anterior and posterior depth of the body and the ratio of these measurements differed between the F and C lines. Body cavity volume index (length x width x height) differed between lines in females and sexes combined. The weights of some internal organs (gizzard, heart, liver, pancreas, and spleen), but not others (proventriculus and lungs), differed between lines, and the total weight of these organs was greater in the C line than in the F line. However, the ratio of total demand organs (muscles and bones) to the total weight of the supply organs was less in the F line than in the C line. Heterosis was a more important source of variation in body weight and weights of the pectoralis major and pectoralis minor muscle weights in males than in females. Heterosis for some body shape measurements (keel length, body depth 1, body depth 2, body depth ratio, body cavity height, and body cavity volume index) was significant in some comparisons. Heterosis (range = 3.64 to 3.99%) for leg muscle measurements (thigh muscles, drumstick muscles, and total leg muscles) was highly significant (P < or = 0.01) based on the analysis for both sexes. Differences between the reciprocal crosses of the F and C lines were more frequent in the present study than in previous studies in which the F line was reciprocally crossed with sire lines from 2 other commercial breeders. However, when the data from the previous studies and the current study were summarized, it appeared that the only reciprocal effect that was consistent was for the weight of the drumstick muscles, indicating sex linkage or maternal effects may influence the weight of these muscles.

Genetic variation in pure lines and crosses of large-bodied turkey lines. 3. Growth-related measurements on live birds

An experimental line (F) selected over 34 generations for increased 16-wk BW was reciprocally crossed with a primary breeding sire line (C) from a large international turkey breeder to study the inheritance of growth-related traits measured on live birds. All genetic groups were grown intermingled in confinement with sexes reared in different houses. The traits measured included BW at 8, 16, and 20 wk of age and shank length, shank width, shank depth, breast width, and walking ability scores at 16 wk of age. Walking ability was rated from 1 to 5 with 1 representing birds with no leg defects and no difficulty walking and 5 indicating birds with extreme lateral deviations of the legs and great difficulty walking. Ratings of 2, 3, and 4 represented intermediate values. The F line had a different growth pattern than the C line with the F line being larger than the C line at 8 wk of age, but the reverse was true at 16 and 20 wk of age. The difference in BW between the C and F lines increased from 16 to 20 wk of age. The C line had wider breasts than the F line at 16 wk of age. The F line had longer shanks than the C line. Shank width was larger in the C line than the F line for females but not males. No line difference in shank depth was observed. Walking ability scores at 16 wk of age were lower (better) in the C line than in the F line for males but not females. Significant heterosis in BW of the crosses of the F and C lines was observed at all ages in males (range = 3.3 to 5.6%) and only at 8 wk of age in females (3.6%). These results were similar to an earlier study in which the F line was crossed with a primary-breeding sire line from 2 other international turkey breeders. No significant heterosis in the crosses of the C and F line was observed for breast width and shank measurements. Heterosis was significant for walking ability scores of females (-3.0%) but not males. Reciprocal effects, a measure of sex linkage and maternal influences, were noted only for shank length and the direction of the difference was not the same in the 2 sexes.

Genetic variation in pure lines and crosses of large-bodied turkey lines. 1. Body weight, walking ability, and body measurements of live birds

An experimental line of turkeys selected for increased BW (F) was reciprocally crossed with sire lines (designated A and B) from each of two major commercial breeders in order to study the inheritance of growth traits. All genetic groups were grown intermingled in confinement with the sexes reared in different houses. Traits measured included BW at 8, 16, and 20 wk of age; shank length, width, and depth; breast width; and walking ability scores at 16 wk of age. The F line had a different growth pattern than the two commercial sire lines. The F line had higher (males) or similar (females) BW in comparison to Line A at 8 wk of age, but by 16 wk of age, Line A was heavier than Line F in both sexes. The difference in BW between the F and A lines increased from 16 to 20 wk of age. Lines F and B did not differ in BW at 8 wk of age, but at 16 and 20 wk of age, Line B birds were heavier than those of F line. Reciprocal effects, a measure of sex linkage and maternal effects, were noted only for breast width of females in crosses of Lines A and F and for shank width and depth of males and 8-wk BW and shank depth of females in crosses of Lines B and F. Heterosis was an important source of variation in BW for males from both crosses. The percentage heterosis at the various ages ranged from 3.1 to 7.5. For females, heterosis (range = 2.6 to 4.9%) was only significant at younger ages (8 wk for the crosses of the A and F lines and 8 and 16 wk for the crosses of the B and F lines). No heterosis for breast width was observed in either cross. Heterosis in walking ability scores was significant only for males from the crosses of Lines B and F. The presence of heterosis was inconsistent for shank measurements.

Genetic relationship among lines and smooth muscle and ovarian follicular development within lines of Japanese quail in two long-term selection studies

Smooth muscle tumor and ovarian follicular development were studied in lines of Japanese quail selected for increased 4-wk BW (HW, P, and T) and their randombred controls (C and R1). The lines studied were from long-term selection studies at The Ohio State University (HW and R1) and The University of Georgia (P, T, and C). To study the genetic relationship among the lines in the two selection studies, the C, P, HW, and R1 lines were DNA-fingerprinted by digestion of the DNA with the HaeIII restriction enzyme and using Jeffreys' 33.6 probe. The BW of females at 4 wk of age and at the end of a 240-d egg production period were similar for the C and R1 lines. The BW of the selected lines was ranked P > T > HW for both measurements. Smooth muscle tumors were found in the oviducal ligaments adjacent to the magnum. A greater percentage of hens from the BW-selected lines had smooth muscle tumors of greater weight than the randombred control lines, which did not differ in tumor incidence or weight. The P and T lines had a greater incidence of multiple-lobed tumors than the HW line. Based on bandsharing (BS) of DNA fingerprints, the Georgia and Ohio lines did not appear to be closely related, suggesting that, perhaps, the smooth muscle tumors in the BW-selected lines in the two studies might have resulted from pleiotrophic effects of genes affecting growth or to genes closely linked to the growth genes. The BW-selected lines in both selection studies had more ovarian follicles in rapid development, which were of greater weight, than the randombred control lines. The HW line had a larger number of ovarian follicles in rapid development than the P and T lines. The percentage of hens with atretic follicles was greater in the BW-selected lines. The results of the present study suggest that the effect of BW selection on ovarian follicular development may occur early in selection (within the first 30 generations) and is not influenced by additional genetic changes in BW.

Measurement of genetic variation within and between Japanese quail lines using DNA fingerprinting

The objective of the present experiment was to study genetic variation within and among well-defined Japanese quail lines by DNA fingerprinting. The Japanese quail lines included a randombred control line (R1) and lines developed from R1 by divergent selection over 30 generations for 4-wk BW (HW, LW) and total plasma phosphorus (TPP) (HP, LP), a measure of yolk precursor in the blood. In addition, two sublines (HW-HP, HW-LP) of HW, developed in the ninth generation, were included in the analysis. Males of the sublines were selected for increased 4-wk BW whereas females were selected for increased (HW-HP) or decreased (HW-LP) TPP. Sixteen individual DNA samples per line were digested with HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs designed to measure band sharing (BS). Within lines, BS ranged from 0.384 to 0.525. The BS within the R1 line was less than that of all selected lines, except for the HP and LP lines, indicating that, in general, selection had increased genetic homogeneity within the selected lines. Between lines, BS was less than within lines and the R1 line had the highest average level of BS (0.278) with the other lines. The BS between lines for the selected lines ranged from 0.230 to 0.308 with an average of 0.265. In the comparison of the R1 line with the selected lines, it appeared that selection for increased TPP or decreased BW may have influenced BS levels. The relationships of the HW line with its sublines (HW-HP and HW-LP) were not accurately predicted by the DNA fingerprinting technique used. All lines were separated, as indicated by the genetic distance between lines.

Ribosomal RNA gene copy number and nucleolar-size polymorphisms within and among chicken lines selected for enhanced growth

Ribosomal (r) DNA genotypes (rRNA gene copy number) and nucleolar phenotypes (nucleoli number and size) were studied in dam and sire commercial broiler pure lines from three primary breeder sources. Thirteen lines were studied to determine whether directionally selected broiler pure lines contain higher numbers of rRNA genes than a control line unselected for performance traits. Eight of the 13 lines exhibited rRNA gene copy averages between 261 and 331 copies, three lines had averages between 365 and 380, and two lines had average copy numbers equal to or greater than 450 rRNA genes. The overall source copy number average from one breeder company exhibited a value (402 rRNA genes) significantly different from the control value (300 rRNA genes). Nucleoli number and relative-size were examined in 9 of the 13 lines to establish ploidy and determine the population incidence of nucleolar size polymorphisms. All of the individuals examined for nucleolar phenotype expressed two nucleoli, indicating that gene copy number variation in those lines was generally unrelated to haploidy, aneuploidy, or polyploidy. A high frequency of individuals exhibited nucleolar size polymorphisms (line values of 57 to 87%). The results suggest that multiple nucleolus organizer region (NOR) types are segregating within and among broiler pure lines and that these NOR types contain variable numbers of rRNA genes that differ in nucleogenesis capacity.

Genetic diversity of commercial turkey primary breeding lines as estimated by DNA fingerprinting

The genetic diversity of primary breeding sire and dam lines from the three largest turkey breeders was estimated by band sharing of DNA fingerprints and by genetic distance estimated from band sharing. For comparison, experimental lines selected for increased egg production (E line) or increased 16-wk body weight (F line) were also included in the analysis. Eighteen individual DNA samples per line were digested with HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs designed to measure band sharing. Within commercial lines, band sharing ranged from 0.370 to 0.508 and was greater in commercial sire lines (average = 0.475) than in commercial dam lines (average = 0.393), indicating that accumulated inbreeding was greater in the sire lines. Band sharing in the F and E lines was 0.479 and 0.522, respectively. The average band sharing among lines was higher for primary breeding sire lines (average = 0.267) than for primary breeding dam lines (0.207), suggesting more genetic diversity in the dam lines. Genetic distance estimated from band sharing was greater among commercial dam lines than commercial sire lines. Based on band sharing between lines and genetic distance estimates, it appears that the experimental E and F lines contain genetic variation not found in the commercial lines. The results of the present study, along with data published in the literature, suggest that commercial primary breeding turkey lines are as diverse, if not more diverse, than similar commercial chicken lines.

Influence of crossing a line selected for increased shank width and a commercial sire line on performance and walking ability of turkeys

The present study was initiated to determine whether walking ability (WA) could be markedly improved without seriously compromising growth rate and body conformation by crossing a relatively unimproved commercial sire line (UC) with a line (FL) selected for increased shank width and backcrossing F1 females to UC line males. Body weights at 8, 16, and 20 wk of age were generally similar for both lines at the time of the initial cross. The UC line had inferior WA, shorter and narrower shanks, and wider breasts compared with the FL line. The F1 birds exhibited overdominance for BW at all ages. Heterosis in BW ranged from 3.2 to 7.8%. At 16 wk of age, the WA scores decreased (indicating improved WA) in the F1 relative to the average of the parental lines. Heterosis of WA scores was -10.5% (P > or = 0.05) for males and -23.5% (P < or = 0.05) for females. Heterosis was observed in the F1 for shank length but not for other shank measurements (width and depth). No heterosis was observed for breast width. Mortality from 8 through 20 wk of age was reduced in the F1 relative to the parental lines. The backcross of the F1 females to UC males still exhibited heterosis for male BW at 16 and 20 wk of age and for WA scores, although the magnitude was reduced 50% or more. Mortality from 8 to 20 wk of age decreased in the backcross compared with the parental lines. The results suggest that a line exhibiting improved leg structure and WA, and poor conformation, such as FL, can be used to greatly improve the WA of a cross involving a sire line with poor WA but excellent conformation. A portion of the gains in BW and breast width obtained in the F1 was retained in a backcross to the sire line, making such a crossing scheme commercially feasible.