Agroecology Is Affecting Village Chicken Producers’ Breeding Objective in Ethiopia

This study assessed factors that determine village chicken producers’ trait preferences in different agroecologies of Ethiopia. Three hundred and eighty village chicken producers were sampled for individual interviews. Data were analyzed using descriptive and inferential statistical techniques. Inbreeding coefficients of chicken populations in the three major agroecologies were estimated. In addition, the multivariate regression model was employed to evaluate the degree to which agroecological difference and socioeconomic and institutional factors impact village chicken producers’ trait preferences. Egg and meat production for consumption and income generation were the three major village chicken production functions in the study. Plumage color and weight were ranked first for male and female chicken, respectively. Red plumage color (52.4%) was the primary choice followed by white color (24.5%). Agroecology and livestock holding (TLU) significantly ( P < 0.05 ) affected farmers’ preference toward economic traits, while land holding significantly ( P < 0.05 ) affected reproductive traits. Distance to market significantly ( P < 0.05 ) affected farmers’ preference toward adaptive traits. The inbreeding coefficient of 0.25, 0.23, and 0.06 was recorded in low, mid, and highland agroecologies, respectively. The agroecological difference is affecting village chicken producers’ breeding objective in Ethiopia. A higher inbreeding coefficient was observed in the low and mid agroecologies. Future breed improvement programs should give due consideration to village chicken producers’ socioeconomic characteristics and agroecological differences.

Inbreeding Coefficient and Distance in MHC Genes of Parents as Predictors of Reproductive Success in Domestic Cat

Inbreeding and low diversity in MHC genes are considered to have a negative effect on reproductive success in animals. This study presents an analysis of the number and body mass of offspring in domestic cat, depending on the inbreeding coefficient and the degree of similarity in MHC genes of class I and II in parents. Inbred partners had a lower number of live kittens at birth than outbred ones. At the same time, the inbreeding coefficient did not affect the litter size and the number of offspring who survived until the period of transition to solid food. The most significant predictor for the number of surviving offspring was the degree of parental similarity in MHC genes: the parents with the maximum distance in MHC genes had more survived kittens. Moreover, this effect was most pronounced immediately after birth. A significant percentage of kittens from parents with a minimum distance in MHC genes were either stillborn or died on the first day after birth. By the age of transition to solid food, this effect is no longer so pronounced. Furthermore, neither the inbreeding coefficient nor the distance in MHC genes of parents had any effect on the body mass of kittens.

Structure and genetic variability of the Mexican Sardo Negro breed

ABSTRACT: This study analyzed the Sardo Negro breed pedigree (41,521 animals registered from 1958 to 2019) to determine its structure, evolution, and genetic variability (GV). The population genetic parameters evaluated were effective number of founders (fe) and ancestors (fa), pedigree integrity, additive genetic relationship (AGR); number of complete generations (NCG), maximum generations traced (NMGT), and equivalent complete generations (NECG); effective population size (Ne), inbreeding coefficient (F), and generation interval (GI). The average GI was 7.45 years. A total of 7,804 founders and 4,856 ancestors were identified for a fe of 185 and a fa of 97. The average and maximum values of NCG, NECG, and NMGT were 1.6 and 5.0, 2.5 and 6.5, 4.3 and 12, with Ne estimates of 15.9, 25.9, and 69.0, respectively. The increase in F, linked to Ne, ranged from 0.72% to 3.1% per generation. The average values for F and AGR were 3.6% and 1.0%, respectively. The proportion of inbred individuals was 32.0%, with F values ranging from 0.01 to 62.2% and an average of 11.3%. The rate of inbred population was 1.3% per year. The annual rate of AGR was 0.04%. For the continuity and projection of the breed, the evolution of F as a function of Ne and the possible implications of the selection schemes must be considered. The genetic variability sustained over time results from the Ne.

Characterization and Genetic Diversity of Taif Chicken Ecotype Using Dense Microsatellites Panel

The current study is the first comprehensive investigation to address the native chicken ecotypes of the Taif region to unravel the genetic diversity using a dense panel of 40 microsatellites (SSR). Blood samples were collected from 25 hens randomly sampled from a village farm at Taif governorate. A total of 147 alleles were detected, with an average of 3.7 alleles per locus. The overall mean of polymorphic information content (PIC) was 0.43. The average observed heterozygosity (Hobs) of 0.28 was lower than the expected heterozygosity (Hexp) of 0.48. Out of 40l ocionly11 loci showed insignificant deviation from Hardy Weinberg expectation. The ecotypes showed low genetic diversity (HS = 0.65) and a high level of inbreeding (FIS= 0.75). The high FIS is indicative of the endangerment potentiality of this ecotype. Nine SSR showed an inbreeding coefficient of one. The significant estimate of the inbreeding coefficient of the present study calls for an immediate breeding plan to preserve such endangered ecotypes. Results of the present study will provide an initial guide to design further investigations for the development of sustainable genetic improvement and conservation programs for the Taif ecotype genetic resources.

PLUM VARIETIES USED AS PARENTS IN ROMANIAN BREEDING PROGRAM

There are about three thousand varieties belonging to Prunus domestica available at present worldwide that can be used as genitors in plum breeding activity. An analysis of the pedigrees of plum cvs. developed in Romanian breeding programs shows that the most are descended from ‘Tuleu gras’, ‘Renclod Althan’, ‘Anna Späth’, ‘Stanley’ and ‘Early Rivers’, called 'ancestors'. That means the majority of plum cvs. have at least one of the ancestors as parent or grandparent. For those 40 plum cvs. registered in Romania in 60 years an increased number of crosses with these 'ancestors' has led to what we call 'inbreeding'. According to data presented in this paper, ‘Tuleu gras’ cv. was the most frequently used parent in the cross combinations, giving origin to 23 cvs. Among the other frequently used genitors were: ‘Renclod Althan’ (7 cvs.), ‘Anna Späth’ (3 cvs.) and ‘Stanley’ (1 cv.). Many of the cultivars – 32 altogether (80%) have originated from hybridization, whereas 4 cvs. have originated from open pollination, others 3 cvs. from mutagenesis and 1 cv. from clonal selection. The goal of this work is to measure genetic diversity presently use in Romanian plum breeding. Pedigrees of each cv. were used to study the genetic contributions of ancestor. Of the 40 cvs. analyzed, 33 had an inbreeding coefficient other than zero. The overall mean inbreeding coefficient was 0.419 for all cvs., where their parentages were known. For cvs. with unknown parentage (nonrelated with known parentage) the inbreeding coefficient is zero. The mean coefficient of coancestry of 40 plum cvs. are 0.081 with ‘Tuleu gras’ cv., 0.019 with ‘Renclod Althan’ and ‘Anna Späth’ cvs., 0.017 with ‘Early Rivers’ cv., 0.014 with ‘d’Agen’ and ‘Renclod Violet’ cvs. and 0.005 with Stanley cv. In conclusion, plum breeders have worked with populations of greatly reduced genetic diversity and this strategy becomes a problem because it leads to genetic impoverishment, and, also, the loss of the genetic resistance to different diseases.

Rank-invariant estimation of inbreeding coefficients

The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.

Assessment of Genetic Diversity and Relationship of the Two Sanga Type Cattle of Botswana Based on Microsatellite Markers

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana; Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INTRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations; Tswana (He=0.7895±0.033 vs Ho=0.631±0.091) and Tuli (He=0.8123±0.033 vs Ho=0.556±0.021). The inbreeding coefficient was 0.200±0.002 and 0.332±0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding program is likely to result in minimal heterosis and therefore not recommended.

Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

PSI-B-23 Assessment of genomic inbreeding in Russian local and commercial dairy breeds of cattle

Drastic decline of population size of Russian local cattle breeds observed during last three decades has led to the decrease of genetic diversity. Due to the limited number of bulls used for artificial insemination, inbreeding in herds can be increased, which can lead to the decrease of reproduction capacity and adaptability of animals. Our aim was to assess genomic inbreeding in two Russian local cattle breeds, including Kholmogor (n = 26) and Istoben (n = 21). Two transboundary cattle breeds used for milk production in Russia including Holstein (n = 49) and Simmental (n = 38) were chosen for comparison. SNP genotyping was performed using the Bovine GGP 150K BeadArray (Illumina, CA, USA). After the quality control, 117591 autosomal SNPs were selected for analyzes. The degree of genomic inbreeding was assessed by calculations of inbreeding coefficient based on run of homozygosity (F(ROH)) and multilocus heterozygosity (sMLH). We found the strong negative correlations between the F(ROH) and sMLH values in animals of all of studied breeds (r2 = -0.805). The average F(ROH) values were 0.065 &lt; mo &gt;±&lt; /mo &gt;&lt; /math &gt;“&gt;±± 0.003 for Kholmogor, 0.048 &lt; mo &gt;±&lt; /mo &gt;&lt; /math &gt;“&gt;±± 0.006 for Istoben, 0.129 &lt; mo &gt;±&lt; /mo &gt;&lt; /math &gt;“&gt;±± 0.007 for Holstein, and 0.102 &lt; mo &gt;±&lt; /mo &gt;&lt; /math &gt;“&gt;±± 0.007 for Simmental breed. The sMLH values in Kholmogor, Istoben, Holstein and Simmental breeds varied from 0,99 to 1,076, from 0,829 to 1,102, from 0,890 to 1,069 and from 0,866 to 1,041, and averaged to 1.030, 1.013, 1.000, and 0.974, respectively. According to our research results, two studied Russian cattle breeds are characterized by lower levels of genomic inbreeding compared to transboundary cattle breeds. Our results will be helpful for developing the conservation programs for Russian Kholmogor and Istoben cattle breeds. The study was funded by the Russian Ministry of Science and Higher Education within theme No. 0445-2019-0024 and RFBR within project 19-316-90017 (the study of Kholmogor cattle).