Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed

The objective of this work was to evaluate the population structure and the genetic and phenotypic progress of Nelore cattle in Northern Brazil. Pedigree information concerning animals born between 1942 and 2006 were analyzed. Population structure was performed using the Endog program. Out of the 140,628 animals studied, 67.7, 14.52 and 3.18% had complete pedigree record of the first, second and third parental generation, respectively. Inbreeding and average relatedness coefficients were low: 0.2 and 0.13%, respectively. However, these parameters may have been underestimated, since information on pedigree was incomplete. The effective number of founders was 370 and the genetic contribution of 10, 50 and 448 most influent ancestors explained 13.2, 28 and 50% of the genetic variability in the population, respectively. The genetic variability for growth traits and population structure demonstrates high probability of increasing productivity through selective breeding. Moreover, management strategies to reduce the currently observed age at first calving and generation intervals are important for Nelore cattle genetic improvement.

Download Full-text

Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands

Scientific Reports ◽

10.1038/s41598-019-49861-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Dagne Wegary ◽

Adefris Teklewold ◽

Boddupalli M. Prasanna ◽

Berhanu T. Ertiro ◽

Nikolaos Alachiotis ◽

...

Keyword(s):

Population Structure ◽

Candidate Genes ◽

Genetic Relatedness ◽

Inbred Lines ◽

Snp Markers ◽

Pedigree Information ◽

Selective Sweeps ◽

Genetic Purity ◽

Heterotic Groups ◽

Maize Inbred Lines

Abstract Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30–36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.

Download Full-text

Putative Variants, Genetic Diversity and Population Structure among Soybean Cultivars Bred at Different Ages in Huang-Huai-Hai Region

10.21203/rs.3.rs-847153/v1 ◽

2021 ◽

Author(s):

Jialin Liu ◽

Huimin Xie ◽

Ting Lin ◽

Congxiao Tie ◽

Huolin Luo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variants ◽

Pedigree Information ◽

Biological Processes ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Soybean Cultivars ◽

Genome Wide

Abstract Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To data, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population that composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38x. In total, 11185589 single nucleotide polymorphisms (SNPs) and 2520208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of the five sub-populations were 290kb, 380kb, 753kb, 182kb, and 227kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increasing in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study was to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and in the hope of providing a theoretical reference for other identical studies.

Download Full-text

Analysis of the population structure of a cattle conservation nucleus Curraleiro Pé Duro

Arquivo Brasileiro de Medicina Veterinária e Zootecnia ◽

10.1590/1678-4162-12042 ◽

2021 ◽

Vol 73 (1) ◽

pp. 231-238

Author(s):

N.L. Ribeiro ◽

G.R. Medeiros ◽

G.V. Nascimento ◽

J.K.G. Arandas ◽

M.N. Ribeiro

Keyword(s):

Population Structure ◽

Management Plan ◽

Inbreeding Coefficient ◽

Pedigree Information ◽

Third Generation ◽

Effective Number ◽

Pedigree Data ◽

Genetic Management ◽

The Third ◽

Genealogical Information

ABSTRACT The objective of this research was to study the population structure of the Cattle Conservation Nucleos Curraleiro Pé Duro of the Instituto Nacional do Semiárido (NCP_INSA) based on pedigree data. Genealogical information from 338 animals registered in the period from 1991 to 2019 was used. The number of founding animals (Nf), the effective number of founders (fe), effective number of ancestors (fa), inbreeding coefficient (F), and average relatedness coefficient (AR), in addition to Fis, Fit and Fst were estimated. It was possible to identify ancestors up to the third generation, with an increase in information over the generations. Of the total pedigree information evaluated, 90.53% had the identification of the father and mother. The effective size of the population was smaller than those proposed by FAO, suggesting the need to redefine the herd management and genetic management plan strategies, promoting gene flow and breed expansion.

Download Full-text

Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.665872 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhiying Wang ◽

Bohan Zhou ◽

Tao Zhang ◽

Xiaochun Yan ◽

Yongsheng Yu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Inbreeding Depression ◽

Inner Mongolia ◽

Inbreeding Coefficient ◽

Production Performance ◽

Pedigree Information ◽

Economic Traits ◽

Inbreeding Coefficients ◽

Cashmere Goats

Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs.Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs.Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD.Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

Download Full-text

Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses

Animals ◽

10.3390/ani11020269 ◽

2021 ◽

Vol 11 (2) ◽

pp. 269

Author(s):

Carmen Marín Navas ◽

Juan Vicente Delgado Bermejo ◽

Amy Katherine McLean ◽

José Manuel León Jurado ◽

Antonio Rodriguez de la Borbolla y Ruiberriz de Torres ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Discriminant Analysis ◽

Genetic Parameters ◽

Canonical Discriminant Analysis ◽

Canonical Analysis ◽

Pedigree Information ◽

Effective Solution ◽

Negative Effects ◽

Generation Interval

Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).

Download Full-text

Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs

Genes ◽

10.3390/genes12030429 ◽

2021 ◽

Vol 12 (3) ◽

pp. 429

Author(s):

Grażyna Polak ◽

Artur Gurgul ◽

Igor Jasielczuk ◽

Tomasz Szmatoła ◽

Jędrzej Krupiński ◽

...

Keyword(s):

Population Structure ◽

Genomic Data ◽

Pedigree Information ◽

Runs Of Homozygosity ◽

Q Value ◽

Horse Population ◽

Livestock Breeding ◽

Genomic Inbreeding ◽

And Control ◽

Shared Alleles

Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (FPED) and genomic inbreeding estimates was found for FROH (runs of homozygosity-based F coefficient) and FUNI (F coefficient based on the correlation between uniting gametes). FROH correlation with FPED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.

Download Full-text

Analysis of population structure and genetic variability in Iranian buffaloes (Bubalus bubalis) using pedigree information

Animal Production Science ◽

10.1071/an14738 ◽

2016 ◽

Vol 56 (7) ◽

pp. 1130 ◽

Cited By ~ 6

Author(s):

Navid Ghavi Hossein-Zadeh

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Bubalus Bubalis ◽

Pedigree Analysis ◽

Inbreeding Coefficient ◽

Pedigree Information ◽

Genome Equivalent ◽

Effective Number ◽

Inbreeding Coefficients

The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P < 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.

Download Full-text