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

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).

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Evaluation of the Romosinuano cattle population structure in Mexico using pedigree analysis

Revista Colombiana de Ciencias Pecuarias ◽

10.17533/udea.rccp.v32n4a05 ◽

2020 ◽

Vol 33 (1) ◽

pp. 44-59

Author(s):

Rafael Núñez-Domínguez ◽

Ricardo E Martínez-Rocha ◽

Jorge A Hidalgo-Moreno ◽

Rodolfo Ramírez-Valverde ◽

José G García-Muñiz

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Population Size ◽

Effective Population Size ◽

Genetic Drift ◽

Pedigree Analysis ◽

Effective Population ◽

Genetic Management ◽

Generation Interval

Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.Palavras-chave: consanguinidade; deriva genética; diversidade genética, estrutura populacional; fluxo de genes; intervalo entre gerações; pedigree; probabilidade de origem do gene; Romosinuano; tamanho efetivo da população.

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Evaluation of genetic variability of the breed Norik of Muran according to pedigree information

Czech Journal of Animal Science ◽

10.17221/20/2017-cjas ◽

2018 ◽

Vol 63 (No. 5) ◽

pp. 195-200 ◽

Cited By ~ 2

Author(s):

M. Halo ◽

E. Mlyneková ◽

M. Horná ◽

M. Ivančíková ◽

A. Hrdá

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Average Length ◽

Pedigree Information ◽

Common Ancestry ◽

Generation Interval ◽

The Core ◽

Equivalent Number ◽

The Common ◽

Gene Origin

The Norik of Muran, a unique draught horse bred in Slovakia, belongs to country’s biodiversity treasures. The genetic diversity of this horse type was evaluated on the basis of indicators derived from the common ancestry and the probability of gene origin. The pedigree file of the analyzed horses involved 115 individuals (15 stallions and 100 mares). The number of complete generations was 4.49 on average. The maximum number of ancestor generations at the examined population of living horses was 5.38 and the equivalent number in the generation of ancestors was 5.14. The highest average length of the generation interval was 10.97 years in the father–son direction compared to father–daughter (9.74), mother–son (10.87), and mother–daughter (8.99 years – the lowest average length). The generation interval overall average length was 10.14 years. The total coefficient of relatedness was 1.72% on average. The efficient number of core ancestors evenly used in breeding in comparison with the core ancestors mildly decreased to 198. Therefore the Austrian Norik incorporation in the breeding program is the opportunity how to maintain genetic diversity.

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Assessment of genetic diversity in goat genetic groups of Kerala, (India) using morphobiometric markers

Indian Journal of Animal Research ◽

10.18805/ijar.b-3119 ◽

2018 ◽

Author(s):

G. Radhika ◽

K. C. Raghavan ◽

K. A. Mercey ◽

C. Sunanda ◽

P. M. Rojan

Keyword(s):

Genetic Diversity ◽

Discriminant Analysis ◽

Analytical Techniques ◽

Coat Colour ◽

Canonical Discriminant Analysis ◽

Morphological Data ◽

Biometric Data ◽

Boer Goat ◽

Canonical Variables ◽

Genetic Groups

Geographical isolation and human interventions resulted in formation of subpopulations among native breeds, which showed differences in morphological or biometric traits. Crossbreeding of indigenous goats with exotic breeds resulted in combining desirable characteristics of many breeds in a composite population. Malabari crossbreds (CB), which had the inheritance of Malabari, Saanen, Alpine and Boer goat breeds were available at University Goat Farm, Mannuthy, Kerala, India. The native goats of Kerala namely, Attappady Black (AB) and populations of Malabari goats from Kannur, Calicut, Thrissur and Malappuram districts (MK, MC, MT and MM) were analysed along with Malabari crossbreds (CB) for genetic diversity. Morphological data were collected from 1776 animals and biometric data from 572 animals representing six goat populations. Qualitative morphological traits analysed were coat colour, presence or absence of horns, tassels, beard, pattern of ear and hair at forequarters and hindquarters. Quantitative biometric traits assessed were chest girth, height at withers, body length and body weight collected from female animals of one to three years of age. Least squares means calculated from SPSS, canonical discriminant analysis by CANDISC, Mahalanobis distance and dendrogram constructed by PROC CLUSTER were used to analyse biometric variables. Canonical discriminant analysis conducted for biometric data identified three statistically significant canonical variables (P less than 0.0001), with CAN1 explaining 57.2 per cent of total variance. Multivariate analytical techniques thus confirmed the existence of six different populations. The discriminatory capacity of biometric variables chosen for the study was also justified.

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Genetic diversity derived from pedigree information and estimation of genetic parameters for reproductive traits of Limousine and Charolais cattle raised in Italy

Italian Journal of Animal Science ◽

10.1080/1828051x.2020.1778547 ◽

2020 ◽

Vol 19 (1) ◽

pp. 762-771 ◽

Cited By ~ 1

Author(s):

Marcos Paulo Gonçalves de Rezende ◽

Carlos Henrique Mendes Malhado ◽

Stefano Biffani ◽

Paulo Luis Souza Carneiro ◽

Riccardo Bozzi

Keyword(s):

Genetic Diversity ◽

Genetic Parameters ◽

Reproductive Traits ◽

Pedigree Information ◽

Charolais Cattle ◽

Estimation Of Genetic Parameters

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PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations

Journal of Animal Science ◽

10.1093/jas/skz258.540 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 265-266

Author(s):

Veronika R Kharzinova ◽

Arsen V Dotsev ◽

Anastasiya Solovieva ◽

Klaus Wimmers ◽

Henry Reyer ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Structure Study ◽

Snp Markers ◽

Negative Effects ◽

Russian Science ◽

Data Set ◽

Northern Territories ◽

High Level ◽

Wild Reindeer

Abstract Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which leads to a loss of the genetic diversity necessary for survival in the changing habitat conditions. To infer the population structure and genome-wide diversity of wild reindeer, the Taymyr (TAI, n = 33) and Yakut populations including Tundra Leno-Olenek (LNO, n = 20), the Island (ISL, n = 6), the Sundrun (SUN, n = 6) and the Taiga (TGA, n = 5) were genotyped with the Illumina Bovine HD BeadChip. Data set consisting of 8801 polymorphic SNP markers was used to calculate population genetic parameters in PLINK 1.9, SplitsTree 4.14.6. software, R packages “diveRsity” and “StAMMP.” We detected the similar level of observed heterozygosity across the TAI, ISL, SUN and LNO: 0.187, 0.188, 0.184, and 0.189 respectively. Meanwhile, allelic richness was slightly higher in Taimyr population compared to the Yakut groups. The lowest level of genetic diversity was recorded in the Taiga reindeer (Ho=0.168; Ar = 1.476). All populations showed heterozygotes deficiency (uFIS 95%, CI > 0) with higher uFIS values in TGA (0.079). MDS analysis revealed the high level of genetic similarity of TAI, ISL and LNO and placed SUN in close proximity to them. The first and the second MDS components (2.36% and 2.15% of the genetic variability) clearly divided the Taiga reindeer, the genetic apartness of which was also confirmed by the results of the Neighbour-Net tree analysis. Information obtained here, might be helpful for further effective use and maintenance of the reindeer populations as well as for overcoming the negative effects of decreasing their number. The study was supported by Russian Science Foundation within Pr. no. 16-16-10068.

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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.

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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.

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Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽

10.3390/genes10100822 ◽

2019 ◽

Vol 10 (10) ◽

pp. 822 ◽

Cited By ~ 2

Author(s):

Kyung Jun Lee ◽

Jung-Ro Lee ◽

Raveendar Sebastin ◽

Myoung-Jae Shin ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Discriminant Analysis ◽

Single Nucleotide Polymorphisms ◽

Genetic Differentiation ◽

Principal Components ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

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