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

Wang, Zhiying; Zhou, Bohan; Zhang, Tao; Yan, Xiaochun; Yu, Yongsheng; Li, Jinquan; Mei, Bujun; Wang, Zhixin; Zhang, Yanjun; Wang, Ruijun; Lv, Qi; Liu, Zhihong; Zhao, Yongju; Du, Chenyu; Su, Rui

doi:10.3389/fvets.2021.665872

Cited by 6 publications

(5 citation statements)

References 37 publications

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“…This ratio was found to be 0.07 for Galla and 0.03 for SEA. Different estimates for this ratio were reported by other authors, such as 0.23 in Cashmere goats 37 , 0.46 in Markhoz goats 28 , and 0.14 in Jamunapari goats 3 . These findings further explain the fact that although the main objective of a breeding plan was to select superior genes for breeding purposes, it ultimately led to reducing the genetic diversity of the population, as few animals were used in subsequent generations.…”

Section: Discussionmentioning

confidence: 55%

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Kichamu,

Wanjala,

Cziszter

et al. 2024

Sci Rep

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Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval (GI) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders (fa/fe) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size (Ne) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.

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Section: Discussionmentioning

confidence: 55%

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Kichamu,

Wanjala,

Cziszter

et al. 2024

Sci Rep

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“…These issues have led to variability in breed quality, degradation, and inconsistency in both meat and cashmere quality, hampering the advancement of the IMCGs brand and industry. Initial conservation efforts relied heavily on government-supported activities, including specialized breeding farms, in situ conservation, and the use of genealogies for estimating genetic diversity [ 26 , 27 ]. Implementing individual-based breeding strategies showed promise, further enhanced by biotechnological innovations like embryo engineering, cryopreservation of sperm, embryos, and oocytes [ 28 , 29 ], and the emergence of molecular markers including AFLP, RAPD, SSR [ 30 , 31 ], and more recently, SNP chips, GBS, and WGRS [ 18 – 20 , 32 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

Wang,

et al. 2024

BMC Genomics

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Background Inner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems. Results In order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals’ genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population. Conclusions The IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs’ germplasm resources.

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“…The effective population size (N e ) is a parameter that quantifies the turnover in genetic variation due to the effect of genetic drift in a population [22]. This parameter was estimated using the SNeP software version 1.1, using Sved's [23] formula: E(r 2 ) = (1 + 4N e c) −1 , where N e is the effective population size, c is the genetic distance between two markers (expressed in Morgans), and E(r 2 ) is the expected r 2 for a given distance c. Time points representing the number of generations in the past were estimated as T = 1/2c [24], with a generation interval of ~4 years [25].…”

Section: Linkage Disequilibrium (Ld) and Effective Population Size (N...mentioning

confidence: 99%

Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data

Vlaic,

Russo

et al. 2024

Animals

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Animal husbandry is one of man’s oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country’s goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.

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

Cited by 6 publications

References 37 publications

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data

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