Elucidating population structure and genetic diversity of intercross sheep through pedigree analysis

IF 1.6 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Small Ruminant Research Pub Date : 2024-06-25 DOI:10.1016/j.smallrumres.2024.107309
Abdul Rahim , Rajni Chaudhary , K.S. Rajaravindra , R. Pourouchottamane , G.R. Gowane , Arun Kumar
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Abstract

The aim of this study was to assess the population structure and genetic diversity along with determining the accuracy of ongoing selection program in a closed flock of Intercross sheep through pedigree analysis. The pedigree records of 2245 animals maintained at CSWRI-NTRS, Garsa, Kullu during the period from 2012 to 2023 were utilized to calculate the genealogical information, genetic conservation index and other parameters based on gene origin probabilities. Lambs born during 2020 and 2023 were considered as reference population. ENDOG version 4.8 software package was used for pedigree analysis. Analysis revealed that the mean generation interval for the reference population was 3.20 years with a longer interval in dam-offspring pathways relative to sire-offspring pathways. Average inbreeding coefficients for whole and reference population were 0.21 and 0.49 % and corresponding average relatedness was 1.24 and 1.72 %, respectively. The average maximum, equivalent and completed generations were 2.50, 1.96 and 1.63 with 0.12 %, 0.17 % and 0.20 % increase in inbreeding coefficient, respectively. This resultant effective population size estimated using individual increase in inbreeding was 156.52. Effective numbers of founders (fe) and ancestors (fa) was 68 and 61, respectively for reference population with a ratio of 1.11, indicating occurrence of minor effects of bottleneck in the flock. The genetic contribution of most influent ancestors contributing 50 % of the gene pool was only 23. The estimated founder genome (fg) and non-founder genome (fng) were 35.87 and 75.91, respectively in the present population. The estimate for fg/fa ratio was 0.59 which explained that 59 % of the original genetic diversity is exit in the reference population. Genetic conservation index (GCI) ranged from 1 % to 20.28 % with a mean value of 4.91 %. Overall, males recorded a slightly higher GCI than females, i.e., 5.23 vs 4.65 %, respectively. The results revealed that, the population has augmented genetic diversity and low level of inbreeding. Small fraction of genetic diversity was vanished due to unequal contribution of founders and minor bottleneck effects occurred due to disproportionate contribution of breeding animals to gene pool of population. Use of a sufficient number of breeding rams and optimum contribution selection (OCS) is recommended to maintain the genetic diversity as well as enhancing production potential in this population.

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通过血统分析阐明杂交绵羊的种群结构和遗传多样性
本研究的目的是评估种群结构和遗传多样性,并通过血统分析确定正在进行的杂交羊群选育计划的准确性。本研究利用库尔勒加尔萨 CSWRI-NTRS 在 2012 年至 2023 年期间保存的 2245 只绵羊的血统记录,根据基因来源概率计算系谱信息、遗传保护指数和其他参数。2020 年和 2023 年出生的羔羊被视为参考种群。使用ENDOG 4.8版软件包进行系谱分析。分析表明,参考群体的平均世代间隔为 3.20 年,相对于父系-子系世代间隔,母系-子系世代间隔更长。整个群体和参照群体的平均近交系数分别为 0.21 % 和 0.49 %,相应的平均亲缘关系分别为 1.24 % 和 1.72 %。平均最大世代数、等效世代数和完成世代数分别为 2.50、1.96 和 1.63,近交系数分别增加了 0.12 %、0.17 % 和 0.20 %。根据近交系数的个体增长估算出的有效种群数量为 156.52。参考种群的有效始祖(fe)和祖先(fa)数量分别为 68 和 61,比值为 1.11,表明鸡群中出现了轻微的瓶颈效应。影响最大的祖先的基因贡献率仅为 23,占基因库的 50%。在本种群中,创始基因组(fg)和非创始基因组(fng)的估计值分别为 35.87 和 75.91。fg/fa比值估计为0.59,说明参照种群中有59%的原始遗传多样性。遗传保护指数(GCI)介于 1 % 到 20.28 % 之间,平均值为 4.91 %。总体而言,雄性的遗传保护指数略高于雌性,分别为 5.23% 和 4.65%。结果表明,该种群的遗传多样性较高,近亲繁殖程度较低。小部分遗传多样性因始祖鸟的贡献不均而消失,种畜对种群基因库的贡献不成比例而产生了轻微的瓶颈效应。建议使用足够数量的种公羊和最佳贡献选择(OCS)来保持遗传多样性并提高该种群的生产潜力。
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来源期刊
Small Ruminant Research
Small Ruminant Research 农林科学-奶制品与动物科学
CiteScore
3.10
自引率
11.10%
发文量
210
审稿时长
12.5 weeks
期刊介绍: Small Ruminant Research publishes original, basic and applied research articles, technical notes, and review articles on research relating to goats, sheep, deer, the New World camelids llama, alpaca, vicuna and guanaco, and the Old World camels. Topics covered include nutrition, physiology, anatomy, genetics, microbiology, ethology, product technology, socio-economics, management, sustainability and environment, veterinary medicine and husbandry engineering.
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