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Claudin and Rab proteins are key molecular components involved in coccidiosis resistance in Portuguese Merino sheep. Claudin和Rab蛋白是葡萄牙美利奴羊抗球虫病的关键分子成分。
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-17 DOI: 10.1186/s12711-025-01020-x
Endika Varela-Martínez,Ana Afonso,Dimitra Mainou,Fábio Teixeira,Telmo Nunes,Pedro Vieira,Inês Sarraguça,Cristina Martins,Natalia Campbell,Rafael Cordeiro da Silva,Tiago Perloiro,Luís Madeira de Carvalho,Ana Cristina Ferreira,Luís Telo da Gama,Helga Waap,Andreia J Amaral
BACKGROUNDAlthough coccidial infection is often asymptomatic in sheep, both clinical and subclinical forms of the disease are linked to considerable production losses, mainly in young lambs. Studies aiming to identify genetic markers for use in selection programs towards increasing genetic resistance to coccidiosis are lacking and have yet to be performed in Portuguese Merino sheep. The purpose of this study was to identify genomic regions associated with resistance to coccidiosis by conducting a genome-wide association study (GWAS) in Portuguese Merino sheep.RESULTSFrom an initial population of 1,022 sheep having known phenotypic characteristics, 206 and 202 distinct animals were genotyped using 50 K and 600 K Single Nucleotide Polymorphism (SNP) arrays, respectively. After the 50 K array was imputed using a 600 K array as reference, an association analysis was performed for faecal oocyst counts (FOC). We identified 12 SNPs that were significantly associated with resistance by using a chromosome-wide significance threshold. The significant SNPs were related to Ccser1, Thsd4, Eci1, Tnfrsf12a, Chrm3 and Slc20a2 genes. We identified 80 candidate genes located in the proximity of the significant SNPs using the defined confidence regions. Two types of gene set enrichment analyses were performed. Enrichment based on the set of candidate genes, identified the terms virus receptor activity and exogenous protein binding to be enriched, both due to two claudins, CLDN6 and CLDN9. Enrichment based on gene interactions, showed enrichment of terms related to transport vesicles, mainly due to the presence of Rab proteins.CONCLUSIONSGiven the role that Rab and Claudins play in host-parasite relationships, these results suggest the existence of reliable markers associated with resistance to coccidiosis. These markers should be explored in future studies to further validate their use in marker assisted selection, with the goal of enhancing sustainability of the breed conservation-management program.
虽然球虫感染在绵羊中通常是无症状的,但该疾病的临床和亚临床形式都与相当大的生产损失有关,主要发生在羔羊中。目前尚无针对葡萄牙美利奴羊的研究,旨在确定遗传标记以用于提高对球虫病的遗传抗性的选择程序。本研究的目的是通过对葡萄牙美利奴羊进行全基因组关联研究(GWAS),确定与球虫病抗性相关的基因组区域。结果在已知表型特征的1022只羊的初始种群中,分别用50 K和600 K单核苷酸多态性(SNP)阵列对206只和202只不同的羊进行了基因分型。以600k阵列作为参考,输入50k阵列后,对粪便卵囊计数(FOC)进行关联分析。我们通过使用全染色体显著性阈值确定了12个与耐药性显著相关的snp。显著snp与Ccser1、Thsd4、Eci1、Tnfrsf12a、Chrm3和Slc20a2基因相关。我们使用定义的置信区域确定了80个位于显著snp附近的候选基因。进行了两种类型的基因集富集分析。基于一组候选基因的富集,确定了病毒受体活性和外源蛋白结合的术语,都是由于两个CLDN6和CLDN9。基于基因相互作用的富集,显示了与运输囊泡相关的术语的富集,主要是由于Rab蛋白的存在。结论考虑到Rab和Claudins在宿主-寄生虫关系中的作用,这些结果表明存在与球虫病抗性相关的可靠标记物。这些标记应在未来的研究中进一步验证其在标记辅助选择中的应用,以提高品种保护管理计划的可持续性。
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引用次数: 0
Multi-ancestry genome-wide association meta-analysis identifies candidate genes for computed tomography-based carcass composition traits in pigs. 多祖先全基因组关联荟萃分析确定了基于计算机断层扫描的猪胴体组成性状的候选基因。
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-17 DOI: 10.1186/s12711-025-01023-8
He Han,Pengfei Yu,Zhenyang Zhang,Ran Wei,Wei Zhao,Xiaoliang Hou,Jianlan Wang,Yongqi He,Yan Fu,Zhen Wang,Yuchun Pan,Qishan Wang,Zhe Zhang
BACKGROUNDCarcass composition traits, such as lean meat percentage, bone percentage, and number of ribs, are critical factors determining meat production and profitability of pigs. Traditional slaughter measurements are time-consuming, labor-intensive and invasive and cannot be evaluated on selection candidates. However, computed tomography scanning, a non-invasive technique, enables in vivo measurement of these traits, facilitating rapid accumulation of extensive phenotypic data. Despite these advances, the genetic mechanisms underlying computed tomography-based carcass traits remain largely unexplored.RESULTSIn this study, we performed a multi-ancestry genome-wide association meta-analysis (MA-GWAMA) using low-coverage whole-genome sequencing data from four breeds (1222 Duroc, 582 Landrace, 1018 Yorkshire, and 448 Piétrain). In total, we identified 11 independent genome-wide significant loci associated with carcass composition traits in the meta-analysis. Compared to standard genomic best linear unbiased prediction, weighting MA-GWAMA-significant SNPs increased genomic prediction accuracy in an independent population (N = 365, including 136 Duroc, 65 Landrace, 50 Piétrain, and 114 Yorkshire) by 16.3% for lean meat percentage, by 6.1% for bone percentage, and by 79.4% for number of ribs. Integrating MA-GWAMA results with public eQTL and single-cell data prioritized ALPK2 as a candidate gene for lean meat percentage, and ABCD4 and SLC8A3 as candidate genes for the number of ribs.CONCLUSIONSOur study demonstrates the efficacy of computed tomography phenotyping coupled with multi-omics integration for dissecting the genetic architecture of porcine carcass composition traits. The prioritized variants and genes provide valuable targets for molecular breeding programs to enhance meat quality in pigs.
胴体组成性状,如瘦肉率、骨率和排骨数,是决定猪肉品产量和盈利能力的关键因素。传统的屠宰测量是耗时、劳动密集型和侵入性的,不能对选择候选者进行评估。然而,计算机断层扫描,一种非侵入性技术,能够在体内测量这些特征,促进广泛表型数据的快速积累。尽管取得了这些进展,但基于计算机断层扫描的胴体性状的遗传机制仍未得到充分研究。在这项研究中,我们使用来自4个品种(1222杜洛克、582长白、1018约克郡和448皮萨梅特)的低覆盖率全基因组测序数据进行了多祖先全基因组关联荟萃分析(MA-GWAMA)。总的来说,我们在荟萃分析中确定了11个与胴体组成性状相关的独立全基因组显著位点。与标准的基因组最佳线性无偏预测相比,加权ma - gwma显著snp使独立人群(N = 365,包括136个杜洛克人,65个长白人,50个皮亚姆斯特人和114个约克郡人)的基因组预测准确率提高了16.3%,瘦肉百分比提高了6.1%,肋骨数量提高了79.4%。将MA-GWAMA结果与公开的eQTL和单细胞数据相结合,优选ALPK2作为瘦肉百分比的候选基因,ABCD4和SLC8A3作为肋骨数量的候选基因。结论本研究证明了计算机断层扫描表型结合多组学整合在解剖猪胴体组成性状遗传结构方面的有效性。优先变异和基因为分子育种计划提供了有价值的靶标,以提高猪的肉质。
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引用次数: 0
Characterization of genomic diversity and population structure of worldwide Duroc subpopulations and other pig breeds. 全球杜洛克猪亚群和其他猪种的基因组多样性和群体结构特征。
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-16 DOI: 10.1186/s12711-025-01017-6
Hui Wen,Harvey D Blackburn,Henrique A Mulim,Hinayah R Oliveira,Susanne Hermesch,Ching-Yi Chen,Justin Holl,Allan P Schinckel,Luiz F Brito
BACKGROUNDDuroc is one of the most popular terminal sire pig breeds worldwide due to its greater growth rate, meat quality, feed efficiency, and carcass characteristics compared to other breeds. Despite the breed's popularity, its developmental history, genetic diversity, and genetic relationships with other pig breeds remain largely unknown. Therefore, the primary objective of this study was to investigate population structure and genetic diversity of Duroc subpopulations from Europe, North America, and Australia, and of other pig breeds.RESULTSThe studied pig populations were differentiated into five subgroups(European and North American Durocs, Australian Durocs, Asian-Pacific pig breeds, and two other breed groups [OBP1 and OBP2]), consistent with their geographical origins, as revealed by population structure analyses. The estimated effective population size (Ne) of Duroc subpopulations ranged from 17 to 47, while the Ne for the combined Duroc subpopulations was 172. A total of 140,713 runs of homozygosity (ROHs) were identified across all individuals, with 98,039 ROHs in Durocs and 42,674 in other pig breeds. Durocs had a greater number and proportion of longer ROHs (> 8 Mb) compared to other pig breeds. The ROH-based inbreeding (FROH) values were significantly greater in Durocs than in most of the other breeds, indicating the need for better management of genetic diversity in the breed. We observed strong correlations (> 0.65) between different inbreeding metrics in all the studied pig populations. A total of 43, 18, 27, 37, and 20 candidate genes were identified in the ROH islands for European and North American Durocs, Australian Durocs, Asian-Pacific pigs, OBP1, and OBP2 pigs, respectively. The significant KEGG pathways were mainly related to growth, metabolism, immune system, cellular processes, and signal transduction.CONCLUSIONSSignificant differences exist in genetic diversity, population structure, and ancestry within Duroc subpopulations and between Duroc and other pig breeds. The observed inbreeding levels in Duroc subpopulations indicate the need for better management of genetic diversity within the breed. Functional enrichment analyses of shared ROH islands provide new insights into biological pathways shaped by selection decisions in the past decades, especially those related to the immune system and energy metabolism.
与其他品种相比,杜洛克是世界上最受欢迎的终端父系猪品种之一,因为它具有更高的生长速度、肉质、饲料效率和胴体特性。尽管这个品种很受欢迎,但它的发展历史、遗传多样性以及与其他猪种的遗传关系在很大程度上仍然未知。因此,本研究的主要目的是调查来自欧洲、北美和澳大利亚的杜洛克猪亚群以及其他猪种的群体结构和遗传多样性。结果猪群结构分析显示,研究猪群根据其地理来源可划分为5个亚群(欧洲和北美杜洛克、澳大利亚杜洛克、亚太地区杜洛克猪品种,以及另外2个品种群[OBP1和OBP2])。杜洛克亚种群的有效种群数(Ne)在17 ~ 47之间,而组合的有效种群数(Ne)为172。在所有个体中共鉴定出140,713个纯合性(ROHs),其中杜洛克猪98,039个,其他猪品种42,674个。杜洛克较长ROHs的数量和比例均高于其他猪种(bbb8mb)。杜洛克的roh近交(FROH)值明显高于大多数其他品种,这表明需要更好地管理该品种的遗传多样性。我们观察到,在所有研究的猪群中,不同近交指标之间存在很强的相关性(> 0.65)。在ROH孤岛中分别鉴定出43个、18个、27个、37个和20个候选基因,分别用于欧洲和北美杜洛克、澳大利亚杜洛克、亚太猪、OBP1和OBP2猪。重要的KEGG通路主要与生长、代谢、免疫系统、细胞过程和信号转导有关。结论杜洛克猪亚群遗传多样性、群体结构和祖先系与其他猪种存在显著差异。观察到的杜洛克亚群的近交水平表明需要更好地管理品种内的遗传多样性。共享ROH岛的功能富集分析为过去几十年的选择决策形成的生物学途径提供了新的见解,特别是那些与免疫系统和能量代谢有关的途径。
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引用次数: 0
Normalized cumulative gain as an alternative evaluation measure for genomic selection models. 归一化累积增益作为基因组选择模型的另一种评估方法。
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-16 DOI: 10.1186/s12711-025-01022-9
Felix Heinrich,Thomas M Lange,Faisal Ramzan,Mehmet Gültas,Armin O Schmitt
BACKGROUNDGenomic selection relies on a variety of statistical and machine learning methods to predict phenotypes from genomic data. Since no single method consistently outperforms others across datasets, evaluating and comparing model performance is essential. However, standard evaluation metrics such as Pearson's correlation coefficient and mean squared error treat genomic prediction as a regression problem, assessing overall fit rather than the effectiveness of selecting top-performing individuals for breeding. This disconnect can lead to suboptimal model selection in practice.RESULTSTo address this, we present the normalized cumulative gain (NCG) as an alternative evaluation measure that directly measures the phenotypic gain achieved from the individuals selected by the model. We applied this measure on four animal and plant datasets to compare nine commonly used methods for genomic prediction.CONCLUSIONSNCG offers an intuitive and interpretable measure of selection efficiency, focusing solely on the individuals that would actually be chosen. We further demonstrate that calculating the performance under all possible selection thresholds provides more information than a single or few arbitrary thresholds. This more granular analysis shows that the performance of the methods may differ under varying selection intensities and can provide guidance for the choice of selection intensity. Our approach is implemented in R and is available at https://github.com/FelixHeinrich/GS_Comparison_with_NCG.
基因组选择依赖于各种统计和机器学习方法来预测基因组数据的表型。由于没有一种方法在数据集上始终优于其他方法,因此评估和比较模型性能是必不可少的。然而,诸如皮尔逊相关系数和均方误差等标准评估指标将基因组预测视为回归问题,评估的是整体拟合,而不是选择表现最佳的个体进行育种的有效性。这种脱节在实践中可能导致次优模型选择。为了解决这个问题,我们提出了归一化累积增益(NCG)作为一种替代评估措施,直接测量从模型选择的个体获得的表型增益。我们将该方法应用于4个动植物数据集,比较了9种常用的基因组预测方法。结论:sncg提供了一种直观且可解释的选择效率测量方法,仅关注实际被选择的个体。我们进一步证明,在所有可能的选择阈值下计算性能比单个或几个任意阈值提供更多的信息。这种更细粒度的分析表明,在不同的选择强度下,方法的性能可能会有所不同,可以为选择强度的选择提供指导。我们的方法是用R实现的,可以在https://github.com/FelixHeinrich/GS_Comparison_with_NCG上找到。
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引用次数: 0
Deriving breeding goals and expected selection responses to reduce environmental impacts in rainbow trout farming. 制定虹鳟鱼养殖的育种目标和预期选择响应,以减少对环境的影响。
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-13 DOI: 10.1186/s12711-025-01018-5
Simon Pouil,Joël Aubin,Florence Phocas
BACKGROUNDWith growing societal concerns about the sustainability of food production systems, there is increasing interest in considering not only economic gains but also environmental issues in breeding programs of farmed species. In this study, we compared expected selection responses for breeding programs aiming to minimize environmental impacts of the production of rainbow trout in France, one of the most important fish species in salmonid aquaculture. The consequences of genetic improvement based on environmental merit indices were investigated in a hypothetical rainbow trout production farm with a constant annual production of 300 tonnes of fish. The merit indices included three different traits: thermal growth coefficient (TGC), daily feed intake (DFI), and survival (SR). A cradle-to-farm-gate life cycle assessment was conducted to evaluate the environmental values of each trait, which served as weightings in breeding goals aiming at minimizing expected environmental impacts by genetic selection. We explored nine different environmental impact categories: climate change, terrestrial acidification, freshwater eutrophication, marine eutrophication, terrestrial ecotoxicology, freshwater ecotoxicology, land use, water dependence, and cumulative energy demand.RESULTSSelection accuracy ranged from 0.34 to 0.43, with the lowest accuracy observed for the breeding goal targeting reduced water dependence, and the highest for those targeting reductions in eutrophication and terrestrial ecotoxicity. Annual genetic gains in reductions of environmental impacts, expressed per tonne of trout, were high for reducing eutrophication potential (- 6.80 to - 2.61%) and terrestrial ecotoxicity (- 4.14 to - 1.59%), but negligible for water use reduction (- 0.04 to - 0.01%). Genetic changes in DFI and TGC led to substantial annual gains in feed conversion ratio, from 1.7 to 4.8%. However, SR showed no improvement and often declined, highlighting the difficulty of balancing genetic gains across traits.CONCLUSIONSWe demonstrated the benefits of using environmental values in breeding goals to minimize environmental impacts at the farm level, while maintaining high genetic gains in feed efficiency traits. Nevertheless, we also showed that selection efficiency was highly dependent of the impact category. Our results suggested that another selection strategy should be considered to avoid unfavourable consequences on SR.
随着社会对粮食生产系统可持续性的关注日益增加,人们越来越有兴趣在养殖物种育种计划中不仅考虑经济收益,还考虑环境问题。在这项研究中,我们比较了养殖计划的预期选择反应,旨在最大限度地减少虹鳟鱼生产对环境的影响,虹鳟鱼是鲑科水产养殖中最重要的鱼类之一。在一个假设的虹鳟鱼养殖场中,研究了基于环境价值指数的遗传改良的后果,该养殖场的年产量为300吨鱼。肥力指标包括热生长系数(TGC)、日采食量(DFI)和成活率(SR) 3个指标。采用从摇篮到养殖场的生命周期评价方法,评价各性状的环境价值,作为遗传选择对环境影响最小的育种目标的权重。我们探讨了9个不同的环境影响类别:气候变化、陆地酸化、淡水富营养化、海洋富营养化、陆地生态毒理学、淡水生态毒理学、土地利用、水依赖和累积能源需求。结果选择精度在0.34 ~ 0.43之间,以减少对水的依赖为目标的养殖目标选择精度最低,以减少富营养化和陆地生态毒性为目标的养殖目标选择精度最高。以每吨鳟鱼为单位,减少环境影响的年度遗传收益在降低富营养化潜力(- 6.80至- 2.61%)和陆地生态毒性(- 4.14至- 1.59%)方面很高,但在减少用水量(- 0.04至- 0.01%)方面可以忽略不计。DFI和TGC的遗传变化导致饲料系数每年大幅提高,从1.7提高到4.8%。然而,SR没有表现出改善,而且经常下降,突出了平衡性状间遗传收益的困难。结论在育种目标中使用环境价值可以最大限度地减少养殖场层面的环境影响,同时保持饲料效率性状的高遗传增益。然而,我们也表明,选择效率高度依赖于影响类别。我们的结果表明,应该考虑另一种选择策略,以避免对SR不利的后果。
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引用次数: 0
Comparison between repeatability, reproductive stage stratified repeatability, and relative risk models for prediction of breeding values for functional survival in rotationally crossbred sows. 轮换杂交母猪可重复性、繁殖阶段分层可重复性和相对风险模型预测功能存活育种值的比较
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-09 DOI: 10.1186/s12711-025-01019-4
Bjarke G Poulsen,Daniela Lourenco,Tage Ostersen,Bjarne Nielsen,Natália G Leite,Mark Henryon,Ole F Christensen
BACKGROUNDThe aim of this study was to compare different statistical models for predicting breeding values for sow survival with right-censored phenotypes from rotationally crossbred and commercial sows. We tested two hypotheses. First, we hypothesized that single-trait relative risk models predict more accurate breeding values than single-trait linear repeatability models. Second, we hypothesized that a reproductive stage stratified linear repeatability model predicts more accurate breeding values than the standard single-trait linear repeatability models. The single-trait models predict breeding values for survival between farrowings, while the reproductive stage stratified models predict breeding values for both survival between a farrowing and the next service, and survival between a service and the next farrowing. The validation criterion was the Pearson correlation between adjusted phenotypes for the lifetime number of litters produced and predicted breeding values for survival converted to lifetime number of litters produced. All validation criteria were compared to one another and against zero using appropriate statistical tests and correction for multiple tests. Each model was constructed with two different multi-breed relationship matrices to ensure that the results were not affected by the choice between them.RESULTSThe values of the validation criteria for the single-trait models were significantly larger than zero and similar (0.02). The values of the validation criteria for the reproductive stage stratified linear repeatability models were both significantly larger than zero and significantly larger than those from the single-trait models (0.04 vs. 0.02).CONCLUSIONSThe relative risk and linear repeatability single-trait models for survival between subsequent farrowings predicted equally accurate breeding values (0.02), while the linear repeatability two-trait models for survival from services to their subsequent farrowings and farrowings to the subsequent services predicted more accurate breeding values than the single-trait models (0.04 vs. 0.02). However, the accuracy of breeding values was small for all models because the survival phenotypes used for prediction were censored and the heritability of complete survival times was moderate (8-9%). Therefore, the comparison would benefit from reevaluation in other populations, and the models should be improved upon before implementation in practical breeding programs.
背景:本研究的目的是比较旋转杂交母猪和商业母猪右删型母猪存活率的不同统计模型。我们检验了两个假设。首先,我们假设单性状相对风险模型比单性状线性可重复性模型预测更准确的育种值。其次,我们假设繁殖阶段分层线性可重复性模型比标准单性状线性可重复性模型预测更准确的育种值。单性状模型预测了两次分娩之间的存活率,而繁殖阶段分层模型预测了一次分娩和下一次分娩之间以及一次分娩和下一次分娩之间的存活率。验证标准是校正后的表型与转换为一生产仔数的预测繁殖值之间的Pearson相关性。使用适当的统计检验和多次检验的校正,将所有验证标准相互比较,并与零进行比较。每个模型都由两个不同的多品种关系矩阵构建,以确保结果不受它们之间选择的影响。结果单性状模型的验证标准值均显著大于零且相似(0.02)。生殖期分层线性重复性模型的验证标准值均显著大于零,且显著大于单性状模型的验证标准值(0.04 vs. 0.02)。结论相对危险度单性状模型和线性可重复性单性状模型预测的后续产仔之间的繁殖值准确度相同(0.02),而从产仔到后续产仔和产仔到后续产仔生存的线性可重复性双性状模型预测的繁殖值准确度高于单性状模型(0.04 vs. 0.02)。然而,所有模型的育种值的准确性都很小,因为用于预测的存活表型被剔除,并且完全存活时间的遗传力中等(8-9%)。因此,在其他种群中进行重新评估将有利于比较,在实际育种计划实施之前,应该对模型进行改进。
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引用次数: 0
Genetics of digital phenotypes of keel bone in layer chickens and correlations with keel bone fractures and deviations. 蛋鸡龙骨数字表型的遗传学及其与龙骨骨折和偏差的相关性。
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-11-27 DOI: 10.1186/s12711-025-01016-7
Moh Sallam,Lina Göransson,Anne Larsen,Helena Wall,Wael Alhamid,Stefan Gunnarsson,Martin Johnsson,Dirk-Jan de Koning
BACKGROUNDPoultry is a global industry with laying hens that are genetically optimized for high egg yield. Keel bone fractures can affect up to 80% of laying hens, posing welfare and production problems. Therefore, genetic selection to reduce keel fractures is important. However, the lack of a reliable, automated, and heritable phenotypes for keel bones makes this a challenging task. The aim of this study was to (1) develop automated analyses of radiographic images to phenotype keel bones, and (2) investigate whether the proposed phenotypes are heritable and genetically correlated with the post-dissection scores of keel bone fractures and deviations. A total of 1051 laying hens (Bovans Brown and Lohmann Brown) from a commercial farm were x-rayed, followed by keel bone dissection and scoring for deviations and fractures. Furthermore, blood was sampled for genotyping using 50 K Illumina SNP chips. Keel bones were segmented (with ~ 0.90 accuracy) from the radiographic images using deep learning models, after which the images were automatically measured for general geometry and radiopacity. Multi-trait genomic restricted maximum likelihood was used to estimate genetic parameters.RESULTSHeritability estimates ranged from 0.28 to 0.30 for both keel deviations and fractures observed post-dissection. The automated phenotypes had heritability estimates ranging from 0.07 to 0.10 for keel radiopacity and from 0.11 to 0.39 for keel geometry. Estimates of genetic correlations of keel geometry with keel deviation and fractures ranged from -0.57 to 0.72.CONCLUSIONSAutomated methods were developed for measuring keel bone radiopacity and geometry. Keel concave area was found to be a reliable and heritable phenotype that breeding companies can use to reduce keel deviations and fractures. These methods can also be adapted to measure other bones (e.g., tibiotarsal) or objects (e.g., eggs), allowing breeders to quickly compute phenotypes for keel, tibia, and egg size from the same radiographic image. The developed methods are well-suited for large-scale studies to assess different housing environments and nutrition strategies aimed at improving keel bone conditions.
家禽业是一个全球性的产业,其蛋鸡是经过基因优化的高产蛋鸡。高达80%的蛋鸡会受到龙骨骨折的影响,造成福利和生产问题。因此,通过遗传选择来减少龙骨骨折是很重要的。然而,缺乏可靠的、自动化的和可遗传的龙骨表型使得这项任务具有挑战性。本研究的目的是:(1)开发自动分析的影像学图像,以龙骨表型,(2)调查所提出的表型是否可遗传,并与龙骨骨折和偏差的解剖后评分遗传相关。对来自某商业农场的1051只蛋鸡(Bovans Brown和Lohmann Brown)进行x光检查,随后进行龙骨解剖并对偏差和骨折进行评分。此外,使用50 K Illumina SNP芯片采集血液进行基因分型。使用深度学习模型从放射图像中分割龙骨(精度约为0.90),然后自动测量图像的一般几何形状和放射不透明度。采用多性状基因组限制性最大似然法估计遗传参数。结果解剖后观察到的龙骨偏差和骨折的评分范围为0.28至0.30。自动表型的遗传率估计范围从0.07到0.10的龙骨放射度和从0.11到0.39的龙骨几何。龙骨几何形状与龙骨偏差和骨折的遗传相关性估计在-0.57到0.72之间。结论建立了测量龙骨放射透明度和几何形状的自动化方法。龙骨凹区被发现是一种可靠的遗传表型,育种公司可以利用它来减少龙骨偏差和骨折。这些方法也可以用于测量其他骨骼(例如,胫跖骨)或物体(例如,鸡蛋),使育种者能够快速计算龙骨、胫骨和鸡蛋大小的表型。开发的方法非常适合大规模研究,以评估不同的住房环境和营养策略,旨在改善龙骨状况。
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引用次数: 0
Interfacing mechanistic and breeding scheme simulation to predict selection response on lactation efficiency in dairy cows under different nutritional environments 界面机制及育种方案模拟预测不同营养环境下奶牛泌乳效率的选择响应
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-11-13 DOI: 10.1186/s12711-025-01013-w
A. Bouquet, M. Slagboom, J. R. Thomasen, M. Kargo, N. C. Friggens, L. Puillet
Predicting selection response for lactation efficiency in dairy cows is challenging, as the expression of this complex trait depends on dynamic interactions between the ability of cows to acquire nutrients and allocate them to different life functions. Moreover, the relative emphasis of these components may change due to energetic trade-offs between life functions when kept in limiting environments. The objective of this study is to present a new approach combining mechanistic and breeding scheme simulations to predict selection response on components of lactation efficiency of dairy cows under a non-limiting nutritional environment and when transferred to a limiting environment with a moderate feed restriction. These predictions were compared to the ones obtained with the conventional method used in quantitative genetics considering a typical dairy cattle breeding scheme and several breeding goals (BG) aiming at improving milk production, lactation efficiency and fertility. In the non-limiting environment, selection responses predicted by the two methods differed for both milk production and fertility. The sign and magnitude of differences depended on BGs. Selection response predictions were consistent only for BGs that did not change much the body reserve mobilization patterns of cows, and hence their conception probability. Indeed, pregnancy status impacted energy allocation of cows and consequently milk production, more energy being allocated to lactation in case of reproductive failure. Differences in selection response between modelling approaches were slightly increased when cows were reared in the limiting environment. Overall, the choice of prediction method led to substantial BG reranking with respect to selection response on milk production and fertility. Mechanistic-based predictions of selection response for lifetime efficiency were also sensitive to the nutritional environment and BG. Combining mechanistic and genetic modelling is a promising approach to benchmark breeding strategies of dairy cow lactation efficiency and better anticipate the impact of changes in energetic trade-offs induced both by selection and changes in the nutritional environment. Moreover, the simulations of phenotypic trajectories over cow lifetime before and after selection enabled a better understanding of the mechanisms underlying genetic improvement.
预测奶牛泌乳效率的选择反应是具有挑战性的,因为这一复杂性状的表达取决于奶牛获取营养并将其分配给不同生命功能的能力之间的动态相互作用。此外,当保持在有限的环境中时,由于生命功能之间的能量权衡,这些成分的相对重点可能会发生变化。本研究的目的是提出一种结合机制模拟和育种方案模拟的新方法,以预测奶牛在非限制性营养环境下和转移到适度限饲的限制性环境时对泌乳效率组成部分的选择响应。考虑到典型的奶牛育种方案和旨在提高产奶量、泌乳效率和育肥力的几个育种目标,将这些预测结果与定量遗传学中使用的传统方法所获得的预测结果进行了比较。在非限制性环境下,两种方法预测的选择响应在产奶量和育性方面存在差异。差异的符号和大小取决于bg。选择反应预测只有在没有改变奶牛身体储备动员模式的情况下才一致,因此它们的受孕概率也不会改变。事实上,怀孕状态会影响奶牛的能量分配,从而影响产奶量,在繁殖失败的情况下,更多的能量被分配给哺乳。当奶牛在限制环境中饲养时,不同建模方法之间的选择反应差异略有增加。总体而言,预测方法的选择导致BG在产奶量和生育力的选择响应方面进行了实质性的重新排序。基于机械的选择响应对终生效率的预测也对营养环境和BG敏感。结合机制和遗传建模是一种很有前途的方法,可以对奶牛泌乳效率的育种策略进行基准测试,并更好地预测由选择和营养环境变化引起的能量权衡变化的影响。此外,对选择前后奶牛一生中表型轨迹的模拟使我们能够更好地理解遗传改进的机制。
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引用次数: 0
Integrative analysis of genome and transcriptome reveals a novel regulator for pork intramuscular fat content 基因组和转录组的综合分析揭示了猪肉肌内脂肪含量的新调控因子
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-11-06 DOI: 10.1186/s12711-025-01014-9
Xueyan Zhao, Jingxuan Li, Wanli Jia, Yifan Ren, Yanping Wang, Tizhong Shan, Jiying Wang
Pork is a primary source of animal protein worldwide, and intramuscular fat (IMF) content is a key determinant of meat quality and consumer preference. To identify genetic regulators of IMF content, we leveraged RNA sequencing and whole-genome resequencing data from 79 Laiwu pigs renowned for high IMF content to conduct expression quantitative trait locus (eQTL) mapping. We integrated eQTL results with genome-wide association study (GWAS) data from 453 Chinese Lulai Black pigs (a crossbreed of Laiwu and Yorkshire pigs), and systematically identified candidate regulatory genes for IMF content by incorporating weighted gene co-expression network analysis (WGCNA) and correlation analysis in this population. We identified 9,763 cis-eQTLs at the genome-wide level (p < 5E−08) and 1,337 cis-eQTLs at the suggestive level (p < 5E−06). A 2.02 Mb cis-QTL region on Sus scrofa chromosome 9, containing 587 cis-eQTLs regulating MED17 expression, overlapped with an IMF-associated QTL detected by GWAS in Lulai Black pigs, a Laiwu-Yorkshire crossbreed. WGCNA identified three critical co-expression modules related to IMF content, with MED17 acting as a critical gene in a module linked to adipogenesis and lipid metabolism. Correlation analysis showed MED17 expression was negatively correlated with IMF content (FDR = 1.58E−02). In 3T3-L1 preadipocytes, adenovirus-mediated Med17 overexpression significantly reduced adipogenic differentiation and altered expression of adipogenesis-related genes (Pparg, Adipoq, Srebf1, Cpt1a, and Atgl), indicating that Med17 modulates adipocyte differentiation and lipid metabolism. This study identifies MED17 as a novel regulator of IMF content in pigs, bridging genomic variation, gene expression networks, and phenotypic traits. These findings provide mechanistic insights into IMF deposition and highlight the potential of integrative multi-omics approaches for genetic improvement of pork quality traits in breeding programs.
猪肉是世界范围内动物蛋白的主要来源,肌内脂肪(IMF)含量是肉品质和消费者偏好的关键决定因素。为了确定IMF含量的遗传调控因子,我们利用79头以IMF含量高而闻名的莱芜猪的RNA测序和全基因组重测序数据进行了表达数量性状位点(eQTL)定位。我们将453只中国鲁来黑猪(莱芜猪和约克猪的杂交品种)的eQTL结果与全基因组关联研究(GWAS)数据相结合,通过加权基因共表达网络分析(WGCNA)和相关分析,系统地鉴定了影响该群体IMF含量的候选调控基因。我们在全基因组水平上鉴定出9763个顺式- eqtl (p < 5E−08),在提示水平上鉴定出1337个顺式- eqtl (p < 5E−06)。在苏氏9号染色体上有一个2.02 Mb的顺式QTL区,包含587个调节MED17表达的顺式QTL,与GWAS在莱芜-约克杂交品种鲁来黑猪中检测到的imf相关QTL重叠。WGCNA确定了三个与IMF含量相关的关键共表达模块,其中MED17是与脂肪形成和脂质代谢相关的模块中的关键基因。相关分析显示,MED17表达与IMF含量呈负相关(FDR = 1.58E−02)。在3T3-L1前脂肪细胞中,腺病毒介导的Med17过表达显著降低了成脂分化,改变了成脂相关基因(Pparg、Adipoq、Srebf1、Cpt1a和Atgl)的表达,表明Med17调节了脂肪细胞分化和脂质代谢。本研究确定MED17是猪体内IMF含量的一种新型调节剂,连接基因组变异、基因表达网络和表型性状。这些发现为IMF沉积提供了机制见解,并强调了在育种计划中综合多组学方法对猪肉品质性状进行遗传改良的潜力。
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引用次数: 0
Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality 揭示肠道中遗传与非遗传相对丰度细菌对公猪精液质量的作用
IF 4.1 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-11-06 DOI: 10.1186/s12711-025-00990-2
Liangliang Guo, Xiaoqi Pei, Jiajian Tan, Haiqing Sun, Siwen Jiang, Hongkui Wei, Jian Peng
The relative abundance of some bacteria in the gut of pigs is heritable, suggesting that host genetics may recursively influence boar semen quality by affecting the composition and function of gut microbiota. Therefore, it is essential to elucidate the specific contributions of heritable versus non-heritable gut microbiota to semen quality traits. Our study aimed to identify heritable and non-heritable bacterial taxa at the genus level in the boar gut and to predict their functions and respective contributions to semen quality traits. At the genus level, 39 heritable and 91 non-heritable bacterial taxa were identified. Functional analysis revealed that predicted microbial functions in both groups were primarily enriched in carbohydrate, nucleotide, and amino acid metabolism. We further analyzed the average microbiability of heritable and non-heritable bacteria on short-chain fatty acids (SCFAs) and semen quality traits. The relative abundance of heritable bacteria was found to contribute more to SCFAs levels and semen quality than non-heritable bacteria. Mediation analysis revealed that SCFAs could mediate the influence of the relative abundance of heritable bacteria on host phenotypes, identifying 99 significant genus-SCFAs-semen quality trait mediation links. Our findings underscore the substantial role of the relative abundance of heritable gut bacteria in shaping porcine semen quality through SCFAs mediation. These results highlight the potential of targeted microbiome interventions to enhance reproductive traits in pigs.
猪肠道中某些细菌的相对丰度是可遗传的,这表明宿主遗传可能通过影响肠道微生物群的组成和功能而递归地影响猪精液质量。因此,有必要阐明遗传与非遗传肠道微生物群对精液质量性状的具体贡献。本研究旨在鉴定猪肠道中可遗传和不可遗传的细菌分类群,并预测它们的功能及其对精液质量性状的贡献。在属水平上鉴定出39个可遗传的细菌类群和91个不可遗传的细菌类群。功能分析显示,两组预测的微生物功能主要富集于碳水化合物、核苷酸和氨基酸代谢。我们进一步分析了遗传和非遗传细菌对短链脂肪酸(SCFAs)的平均微生物率和精液质量性状。可遗传细菌的相对丰度比不可遗传细菌对SCFAs水平和精液质量的贡献更大。中介分析显示,SCFAs可以介导可遗传细菌相对丰度对宿主表型的影响,鉴定出99个显著的属-SCFAs-精液质量性状中介联系。我们的研究结果强调了相对丰富的可遗传肠道细菌在通过SCFAs介导塑造猪精液质量中的重要作用。这些结果突出了靶向微生物组干预提高猪繁殖性状的潜力。
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引用次数: 0
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Genetics Selection Evolution
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