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Integrating Analytic Hierarchy Process and Weighted Goal Programming to Define Economic Traits and Consensus Desired Genetic Gains for the Russian Sturgeon (Acipenser gueldenstaedtii) Breeding Objective. 结合层次分析法和加权目标规划确定俄罗斯鲟鱼(Acipenser gueldenstaedtii)育种目标的经济性状和一致期望遗传增益。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2026-03-01 Epub Date: 2025-10-22 DOI: 10.1111/jbg.70019
Mina Rahbar, Roghieh Safari, Carlos I Perez-Rostro

This study employed participatory methods to identify breeding objectives and define desired genetic gains for economically important traits in the Russian sturgeon (Acipenser gueldenstaedtii). Two structured questionnaires were distributed to all Russian sturgeon farmers in Iran. The first questionnaire collected farm management information and asked farmers to prioritise five important traits from a list of thirteen. The top-ranked traits were ovarian fat lobe weight (OFW), total caviar weight (TCW), body weight of broodstock (BWB), larval body area at hatching (LBA), and yolk sac area (YSA). In the second questionnaire, pairwise comparisons were applied to derive individual trait preferences through the Analytical Hierarchy Process (AHP). Social group preference (Soc-p) values were computed for each social group using the weighted goal programming (WGP) model implemented in LINGO software. The greatest disagreement in Soc-p values emerged between the commercial product and water temperature categories. Subsequently, the extended WGP models were employed to derive consensus preference (Con-p) values for these categories. The average of the Con-p values was 0.28 (OFW), 0.22 (BWB), 0.14 (TCW), 0.13 (LBA), and 0.05 (YSA). These Con-p values were then used to determine the desired genetic gains, which were highest for TCW (1.39%) and lowest for YSA (0.34%). The use of AHP and WGP, rather than economic indices, was justified by the limited availability of reliable economic data in Iranian sturgeon aquaculture and the need for farmer-driven, consensus-based breeding goals. This research demonstrates that participatory approaches can successfully define genetic priorities, improve consensus among diverse farmer groups, and guide sustainable breeding strategies for Russian sturgeon in Iran.

本研究采用参与式方法确定俄罗斯鲟鱼(Acipenser gueldenstaedtii)的育种目标和确定经济上重要性状的期望遗传增益。向伊朗的所有俄罗斯鲟鱼养殖者分发了两份结构化问卷。第一份问卷收集了农场管理信息,并要求农民从13项特征中选出5项重要特征。卵巢脂肪瓣重(OFW)、鱼子酱总重(TCW)、幼鱼体重(BWB)、孵化体面积(LBA)和卵黄囊面积(YSA)排在前几位。在第二份问卷中,采用两两比较的方法,通过层次分析法(AHP)得出个体的性状偏好。使用LINGO软件实现的加权目标规划(WGP)模型计算每个社会群体的社会群体偏好(Soc-p)值。Soc-p值的最大差异出现在商业产品和水温类别之间。随后,采用扩展的WGP模型来推导这些类别的共识偏好(Con-p)值。Con-p值的平均值为0.28 (OFW)、0.22 (BWB)、0.14 (TCW)、0.13 (LBA)和0.05 (YSA)。然后用这些Con-p值来确定期望的遗传增益,TCW最高(1.39%),YSA最低(0.34%)。使用层次分析法和WGP而不是经济指数是合理的,因为伊朗鲟鱼水产养殖的可靠经济数据有限,而且需要农民驱动的、基于共识的养殖目标。这项研究表明,参与式方法可以成功地确定遗传优先级,提高不同农民群体之间的共识,并指导伊朗俄罗斯鲟鱼的可持续繁殖策略。
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引用次数: 0
Genomic Prediction Ability for Novel Profitability Traits Using Different Models in Nelore Cattle. 利用不同模型对耐洛尔牛新盈利性状的基因组预测能力。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2026-03-01 Epub Date: 2025-09-22 DOI: 10.1111/jbg.70016
Letícia Silva Pereira, Cláudio Ulhôa Magnabosco, Guilherme Rosa, Nedenia Bonvino Stafuzza, Tiago Zanett Albertini, Minos Carvalho, Raysildo Barbosa Lobo, Elisa Peripolli, Eduardo da Costa Eifert, Fernando Baldi

The aim of this study was to assess the accuracy, bias and dispersion of genomic predictions for accumulated profitability (APF) and profit per kilogram of liveweight gain (PFT) in Nelore cattle using different prediction approaches. The dataset consisted of 3969 phenotypic records for each trait. The pedigree harboured information from 38,930 animals born between 1998 and 2016, including 2691 sires and 19,884 dams. A total of 2449 animals were genotyped using the Clarifide Nelore 3.0 SNP panel. Nine models for genomic prediction were evaluated: a linear animal model was applied to estimate genetic parameters and perform the genomic single-trait best linear unbiased prediction (ST_ss-default). Additionally, a two-trait (ssGBLUP TT_W450 and TT_DMI), three-trait (TTT_CAR) and multi-trait ssGBLUP (MT_ss) were tested. Finally, two models employing the weighted linear (ST_sswl1 and ST_sswl2) and non-linear (ST_sswnl1 and ST_sswnl2) single-step genomic approach (WssGBLUP) were used to predict genomic breeding values (GEBV). The ability to predict future performance was assessed by calculating the correlation between GEBV and adjusted phenotypes. The average prediction accuracy of the GEBV models ranged from 0.345 to 0.665 for PFT and from 0.425 to 0.603 for APF. The predictive capability of the MT_ss model (0.665) was significantly higher than that of the other models for PFT, except for the TTT_CAR model (0.604), which also showed an improvement in predictive performance. For APF, the MT_ss (0.561) and TT_W450 (0.556) models demonstrated improved genomic prediction accuracy compared to the other models. In general, the single trait ssGBLUP (ST_ss-default) models and the non-linear weighting approach did not enhance prediction accuracy for either trait. For the phenotypic prediction ability of PFT, the linear WssGBLUP models ST_sswl1 (0.65) and ST_sswl2 (0.70), TT_W450 (0.64) and ssGBLUP-M (0.66) demonstrated the highest prediction accuracies. Similar results were observed for the phenotypic prediction ability of APF for both models. However, the linear WssGBLUP models ST_sswl1 (0.84) and ST_sswl2 (0.94) provided higher prediction performance compared to the two-, three- and multi-trait models. The results indicate that the multi-trait model achieved better predictive ability for the novel traits PFT and APF. Multi-trait genomic selection may yield greater genetic gains than other models for these forthcoming economically important traits in breeding programmes.

本研究的目的是评估使用不同预测方法对内洛雷牛累积盈利能力(APF)和每公斤活重增重利润(PFT)基因组预测的准确性、偏倚性和分散性。该数据集由每个性状的3969个表型记录组成。该谱系包含了1998年至2016年间出生的38930只动物的信息,其中包括2691只公鹿和19884只母鹿。使用Clarifide Nelore 3.0 SNP面板共对2449只动物进行基因分型。对9种基因组预测模型进行了评估:采用线性动物模型估计遗传参数,并进行基因组单性状最佳线性无偏预测(ST_ss-default)。此外,还对ssGBLUP (TT_W450和TT_DMI)、TTT_CAR和多性状ssGBLUP (MT_ss)进行了双性状测试。最后,采用加权线性(ST_sswl1和ST_sswl2)和非线性(ST_sswnl1和ST_sswnl2)单步基因组法(WssGBLUP)预测基因组育种值(GEBV)。通过计算GEBV和调整后表型之间的相关性来评估预测未来表现的能力。GEBV模型对PFT的平均预测精度为0.345 ~ 0.665,对APF的平均预测精度为0.425 ~ 0.603。除TTT_CAR模型(0.604)外,MT_ss模型对PFT的预测能力(0.665)显著高于其他模型,TTT_CAR模型的预测能力也有所提高。对于APF,与其他模型相比,MT_ss(0.561)和TT_W450(0.556)模型显示出更高的基因组预测精度。总体而言,单性状ssGBLUP (ST_ss-default)模型和非线性加权方法对两种性状的预测精度都没有提高。对于PFT的表型预测能力,线性WssGBLUP模型ST_sswl1(0.65)和ST_sswl2(0.70)、TT_W450(0.64)和ssGBLUP-M(0.66)的预测精度最高。两种模型的APF表型预测能力结果相似。然而,线性WssGBLUP模型ST_sswl1(0.84)和ST_sswl2(0.94)的预测性能优于两性状、三性状和多性状模型。结果表明,多性状模型对新性状PFT和APF具有较好的预测能力。在育种计划中,多性状基因组选择可能比其他模式产生更大的遗传收益。
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引用次数: 0
Estimating the Value of Including Resilience in a Multi-Trait Selection Index Designed for Australian Merino Sheep. 澳大利亚美利奴羊多性状选择指标中弹性的价值评估。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2026-03-01 Epub Date: 2025-10-23 DOI: 10.1111/jbg.70021
Erin G Smith, Samuel F Walkom, Sam A Clark

General resilience in livestock can be estimated from the variability in longitudinal data and may support balanced breeding objectives by helping animals better cope with environmental stress. However, its economic value and inclusion within multi-trait selection indexes remain largely unexplored. Current genetic improvement programs for sheep primarily focus on wool growth, reproduction and lean meat production. This study developed a bioeconomic model to estimate the economic value of general resilience, using the natural logarithm of variance of wool fibre diameter as a resilience indicator trait in sheep. A commercial Merino sheep enterprise was considered, and the economic value of resilience was derived from its association with health, mortality, and energy allocation for production. The breeding objective included key traits related to meat production, reproduction, and wool quality and quantity, to compare the economic impact of resilience with these traits. Among 13 traits, resilience contributed 2.02% to the total value of the index and ranked 11th in economic importance. After 10 years of simulated selection, resilience was expected to improved by 0.07 genetic standard deviations, translating to a modest economic gain of $0.08 per ewe. A sensitivity analysis was conducted to assess the impacts of increasing the relative contribution of resilience within the index on selection responses under four scenarios: (i) base genetic correlations, (ii) stronger correlations, (iii) weaker correlations, and (iv) adding genomic information. Resilience responded 50%-75% more effectively to selection when it had stronger genetic correlations with production traits or when genomic information was incorporated. However, placing greater emphasis on resilience (> 10% of the index) reduced progress in key production traits. Future research should explore these trade-offs in industry selection indexes to integrate resilience effectively without compromising productivity.

牲畜的一般恢复力可以从纵向数据的可变性中估计出来,并可能通过帮助动物更好地应对环境压力来支持平衡的育种目标。然而,它的经济价值和在多性状选择指标中的包容性在很大程度上仍未被探索。目前的绵羊遗传改良项目主要集中在羊毛生长、繁殖和瘦肉生产方面。本研究利用羊毛纤维直径方差的自然对数作为绵羊的弹性指标性状,建立了一个生物经济模型来估计一般弹性的经济价值。以一家商业美利奴羊企业为例,复原力的经济价值来源于其与健康、死亡率和生产能量分配的关系。育种目标包括与肉类生产、繁殖和羊毛质量和数量相关的关键性状,以比较弹性与这些性状的经济影响。在13个特征中,弹性对指数总价值的贡献率为2.02%,经济重要性排名第11位。经过10年的模拟选择,恢复力有望提高0.07个遗传标准差,转化为每只母羊0.08美元的适度经济收益。通过敏感性分析,在基础遗传相关、强相关、弱相关和添加基因组信息四种情况下,增加弹性指数相对贡献对选择反应的影响。当弹性与生产性状具有更强的遗传相关性或纳入基因组信息时,弹性对选择的反应效率提高50%-75%。然而,过分强调弹性(占指数的10%)会降低关键生产性状的进展。未来的研究应该在行业选择指标中探索这些权衡,在不影响生产率的情况下有效地整合弹性。
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引用次数: 0
Genetic Parameter Estimation for Pregnancy Loss and Their Association With Reproductive and Growth Traits in Brahman Cattle Under Extensive Tropical Conditions. 热带条件下婆罗门牛妊娠损失的遗传参数估计及其与繁殖和生长性状的关系。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2026-03-01 Epub Date: 2025-11-03 DOI: 10.1111/jbg.70025
Daniel Cardona-Cifuentes, Lucia G de Albuquerque, Milagros Arias, Sindy Caivio-Nasner, Luis Camaripano, Luis G Gonzalez-Herrera, Patricia I Schmidt, Fernando Baldi

This study estimated genetic parameters for pregnancy loss (PL) in Brahman cattle and evaluated the genetic correlation of PL with growth and reproductive traits using both the pedigree relationship matrix (A) and pedigree plus genomic relationship matrix (H). Data were collected from two herds in Bolivia, focusing on three age groups: heifers, primiparous and multiparous cows. Threshold animal models were fitted to each group. Multitrait models were fitted between the PL at different age group and between PL and the following traits: adjusted weights at 450 (W450) and 550 (W550) days, scrotal circumference adjusted at 450 (SC450) and 550 (SC550) days, accumulated cow productivity (ACP), age at first calving (AFC) and stayability (STAY). The H matrix increased the heritability for PL in heifers from 0.06 to 0.11. The genetic correlation between PL in heifers and primiparous cows changed using H (from 0.18 to 0.7), and it was high between heifers and multiparous cows. Moderate-high negative genetic correlation was observed between PL and STAY, with changes in heifers when using H (-0.17 to -0.57). AFC and PL presented medium-high positive genetic correlations. Negative correlations between PL and SC450 or SC550 were found in primiparous and multiparous cows. Using H, the correlation between PL in heifers and ACP shifted from 0.08 to -0.31, showing medium-high negative correlations for the other two age groups. Genetic correlations were low between PL and W450 or W550. Genomic information allows the use of PL as a selection criterion in heifers. Selection for major sexual precocity, longevity and productivity would enable the reduction of pregnancy loss.

本研究利用家系关系矩阵(A)和家系加基因组关系矩阵(H)估算了婆罗门牛妊娠损失(PL)的遗传参数,并评估了PL与生长和生殖性状的遗传相关性。数据收集自玻利维亚的两个牛群,重点关注三个年龄组:小母牛、初产母牛和多产母牛。各组均拟合阈值动物模型。采用多性状模型拟合了不同年龄层泌乳仔猪之间以及泌乳仔猪与450 (W450)和550 (W550) d调整体重、450 (SC450)和550 (SC550) d调整阴囊围、累积产奶量(ACP)、初产龄(AFC)和留犊性(STAY)之间的关系。H矩阵使小母牛的PL遗传率由0.06提高到0.11。小母牛与初产母牛的PL遗传相关随H的变化而变化(从0.18变为0.7),且小母牛与多产母牛的PL遗传相关较高。PL与STAY之间存在中高的负相关遗传关系,使用H时,小母牛的PL与STAY之间存在变化(-0.17 ~ -0.57)。AFC与PL呈中-高正相关。初产和多产奶牛的PL与SC450或SC550呈负相关。使用H时,小母牛的PL与ACP的相关性从0.08转变为-0.31,其余两个年龄组呈中-高负相关。PL与W450和W550的遗传相关性较低。基因组信息允许使用PL作为小母牛的选择标准。选择主要的性早熟,长寿和生产力将使怀孕损失减少。
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引用次数: 0
Use of Cluster Analysis for Identifying Metafounders. 使用聚类分析识别元创始人。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2026-01-23 DOI: 10.1111/jbg.70039
Christine Anglhuber, Christian Edel, Eduardo C G Pimentel, Reiner Emmerling, Kay-Uwe Götz, Georg Thaller

In the metafounder approach, the relationship matrix of metafounders, Γ $$ boldsymbol{Gamma} $$ is used to transfer information on relationships between pedigree founders into the numerator relationship matrix A $$ mathbf{A} $$ , creating matrix A Γ $$ {mathbf{A}}^{boldsymbol{Gamma}} $$ . Commonly metafounders are defined based on the available information of the animal (e.g., country, sex, breed) similar to unknown parent groups (UPG). This limits the ability of metafounders to correctly reflect the population structure. In Single-Step Models, hidden stratification in the population may cause inconsistencies between matrix A $$ mathbf{A} $$ and the genomic relationship matrix G $$ mathbf{G} $$ when they are combined into matrix H $$ mathbf{H} $$ . Reliable information on the true structure in a population can be obtained from genotypes. In this study, we investigate an approach to transfer information on population structure from the genotyped animals to the ungenotyped ancestors. We used an unsupervised clustering approach to assign pedigree founders to metafounders and performed Single-Step genomic evaluation for an increasing number of metafounders (nMF) assumed. The optimum nMF to model was determined by harmonising the trend in inbreeding in G $$ mathbf{G} $$ and A Γ $$ {mathbf{A}}^{boldsymbol{Gamma}} $$ and by monitoring of elements in Γ $$ boldsymbol{Gamma} $$ . A semi-stochastic simulation based on real genotypes from Fleckvieh was used to investigate two scenarios: a trait with a strong genetic trend and a trait with no genetic trend. The quality of the prediction was determined by a regression of true breeding value as obtained from the simulation on estimated breeding value. The modelling of metafounders defined by population structure analysis led to a slight reduction in prediction quality in a trait with no trend, but was still stable in the range of the optimum nMF. In a trait with a strong genetic trend, prediction qualtity was improved compared to a common Single-Step model. The largest improvement was achieved in the range of the proposed optimum nMF.

在元创始人方法中,元创始人的关系矩阵Γ $$ boldsymbol{Gamma} $$用于将系谱创始人之间的关系信息传递到分子关系矩阵A $$ mathbf{A} $$中,创建矩阵A Γ $$ {mathbf{A}}^{boldsymbol{Gamma}} $$。通常根据动物的可用信息(例如,国家,性别,品种)来定义元创建者,类似于未知的亲本群体(UPG)。这限制了元创始人正确反映人口结构的能力。在单步模型中,群体中的隐性分层可能导致矩阵A $$ mathbf{A} $$与基因组关系矩阵G $$ mathbf{G} $$组合成矩阵H $$ mathbf{H} $$时不一致。从基因型中可以获得关于群体真实结构的可靠信息。在本研究中,我们研究了一种将种群结构信息从基因型动物传递给非基因型祖先的方法。我们使用无监督聚类方法将谱系创始人分配给元创始人,并对越来越多的元创始人(nMF)假设进行单步基因组评估。通过协调G $$ mathbf{G} $$和A Γ $$ {mathbf{A}}^{boldsymbol{Gamma}} $$的近交趋势和监测Γ $$ boldsymbol{Gamma} $$中的元素,确定了模型的最佳nMF。基于Fleckvieh真实基因型的半随机模拟研究了两种情况:具有强遗传趋势的性状和没有遗传趋势的性状。通过对估计育种值的模拟得到的真实育种值的回归来确定预测的质量。由种群结构分析定义的元奠基人建模导致无趋势性状的预测质量略有下降,但在最优nMF范围内仍然稳定。在遗传趋势较强的性状上,与普通单步预测模型相比,预测质量得到了提高。在提出的最佳nMF范围内取得了最大的改进。
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引用次数: 0
Economic Benefit of Genetic Progress in Five Wool Sheep Breeds of Argentina. 阿根廷五个毛羊品种遗传进展的经济效益。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2026-01-12 DOI: 10.1111/jbg.70040
Joaquín Pablo Mueller, Nicolás Giovannini, Juan Mauricio Álvarez, Pedro Alejandro Vozzi, Daniel Omar Maizon, Emilio Rivera, Francisco Milicevic, María Virginia Sturzenbaum, Alan Maxs Pardo

The economic benefits of genetic improvement were estimated based on genetic trends observed for economically important traits in stud herds participating in Argentina's genetic evaluation scheme. The analysis included Horned Merino, Polled Merino, Dohne Merino, Corriedale and Polwarth sheep born between 2014 and 2023. This benefit was calculated as the difference between the additional income generated by the increased value of meat and wool in multiplier and commercial herds, and the costs associated with genetic improvement at the stud tier and additional cost of improved rams at multiplier and commercial tiers. The benefits of 10 years of genetic improvement and their residual effect for another 10 years were computed, updating the annual results with a discount rate of 5%. The benefit obtained in the five breeds reached USD 4.95 million considering only breeding program costs at the stud tier. Including additional ram buying costs, the benefit reached USD 3.75 million, the difference being captured by the ram selling tiers. At the breed level (ignoring ram buying costs) the return to investment (ROI) amounted to 33.6. At multiplier and commercial herd tiers (including ram buying costs) the income to cost ratios were 5.5 and 4.0, respectively. The Corriedale breed was responsible for 39% of the total benefit. Altogether, genetic improvement in the stud tier reached 1.47 million lambs annually or about 54% of the five wool sheep populations of the country. Thus, conventional genetic improvement efforts of economically important traits of wool sheep breeds proved to have been highly profitable.

根据参与阿根廷遗传评估计划的种马群中重要经济性状的遗传趋势,对遗传改良的经济效益进行了估计。分析对象包括2014年至2023年间出生的角美利奴羊、poll美利奴羊、Dohne美利奴羊、Corriedale羊和Polwarth羊。这一收益的计算方法是,倍率和商业畜群的肉和羊毛价值增加所产生的额外收入,与种马群遗传改良相关的成本以及倍率和商业畜群改良公羊的额外成本之间的差额。计算了10年遗传改良的收益及其未来10年的剩余效应,并以5%的贴现率更新了年度结果。仅考虑种马一级的育种计划成本,五个品种获得的效益达到495万美元。包括额外的公羊购买成本在内,收益达到375万美元,差额由公羊销售层抵消。在品种层面(忽略公羊购买成本),投资回报率(ROI)为33.6。在乘数和商业牧群层(包括公羊购买成本),收入成本比分别为5.5和4.0。Corriedale品种占总收益的39%。总的来说,种马群的遗传改良每年达到147万只羔羊,约占该国五个毛羊种群的54%。因此,对毛羊品种重要经济性状的传统遗传改良工作已被证明是高利润的。
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引用次数: 0
Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed. 加勒加鲁比亚肉牛近交系生产性状抑制的基因组分析。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-16 DOI: 10.1111/jbg.70034
N Mejuto-Vázquez, C Hervás-Rivero, R Rodríguez-Bermúdez, D López-Carbonell, M Hermida, P Martínez, L Varona

In autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using ~63,000 SNPs to assess inbreeding depression in four key traits: age at first calving (AFC) with 3503 records, calving interval (CI) with 3315 records, birth weight (BW) with 4878 records and weight at 210 days (W210) with 3285 records. Runs of homozygosity were sorted by length ([1,2], (2,4], (4,8], (8,16], > 16 Mb), and the corresponding inbreeding coefficients (FROH>1, FROH>2, FROH>4, FROH>8, FROH>16) were calculated using the consecutiveRUNs R package. A Genomic BLUP (GBLUP) was conducted for each FROH estimate using the BLUPF90+ programs. The results revealed significant inbreeding depression for AFC and CI, whereas W210 and BW exhibited similar inbreeding trends, but the effects of inbreeding on these traits were not statistically significant. To further explore the genetic basis of inbreeding depression, SNPs located within ROHs were tested, though a t-test, for their association with phenotypic traits. Genes located in significant regions (-log(p-value) > 3 from t-test) were annotated using Ensembl BioMart within a ± 0.5 Mb window. Recent inbreeding (ROH > 8 Mb) showed significant negative effects on reproductive traits, and key genomic regions-particularly on chromosome 2 involving MSTN, NAB1, and COL5A2-were linked to increased AFC and reduced BW and W210; ROH-based inbreeding estimates proved effective in detecting inbreeding depression in this native breed. Overall, ROH-based analyses revealed genomic regions and candidate genes, notably MSTN, contributing to inbreeding depression and key production traits in Rubia Galega cattle.

在人口较少的本土家畜品种中,如来自加利西亚(西班牙)的Rubia Galega,近亲之间的交配很常见,并可能导致近亲繁殖的抑制。利用约63,000个snp估计了4984只动物的基因组近交系数,以评估4个关键性状的近交抑制:初产龄(AFC)记录3503条,产犊间隔(CI)记录3315条,出生体重(BW)记录4878条,210天体重(W210)记录3285条。按长度([1,2],(2,4],(4,8],(8,16],>16 Mb)对纯合子进行排序,并使用连续veruns R包计算相应的近交系数(FROH>1, FROH>2, FROH>4, FROH>8, FROH>16)。使用BLUPF90+程序对每个FROH估计进行基因组BLUP (GBLUP)。结果表明,AFC和CI的近交抑制显著,而W210和BW的近交趋势相似,但近交对这些性状的影响无统计学意义。为了进一步探索近交抑郁症的遗传基础,我们通过t检验对位于ROHs内的snp与表型性状的相关性进行了测试。在±0.5 Mb的窗口内,使用Ensembl BioMart对位于显著区域的基因(t检验的-log(p值)>.3)进行注释。最近的近亲繁殖(ROH > 8mb)对生殖性状有显著的负面影响,关键基因组区域-特别是涉及MSTN、NAB1和col5a2的2号染色体-与AFC升高、体重和W210降低有关;结果表明,基于roh的近交估计可以有效地检测到该本地品种的近交抑制。总体而言,基于roh的分析揭示了Rubia Galega牛近交抑制和关键生产性状的基因组区域和候选基因,特别是MSTN。
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引用次数: 0
Genetic Parameters of Methane Emission, Feed Efficiency, Feeding Behaviour, and Growth Traits in Beef Cattle. 肉牛甲烷排放、饲料效率、摄食行为和生长性状的遗传参数
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-12 DOI: 10.1111/jbg.70037
J A Silva, J P S Valente, L F M Mota, G R D Rodrigues, T L S Soares, J O S Marcatto, A M Pelaez, F M Monteiro, R C Canesin, L G Albuquerque, M E Z Mercadante

Climate change has intensified the need to reduce greenhouse gas emissions, particularly methane (CH4) from enteric fermentation. Genetic selection has emerged as a promising mitigation strategy; however, studies on Bos taurus indicus , especially Nellore cattle, remain limited. This study aimed to estimate heritabilities and genetic correlations for CH4 emission traits and their relationships with feeding behaviour, feed efficiency, and performance, as well as to evaluate the direct and correlated responses to selection for lower CH4 emissions. Data were from 2418 Nellore cattle evaluated in feed efficiency trials. Traits included dry matter intake (DMI), feeding time per day (FTd), feed events per day (FEd), and feeding rate (FR), residual feed intake (RFI), average daily gain (ADG), and mid-test body weight (MBW). Methane emissions were measured in 1153 animals using the SF6 tracer technique, providing daily CH4 emission (g/day), CH4 per unit of DMI (CH4DMI, g/day), and residual CH4 (CH4res). Variance components were estimated using the single-step genomic BLUP (ssGBLUP) method through Bayesian inference. Heritability estimates were moderate for CH4 (0.25), CH4DMI (0.14), CH4res (0.14), and performance traits such as DMI (0.35), ADG (0.36), and MBW (0.40). Higher estimates were observed for feeding behaviour traits FTd (0.49) and FR (0.42). Genetic correlations between CH4 and production traits were high, particularly with DMI (0.79), ADG (0.90), and MBW (0.91), indicating that selection for reduced CH4 emissions may affect growth. Direct selection for CH4 led to a modest annual reduction in emissions but also a correlated decline in MBW. These results demonstrate that while CH4 emissions are heritable, their strong genetic association with productivity traits indicates that isolated selection for reduced emissions may lead to undesirable outcomes in feed intake and performance. Therefore, strategies aiming to reduce CH4 emissions should consider the genetic relationships with growth and efficiency traits to avoid compromising animal productivity.

气候变化加剧了减少温室气体排放的需要,特别是肠道发酵产生的甲烷(CH4)。基因选择已成为一种有希望的缓解策略;然而,对印度牛,特别是内罗牛的研究仍然有限。本研究旨在评估CH4排放性状的遗传力和遗传相关性及其与取食行为、饲料效率和生产性能的关系,并评估选择降低CH4排放的直接和相关响应。数据来自饲料效率试验中评估的2418头Nellore牛。性状包括干物质采食量(DMI)、日采食量(FTd)、日采食量(FEd)、采食量(FR)、剩余采食量(RFI)、平均日增重(ADG)和试验中体重(MBW)。利用SF6示踪技术测量了1153只动物的甲烷排放量,提供了每日CH4排放量(g/day)、单位DMI的CH4排放量(CH4DMI, g/day)和剩余CH4 (CH4res)。通过贝叶斯推断,采用单步基因组BLUP (ssGBLUP)方法估计方差成分。CH4(0.25)、CH4DMI(0.14)、CH4res(0.14)以及DMI(0.35)、ADG(0.36)和MBW(0.40)等性能性状的遗传力估计中等。摄食行为性状FTd(0.49)和FR(0.42)的估计值较高。CH4与生产性状的遗传相关性较高,尤其是DMI(0.79)、ADG(0.90)和MBW(0.91),表明选择减少CH4排放可能影响生长。直接选择CH4导致了每年排放量的适度减少,但也导致了MBW的相关下降。这些结果表明,虽然甲烷排放是可遗传的,但其与生产力性状的强烈遗传关联表明,减少甲烷排放的孤立选择可能会导致采食量和生产性能方面的不良结果。因此,旨在减少CH4排放的策略应考虑与生长和效率性状的遗传关系,以避免损害动物生产力。
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引用次数: 0
Is There a Genetic Link Between Resting Infrared Thermography in Young Horses and Longevity in Jumping Competition? 静止红外热成像与赛马寿命是否存在遗传联系?
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-09 DOI: 10.1111/jbg.70038
Anne Ricard, Séverine Deretz, Cathy Menard, Bernard Dumont Saint Priest

The objective was to evaluate the genetic relationship between the surface temperature of regions of interest, measured using infrared images of young horses and functional longevity in jumping. This relationship was assessed by comparing the temperatures measured in the offspring of two groups of sires, one favourable and one unfavourable, to longevity. The study used a specific data collection protocol on a sample of 921 young progeny, before they began competing, of 141 extreme stallions, comprising 61 favourable and 80 unfavourable sires. These stallions had been selected based on estimated breeding values for functional longevity derived from official competition data of 202,320 horses. Infrared imaging provided 49 temperature variables, including average and maximum values for regions of interest such as temperature differences from the body for eyes, hocks, fetlocks, feet, carpi and back. It also included differentials between these regions, asymmetry between right and left sides and variability within each area. Heritability was estimated using a mixed model with fixed effects, of age, sex, coat colour, weight and visit, along with random genetic effects (considering a pedigree of 8002 horses). The effect of temperature on the group of sires was assessed using multivariate partial least squares logistic regression, adjusting temperature for fixed effects. Results indicated high heritability for the temperature of regions of interest: body (0.53 ± 0.14), carpi (0.55 ± 0.19), fetlocks (0.47 ± 0.12), feet (0.46 ± 0.12 and 0.38 ± 0.12). Lower heritability was observed for differences between regions (around 0.20) and even lower for asymmetry and variability. Lower average and maximum eye temperatures, lateral asymmetry in hind feet temperature and temperature variability in the back were associated with a higher probability of belonging to the favourable group of sires for functional longevity. Infrared imaging may be a tool for identifying easily measurable selection criteria associated with longevity. Given the limited number of horses, the limited number of significant variables associated with the group of sires and the specificity of the protocol, verification and validation studies are necessary before its use.

目的是评估感兴趣区域的表面温度之间的遗传关系,用年轻马的红外图像测量和功能寿命的跳跃。这种关系是通过比较两组后代的温度来评估的,一组对长寿有利,一组对长寿不利。该研究采用了一种特定的数据收集方案,在141种极端种马的921个年轻后代开始竞争之前,其中包括61种有利种和80种不利种。这些种马是根据202,320匹马的官方比赛数据得出的功能性寿命的估计育种值来选择的。红外成像提供了49个温度变量,包括感兴趣区域的平均值和最大值,例如眼睛、飞节、脚、腕关节和背部的温差。它还包括这些区域之间的差异,左右两侧的不对称以及每个区域内的可变性。遗传率是用一个混合模型来估计的,该模型具有固定的影响,包括年龄、性别、毛色、体重和访问,以及随机的遗传影响(考虑到8002匹马的血统)。使用多变量偏最小二乘逻辑回归评估温度对组sires的影响,调整温度为固定效应。结果表明,感兴趣区域的温度遗传率较高:体(0.53±0.14),腰(0.55±0.19),腿(0.47±0.12),脚(0.46±0.12和0.38±0.12)。区域间差异的遗传率较低(约0.20),不对称和变异的遗传率更低。较低的平均和最高眼睛温度、后脚温度的横向不对称以及背部温度的变化,与属于功能长寿的有利种群的可能性较高有关。红外成像可能是一种工具,用于识别与寿命相关的易于测量的选择标准。考虑到马的数量有限,与组种相关的重要变量数量有限,以及方案的特殊性,在使用之前需要进行验证和验证研究。
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引用次数: 0
The Changes in Genetic Parameters and Genomic Selection of Lambing Rate in Hu Sheep Following Marker-Assisted Selection. 标记辅助选择下湖羊产羔率遗传参数的变化及基因组选择。
IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Pub Date : 2025-12-08 DOI: 10.1111/jbg.70036
Yuan Zhao, XiaoXue Zhang, FaDi Li, Huibin Tian, DeYin Zhang, Xiaolong Li, YuKun Zhang, JiangBo Cheng, ZongWu Ma, ChangChun Lin, XiWen Zeng, LiMing Zhao, WeiMin Wang

The identification of quantitative trait locus (QTL) or genes responsible for key agronomic traits has significantly enhanced genetic improvement through marker-assisted selection (MAS). However, the impacts of MAS on genetic parameters and subsequent selection processes have not been thoroughly characterised. Here, through genome-wide selective sweep analysis, we identified a diverse set of genes involved in oocyte meiosis, including PPP3CA, AR, PPP1CB, SPDYA, MAD1L1, and BMPR1B. The genome-wide association study (GWAS) further identified three genes UNC5C, BMPR1B, and PDLIM5 as being associated with lambing rate in Hu sheep. From these analyses, the FecB loci emerged as a potential molecular marker for lambing rate. with an increase of 0.5 lambs per G allele. The heritability of the lambing rate was estimated to be 0.19 (±0.02). Moreover, based on 10-fold cross-validation, the accuracy of genomic selection (GS) was found to be 0.30. Simulated MAS resulted in a reduction of the additive genetic variance components, with estimated heritability dropping to 0.14 (±0.02) and GS accuracy decreasing to 0.18-representing a decline of 26.42% and 34.81%, respectively. To address the reduced GS accuracy, we performed GWAS on the reference set to identify weighted single nucleotide polymorphisms (SNPs). This method has the potential to increase accuracy by 13.8%. Our study found that MAS has a negative impact on GS. To address this issue, we integrated prior information on SNPs from GWAS, which exhibit pleiotropic genetic architecture. This integration enables us to utilise genetic markers for complex traits more effectively, thereby improving the accuracy and efficiency of GS.

数量性状位点(QTL)或关键农艺性状相关基因的鉴定,极大地促进了标记辅助选择(MAS)的遗传改良。然而,MAS对遗传参数和随后的选择过程的影响尚未得到彻底的表征。在这里,通过全基因组选择性扫描分析,我们确定了一组不同的参与卵母细胞减数分裂的基因,包括PPP3CA、AR、PPP1CB、SPDYA、MAD1L1和BMPR1B。全基因组关联研究(GWAS)进一步确定了3个基因UNC5C、BMPR1B和PDLIM5与湖羊产羔率相关。从这些分析中,FecB基因座成为产羔率的潜在分子标记。每个G等位基因增加0.5只羔羊。估计产羔率的遗传率为0.19(±0.02)。此外,基于10倍交叉验证,基因组选择(GS)的准确性为0.30。模拟MAS导致加性遗传方差成分降低,估计遗传力降至0.14(±0.02),GS精度降至0.18,分别下降26.42%和34.81%。为了解决GS准确性降低的问题,我们对参考集进行了GWAS,以确定加权单核苷酸多态性(snp)。该方法有可能将准确度提高13.8%。我们的研究发现MAS对GS有负向影响。为了解决这个问题,我们整合了来自GWAS的snp的先前信息,这些snp表现出多效性遗传结构。这种整合使我们能够更有效地利用复杂性状的遗传标记,从而提高GS的准确性和效率。
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引用次数: 0
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Journal of Animal Breeding and Genetics
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