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Abstract：
BACKGROUND: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits.
RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits.
CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.
RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits.
CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.
摘要：
背景：基于其预测的育种值和相关个体的交配来选择个体，可以增加按血统相同的等位基因的比例。在这种情况下，这项研究的目的是根据替代指标和数据来源，如谱系(FPED)，估计近交系数。混合基因组关系矩阵H(FH)，和不同长度的ROH（FROH）；并计算选择体重调整为378日龄（W378）的封闭Nellore牛种群中不同指标之间的Pearson相关性。除了总FROH（所有类别）系数外，还根据ROH段的大小类别进行了估算：FROH1（1-2Mb），FROH2(2-4Mb),FROH3（4-8Mb），FROH4（8-16Mb），和FROH5（>16Mb），和每个染色体(FROH_CHR)。此外，我们评估了每种近亲繁殖指标对出生体重（BW）的影响，体重调整为210（W210）和W378，阴囊周长（SC），和剩余饲料摄入量(RFI)。我们还评估了近交对生长性状的染色体特异性影响。
结果：FPED与FROH的相关性为0.60，FH与FROH的相关性为0.69和0.61。FPED的近亲繁殖年比率为0.16%,FH为0.02%，FROH为0.16%。FROH5的1%增加导致W210和W378的减少高达-1.327±0.495kg。四个近交系数(FPED，FH,FROH2和FROH5）对W378有显著影响，FROH2每增加1%，减少量高达-3.810±1.753kg。FPED对RFI（0.01±0.0002kg干物质/天）和FROH对SC（-0.056±0.022cm）有不利影响。计算的BTA3，BTA5和BTA8的FROH_CHR系数显着影响生长性状。
结论：所有评价性状均观察到近交抑郁。然而,对于用于选择动物的标准，这些影响更大(即，W378).与基于系谱的近交相比，基因组近交的增加与所评估性状的近交抑制更高相关。在交配过程中，基因组信息应用作优化近亲繁殖控制的工具，因此,最大限度地减少内洛尔牛的近亲繁殖抑郁症。
结果：FPED与FROH的相关性为0.60，FH与FROH的相关性为0.69和0.61。FPED的近亲繁殖年比率为0.16%,FH为0.02%，FROH为0.16%。FROH5的1%增加导致W210和W378的减少高达-1.327±0.495kg。四个近交系数(FPED，FH,FROH2和FROH5）对W378有显著影响，FROH2每增加1%，减少量高达-3.810±1.753kg。FPED对RFI（0.01±0.0002kg干物质/天）和FROH对SC（-0.056±0.022cm）有不利影响。计算的BTA3，BTA5和BTA8的FROH_CHR系数显着影响生长性状。
结论：所有评价性状均观察到近交抑郁。然而,对于用于选择动物的标准，这些影响更大(即，W378).与基于系谱的近交相比，基因组近交的增加与所评估性状的近交抑制更高相关。在交配过程中，基因组信息应用作优化近亲繁殖控制的工具，因此,最大限度地减少内洛尔牛的近亲繁殖抑郁症。
