Data for: Comparative evaluation of phenotypic, pedigree, and family-based selection in insect breeding using stochastic simulation

Selective breeding in insects has predominantly relied on phenotypic
selection without considering relatedness. Selection on estimated breeding
values could potentially increase genetic gain, but the challenge of
pedigree tracking complicates this. Family selection can be used as an
alternative to individual selection, either using combined between- and
within-family selection, or strict between-family selection with full-sib
group records as a proxy for individual data. The effectiveness of family
selection can however be compromised by the presence of unmitigated common
environment effects. In this study, we employ stochastic simulations to
explore expected genetic gain and rate of inbreeding in insect populations
under four single-trait selection schemes: phenotypic selection,
individual pedigree selection, combined selection using both family and
individual breeding values for selection, and between-family selection
using full-sib average phenotypes for breeding value estimation. These
schemes are compared on genetic gain and rate of inbreeding across five
trait heritabilities (0.05, 0.1, 0.2, 0.4 and 0.6), two variations in
number of families in the population (60 or 200), and two offspring group
structures for the family breeding schemes (1 or 3 sib groups per female)
with a fixed common environment effect. Selection based on individual
breeding values results in significantly higher genetic gain than
phenotypic selection at low heritability (≤0.1), and similar gain at
heritability >0.1. Phenotypic selection results in a lower rate of
inbreeding (0.003-0.011) compared to other schemes (0.005-0.055) at low
heritability (≤0.1), but this difference is reduced as heritability
increases. Combined selection results in genetic gain between that of the
phenotypic and individual pedigree schemes, depending on sib group
structure and heritability. Using between-family selection reduces genetic
gain (0.23-1.97) compared to other schemes (0.40-4.34). Establishing
multiple sib-groups mitigates the confounding of genetic and common
environment effects, and thus the reduction in genetic gain from family
selection schemes. Increasing the number of families from 60 to 200 in the
breeding population reduces inbreeding in all scenarios (ΔF at 60 families
is 0.009-0.055, at 200 families is 0.003-0.031). We conclude that
selection on individual breeding values yields greater genetic gain
compared to family breeding values and selection on phenotypes. The
between-family approach is an alternative when individual pedigrees are
not feasible to maintain. Phenotypic selection results in both high
genetic gain and generally low rates of inbreeding, but as heritability
increases, so does the rate of inbreeding. Therefore, phenotypic selection
should not be implemented without any inbreeding control in long term
selection.

昆虫选择育种（selective breeding）长期以来主要依赖不考虑亲缘关系的表型选择（phenotypic selection）。基于估计育种值（estimated breeding values）的选择理论上可提升遗传进展（genetic gain），但系谱追踪（pedigree tracking）的难度使该方案的实施复杂化。家系选择（family selection）可作为个体选择（individual selection）的替代方案，具体可采用家系间与家系内综合选择法（combined between- and within-family selection），或以全同胞组记录（full-sib group records）作为个体数据替代物的严格家系间选择法（strict between-family selection）。但未被控制的共同环境效应（common environment effects）会削弱家系选择的实施效果。本研究采用随机模拟（stochastic simulations）方法，探究4种单性状选择方案（single-trait selection schemes）下昆虫群体的预期遗传进展与近交速率（rate of inbreeding），4种方案分别为：表型选择、个体系谱选择（individual pedigree selection）、同时利用家系与个体育种值开展选择的综合选择法，以及以全同胞平均表型值估计育种值（breeding value estimation）的家系间选择法。本研究设置5个性状遗传力（trait heritabilities）水平（0.05、0.1、0.2、0.4和0.6）、2个群体家系数量梯度（60或200），并针对家系选育方案设置2种后代组结构（每头雌虫对应1或3个同胞组（sib groups）），同时固定共同环境效应，以此比较不同选择方案的遗传进展与近交速率。在低遗传力（≤0.1）条件下，基于个体育种值的选择可获得显著高于表型选择的遗传进展；当遗传力＞0.1时，二者的遗传进展则无显著差异。在低遗传力（≤0.1）条件下，表型选择的近交速率（0.003~0.011）低于其他选择方案（0.005~0.055），但该差异会随遗传力升高而逐渐缩小。综合选择法的遗传进展介于表型选择与个体系谱选择之间，具体水平取决于同胞组结构与遗传力大小。家系间选择法的遗传进展（0.23~1.97）低于其他选择方案（0.40~4.34）。设置多个同胞组可减轻遗传效应与共同环境效应的混杂问题，从而缓解家系选择方案带来的遗传进展损失。将选育群体（breeding population）的家系数量从60提升至200，可在所有情景下降低近交（inbreeding）水平：家系数量为60时的近交速率ΔF为0.009~0.055，家系数量为200时则为0.003~0.031。本研究结论如下：基于个体育种值的选择可获得高于家系育种值选择与表型选择的遗传进展；当无法维持个体系谱记录时，家系间选择法可作为替代方案。表型选择可同时实现较高的遗传进展与较低的近交速率，但近交速率会随遗传力升高而增加。因此，在长期选择（long term selection）过程中，表型选择若不辅以近交控制措施则不可取。