مقایسه‌ی راهبردهای انتخاب فنوتیپی، شجره‌ای و ژنومی در برنامه‌ی اصلاح نژاد مرغان بومی ایران: مدیریت همبستگی منفی صفات تخم‌مرغ و کنترل هم‌خونی (یک مطالعه‌ی شبیه‌سازی)

Introduction: Iranian native chickens represent a valuable genetic resource, valued for its adaptation to harsh environmental condition and relative disease resistance. To conserve and improve this resource, breeding stations in several provinces including Fars, Mazandaran, Esfahan, Yazd, West Azerbaijan and Khorasan have impelemnted selection programmes. The research mainly focused on estimating genetic parameters for productive and reproductive traits in this population, and a meta-analysis of these estimates has also been published. In contrast, studies that focus on optimizing and comparing alternative breeding strategies, remain scarce for the Iranian native chicken. Two structural challenges are particularly relevant to such programmes: (i) a reported negative genetic correlation between egg number and egg weight, which whereby selection for one trait may adversely affect to other; and (ii) the low heritability and sex-limited expression of egg number, which prevent direct selection of cocks based on their own laying records. These conditions are precisely those under which genomic selection is expected to provide substantial advantages, as it can generate breeding values for both sexes and at an early age.
Materials and Methods: A stochastic, multi-trait breeding-program simulation was developed and parameterized using real, published genetic parameters for Iranian native chickens. Three economically important traits were considered including body weight at 12 weeks (BW12), egg number over the first 12 weeks of lay (EN) and mean egg weight (EW), with heritabilities of 0.40, 0.20 and 0.45 respectively, and a negative genetic correlation of −0.27 between EN and EW. A closed nucleus population comprising 60 sires and 300 dams was simulated under discrete generations, with each dam produced 6 offspring (approximately 1800 per generation), over 10 generations and 20 replicates. This resulted approximately 18,000 body-weight records per replicate and approximately 9,000 records for each egg production trait, which were expressed only in females. The nucleus size and the 1:5 mating ratio reflect the operational scale of Iranian native-chicken breeding stations and resulting in an effective population size of 200. Rather than assuming selection accuracy, a structured genome comprising 20 chromosomes (approximately 20 Morgan) was simulated and evolved through a historical population with an effective size 80, 120 generations to generate realistic linkage disequilibrium. approximately 2110 polymorphic loci remained, of which 600 were sampled as hidden QTL and approximately 1510 as predictive markers, thus, none of the selection method had access to the causal loci. Three selection strategies were compared including: phenotypic (mass) selection, pedigree-BLUP and genomic selection (GBLUP). Estimated breeding values were obtained by actually solving the corresponding models, and the realized accuracy of each strategy was calculated as the correlation between estimated and true breeding values. Because egg traits were expressed only in females, so cocks' breeding values for these traits were derived exclusively from information provided by relatives or genomic data. Inheritance was modeled using recombined gametes, allowing the reduction in additive genetic variance by selection (Bulmer effect) to arise naturally. Selection was based on a standardized multi-trait economic index; while inbreeding was quantified as the reduction in molecular heterozygosity relative to the base generation. Sensitivity analysis was also conducted to evaluate the effect of genomic reference-population size and the negative EN-EW genetic correlation under three alternative index weightings.
Results and Discussion: Mass selection was virtually ineffective for egg number, resulting in a gain of only +0.03 additive genetic standard deviations (σa), after 10 generations, because cocks lacked own records and the trait had relatively low heritability. It also resulted in an excessive and unbalanced increase in body weight. Pedigree-based BLUP and, particularly, genomic selection produced substantial and more balanced gains in egg number (+1.58 and +1.40 σa, respectively), with genomic selection produced greatest gain in egg-weight (+5.60 σa). Genomic selection achieved the highest realized accuracy for all three traits; however, when a single-generation reference population was used, its advantage over pedigree-BLUP for egg number was relatively small. Contrary to a common assumption that pedigree-based BLUP necessarily results in the lowest inbreeding: BLUP and genomic selection resulted in similar levels of molecular inbreeding (approximately 13.1% and 10.9%, respectively), both of which were higher than that observed phenotypic selection (6.1%), because both approaches concentrate selection on families. Increasing the genomic reference population size from 500 to 4000 individuals increased the realized genomic accuracy of egg number from 0.43 to 0.69. The EN–EW Negative Correlations was clearly demonstrated: selecting solely for egg number increased EN by +5.49 σa but reduced EW by −1.26 (σa,) whereas a balanced economic index simultaneously improved both traits (+1.71 and +5.43 σa).
Conclusion: In a simulated Iranian native chicken breeding program, genomic selection embedded in a balanced multi-trait economic index was the most effective strategy for the simultaneous improvement of growth and egg-production traits, particularly for the lowly heritable and sex-limited egg number. Phenotypic selection was inadequate for improving this trait, whereas pedigree-BLUP represented an effective intermediate strategy. The advantage of genomic selection depends on assembling a sufficiently large reference population and, because both pedigree-based BLUP and genomic selection raise inbreeding, must be accompanied by inbreeding management. Therefore, Iranian Native-chicken breeding stations are encouraged to gradually shift from conventional phenotypic selection to genomic evaluation based on balanced economic indices.