AUTHOR=Barani Somayeh , Miraie Ashtiani Sayed Reza , Nejati Javaremi Ardeshir , Khansefid Majid , Esfandyari Hadi 

TITLE=Optimizing purebred selection to improve crossbred performance

JOURNAL=Frontiers in Genetics

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1384973

DOI=10.3389/fgene.2024.1384973

ISSN=1664-8021

ABSTRACT=<p>Crossbreeding is a widely adopted practice in the livestock industry, leveraging the advantages of heterosis and breed complementarity. The prediction of Crossbred Performance (CP) often relies on Purebred Performance (PB) due to limited crossbred data availability. However, the effective selection of purebred parents for enhancing CP depends on non-additive genetic effects and environmental factors. These factors are encapsulated in the genetic correlation between crossbred and purebred populations (<inline-formula id="inf1"><mml:math id="m1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>). In this study, a two-way crossbreeding simulation was employed to investigate various strategies for integrating data from purebred and crossbred populations. The goal was to identify optimal models that maximize CP across different levels of <inline-formula id="inf2"><mml:math id="m2" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Different scenarios involving the selection of genotyped individuals from purebred and crossbred populations were explored using ssGBLUP (single-step Genomic Best Linear Unbiased Prediction) and ssGBLUP-MF (ssGBLUP with metafounders) models. The findings revealed an increase in prediction accuracy across all scenarios as <inline-formula id="inf3"><mml:math id="m3" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> values increased. Notably, in the scenario incorporating genotypes from both purebred parent breeds and their crossbreds, both ssGBLUP and ssGBLUP-MF models exhibited nearly identical predictive accuracy. This scenario achieved maximum accuracy when <inline-formula id="inf4"><mml:math id="m4" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> was less than 0.5. However, at <inline-formula id="inf5"><mml:math id="m5" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> = 0.8, ssGBLUP, which exclusively included sire breed genotypes in the training set, achieved the highest overall prediction accuracy at 73.2%. In comparison, the BLUP-UPG (BLUP with unknown parent group) model demonstrated lower accuracy than ssGBLUP and ssGBLUP-MF across all <inline-formula id="inf6"><mml:math id="m6" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> levels. Although ssGBLUP and ssGBLUP-MF did not demonstrate a definitive trend in their respective scenarios, the prediction ability for CP increased when incorporating both crossbred and purebred population genotypes at lower levels of <inline-formula id="inf7"><mml:math id="m7" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mrow><mml:mtext> </mml:mtext><mml:mi>r</mml:mi></mml:mrow><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Furthermore, when <inline-formula id="inf8"><mml:math id="m8" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> was high, utilizing paternal genotype for CP predictions emerged as the most effective strategy. Predicted dispersion remained relatively similar in all scenarios, indicating a slight underestimation of breeding values. Overall, the <inline-formula id="inf9"><mml:math id="m9" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula> value emerged as a critical factor in predicting CP based on purebred data. However, the optimal model to maximize CP depends on the factors influencing <inline-formula id="inf10"><mml:math id="m10" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>p</mml:mi><mml:mi>c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math></inline-formula>. Consequently, ongoing research aims to develop models that optimize purebred selection, further enhancing CP.</p>