Abstract：Abstract Fertility performance of pig (Sus scrofa) is a main objective trait in pig genetic improvement, which is difficult to achieve great genetic progress with traditional breeding method due to its relative lower heritability. To investigate the performance of the restriction association site DNA sequencing (RAD-seq) technology on genomic prediction of the breeding value for fertility traits, 725 sows with records of total number born (TNB), number born alive (NBA) and litter weight (LW) from Shenzhen Agroi Pastoral Enterprises Co., Ltd. were collected. 618 sows in all of 725 sows with RAD-seq were sequenced and 79 725 genome-wide distributed SNPs after quality control were produced. To validate the efficiency of the RAD-seq on genomic selection, the 618 sows into two parts with 4∶1 ratio were divided, which served as the reference and validation population, respectively. Then, the predictive accuracy and biasness of three methods including best linear unbiased prediction (BLUP), genomic BLUP (GBLUP) and single-step genomic BLUP (SS-GBLUP) were studied, respectively, for validation population for which phenotypic records were masked. The results showed that GBLUP increased the prediction accuracy of breeding value from 0.109 (TNB), 0.067 (NBA) and 0.009 (LW) with BLUP to 0.220 (TNB), 0.184 (NBA) and 0.205 (LW), respectively, and SS-GBLUP performed similar prediction accuracy as GBLUP. Furthermore, GBLUP and SS-GBLUP improved the prediction biasness in comparison with BLUP. The results suggested RAD-seq based genomic selection method was effective in breeding value prediction for fertility traits. The exploration of the application of RAD-seq technology on pig genomic selection has theoretical and practical significance.
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