Abstract

Sow fertility traits, such as litter size and the number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable and expressed late in life. Age at puberty (AP) is an early indicator of reproductive longevity. Here, we utilized a custom Affymetrix single-nucleotide polymorphisms (SNPs) array (SowPro90) enriched with positional candidate genetic variants for AP and a haplotype-based genome-wide association study to fine map the genetic sources associated with AP and other fertility traits in research (University of Nebraska-Lincoln [UNL]) and commercial sow populations. Five major quantitative trait loci (QTL) located on four Sus scrofa chromosomes (SSC2, SSC7, SSC14, and SSC18) were discovered for AP in the UNL population. Negative correlations (r = −0.96 to −0.10; P < 0.0001) were observed at each QTL between genomic estimated breeding values for AP and reproductive longevity measured as lifetime number of parities (LTNP). Some of the SNPs discovered in the major QTL regions for AP were located in candidate genes with fertility-associated gene ontologies (e.g., P2RX3, NR2F2, OAS1, and PTPN11). These SNPs showed significant (P < 0.05) or suggestive (P < 0.15) associations with AP, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. For example, in the UNL population, when the number of favorable alleles of an SNP located in the 3′ untranslated region of PTPN11 (SSC14) increased, AP decreased (P < 0.0001), while LTNP increased (P < 0.10). Additionally, a suggestive difference in the observed NR2F2 isoforms usage was hypothesized to be the source of the QTL for puberty onset mapped on SSC7. It will be beneficial to further characterize these candidate SNPs and genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect the phenotypic variation of fertility traits.

中文翻译：

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使用 Sowpro90 基因分型芯片精细定位与青春期年龄和母猪生育力相关的遗传变异。

摘要

母猪繁殖力特征，如产仔数和终生胎次数（繁殖寿命），在经济上很重要。这些性状的选择很困难，因为它们遗传性低，并且在晚年表现出来。青春期年龄 ( AP ) 是生殖寿命的早期指标。在这里，我们利用定制的 Affymetrix 单核苷酸多态性 ( SNPs ) 阵列 ( SowPro90 )，富含 AP 的位置候选遗传变异和基于单倍型的全基因组关联研究，以精细定位与 AP 和其他生育性状相关的遗传来源。研究（内布拉斯加大学林肯分校 [ UNL ]）和商业母猪种群。五个主要数量性状基因座（QTL) 位于四个Sus scrofa染色体（SSC2、SSC7、SSC14 和 SSC18）上被发现用于 UNL 群体中的 AP。在每个 QTL 处观察到 AP 的基因组估计育种值与生殖寿命（以胎次终生数 ( LTNP )衡量）之间的负相关性（r = -0.96 至 -0.10；P < 0.0001 ）。在 AP 的主要 QTL 区域中发现的一些 SNP 位于具有生育相关基因本体的候选基因中（例如，P2RX3、NR2F2、OAS1和PTPN11）。这些 SNP 显示出显着性 ( P < 0.05) 或暗示性 ( P< 0.15) 与 UNL 种群中 AP、繁殖寿命和窝产仔数性状以及商品母猪的窝产仔数性状的关联。例如，在UNL人群中，当位于PTPN11（SSC14）3'非翻译区的SNP的有利等位基因数量增加时，AP减少（P < 0.0001），而LTNP增加（P < 0.10）。此外，观察到的NR2F2的暗示性差异假设同种型的使用是映射到 SSC7 上的青春期开始 QTL 的来源。进一步表征这些候选 SNP 和基因以了解它们对蛋白质序列和功能、基因表达、剪接过程的影响以及这些变化如何影响生育性状的表型变异将是有益的。