State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Sanya Institute of China Agricultural University, Sanya, 572025, China.
BMC Genomics. 2024 Jan 4;25(1):30. doi: 10.1186/s12864-023-09925-x.
Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual's whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog).
A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR-RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells.
Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.
沙孜利猪是中国著名的本土品种，具有优异的肉质特性。然而，沙孜利猪肉质特性的遗传机制和基因组证据尚不清楚。为了探索和研究沙孜利猪的种质特性，我们首次对 67 个个体的全基因组测序数据进行了全面分析（20 头沙孜利猪[S]、20 头达巴沙猪[DBS]、11 头约克夏猪[Y]、10 头伯克夏猪[BKX]、5 头巴山猪[BS]和 1 头野猪）。
共检测到 2538577 个高质量 SNP，利用一致性分析法（IBD）和选择扫描法，采用综合分析策略，精确挖掘和筛选出 9 个 S 和 S 与 DBS 共有的候选基因。其中，Wnt 信号通路拮抗剂 dickkopf WNT 信号通路抑制剂 2（DKK2）是最有前途的候选基因，不仅在 PigQTLdb 中鉴定出与棕榈酸和棕榈油酸数量性状位点的关联，而且与其他 12 个群体的 48 头中国本地猪和 4 个群体的 39 头外来猪相比，S 中也有特异性选择。随后，在 21 个不同的猪群体中，利用 PCR-RFLP 方法，在 DKK2 内含子 1 的 12726bp 处（g.114874954 A> C）发现了与肌内脂肪含量相关的突变。我们观察到 DKK2 特异性表达于脂肪组织。DKK2 的过表达降低了甘油三酯、脂肪酸合成酶和脂肪生成及 Wnt 信号通路相关基因的表达，而在猪前体脂肪细胞和 3T3-L1 细胞的脂肪生成分化过程中，干扰 DKK2 则得到相反的效果。
我们的研究结果为挖掘重要经济性状的功能基因提供了一种分析策略，为提高猪的肉质性状和分子育种提供了基础数据和分子证据。
