Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population

被引:1
作者
Wang, Huiyu [1 ,2 ]
Wang, Xiaoyi [1 ]
Yang, Yongli [1 ]
Zhu, Yixuan [1 ]
Wang, Shuyan [1 ]
Chen, Qiang [1 ]
Yan, Dawei [1 ]
Dong, Xinxing [1 ]
Li, Mingli [1 ]
Lu, Shaoxiong [1 ]
机构
[1] Yunnan Agr Univ, Fac Anim Sci & Technol, Kunming 650201, Yunnan, Peoples R China
[2] Xichang Univ, Fac Anim Sci, Xichang 615000, Sichuan, Peoples R China
来源
BMC GENOMICS | 2024年 / 25卷 / 01期
关键词
GWAS; SLAF-seq; Pigs; Carcass traits; Candidate genes; QUALITY TRAITS; MEAT QUALITY; ZINC; MUSCLE; ASSOCIATION; EVOLUTION; PROTEINS; APOPTOSIS; COMPLEX; GROWTH;
D O I
10.1186/s12864-024-10484-y
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET). Results A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 x 10(- 5)), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs. Conclusions The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.
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页数:14
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共 64 条
  • [1] Fast model-based estimation of ancestry in unrelated individuals
    Alexander, David H.
    Novembre, John
    Lange, Kenneth
    [J]. GENOME RESEARCH, 2009, 19 (09) : 1655 - 1664
  • [2] Andersson-Eklund L, 1998, J ANIM SCI, V76, P694
  • [3] Counting the zinc-proteins encoded in the human genome
    Andreini, C
    Banci, L
    Bertini, I
    Rosato, A
    [J]. JOURNAL OF PROTEOME RESEARCH, 2006, 5 (01) : 196 - 201
  • [4] A bioinformatics view of zinc enzymes
    Andreini, Claudia
    Bertini, Ivano
    [J]. JOURNAL OF INORGANIC BIOCHEMISTRY, 2012, 111 : 150 - 156
  • [5] Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins
    Andreini, Claudia
    Bertini, Ivano
    Cavallaro, Gabriele
    [J]. PLOS ONE, 2011, 6 (10):
  • [6] INHBA transfection regulates proliferation, apoptosis and hormone synthesis in sheep granulosa cells
    Bao, Yongjin
    Yao, Xiaolei
    Li, Xiaodan
    EI-Samahy, M. A.
    Yang, Hua
    Liang, Yaxu
    Liu, Zifei
    Wang, Feng
    [J]. THERIOGENOLOGY, 2021, 175 : 111 - 122
  • [7] A Genetic Predictive Model for Canine Hip Dysplasia: Integration of Genome Wide Association Study (GWAS) and Candidate Gene Approaches
    Bartolome, Nerea
    Segarra, Sergi
    Artieda, Marta
    Francino, Olga
    Sanchez, Elisenda
    Szczypiorska, Magdalena
    Casellas, Joaquim
    Tejedor, Diego
    Cerdeira, Joaquin
    Martnez, Antonio
    Velasco, Alfonso
    Sanchez, Armand
    [J]. PLOS ONE, 2015, 10 (04):
  • [8] The galvanization of biology: A growing appreciation for the roles of zinc
    Berg, JM
    Shi, YG
    [J]. SCIENCE, 1996, 271 (5252) : 1081 - 1085
  • [9] Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs
    Blaj, Iulia
    Tetens, Jens
    Preuss, Siegfried
    Bennewitz, Joern
    Thaller, Georg
    [J]. PLOS ONE, 2018, 13 (10):
  • [10] Allelic frequencies of NR6A1 and VRTN, two genes that affect vertebrae number in diverse pig breeds: A study of the effects of the VRTN insertion on phenotypic traits of a Duroc x Landrace-Large White cross
    Burgos, Carmen
    Latorre, Pedro
    Altarriba, Juan
    Carrodeguas, Jose Alberto
    Varona, Luis
    Lopez-Buesa, Pascual
    [J]. MEAT SCIENCE, 2015, 100 : 150 - 155