Identification of loci affecting teat number by genome-wide association studies on three pig populations

Tang, Jiaxi; Zhang, Zhiyan; Yang, Bin; Guo, Yuanmei; Ai, Huashui; Yi, Long; Su, Ying; Cui, Leilei; Zhou, Liyu; Wang, Xiaopeng; Zhang, Hui; Wang, Chengbin; Ren, Jun; Huang, Lusheng; Ding, Nengshui

doi:10.5713/ajas.15.0980

Cited by 19 publications

(16 citation statements)

References 40 publications

(48 reference statements)

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“…), lysine demethylase 6B ( KDM6B ) (Tang et al . ), Rap guanine nucleotide exchange factor ( RAPGEF1 ) (Verardo et al . ), secretory carrier membrane protein 2 ( SCAMP2 ) (Lee et al .…”

Section: Effect Of the Ssc5:60296617 Snp On Teat Number Traitsmentioning

confidence: 99%

Genotyping by sequencing reveals a new locus for pig teat number

Wang

Zhang

et al. 2017

Animal Genetics

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Teat number is an extremely valuable trait for sow reproduction performance and piglet survival. Here, we used genotyping-by-sequencing and a general liner model to carry out genome-wide analysis of sow total teat number in an Erhualian population. The results indicated that eight SNPs on chromosomes 4, 5, 9 and 10 were significant genome wide (Bonferroni method, P < 2.85E-7) for sow total teat number. Validation analyses were performed in 298 Erhualian and 904 Large White sows using these significant SNPs and the general liner model procedure in sas. Finally, only the SNP on chromosome 5 was found to be significantly associated with sow teat number in both populations. The GG genotype individuals had 2.23 and 0.82 more teat numbers respectively than did the AA genotype individuals in these two populations (P < 0.05). According to the expression and annotation analyses, we inferred the presence of a gene or lincRNA that could affect teat number by regulating other genes and ultimately affecting the mammogenesis of pigs. Further studies using methods such as Cas9 editing and gene silencing analysis are necessary for additional function analysis.

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“…), lysine demethylase 6B ( KDM6B ) (Tang et al . ), Rap guanine nucleotide exchange factor ( RAPGEF1 ) (Verardo et al . ), secretory carrier membrane protein 2 ( SCAMP2 ) (Lee et al .…”

Section: Effect Of the Ssc5:60296617 Snp On Teat Number Traitsmentioning

confidence: 99%

Genotyping by sequencing reveals a new locus for pig teat number

Wang

Zhang

et al. 2017

Animal Genetics

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“…Wada et al 2000 ; Hirooka et al 2001 ; Rodríguez et al 2005 ; Bidanel et al 2008 ; Ding et al 2009 ; Hernandez et al 2014 ) or by applying genome‐wide association studies (GWAS) within breeds (e.g. Arakawa et al 2015 ; Rohrer & Nonneman 2017 ; Tang et al 2017 ; Lee et al 2019 ; van Son et al 2019 ). Results of these studies evidenced many different QTL affecting this trait and confirmed its polygenic nature.…”

Section: Introductionmentioning

confidence: 99%

Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

et al. 2021

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Summary The number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.

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“…Number of teats (NTE) in pigs is a highly heritable trait and shows considerable variation across breeds (8–21) (Rohrer and Nonneman, 2017) and also within breeds (e.g., 12–20 in Landrace) (Lopes et al, 2014). Several genome-wide association studies (GWAS) have shown that NTE is a polygenic trait influenced by many different quantitative trait loci (QTL) scattered over nearly all chromosomes of the pig genome (Duijvesteijn et al, 2014; Lopes et al, 2014; Arakawa et al, 2015; Verardo et al, 2016; Yang et al, 2016; Tang et al, 2017; Uzzaman et al, 2018). Among these, a QTL on Sus scrofa chromosome 7 (SSC7) has been identified showing a large effect on NTE in several commercial breeding lines and crosses (e.g., Duijvesteijn et al, 2014; Rohrer and Nonneman, 2017; Dall’Olio et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

A QTL for Number of Teats Shows Breed Specific Effects on Number of Vertebrae in Pigs: Bridging the Gap Between Molecular and Quantitative Genetics

et al. 2019

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Modern breeding schemes for livestock species accumulate a large amount of genotype and phenotype data which can be used for genome-wide association studies (GWAS). Many chromosomal regions harboring effects on quantitative traits have been reported from these studies, but the underlying causative mutations remain mostly undetected. In this study, we combine large genotype and phenotype data available from a commercial pig breeding scheme for three different breeds (Duroc, Landrace, and Large White) to pinpoint functional variation for a region on porcine chromosome 7 affecting number of teats (NTE). Our results show that refining trait definition by counting number of vertebrae (NVE) and ribs (RIB) helps to reduce noise from other genetic variation and increases heritability from 0.28 up to 0.62 NVE and 0.78 RIB in Duroc. However, in Landrace, the effect of the same QTL on NTE mainly affects NVE and not RIB, which is reflected in reduced heritability for RIB (0.24) compared to NVE (0.59). Further, differences in allele frequencies and accuracy of rib counting influence genetic parameters. Correction for the top SNP does not detect any other QTL effect on NTE, NVE, or RIB in Landrace or Duroc. At the molecular level, haplotypes derived from 660K SNP data detects a core haplotype of seven SNPs in Duroc. Sequence analysis of 16 Duroc animals shows that two functional mutations of the Vertnin ( VRTN ) gene known to increase number of thoracic vertebrae (ribs) reside on this haplotype. In Landrace, the linkage disequilibrium (LD) extends over a region of more than 3 Mb also containing both VRTN mutations. Here, other modifying loci are expected to cause the breed-specific effect. Additional variants found on the wildtype haplotype surrounding the VRTN region in all sequenced Landrace animals point toward breed specific differences which are expected to be present also across the whole genome. This Landrace specific haplotype contains two missense mutations in the ABCD4 gene, one of which is expected to have a negative effect on the protein function. Together, the integration of largescale genotype, phenotype and sequence data shows exemplarily how population parameters are influenced by underlying variation at the molecular level.

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Identification of loci affecting teat number by genome-wide association studies on three pig populations

Cited by 19 publications

References 40 publications

Genotyping by sequencing reveals a new locus for pig teat number

Genotyping by sequencing reveals a new locus for pig teat number

Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

A QTL for Number of Teats Shows Breed Specific Effects on Number of Vertebrae in Pigs: Bridging the Gap Between Molecular and Quantitative Genetics

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