Genotyping by sequencing reveals a new locus for pig teat number

Wang, L; Zhang, Y; Zhang, T; Zhang, L; Hua, Yan; Liu, X

doi:10.1111/age.12547

Cited by 15 publications

(13 citation statements)

References 15 publications

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“…Genotype marker density is one important factor affecting the efficiency of GWAS (Brondum et al, 2012).With the increase of marker density, the linkage disequilibrium between markers and the target trait QTL is increased, which is helpful for QTL detection. In previous studies, the advantages of whole genome sequencing data have been demonstrated (Wang L. et al, 2017). However, its high cost hampered the wide application of sequencing data.…”

Section: Discussionmentioning

confidence: 99%

A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

et al. 2021

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The body shape of a pig is the most direct production index, which can fully reflect the pig’s growth status and is closely related to important economic traits. In this study, a genome-wide association study on seven body size traits, the body length (BL), height (BH), chest circumference (CC), abdominal circumference (AC), cannon bone circumference (CBC), rump width (RW), and chest width (CW), were conducted in Yorkshire pigs. Illumina Porcine 80K SNP chips were used to genotype 589 of 5,572 Yorkshire pigs with body size records, and then the chip data was imputed to sequencing data. After quality control of imputed sequencing data, 784,267 SNPs were obtained, and the averaged linkage disequilibrium (r2) was 0.191. We used the single-trait model and the two-trait model to conduct single-step genome wide association study (ssGWAS) on seven body size traits; a total of 198 significant SNPS were finally identified according to the P-value and the contribution to the genetic variance of individual SNP. 11 candidate genes (CDH13, SIL1, CDC14A, TMRPSS15, TRAPPC9, CTNND2, KDM6B, CHD3, MUC13, MAPK4, and HMGA1) were found to be associated with body size traits in pigs; KDM6B and CHD3 jointly affect AC and CC, and MUC13 jointly affect RW and CW. These genes are involved in the regulation of bone growth and development as well as the absorption of nutrients and are associated with obesity. HMGA1 is proposed as a strong candidate gene for body size traits because of its important function and high consistency with other studies regarding the regulation of body size traits. Our results could provide valuable information for pig breeding based on molecular breeding.

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Section: Discussionmentioning

confidence: 99%

A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

et al. 2021

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“…Genome-wide association studies (GWAS) have been widely used to analyze the genetic architecture of reproduction, meat quality, and production traits in the pig population ( Verardo et al, 2016 ; Schmid et al, 2018 ; Ding et al, 2019 ). Previous GWAS found that several single nucleotide polymorphisms (SNPs) in or near the bone morphogenetic protein 2 ( BMP2 ) gene were associated with body length and body height, and many reported that the vertebrae development-associated ( VRTN ) gene was significantly associated with total teat number in pigs ( Lee et al, 2014 , 2019 ; Arakawa et al, 2015 ; Wang et al, 2017 ). Almost all GWAS for body length, body height, and total teat number were performed by single-locus GWAS.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs

Hong

Dong

et al. 2021

Front. Genet.

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Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

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“…During the last decade, GWAS has been widely used to identify quantitative trait loci (QTL) and quantitative trait nucleotides (QTN) in important quantitative traits, such as teat number (48), growth traits (37), and meat traits (28). Reproductive traits are among the important economic traits in pig breeding.…”

Section: Introductionmentioning

confidence: 99%

Identifying SNPs and candidate genes for three litter traits using single-step GWAS across six parities in Landrace and Large White pigs

Wang

Zhou

et al. 2018

Physiological Genomics

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Total number born (TNB), number born alive (NBA), and litter weight born alive (LWB) are critically important traits in pig production. The sow’s parity is one of the major factors influencing litter traits. Because of monogenic or polygenic contributions and the presence of temporal gene effects in different sows’ parities, it is difficult to clarify the biological and genetic background. To systematically explore the genetic mechanism of litter traits, we conducted 18 GWASs using single-step GWAS (ssGWAS) based on two breeds (908 Landrace and 1,130 Large White sow litter records) for each litter trait in different parities. A total of 300 Landrace and 300 Large White sows were genotyped by sequencing (GBS). ssGWAS was performed separately for each breed and each parity due to population stratification and temporal gene effect. In summary, we identified 80 (15 for Landrace and 65 for Large White), 227 (52 for Landrace, 175 for Large White), and 187 (34 for Landrace, 153 for Large White) single nucleotide polymorphisms (SNPs) affecting TNB, NBA, and LWB, respectively. Of them, we suggest that a total of 22 loci (SSC1: 125098202, SSC1: 117560058, SSC14: 147794697, SSC8: 84823302, SSC9: 143554876, and SSC9: 138766097 for Landrace; SSC1: 4023577, SSC1: 3859573, SSC1: 4891063, SSC16: 5197665, SSC10: 32050819, SSC13: 13552924, SSC13: 92819, SSC17: 3579607, SSC13: 196698221, SSC7: 30918403, SSC16: 46221484, SSC16: 46169204, SSC2: 41988642, SSC2: 44475457, SSC2: 42521875, and SSC7: 58411951 for Large White) are shared by TNB, NBA, and LWB. These results indicate the existence of gene temporal effect in each parity. Furthermore, our findings suggest four interesting candidate genes (FBXL7, ALDH1A2, LEPR, and DDX1) associated with litter traits in different parities that have a major effect on embryonic development progression. In conclusion, 22 crucial SNPs and four interesting candidate genes were identified for three litter traits across six parities. These findings advance our understanding of the genetic architecture of litter traits and confirm the presence of temporal gene effects in different parities. Importantly, functional validation studies for findings of particular interest are recommended in litter traits.

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Genotyping by sequencing reveals a new locus for pig teat number

Cited by 15 publications

References 15 publications

A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs

Identifying SNPs and candidate genes for three litter traits using single-step GWAS across six parities in Landrace and Large White pigs

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