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

Abstract

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.

Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle

“…The BovineHD4100014792-rs134139959 SNP located within F-box and leucine rich repeat protein 7 gene (FBXL7) was associated with the rear leg rear view trait in the present study, but, in previous studies, was associated with body length in water buffaloes (Bubalus bubalis) [69], clinical mastitis in first lactating US Holstein dairy cattle [70], subclinical ketosis in second and later lactations in Canadian Holstein dairy cattle [71] and also litter traits in Landrace and Large White pigs [62].…”

“…Meanwhile, the aldehyde dehydrogenase 1 family member A2 gene ( ALDH1A2 ) was associated with the growth trait in the Blanco Orejinegro cattle breed from Colombia [ 58 ], as well as intramuscular fatty acid composition in rabbits [ 59 ]. ALDH1A2 was also associated with lactation persistency in Canadian Holstein cattle [ 60 ], carcass traits in Chinese Simmental beef cattle [ 61 ] and litter traits in Landrace and Large White pigs [ 62 ]. Moreover, ALDH1A2 has been reported to play critical roles in the synthesis of retinoic acid, the active derivative of vitamin A, which is important for limb and organ development [ 63 ].…”

A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

“…3) The associated gene in bold in this column represent these genes were associated with traits based on annotation. 4) down/up = the location of SNP in downstream/upstream of the nearest gene.…”

“…The bold data in this column represent the SNP at suggestive genome-wide significant level. 4) The associated gene in bold in this column represent these genes were associated with traits based on annotation. 5) down/up = the location of SNP in downstream/upstream of the nearest gene.…”

“…Up to the present, selection based on traditional breeding methods using best linear unbiased prediction has been successful in improving maternal reproductive traits [3]. However, the genetic architecture of reproductive traits is very complicated due to low heritability, minor genes, maternal effects and environmental factors [4], resulting in the difficulty deciphering the genetic architecture of reproduction traits. Over the past 20 years, the dense genome coverage provided by high-throughput chip genotyping makes it possible to exploit the linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) and quantitative trait locus (QTL) through genome-wide association study (GWAS) to identify genes related to traits of interest.…”