Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583-52724713) and (TG)n (Chr4:90732644-90732802) could be utilized as the candidate locus for MAS in pig industry.HIGHLIGHTSFive novel SSR loci was identified in pigs through MALDI-TOF MS.V1, V2 and V3 loci was were significantly associated to the backfat of pigs.

The body status of livestock affects their physiological function and productive performances. Microsatellites, one of the most used DNA markers, have been found to be associated with pig productive traits. However, their identifications and effects on body measurement traits of the Chinese Qinghai Bamei pig still uncovered. According to our previous sequencing data, in this study, three novel microsatellites were found in this breed. Using time of flight-mass spectrometry (TOF-MS) method, these microsatellites were further identified in a large Bamei pig population. TOF-MS spectra showed that there are three microsatellites loci, named P1, P2 and P3. These microsatellites were linkage equilibrium based on the values of D' and r2 tests. Association results demonstrated that P1 locus was associated with the body length, body height and chest width and the beneficial genotype was 150-/150-bp (p < 0.05); and P2 locus was associated with the body height (p < 0.05), and the 145-/145-bp, 145-/147-bp and 145-/149-bp were claimed as favorable genotypes and 145-bp allele was considered as the favorable allele. These findings suggested that P1 and P2 microsatellites might be considered as the candidate genetic markers to select pigs with superior body sizes, especially in local breed.

Teat number is an important economic trait in the pig breeding industry and is directly related to the livability and growth status of piglets. By applying genetic technology, it may be possible to increase the number of teats and thus enhance production. Previous research has shown that teat number exhibits moderate levels of heritability that could be accelerated by the use of a genetic marker, such as microsatellites. Based on our preliminary sequencing data, the present study describes the use of time-of-flight mass spectrometry (TOF-MS) to identify the locations of four new microsatellites in Qinghai Bamei pig (n=256), an indigenous breed of Chinese pig. TOF-MS demonstrated that the L1-(GT)(n) locus had three alleles: 152 bp, 164 bp, and 166 bp. The three other loci, L2-(AC)(n), L3-(TC)(n), and L4-(TGA)(n), all had two alleles. Alignment of our sequencing data with the Sus scrofa reference genome (Sscrofa11.1) revealed that the L1-(GT)(n) microsatellite, which features a GT repeat motif, was located in the retinoic acid induced 2 gene (RAI2) on chromosome X in Sus scrofa (SSCX). Analysis further revealed that the L2-(AC)(n) locus, featuring AC repeats, and the L3-(TC)(n) locus, featuring TC repeats, were located in intergenic regions on SSC14 and SSC5, respectively. TGA repeats within the L4-(TGA)(n) locus were located in the inner mitochondrial membrane peptidase subunit 2 gene (IMMPL2) on SSC18. Further association analysis revealed that the L1-(GT)(n) locus was significantly associated with teat number (p < 0.05) and that the 152-bp allele exhibited the most positive association. Our data indicate that the L1-(GT)(n) microsatellite could represent a potential DNA marker with which to increase the number of teats. Thus could help to improve production in the pig breeding industry.

Abstract Simple sequence repeats (SSRs) are an important part of the genome and have become powerful auxiliary DNA markers in animal breeding using marker‐assisted selection (MAS). Based on previous sequencing data of Qinghai Bamei pigs, a total of three novel candidate SSR loci were analysed in this study. Time‐of‐flight mass spectrometry (TOF‐MS) was used for SSR genotyping, and association analyses between SSRs and the litter size of Qinghai Bamei sows was also performed. The results of genotyping showed that the (ATC)n‐P1, (AC)n‐P2 and (AC)n‐P3 loci had 2, 3 and 18 genotypes, respectively; 2, 3 and 8 alleles were also identified at these loci. Except for the (AC)n‐P2 locus, the polymorphism information content (PIC) values of other loci were greater than 0.25. Association analyses indicated that only the (ATC)n‐P1 locus was significantly associated with the litter size of Qinghai Bamei sows (p = .047). Compared to 189‐/189‐ genotype, individuals with the 189‐/195‐ genotype had the senior litter size, which was 9.04 ± 0.21. Our results enrich the data on SSRs in Qinghai Bamei pigs and indicate that (ATC)n‐P1 is a candidate locus for MAS in the pig industry.