Detection Of Quantitative Trait Loci For Teat Number And Body Weight At Weaning Using High-Density SNP Markers Across The Pig Genome

Four F2 resource populations of Erhualian×Tongcheng, Erhualian×Rongchang, Erhualian×Bamaxiang and Erhualian×Shaziling were constructed, and genomic DNA of 392 piglets and their parents and grandparents was genotyped with Illumina porcine 60k DNA chips. Genome-wide association analysis was conducted to detect QTL for teat number in pigs.Results showed that thirteen QTLs for total teat number including seven at 5% and six at 1% genome-wide significance level were mapped to SSC1, SSC3, SSC5, SSC6, SSC7, SSC9, SSC10, SSC12, SSC13 and SSC14. Eight QTLs on SSC1, SSC3, SSC5, SSC6, SSC10 and SSC12 were overlaped with the previous QTLs, and 5 QTLs on SSC7, SSC9, SSC13 and SSC14 were detected only in this study. Eleven QTLs for teat number at left side including two at 5% and nine at 1% genome-wide significance level were detected on SSC3, SSC4, SSC7, SSC8, SSC9, SSC10, SSC13, SSC14, SSC15 and SSC18, and 5 Of the 11 QTLs were overlaped with the QTLs for total teat number, QTL for left teat number on SSC8 was consistent with the previous reports, and the other chromosomes including SSC3, SSC4, SSC7, SSC9, SSC10, SSC13, SSC14, SSC15 and SSC18 contained novel QTLs for this trait. Nine QTLs for teat number at right side including one at 5% and eight at 1% genome-wide significance level were detected on SSC1, SSC3, SSC5, SSC6, SSC7, SSC12 and SSC13, and of them,7 QTLs were overlaped with the QTLs for total teat number, QTL on SSC1 confirmed previous report, and QTLs for right teat number on SSC3, SSC5, SSC6, SSC7, SSC12 and SSC13 were detected for the first time.The confidence intervals of QTL were defined by SNPs with lower F values of 3 compared with the most significantly associated SNP marker. Twelve positional candidate genes within the QTL confidence intervals were characterized for teat number including RBFOX2, ARID5A, PDIA2, ACTB, DYRK1A, TUBAL3, MYOCD, NEDD9, PPRC1, CUEDC2, CYP17A1 and INSIG1. These results would benefit the final characterization of the responsible genes for teat number.This study detected multiple QTLs for teat number in 4 F2 resource populations from Chinese indigenous pig crosses. A majority of QTLs for teat number at left and right sides were found in different chromsomal regions. The favourable QTL alleles for increased teat number were originated from different Chinese founder breeds. The results reflected the genetic basis of teat asymmetry and the complex genetic architecture of teat number in pigs. Four F2 resource populations including Erhualian x Tongcheng, Erhualian x Rongchang, Erhualian x Bamaxiang and Erhualian x Shaziling intercross were constructed, and genomic DNA of 392 piglets and their parents and grandparents was genotyped with Illumina Porcine 60k DNA chips. Genome-wide association analysis was conducted to detect QTL for body weight of piglets weaned at day 45. Nine QTLs for this trait were mapped to SSC1, SSC2, SSC5, SSC7, SSC11 and SSC14, respectively, including five 5% genome-wide significant QTLs and four 1% genome-wide significant QTLs. The most significant QTL with Erhualian-derived favorable alleles was detected at 103.85 Mb on SSC7 in the Erhualian x Bamaxiang cross, and the most significant QTL with non-Erhualian originated favourable alleles was evidenced at 43.77 Mb on SSC14 in the Erhualian×Shaziling resource population.The previous studies showed that the QTLs for body weight of piglets weaned at days 28 to 42 were mapped to SSC1, SSC2, SSC4, SSC7, SSC9, SSC15, SSC17 and SSC18. In this study, QTLs for weaned body weight were also deteced on SSC1, SSC2 and SSC7, including one QTL located at 291.24 Mb on SSC1 in the Erhualian x Rongchang resource population, one at 40.31 Mb on SSC2 in the Erhualian×Shaziling resource population, three at 7.23Mb,28.13 Mb and 103.85 Mb on SSC7 in the Erhualian x Tongcheng, Erhualian x Rongchang and Erhualian x Bamaxiang resource population, respectively, QTL on SSC7 in the Erhualian x Rongchang resource population was consistent with the previous report.Positional candidate genes in the QTL regions were characterized from pig genome database on Ensemble and NCBI. Nine positional candidate genes were identified, including AGPAT1, RNF5, NOTCH4, DPF3, CYP2R1, COPB1, PDE3B, NOP2 and GDF3.These findings revealed the genetic architecture of weaned body weight and could benefit the final chracterization of the causative genes and mutations for weaned body weight.