Skip to main content
. 2021 Feb 25;12:634986. doi: 10.3389/fgene.2021.634986

TABLE 4.

The genome-wide significant SNPs and candidate genes associated with longevity traits in Chinese Holsteins.

Chromosome Position1(bp) SNP Trait2 MAF3 P-value Effect size4 (%) Candidate gene5
2 91,629,36 rs135750821 Lon15 0.43 1.71 E-07 0.49 CALCRL
2 42,630,124 rs137712544 Lon11 0.39 1.82 E-08 1.00 RPRM
2 46,201,858 rs110628337 Lon15 0.35 3.48 E-07 0.67 –
3 64,114,128 rs42867525 ML 0.33 2.96 E-09 0.73 –
3 118,421,054 rs137402734 Lon14 0.39 1.72 E-08 0.65 –
4 11,190,947 rs41613051 Lon11 0.36 5.72 E-08 0.58 TFPI2, GNGT1, GNG11, BET1
4 38,428,113 rs136492033 PL 0.36 1.28 E-07 0.58 CACNA2D1
4 85,565,338 rs109342356 ML 0.18 1.10 E-07 0.50 ING3
5 115,983,568 rs135565406 HL, ML, PL, Lon11, Lon15, 0.42 9.96 E-10, 3.20 E-09, 7.95 E-08, 4.34 E-08, 7.01 E-08 0.73, 0.74, 0.55, 0.66, 0.63 RIBC2, FBLN1, ATXN10
6 2,639,865 rs137700260 HL, Lon13, Lon14 0.07 3.42 E-07, 2.87 E-08, 1.35 E-07 0.47, 0.60, 0.54 NPY1R, NAF1
6 6,916,170 rs43451042 Lon15 0.43 2.69 E-08 0.46 PRSS12, NDST3
7 43,904,171 rs29012367 HL 0.36 1.27 E-08 0.53 CIRBP, FAM174C, PWWP3A, NDUFS7, GAMT, DAZAP1, RPS15, C7H19orf25, REEP6, MBD3, UQCR11, TCF3
7 54,635,988 rs132789189 HL 0.45 5.21 E-09 0.65 NR3C1
7 95,581,783 rs109221022 Lon15 0.39 4.11 E-07 0.68 PCSK1
8 72,165,064 rs43559099 Lon12 0.26 6.83 E-08 0.49 NEFM, NEFL
8 72,275,281 rs134248248 Lon13 0.43 3.68 E-07 0.70 NEFM, NEFL
9 15,157,597 rs42693004 Lon12 0.15 3.46 E-07 0.55 FILIP1, SENP6
9 94,882,463 rs134672623 Lon12, Lon15 0.45 2.59 E-07, 2.35 E-08 0.55, 0.95 SERAC1, GTF2H5, DYNLT1
9 99,144,354 rs109415769 Lon14 0.24 9.83 E-08 0.44 QKI
11 14,367,967 rs133167045 ML 0.17 8.37 E-09 0.53 XDH, SRD5A2, MEMO1
11 24,568,406 rs41592158 PL 0.38 3.61 E-07 0.42 PKDCC, EML4, COX7A2L
12 12,473,832 rs43691605 Lon13, Lon14 0.41 3.73 E-08, 2.14 E-08 0.48, 0.53 –
12 18,879,230 rs109505275 Lon11 0.30 9.14 E-09 0.80 FNDC3A, CDADC1, SETDB2, PHF11
13 71,211,797 rs109520811 PL 0.19 2.99 E-10 0.94 –
14 9,447,596 rs110760208 PL 0.15 3.16 E-08 0.61 –
14 11,909,376 rs110417753 HL 0.29 3.94 E-08 0.65 –
14 17,597,579 rs110392124 HL 0.35 8.15 E-08 0.53 –
14 52,854,862 rs133758639 Lon11 0.33 3.45 E-07 0.60 –
15 23,500,595 rs110052834 Lon12 0.39 1.87 E-07 0.46 NCAM1
16 13,142,992 rs136880011 PL 0.14 7.51 E-08 0.55 RGS18
17 39,552,453 rs135929367 Lon11 0.21 4.18 E-08 0.81 RAPGEF2
17 70,229,172 rs135552789 PL 0.48 1.63 E-07 0.52 RNF185, LIMK2, PIK3IP1, PATZ1, DRG1, PISD
18 13,532,413 rs134612709 Lon13, Lon14, Lon15 0.45 1.12 E-08, 1.23 E-09, 1.11 E-07 0.69, 0.73, 0.63 CA5A, BANP
18 62,531,696 rs134066287 Lon14 0.21 1.47 E-07 0.48 RDH13, NCR1, FCAR, KIR2DL5A, KIR3DL1, KIR2DS1, KIR3DL2
20 30,741,701 rs41567172 ML 0.15 4.07 E-07 0.43 FGF10
22 19,689,530 rs136814811 PL 0.50 3.85 E-07 0.54 GRM7
23 40,794,975 rs109782010 Lon12 0.37 4.58 E-11 1.01 LOC574091, GMPR, MYLIP
24 4,941,502 rs109618980 HL, Lon14 0.25 1.28 E-07, 2.40 E-08 0.51, 0.59 NETO1
24 39,596,108 rs110544386 PL 0.22 1.39 E-08 0.58 –
24 50,494,672 rs110534364 HL 0.10 1.27 E-09 0.66 MRO, ME2, ELAC1, SMAD4
24 52,840,962 rs136448037 Lon12, Lon15 0.37 1.19 E-10, 3.27 E-08 0.80, 0.59 –
25 3,628,922 rs109064423 PL 0.39 8.83 E-08 0.57 TFAP4, GLIS2, CORO7, VASN, DNAJA3, NMRAL1, HMOX2, CDIP1, UBALD1, MGRN1, NUDT16L1, ANKS3, C25H16orf71
25 28,648,581 rs109457044 Lon15 0.16 9.62 E-08 0.62 TYW1, CALN1
26 1,207,558 rs109520495 Lon12 0.15 2.30 E-07 0.51 –
27 42,337,167 rs110187242 Lon11 0.42 1.34 E-07 0.48 UBE2E1, UBE2E2, MIR6532
28 22,970,021 rs42105434 Lon11, Lon12 0.05 4.97 E-08, 3.83 E-07 0.63, 0.50 CTNNA3
X 7,058,580 rs134612804 HL 0.16 6.92 E-09 0.67
X 7,387,994 rs135876977 Lon11 0.30 2.58 E-12 1.43 GRIA3
X 7,811,883 rs41622390 Lon13, Lon14 0.08 4.39 E-09, 2.18 E-07 0.64, 0.49 GRIA3, THOC2
X 32,975,187 rs137272895 Lon13 0.41 6.21 E-09 0.96 –
X 46,704,483 rs137840659 Lon13, Lon14 0.40 5.41 E-08, 8.61 E-09 0.59, 0.62 –
X 55,267,455 rs137389486 PL 0.40 3.89 E-09 0.85 RNF128
X 52,406,362 rs137119176 HL, ML, Lon13 0.25 1.47 E-08, 4.37 E-08, 9.37 E-10 0.81, 0.99,0.75 TCEAL1, MORF4L2, GLRA4, PLP1, RAB9B
X 57,778,726 rs41612337 Lon11, Lon12 0.36 8.51 E-09, 9.69 E-08 1.19, 0.76 GUCY2F, NXT2
X 128,252,398 rs110389261 HL 0.42 1.26 E-07 0.70 PIR, VEGFD, ASB11, ASB9

1The base pair position on chromosome.2Lon11, the days from the first calving to the end of the first lactation or culling; Lon12, the days from the first calving to the end of the second lactation or culling; Lon13, the days from the first calving to the end of the third lactation or culling; Lon14, the days from the first calving to the end of the fourth lactation or culling; Lon15, the days from the first calving to the end of the fifth lactation or culling; PL, productive life referring the days from the first calving to culling or death; ML, milking life referring the days from the first calving to culling or death but excluding all dry periods; HL, herd life referring the days from birth to culling or death.3Minor allele frequency of the significant SNP.4The percentage of the phenotypic variance explained by the significant SNP.5Genes harbor or closest (200 kb) to the significant SNPs.