Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models

Wen, Hui; Johnson, Jay S.; Freitas, Pedro H. F.; Maskal, Jacob M.; Gloria, Leonardo S.; Araujo, Andre C.; Pedrosa, Victor B.; Tiezzi, Francesco; Maltecca, Christian; Huang, Yijian; Schinckel, Allan P.; Brito, Luiz F.

doi:10.1186/s12711-023-00868-1

Genetics Selection Evolution

Table 2 Relevant genomic regions identified for the four heat stress (HS) time-periods

From: Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models

Time-period^a	Chromosome bp positions	% of variance explained	Positional candidate genes
HS time-period 1	10:59,369,633:59,776,918	0.66	CAMK1D, RNU6ATAC39P, CDC123, NUDT5, SEC61A2, KATNAL1, USPL1, ALOX5AP, EFTUD2, HIGD1B, GJC1, ADAM11, DBF4B, CCDC43, MEIOC, FZD2, GPATCH8, ITGA2B, FAM171A2, GRN, SLC25A39, RUNDC3A, SLC4A1, HOXB4, MIR10A, HOXB5, HOXB6, HOXB7, HOXB8, HOXB9, MIR196A1, HOXB13, TTLL6, CALCOCO2, ATP5MC1, UBE2Z, SNF8, GIP, IGF2BP1, PISD, PRR14L, DEPDC5, YWHAH, SLC5A1, SLC5A4, RANBP3L, SLC1A3, U6, MYLK2, FOXS1, DUSP15, TTLL9, PDRG1, XKR7, CCM2L, HCK, TM9SF4, PLAGL2, POFUT1, KIF3B, ASXL1, MIR148A, SDK1, SNORA70
(T_V: 39.741 ± 0.724 DP: 22.080 ± 2.060 Total explained variance: 4.086%)	16:21,601,170:21,965,767	0.45
	12:18,499,751:18,974,836	0.379
	17:35,507,357:36,063,488	0.349
	3:3,029,529:3,257,462	0.317
	18:46,374,852:46,983,072	0.293
	12:24,812,751:25,420,666	0.284
	11:7,020,997:7,540,141	0.280
	17:67,332,252:67,844,392	0.279
	17:65,356,677:65,763,082	0.275
	14:48,306,021:48,731,419	0.274
	6:134,063,309:134,266,656	0.253
HS time-period 2	16:21,601,170:21,965,767	0.490	CAMK1D, CDC123, NUDT5, SEC61A2, RNU6ATAC39P, KATNAL1, USPL1, ALOX5AP, PSMB3, PCGF2, CISD3, MLLT6, SRCIN1, ARHGAP23, GPR179, MRPL45, EPOP, ADAM11, GJC1, SLC25A39, RUNDC3A, SLC4A1, DBF4B, MEIOC, FZD2, ITGA2B, FAM171A2, EFTUD2, HIGD1B, U6, GPATCH8, PISD, PRR14L, DEPDC5, YWHAH, SLC5A1, SLC5A4, RANBP3L, SLC1A3, MYLK2, FOXS1, DUSP15, TTLL9, PDRG1, XKR7, CCM2L, HCK, TM9SF4, PLAGL2, POFUT1, KIF3B, ASXL1, MIR148A, SDK1, CEBPG, PEPD, CHST8, KCTD15, CALCR, GNGT1, CDK6, SAMD9, HEPACAM2, VPS50, ssc-mir-489
(T_V: 39.134 ± 0.620 DP: 22.844 ± 2.084 Total explained variance: 4.840%)	10:59,369,633:59,776,918	0.481
	3:3,029,529:3,257,462	0.414
	14:48,306,021:48,731,419	0.394
	18:46,374,852:46,983,072	0.383
	12:18,499,751:18,974,836	0.380
	6:43,090,860:43,731,895	0.359
	11:7,020,997:7,540,141	0.318
	17:65,356,677:65,763,082	0.292
	17:67,332,252:67,844,392	0.289
	12:23,350,211:23,791,623	0.279
	17:35,507,357:36,063,488	0.271
	16:21,601,170:21,965,767	0.490
HS time-period 3	16:21,548,342:21,840,246	0.364	CAMK1D, CDC123, NUDT5, SEC61A2, DHTKD1, UPF2, RNU6ATAC39P, KATNAL1, USPL1, ALOX5AP, PIP4K2B, PSMB3, PCGF2, CISD3, MLLT6, SRCIN1, ARHGAP23, SOCS7, GPR179, MRPL45, EPOP, ADAM11, GJC1, SLC25A39, RUNDC3A, SLC4A1, DBF4B, CCDC43, MEIOC, FZD2, ITGA2B, FAM171A2, GRN, EFTUD2, HIGD1B, U6, GPATCH8, PISD, PRR14L, DEPDC5, YWHAH, SLC5A1, SLC5A4, NADK2, RANBP3L, MIR148A, SDK1, ZFAT, WNT10B, WNT1, CACNB3, DDX23, RND1, CCDC65, FKBP11, DDN, C12orf75, CCNT1, TEX49, ADCY6, PRKAG1, RHEBL1, DHH, ARF3, CEBPG, PEPD, CHST8, KCTD15, GRID2, FSTL5
(T_V: 39.771 ± 0.729 DP: 23.843 ± 2.478 Total explained variance: 4.793%)	17:67,332,252:67,844,392	0.353
	8:144,423,490:145,098,780	0.351
	18:46,374,852:46,983,072	0.327
	6:43,097,060:43,829,382	0.319
	8:125,810,305:126,470,348	0.314
	3:3,029,529:3,257,462	0.301
	5:14,539,752:15,115,540	0.294
	11:7,020,997:7,540,141	0.290
	8:49,296,088:50,537,893	0.282
	10:59,507,616:59,997,776	0.282
	12:18,499,751:18,974,836	0.276
	14:48,306,021:48,731,419	0.272
	4:7,002,305:7,146,525	0.265
	14:119,028,054:119,983,210	0.252
	12:23,321,216:2,3760,296	0.251
HS time-period 4	10:59,507,616:59,997,776	0.398	CAMK1D, RNU6ATAC39P, CDC123, NUDT5, SEC61A2, DHTKD1, UPF2, EFTUD2, HIGD1B, GJC1, ADAM11, DBF4B, CCDC43, MEIOC, U6, FZD2, GPATCH8, ITGA2B, FAM171A2, GRN, SLC25A39, RUNDC3A, SLC4A1, NADK2, RANBP3L, MYLK2, FOXS1, DUSP15, TTLL9, PDRG1, XKR7, CCM2L, HCK, TM9SF4, PLAGL2, POFUT1, KIF3B, ASXL1, NT5C3A, FKBP9, RP9, KBTBD2, AVL9, PDE1C, INCENP, BEST1, RAB3IL1, FADS3, U1, ZFAT, GRID2
(T_V: 40.125 ± 0.687 DP: 23.226 ± 1.996 Total explained variance: 3.141%)	3:64,224,248:65,386,969	0.374
	4:7,002,305:7,146,525	0.335
	17:67,332,252:67,844,392	0.328
	17:35,507,357:36,063,488	0.310
	18:40,471,432:40,882,202	0.304
	16:21,548,342:21,840,246	0.291
	2:9,425,931:9,613,380	0.273
	8:125,810,305:126,470,348	0.265
	12:18,499,751:18,974,836	0.263

HS: heat stress
^aTime-period: mean ± standard deviation of vaginal temperature (Tv), dew point (DP) and total explained variance for each stage; 1: from 23h00 to 06h30, 2: from 06h30 to 09h30, 3: from 09h30 to 18h30, and 4: from 18h30 to 23h00

Back to article page

ISSN: 1297-9686

Contact us

Submission enquiries: gse@inrae.fr
General enquiries: info@biomedcentral.com