Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success

Table 3 List of haplotypes in the Brown Swiss population identified by the trio-based approach

Name	Chr	Start	End	Allele frequency	Proposed associated gene^a
BH1^b	7	41371808	42545291	3.02	TCF3
BH2^c	19	9726237	10819756	4.22	TUBD1
BH3	1	34908448	36034631	2.05
BH4	1	76587512	77861430	2.20	GMNC
BH5	2	57787148	58768161	2.87	LRP1B
BH6	2	86065338	87460373	3.41	MARS2
BH7	2	120284002	121473182	1.93	SPATA3
BH8	2	127933873	129004898	2.98
BH9	3	52432936	52,689742	1.43	HFM1
BH10	3	101636810	102827915	2.26
BH11	4	108811998	109953666	2.66
BH12	5	57653479	59777422	2.32	RNF41 and LRP1
BH13	5	110617654	111664596	1.63
BH14	7	2588873	3357718	3.04	MRPL55
BH15	7	33954389	34956540	4.12
BH16	7	79845977	80708046	2.20
BH17	11	82034654	82881173	2.39	PGGHG
BH18	11	91766016	92804942	2.54
BH19	11	103891372	105003404	1.77
BH20	12	10254014	10967287	2.02
BH21	12	74954939	75817277	1.61
BH22	14	12290759	13350202	2.64
BH23	17	69786512	70645226	2.98
BH24	18	52977041	54113281	2.32	CPT1C
BH25	19	35808547	36844178	1.86	SNF8
BH26	19	47874708	48724082	1.89
BH27	20	50058036	51370414	2.56
BH28	21	19368258	20362870	1.60
BH29	22	311724	1277064	2.07
BH30	23	39600366	40609442	2.49
BH31	25	27713801	29132187	1.80	ITGAD and SPN
BH32	26	9215188	10180467	1.72
BH33	26	26659976	27689471	2.72
BH34	26	31353340	32429589	2.37	ACSL5
BH35	27	28524504	29550764	1.80
BH36	28	26661955	27743768	1.75
BH37	28	45215132	45913154	2.07
BH38	29	14497752	15554643	3.08

BH BS haplotype, Chr chromosome number, Start and End start and end positions according to the reference sequence ARS-UCD1.2 [36]
^aAccording to NCBI Annotation Release 106 [54]
^bPreviously described haplotype [19]
^ePreviously described haplotype and associated gene [11, 19]

ISSN: 1297-9686