TY - JOUR
T1 - A Million-Cow Validation of a Chromosome 14 Region Interacting with All Chromosomes for Fat Percentage in U.S. Holstein Cows
AU - Prakapenka, Dzianis
AU - Liang, Zuoxiang
AU - Zaabza, Hafedh B.
AU - VanRaden, Paul M.
AU - Van Tassell, Curtis P.
AU - Da, Yang
N1 - Publisher Copyright:
© 2024 by the authors.
PY - 2024/1
Y1 - 2024/1
N2 - A genome-wide association study (GWAS) of fat percentage (FPC) using 1,231,898 first lactation cows and 75,198 SNPs confirmed a previous result that a Chr14 region about 9.38 Mb in size (0.14–9.52 Mb) had significant inter-chromosome additive × additive (A×A) effects with all chromosomes and revealed many new such effects. This study divides this 9.38 Mb region into two sub-regions, Chr14a at 0.14–0.88 Mb (0.74 Mb in size) with 78% and Chr14b at 2.21–9.52 Mb (7.31 Mb in size) with 22% of the 2761 significant A×A effects. These two sub-regions were separated by a 1.3 Mb gap at 0.9–2.2 Mb without significant inter-chromosome A×A effects. The PPP1R16A-FOXH1-CYHR1-TONSL (PFCT) region of Chr14a (29 Kb in size) with four SNPs had the largest number of inter-chromosome A×A effects (1141 pairs) with all chromosomes, including the most significant inter-chromosome A×A effects. The SLC4A4-GC-NPFFR2 (SGN) region of Chr06, known to have highly significant additive effects for some production, fertility and health traits, specifically interacted with the PFCT region and a Chr14a region with CPSF1, ADCK5, SLC52A2, DGAT1, SMPD5 and PARP10 (CASDSP) known to have highly significant additive effects for milk production traits. The most significant effects were between an SNP in SGN and four SNPs in PFCT. The CASDSP region mostly interacted with the SGN region. In the Chr14b region, the 2.28–2.42 Mb region (138.46 Kb in size) lacking coding genes had the largest cluster of A×A effects, interacting with seventeen chromosomes. The results from this study provide high-confidence evidence towards the understanding of the genetic mechanism of FPC in Holstein cows.
AB - A genome-wide association study (GWAS) of fat percentage (FPC) using 1,231,898 first lactation cows and 75,198 SNPs confirmed a previous result that a Chr14 region about 9.38 Mb in size (0.14–9.52 Mb) had significant inter-chromosome additive × additive (A×A) effects with all chromosomes and revealed many new such effects. This study divides this 9.38 Mb region into two sub-regions, Chr14a at 0.14–0.88 Mb (0.74 Mb in size) with 78% and Chr14b at 2.21–9.52 Mb (7.31 Mb in size) with 22% of the 2761 significant A×A effects. These two sub-regions were separated by a 1.3 Mb gap at 0.9–2.2 Mb without significant inter-chromosome A×A effects. The PPP1R16A-FOXH1-CYHR1-TONSL (PFCT) region of Chr14a (29 Kb in size) with four SNPs had the largest number of inter-chromosome A×A effects (1141 pairs) with all chromosomes, including the most significant inter-chromosome A×A effects. The SLC4A4-GC-NPFFR2 (SGN) region of Chr06, known to have highly significant additive effects for some production, fertility and health traits, specifically interacted with the PFCT region and a Chr14a region with CPSF1, ADCK5, SLC52A2, DGAT1, SMPD5 and PARP10 (CASDSP) known to have highly significant additive effects for milk production traits. The most significant effects were between an SNP in SGN and four SNPs in PFCT. The CASDSP region mostly interacted with the SGN region. In the Chr14b region, the 2.28–2.42 Mb region (138.46 Kb in size) lacking coding genes had the largest cluster of A×A effects, interacting with seventeen chromosomes. The results from this study provide high-confidence evidence towards the understanding of the genetic mechanism of FPC in Holstein cows.
KW - GWAS
KW - Holstein
KW - SNP
KW - cow
KW - epistasis
KW - fat percentage
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U2 - 10.3390/ijms25010674
DO - 10.3390/ijms25010674
M3 - Article
C2 - 38203848
AN - SCOPUS:85182094178
SN - 1661-6596
VL - 25
JO - International journal of molecular sciences
JF - International journal of molecular sciences
IS - 1
M1 - 674
ER -