Søren Østergaard

TY - JOUR

T1 - A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach

AU - Atashi, H.

AU - Salavati, Mazdak

AU - De Koster, Jenne

AU - Crowe, Mark

AU - Opsomer, Gert

AU - Hostens, Miel

AU - GplusE Consortium

AU - Foldager, Leslie

AU - Larsen, Torben

AU - Rousing, Tine

AU - Ettema, Jehan

AU - Østergaard, Søren

AU - Sørensen, Martin Tang

AU - Ingvartsen, Klaus Lønne

PY - 2020/3

Y1 - 2020/3

N2 - The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.

AB - The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.

KW - genome-wide association study

KW - Holstein

KW - calving interval

KW - PREIMPLANTATION MOUSE EMBRYOS

KW - IDENTIFICATION

KW - FERTILITY

KW - ACID-TRANSPORT REGULATION

KW - QUANTITATIVE TRAIT LOCI

KW - IN-VITRO

KW - HERDS

KW - REPRODUCTIVE TRAITS

KW - GENETIC-PARAMETERS

KW - AMINO-ACIDS

U2 - 10.3390/ani10030500

DO - 10.3390/ani10030500

M3 - Journal article

C2 - 32192064

VL - 10

SP - 1

EP - 13

JO - Animals

JF - Animals

SN - 2076-2615

IS - 3

M1 - 500

ER -