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<p>The present genome-wide association studies (GWAS) were conducted on the Badri breed of indicine cattle, a breed renowned for its disease resistance and adaptability to the challenging terrain of the Himalayan mountains. The milk production of Badri cattle is lower as compared to indicine and taurine dairy cattle breeds. However, contemporary techniques, particularly the GWAS, offer opportunity for systematic improvement in milk production and fertility of indicine cattle by identifying genomic variations associated with production and reproduction traits. The DNA samples of 96 Badri cows were genotyped using a double digestion restriction associated DNA sequencing approach. Subsequently, a standardized bioinformatics pipeline was employed to identify variants, wherein only single-nucleotide polymorphisms (SNPs) meeting stringent quality control criteria were retained for further analysis. Following filtration, a total of 65,483 high-confidence SNPs were utilized to conduct GWAS on production traits (including lactation length, peak yield, total milk yield, and days to attain peak yield within lactation) and reproduction traits (encompassing dry period and calving interval). Various genomic regions and candidate genes (<i>LOC785621</i>, <i>ADCK1</i>, <i>DIP2C</i>, <i>WDR26</i>, <i>LOC510860</i>, <i>RPS6KC1</i>, <i>KCTD1</i>, <i>GPC3</i>, <i>SLC16A2</i>, <i>TIPRL</i>, <i>DYNC1I1</i>, <i>GRM1</i>, <i>PBX3</i>, <i>AKR1C4</i>, <i>SRGAP2</i>, <i>RPS6KC1</i>, <i>bPLP-II</i>, <i>NRG1</i> and <i>TENM1</i>) and their enrichment pathways were identified which may have a potential role in regulating milk production and female fertility in Badri breed of indicine cattle. The identified genomic regions will aid in early and best individual selection of cattle for higher milk production, improved fertility and in the long term, this may assist to shape future genetic improvement efforts of indicine cattle.</p>

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Genome-wide association studies revealed genomic regions associated with production and reproduction traits in indicine cattle

  • 期刊论文

  • 发表日期：

    2025年2月5日

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  • Javid Ur Rahman,
  • Devendra Kumar,
  • Satya Pal Singh,
  • Bijendra Narayan Shahi,
  • Ashis Kumar Ghosh,
  • Tarannum Jahan

摘要

The present genome-wide association studies (GWAS) were conducted on the Badri breed of indicine cattle, a breed renowned for its disease resistance and adaptability to the challenging terrain of the Himalayan mountains. The milk production of Badri cattle is lower as compared to indicine and taurine dairy cattle breeds. However, contemporary techniques, particularly the GWAS, offer opportunity for systematic improvement in milk production and fertility of indicine cattle by identifying genomic variations associated with production and reproduction traits. The DNA samples of 96 Badri cows were genotyped using a double digestion restriction associated DNA sequencing approach. Subsequently, a standardized bioinformatics pipeline was employed to identify variants, wherein only single-nucleotide polymorphisms (SNPs) meeting stringent quality control criteria were retained for further analysis. Following filtration, a total of 65,483 high-confidence SNPs were utilized to conduct GWAS on production traits (including lactation length, peak yield, total milk yield, and days to attain peak yield within lactation) and reproduction traits (encompassing dry period and calving interval). Various genomic regions and candidate genes (LOC785621, ADCK1, DIP2C, WDR26, LOC510860, RPS6KC1, KCTD1, GPC3, SLC16A2, TIPRL, DYNC1I1, GRM1, PBX3, AKR1C4, SRGAP2, RPS6KC1, bPLP-II, NRG1 and TENM1) and their enrichment pathways were identified which may have a potential role in regulating milk production and female fertility in Badri breed of indicine cattle. The identified genomic regions will aid in early and best individual selection of cattle for higher milk production, improved fertility and in the long term, this may assist to shape future genetic improvement efforts of indicine cattle.