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<p>Runs of homozygosity (ROH) are continuous stretches of homozygous loci generated from identical haplotypes inherited from a common ancestor. ROH hotspots could be an indicator of footprints from artificial and/or natural selection processes. Here, genomic information of 937 individuals from commercial Saanen herds selected in Brazilian tropical environments was used to characterize the population genetic diversity through a genome-wide assessment of autozygosity and effective population size (Ne), in addition to investigate ROH hotspots for pinpointing genomic regions subjected to selective pressures in Saanen in the tropics. Inbreeding levels are relatively under control in this population, but the <i>Ne</i> estimate above but close to 50 animals would be considered critical for this population to be long-term viable in terms of genetic diversity, demanding extra attention on <i>Ne</i> monitoring by the breeders. Nine ROH hotspots were identified on chromosomes 7, 10, 11, 12, 13, 14, 18, and 24, harboring genes directly related to production and adaptive traits. This includes genes associated with milk and protein yield and somatic cell count (<i>CSNK1G1</i>, <i>PCLAF</i>, <i>TRIP4</i>, <i>ZNF609</i>, <i>OAZ2</i>, <i>PIF1</i>, <i>PLEKHO2</i>, and <i>PTGDR</i>); reproduction (<i>ZNF609</i>, <i>OAZ2</i>, <i>PTGDR</i>,<i> GJA3</i>, <i>GJB2</i>, and <i>GJB6</i>); adaptation to heat stress (<i>HSPA9</i>, <i>SIL1</i>, <i>CTNNA1</i>, <i>RNF17</i>, <i>ZMYM2</i>, <i>PARP4</i>, and <i>XPO4</i>); immune system response to mastitis and other infections (<i>HCK</i>, <i>BPIFA1</i>, and <i>BPIFB1</i>), among others. The various loci directly related to the genetic control of productive and adaptive traits in goats identified in this study suggest possible footprints from artificial and/or natural selection processes related to adaptability of Saanen to tropical production systems.</p>

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Genome scan for runs of homozygosity in Saanen goats selected under tropical environments reveals candidate genes for adaptive and production traits

  • 期刊论文

  • 发表日期：

    2025年11月3日

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  • Gerardo Alves Fernandes Júnior,
  • Marcos Vinicius Gualberto Barbosa da Silva,
  • Ana Maria Bezerra Oliveira Lobo,
  • João Cláudio do Carmo Panetto,
  • Kleibe de Moraes Silva,
  • Samuel Rezende Paiva,
  • Olivardo Facó

摘要

Runs of homozygosity (ROH) are continuous stretches of homozygous loci generated from identical haplotypes inherited from a common ancestor. ROH hotspots could be an indicator of footprints from artificial and/or natural selection processes. Here, genomic information of 937 individuals from commercial Saanen herds selected in Brazilian tropical environments was used to characterize the population genetic diversity through a genome-wide assessment of autozygosity and effective population size (Ne), in addition to investigate ROH hotspots for pinpointing genomic regions subjected to selective pressures in Saanen in the tropics. Inbreeding levels are relatively under control in this population, but the Ne estimate above but close to 50 animals would be considered critical for this population to be long-term viable in terms of genetic diversity, demanding extra attention on Ne monitoring by the breeders. Nine ROH hotspots were identified on chromosomes 7, 10, 11, 12, 13, 14, 18, and 24, harboring genes directly related to production and adaptive traits. This includes genes associated with milk and protein yield and somatic cell count (CSNK1G1, PCLAF, TRIP4, ZNF609, OAZ2, PIF1, PLEKHO2, and PTGDR); reproduction (ZNF609, OAZ2, PTGDR, GJA3, GJB2, and GJB6); adaptation to heat stress (HSPA9, SIL1, CTNNA1, RNF17, ZMYM2, PARP4, and XPO4); immune system response to mastitis and other infections (HCK, BPIFA1, and BPIFB1), among others. The various loci directly related to the genetic control of productive and adaptive traits in goats identified in this study suggest possible footprints from artificial and/or natural selection processes related to adaptability of Saanen to tropical production systems.