High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Tolone, Marco; Sardina, Maria Teresa; Criscione, Andrea; Lasagna, Emiliano; Senczuk, Gabriele; Rizzuto, Ilaria; Riggio, Silvia; Moscarelli, Angelo; Macaluso, Vito; Gerlando, Rosalia Di; Cassandro, Martino; Portolano, Baldassare; Mastrangelo, Salvatore

doi:10.1016/j.psj.2023.102692

Cited by 3 publications

(1 citation statement)

References 51 publications

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“…In recent years, due to the extensive utilization of SNP microarray gene chip and whole-genome resequencing technologies [8][9][10][11], research into ROHs based on livestock and poultry genomic information has been increasing. This includes research on various species, such as goats [12][13][14], sheep [15][16][17], cattle [7,18,19], pigs [3,20,21], chickens [22][23][24] and so on. Genomic regions that were abundant with ROHs were defined as ROH islands, potentially signaling selection sweeps.…”

Section: Introductionmentioning

confidence: 99%

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Zhao,

Huang,

Chen

et al. 2024

Animals

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Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.

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Section: Introductionmentioning

confidence: 99%

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Zhao,

Huang,

Chen

et al. 2024

Animals

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Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Wu,

Chen,

Zhou

et al. 2024

Poultry Science

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Development and validation of a 5K low-density SNP chip for Hainan cattle

Wang,

Wu,

Zhang

et al. 2024

BMC Genomics

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Background This study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included. Results A total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65–99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways. Conclusion The development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-10753-w.

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High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Cited by 3 publications

References 51 publications

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Development and validation of a 5K low-density SNP chip for Hainan cattle

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