Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness

Simple Summary Cashmere goats are valuable genetic resources which are famous for their high-quality fiber. Runs of homozygosity (ROHs) refer to uninterrupted sequences of homozygous genotypes present within the DNA sequence of an individual. To enhance the preservation, improvement and enduring utilization of this valuable genetic resource, we performed a comprehensive study on the genetic variance, degree of inbreeding, patterns of ROHs and selected genes situated in ROH islands which are associated with economic attributes in goats via whole-genome sequencing analysis. Our research showed that the Inner Mongolia cashmere goat possesses a notably high level of genetic diversity and presented the lowest inbreeding coefficient. On the contrary, the highest Froh and lowest levels of diversity were observed in wild goats compared to domesticated goats. The analysis of selection signal through ROHs identified some genes related to meat, fiber and milk production; fertility, disease and cold resistance and adaptability; and body size and growth. Abstract 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.

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

/pdf/deep-learning-in-neural-networks-and-their-application-in-2ral3m5i.pdf

Deep Learning in Neural Networks and their Application in Genomics

Riverine buffalo domestication likely occurred around 6300 years ago in Northwestern India. Murrah and Surti are important buffalo breeds that originated in this region and the gene flow from these buffaloes to Mehsana buffalo has long been proposed. However, the extent to which Murrah and Surti ancestry diffused across Mehsana has not been investigated thoroughly. Therefore, we investigated the global and local ancestry of Indian Mehsana buffalo using double digest restriction-site associated DNA sequencing data. Principal component analysis, global ancestry analysis, admixture dating, and three population tests revealed with statistical significance that Mehsana is a unique population. Hence, the hypothesis that Mehsana is a crossbreed between Murrah and Surti is not supported by these findings. However, we noticed that some individuals of Mehsana, 6 out 15, were admixed having 41% Murrah-specific ancestry and 11% Surti-specific ancestry. Local ancestry and post-admixture selection signatures (PASS) in admixed Mehsana individuals revealed PASS in the Mehsana genome, that is, on Bubalus bubalis autosomes (BBA), 1–23 linked from Surti and on BBA, 24 linked from Murrah. Interestingly, upon functional enrichment of these signatures, several adaptation-related genes and pathways were ascertained to Surti, while Murrah-derived regions featured genes involved in fatty acid synthesis (Acyl-CoA Synthetase Short-Chain Family Member 2 (ACSS2)) and milk production. Based on local ancestry analysis, we infer that the introgression of the Murrah genome into Mehsana happened in recent times and that of the Surti genome happened in ancient generations. The finding that Mehsana is an independent population highlights the importance of recognizing distinct genetic lineages in domesticated species. This has global implications for reevaluating the origins and uniqueness of other livestock breeds often assumed to be hybrids. Practically, these findings open up new avenues for selective breeding to preserve traits such as disease resistance, adaptability, and production efficiency. Further studies in larger samples are called for.

Rethinking River Buffalo Domestication Through the Lens of Population Genetics Tools: Mehsana Buffalo Is a Unique Population.

Genome wide mapping of nuclear mitochondrial DNA sequences (NUMTs) and their functionality in domestic water buffalo (Bubalus bubalis)



The fastest way to significantly change the composition of a population is through admixture,
an evolutionary mechanism. In animal breeding history, genetic admixture has provided
both short-term and long-term advantages by utilizing the phenomenon of complementarity and
heterosis in several traits and genetic diversity, respectively. The traditional method of admixture
analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables
more precise estimations. Among these markers, SNPs have been the popular choice since
they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers
can suggest the possibility of a population's origin from a sample of DNA where the source individual
is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative
Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry
and can be exploited to identify signs of recent selective response and can account for genetic
drift. Considering the importance of genetic admixture and local ancestry, in this mini-review,
both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/-
software used and their applications.


Global and Local Ancestry and its Importance: A Mini-Review

Genome-wide runs of homozygosity signatures in diverse Indian goat breeds

Mendelism: Connecting the Dots Across Centuries

/pdf/epitope-tailored-vaccine-construct-for-goat-milk-allergy-1o8ehxzz.pdf

Epitope Tailored Vaccine Construct for Goat Milk Allergy

Mitochondrial genetic diversity analysis of cattle using high density SNP array

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