Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production

Lee, Hyun-Jeong; Kim, Jaemin; Lee, Taeheon; Son, Jun-Kyu; Yoon, Hobaek; Baek, Ki Hyun; Jeong, Jin Young; Cho, Yong-Min; Lee, Kyung-Tai; Yang, Byoung‐Chul; Lim, Hyun-Joo; Cho, Kwang-Hyun; Kwon, Eung Gi; Nam, Jungrye; Cho, Seoae; Kim, Heebal

doi:10.1093/gbe/evu102

Cited by 39 publications

(30 citation statements)

References 69 publications

(91 reference statements)

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“…For example, ATP1A2 was recently reported to be subject to artificial selection for milk production and fertility traits in multiple Holstein populations (Larkin et al. 2012; Lee et al. 2014).…”

Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

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Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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“…The regions with XP‐CLR values in the top 1% of the empirical distribution were designated as candidate sweeps and the genes that span the window regions were defined as candidate genes (Lee et al . ). We annotated genes located in the significant genomic regions identified from XP‐EHH and XP‐CLR tests based on UMD 3.1.…”

Section: Methodsmentioning

confidence: 97%

Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance

Taye

Lee

Caetano-Anollés

et al. 2017

Animal Science Journal

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As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light-colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross-population composite likelihood ratio (XP-CLR) and cross-population extended haplotype homozygosity (XP-EHH) statistical methods. We identified 296 (XP-EHH) and 327 (XP-CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study.

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“…This window overlaps regions found to be under selection in HOL using various tests (for review, see Randhawa et al 2016). Some of the outlier genes that were also identified in an earlier XP-EHH scan (Lee et al 2014) include VPS18, implicated in neurodegeneration (Peng et al 2012), and CAPN3, associated with muscle dystrophy. The window also contains genes that are differentially expressed between high and low milk yield cows (PLCB2 and CCDC9B) (Yang et al 2016).…”

Section: Cattle Breeding: Morphology Tameness and Milk Yieldmentioning

confidence: 99%

Identifying loci under positive selection in complex population histories

et al. 2019

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Detailed modeling of a species' history is of prime importance for understanding how natural selection operates over time.Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method-called graph-aware retrieval of selective sweeps (GRoSS)-has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

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Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production

Cited by 39 publications

References 69 publications

Systematic profiling of short tandem repeats in the cattle genome

Systematic profiling of short tandem repeats in the cattle genome

Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance

Identifying loci under positive selection in complex population histories

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