Identification of Genetic Variants in &lt;I&gt;PDC, RHO, PDE6A&lt;/I&gt; and &lt;I&gt;PDE6B&lt;/I&gt; in Dogs with Progressive Retinal Atrophy

Pandya, Dipal; Kelawala, D.N.; Patel, Namrata; Shah, Tejas; Patel, Anand; Parmar, Nidhi; Reddy, Bhaskar; Patil, D. B.; Joshi, Chaitanya G.

doi:10.18520/cs/v111/i10/1640-1648

Cited by 2 publications

(2 citation statements)

References 31 publications

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“…This is contradictory to the observed behaviour of caching of unripe but mature stages of both native and non-native fruit by tayras (Soley and Alvarado-Díaz 2011). We detected variation in several genes implicated with lens fiber formation and retina vascularization, including gene expansions of ANKRD13A (Avellino et al 2013) andRBP2 (D'Ambrosio et al 2011), along with the inversion of PDC (Pandya et al 2016), suggesting that tayras might not in fact exhibit poor eyesight. The caching behavior mentioned above (Soley & Alvaro-Diaz, 2011) indicates remarkable sensory perception, especially olfaction (Presley 2000) and memory and recognition of different stages of fruit development, likely evolved as a response to avoid competition with other species during seasons when fruit becomes ripe.…”

Section: Resource Availability In the Neotropics: Tayracontrasting

confidence: 72%

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

Derežanin

Blažytė

Dobrynin

et al. 2021

Preprint

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Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci that appear to be associated with phenotypic traits, we observed many genes related to diet, body condition and reproduction. For the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many specific changes in genes associated with diet and body condition. Despite restricting some of our analyses to single-copy orthologs present in all three study species, we observed many candidate loci that may be linked to species traits related to environment-specific challenges in their respective habitats.

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Section: Resource Availability In the Neotropics: Tayracontrasting

confidence: 72%

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

Derežanin

Blažytė

Dobrynin

et al. 2021

Preprint

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“…; Pandya et al . ). A deleterious mutation of the HEXB gene probably causes Sandhoff disease, which can lead to visual defects in domestic cats (Kanae et al .…”

Section: Introductionmentioning

confidence: 97%

Accumulation of deleterious mutations in the domestic yak genome

et al. 2018

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Deleterious mutations play an important functional role, affecting trait phenotypes in ways that decrease the fitness of organisms. Estimating the frequency of occurrence and abundance has been a topic of much interest, especially in crops and livestock. The processes of domestication and breeding allow deleterious mutations to persist at high frequency, and identifying such deleterious mutations is particularly important for breed improvement. Here, we assessed genome-wide patterns of deleterious variation in 59 domestic and 13 wild yaks using genome resequencing data. Based on the intersection of results given by three methods (provean, polyphen2 and sift4g), we identified 3187 putative deleterious mutation sites affecting 2586 genes in domestic yaks and 2067 affecting 1701 genes in wild yaks. Multiple lines of evidence indicate a significant increase in the load of deleterious mutations in domesticated yaks compared to wild yaks. Private deleterious genes were found to be associated with the perception of smell and detection of chemical stimulus. We also identified 36 genes related to Mendelian genetic diseases involved in sensory perception, skeletal development and the nervous and immune systems. This study not only adds to the understanding of the genetic basis of yak domestication but also provides a rich catalog of variants that will facilitate future breeding-related research on the yak genome and on other bovid species.

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Identification of Genetic Variants in <I>PDC, RHO, PDE6A</I> and <I>PDE6B</I> in Dogs with Progressive Retinal Atrophy

Cited by 2 publications

References 31 publications

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

Accumulation of deleterious mutations in the domestic yak genome

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