Detection of whole genome selection signatures of Pakistani Teddy goat

Saif, Rashid; Henkel, Jan; Mahmood, Tania; Ejaz, Aniqa; Ahmad, Faiz; Zia, Saeeda

doi:10.1007/s11033-021-06726-x

Cited by 7 publications

(2 citation statements)

References 27 publications

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“…Out of total 40 milk production genes, only 4 genes ( VPS13B, TTC27, RNPC3 , and SPAG17) harbor the common putative windows. Four SNPs at 15~15.3 Mb region within TTC27 gene were significant (FDR < 5%) in Bovine genome (42), while TTC27 along with VPS13B gene was found to be under-selection in Pakistani Teddy goat breed (13). Only two of five fiber production genes ( PKIA and RHOG ) captured by more than one statistical method used in the current research.…”

Section: Discussionmentioning

confidence: 99%

“…Only two of five fiber production genes ( PKIA and RHOG ) captured by more than one statistical method used in the current research. PKIA gene with – ZHp = 7.520 was under high selection in Teddy goat (13) while currently in DDP goat it is significantly associated with score – ZHp = 5.35 (Table S3). Interestingly, RHOG was found as candidate gene involved in number of hair whorls on right side in horses thus evidencing the curly hair in DDP goat as well (43).…”

Section: Discussionmentioning

confidence: 99%

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Genomic Selection Pressure Discovery using Site-Frequency Spectrum & Reduced Local-Variability Statistics in Pakistani Dera-Din-Panah Goat

Saif

Mahmood

Ejaz

et al. 2022

Preprint

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Population geneticists have long sought to comprehend various selection traces present in the goat genome due to natural or human-driven selection and breeding practices. As a step forward to pinpoint the selection signals in the Pakistani Dera-Din-Panah (DDP) goat breed, whole-genome pooled-sequencing (n=12) was performed and 618,236,192 clean paired-end reads were mapped against ARS1 reference goat assembly. Five different selection signal statistics were applied here using four Site-Frequency Spectrum (SFS) methods (Tajimas D (TD), Fay & Wus H (H), Zengs E (E), Pool-HMM) and one Reduced Local-Variability approach named pooled-heterozygosity (Hp). The under-selection regions were annotated with significant threshold values of -ZTD≥4.7, -ZH≥6, -ZE≥2.5, Pool-HMM≥12, and -ZHp≥5, which resulted in accumulative 364 candidate gene hits, while the highest signals were observed on Chr. 4, 6, 10, 12, 15, 16, 18, 20, 27 harbor ADAMTS6, CWC27 genes associated with body-height, RELN, MYCBP2, FGF14, STIM1, CFAP74, GNB1, CALML6, TMEM52, FAM149A, NADK, MMP23B, OPN3 with body-weight/meat production, FH, MFHAS1, KLKB1 with milk production, RRM1, KMO, SPEF2, F11 with fecundity rate/reproduction, ATP8B4 with immunity, KIT, KMO with pigmentation, ERI1 with olfaction and RHOG with wool production traits. Furthermore, we accentuate to highlight the putative windows that were captured commonly by any of the five statistical methods applied which harbor meat production, immunity and reproduction-associated genes validating the genotype-phenotype relationship of aforementioned traits private to this goat breed. Current insight into the genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other vested traits of large body size and fiber production by updating the breeding strategies to boost the livestock-based agricultural economy of the country.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genomic Selection Pressure Discovery using Site-Frequency Spectrum & Reduced Local-Variability Statistics in Pakistani Dera-Din-Panah Goat

Saif

Mahmood

Ejaz

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat

Saif,

Mahmood,

Zia

et al. 2023

Trop Anim Health Prod

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with fecundity rate/reproduction, ATP8B4 with immunity, KIT, KMO with pigmentation, ERI1 with olfaction and RHOG with wool production traits. Furthermore, we accentuate to highlight the putative windows that were captured commonly by any of the five statistical methods applied which harbor meat production, immunity and reproduction-associated genes validating the genotype-phenotype relationship of aforementioned traits private to this goat breed. Current insight into the genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other vested traits of large body size and fiber production by updating the breeding strategies to boost the livestock-based agricultural economy of the country.

show abstract