Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China

Sun, Xiaoyan; Jiang, Jing; Wang, Gaofu; Zhou, Peng; Li, Jie; Chen, Cancan; Liu, Liangjia; Li, Nianfu; Xia, Yuanyou; Ren, Hangxing

doi:10.5713/ab.21.0577

Cited by 9 publications

(12 citation statements)

References 32 publications

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“…NR1H3 ( LXR-a ) is present in human sebocytes, and LXR agonists inhibit hair follicle growth [ 65 ]. The GRIA2 gene is associated with hind leg wool traits in goats [ 66 ]. The Sox family is expressed in early hair follicle development, and network predictions suggest that the MSTRG.223165-miR-21-SOX6 axis is involved in hair follicle development [ 67 ]; the targeting relationship between miR-21 and SOX6 and MSTRG.223165 has been validated in a dual luciferase assay [ 67 ].…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

Zhang,

Jin,

et al. 2023

Animals

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Wool fineness affects the quality of wool, and some studies have identified about forty candidate genes that affect sheep wool fineness, but these genes often reveal only a certain proportion of the variation in wool thickness. We further explore additional genes associated with the fineness of sheep wool. Whole-genome resequencing of eight sheep breeds was performed to reveal selection signals associated with wool fineness, including four coarse wool and four fine/semi-fine wool sheep breeds. Multiple methods to reveal selection signals (Fst and θπ Ratio and XP-EHH) were applied for sheep wool fineness traits. In total, 269 and 319 genes were annotated in the fine wool (F vs. C) group and the coarse wool (C vs. F) group, such as LGR4, PIK3CA, and SEMA3C and NFIB, OPHN1, and THADA. In F vs. C, 269 genes were enriched in 15 significant GO Terms (p < 0.05) and 38 significant KEGG Pathways (p < 0.05), such as protein localization to plasma membrane (GO: 0072659) and Inositol phosphate metabolism (oas 00562). In C vs. F, 319 genes were enriched in 21 GO Terms (p < 0.05) and 16 KEGG Pathways (p < 0.05), such as negative regulation of focal adhesion assembly (GO: 0051895) and Axon guidance (oas 04360). Our study has uncovered genomic information pertaining to significant traits in sheep and has identified valuable candidate genes. This will pave the way for subsequent investigations into related traits.

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Section: Discussionmentioning

confidence: 99%

Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

Zhang,

Jin,

et al. 2023

Animals

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“…In vicugna, overlapping ROHs in DLG1 suggest selection for feeding efficiency in poor pasture quality [ 65 ] while the selection signals found in PDE4D hint the adaptation of the species to UV radiation exposure through the modulation of pigmentation and/or eye-protective phenotypes. Indeed, this gene was recently described as essential in signaling pathways of melanin encompassing signatures of selection for variation in pigmentation in Groningen White Headed cattle [ 66 ] and goat breeds from Southern China [ 67 ]. Potential environmental adaptation was also observed in guanaco as the species showed overlapping ROHs in BCL2L13 , a gene selected for heat stress tolerance [ 68 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide scan for runs of homozygosity in South American Camelids

Pallotti,

Picciolini,

Antonini

et al. 2023

BMC Genomics

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Background Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

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“…In numerous studies, KCNG4 , ZBTB24 and SORCS3 have been related to the immune system and some diseases in human, but there is no information on the relationship with animal body conformation traits in the previous studies. On the other hand, the SORCS3 gene has been associated with coat color trait in goats [ 72 ]. Furthermore, we found an association between the ADIPOQ (adiponectin) gene and chest width.…”

Section: Discussionmentioning

confidence: 99%

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Easa

Selionova

Aibazov

et al. 2022

Genes

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The objective of this study was to identify the SNPs and candidate genes related to body weight and seven body conformation traits at the age of 8 months in the Russian aboriginal Karachai goats (n = 269) by conducting genome-wide association studies (GWAS), using genotypes generated by Goat SNP BeadChip (Illumina Inc., San Diego, CA, USA). We identified 241 SNPs, which were significantly associated with the studied traits, including 47 genome-wide SNPs (p < 10−5) and 194 suggestive SNPs (p < 10−4), distributed among all goat autosomes except for autosome 23. Fifty-six SNPs were common for two and more traits (1 SNP for six traits, 2 SNPs for five traits, 12 SNPs for four traits, 20 SNPs for three traits, and 21 SNPs for two traits), while 185 SNPs were associated with single traits. Structural annotation within a window of 0.4 Mb (±0.2 Mb from causal SNPs) revealed 238 candidate genes. The largest number of candidate genes was identified at Chr13 (33 candidate genes for the five traits). The genes identified in our study were previously reported to be associated with growth-related traits in different livestock species. The most significant genes for body weight were CRADD, HMGA2, MSRB3, MAX, HACL1 and RAB15, which regulate growth processes, body sizes, fat deposition, and average daily gains. Among them, the HMGA2 gene is a well-known candidate for prenatal and early postnatal development, and the MSRB3 gene is proposed as a candidate gene affecting the growth performance. APOB, PTPRK, BCAR1, AOAH and ASAH1 genes associated with withers height, rump height and body length, are involved in various metabolic processes, including fatty acid metabolism and lipopolysaccharide catabolism. In addition, WDR70, ZBTB24, ADIPOQ, and SORCS3 genes were linked to chest width. KCNG4 was associated with rump height, body length and chest perimeter. The identified candidate genes can be proposed as molecular markers for growth trait selection for genetic improvement in Karachai goats.

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Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China

Abstract: Title of the manuscript: Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China.

Cited by 9 publications

References 32 publications

Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

Genome-wide scan for runs of homozygosity in South American Camelids

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

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