Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

Sun, Xuemei; Guo, Jiazhong; Li, Li; Zhong, Tao; Wang, Linjie; Zhan, Siyuan; Lü, Juan; Wang, Decheng; Dai, Dinghui; Liu, George E.; Zhang, Hongping

doi:10.3390/ani12182365

Cited by 11 publications

(8 citation statements)

References 65 publications

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“…The results show a high correlation between ROH and F ROH . In previous studies of the Jianchang black goat [45], there was a strong positive correlation between the number of ROHs on each chromosome and the chromosome length. Similar results were also found in studies of the German white cashmere goat [46].…”

Section: Discussionmentioning

confidence: 75%

Genome-wide association studies and mapping of ROH identifies candidate genes for growth traits in hybrid rabbits

Jia,

Xiao,

et al. 2024

Preprint

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Screening and identifying genes related to growth traits are critically important for the production of meat rabbits. Genome-wide association studies is an effective method for large-scale screening of genetic markers related to target traits. However, the performance of whole-genome association studies in meat rabbits candidate genes associated with the heterosis remains largely unknown. In this study, after quality control and filtering of genotype data, a total of 380 F2 hybrid rabbits (205 male rabbits, 175 female rabbits) with 78579 SNPs and 42018 ROH on the autosome were obtained. The phenotypic values and heterosis of 380 F2 hybrid rabbits at seven growth stages were compared and analyzed. The fitting of the Logistic growth curve model indicated that the rabbit at 49 days of age was a growth inflection point. At this time, the correlation between weight heterosis and ROH was − 0.1267 to 0.07436. Ultimately, we conducted a genome-wide association studies of genotypes and growth trait heterosis after quality control using a mixed linear model. A total of 10 significant SNP-sites were significantly associated with weight at 84 days of age, and 7 candidate genes associated with growth traits were identified in meat rabbits. Additionally, we also uncovering the functional roles and positions of 20 candidate genes associated with economic traits of meat rabbits in high-frequency ROH regions. This study identified potential genes related to meat rabbit growth, development and adaptability in high-frequency ROH regions. These research findings will provide a genomic reference and new insights for the selection and improvement of hybrid meat rabbits, as well as useful genetic markers for breeding important economic traits in domestic rabbits.

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Section: Discussionmentioning

confidence: 75%

Genome-wide association studies and mapping of ROH identifies candidate genes for growth traits in hybrid rabbits

Jia,

Xiao,

et al. 2024

Preprint

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“…Nonetheless, they have partially clustered together because of breeders’ efforts to improve growth and milk performance of Barki by crossing with Damascus [ 6 ]. The PCA results showed that Damascus and Boer goats are genetically connected, indicating gene flows between these breeds, in contrast to the Egyptian Nubian that was genetically distinct and has a separate genetic structure due to the application of specific breeding programs [ 52 ]. Boer goats were shown to be quite scattered in PCA plot despite implementing some sort of breeding programs.…”

Section: Discussionmentioning

confidence: 99%

“…Two candidate gene were detected on CHR6 at 70.74 and 71.14 Mb: (1) the KIT (KIT Proto-Oncogene, Receptor Tyrosine Kinase) gene, which plays an essential role in the regulation of cell survival and proliferation, hematopoiesis, stem cell maintenance, gametogenesis, mast cell development, migration and function, melanogenesis [ 73 ], and a possible pleotropic role in reproductive performance in livestock. The KIT and its ligand (i.e., KITLG ), are two well-known pigmentation genes in livestock [ 52 , 74 ], and selection signals have been detected in many different goat [ 75 ] and sheep populations [ 76 ]. Interestingly, the same gene was identified to differentiate between the Egyptian Nubian and Boer (F ST = 0.89), which may explain their difference in the dominant hair colors.…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, the same candidate genes and genomic regions on CHR6 (70.74 Mb, KIT ) and CHR18 (15.73 Mb, SPG ) were recently identified by whole genome sequencing as top ROH hotspots in Jianchang Black goats [ 52 ]. Furthermore, the RNF17 (Ring Finger Protein 17) gene that encodes a testis-specific protein containing a RING finger domain and may be involved in spermiogenesis [ 78 ] was detected on CHR12 (50.04 Mb).…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

Sallam,

Reyer,

Wimmers

et al. 2023

BMC Genomics

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Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.

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“…Following recent guidelines, SNP pruning was not applied before ROH detection [40]. The detection of ROHs in LSS and other breeds was carried out using PLINK (v1.9) [33] with the '--homozyg group' command.…”

Section: Genetic Diversity and Genome-wide Detection Of Rohsmentioning

confidence: 99%

Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep

Sun,

Guo,

et al. 2024

Animals

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Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2—an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher’s exact test, p < 2.2 × 10−16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.

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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

Cited by 11 publications

References 65 publications

Genome-wide association studies and mapping of ROH identifies candidate genes for growth traits in hybrid rabbits

Genome-wide association studies and mapping of ROH identifies candidate genes for growth traits in hybrid rabbits

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep

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