Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Jin, Liangliang; Qu, Kaixing; Hanif, Quratulain; Zhang, Jicai; Liu, Jianyong; Chen, Ningbo; Quji, Suolang; Lei, Chuzhao; Huang, Bizhi

doi:10.3389/fgene.2022.833475

Cited by 10 publications

(8 citation statements)

References 54 publications

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“…The results show that short ROH segments account for a large proportion (72.29%) in the research population, with an average size of 0.93 Mb. Due to the lower breeding level of local breeds compared to commercial breeds, the proportion of short ROH segments in local breeds was found to be higher than that in commercial breeds [39][40][41]. The two parental rabbit populations in this study had a low probability of inbreeding, which is consistent with previous research.…”

Section: Discussionsupporting

confidence: 89%

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: Discussionsupporting

confidence: 89%

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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“…After mapping, the “Haplotype Caller”, “Genotype GVCFs” and “Select Variants” modules of the Genome analysis toolkit (GATK, version 3.8-1-0-gf15c1c3ef) [ 15 ] were used to call the SNPs. The mapping and filtering parameters were as shown previously [ 8 ]. SNPs were functionally annotated using ANNOVAR [ 16 ].…”

Section: Methodsmentioning

confidence: 99%

“…Numerous studies on the genetic diversity and lineage origins of local cattle breeds are becoming more prevalent as the use and price of whole-genome sequencing increase. [ 8 , 9 ]. However, there are no previous studies on Loudi cattle from central Hunan, only research work on Xiangxi cattle from western Hunan has been found [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan

Jin

Luo

et al. 2022

Biology

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Due to the geographical, cultural and environmental variability in Xiangxi, China, distinctive indigenous cattle populations have formed. Among them, Loudi cattle and Xiangxi cattle are the local cattle in Hunan, and the environment in Loudi is relatively more enclosed and humid than that in Xiangxi. To study the genome and origin of Loudi cattle in hot and humid environments, 29 individuals were collected and sequenced by whole-genome resequencing. In addition, genomic data were obtained from public databases for 96 individuals representing different cattle breeds worldwide, including 23 Xiangxi cattle from western Hunan. Genetic analysis indicated that the genetic diversity of Loudi cattle was close to that of Chinese cattle and higher than that of other breeds. Population structure and ancestral origin analysis indicated the relationship between Loudi cattle and other breeds. Loudi has four distinctive seasons, with a stereoscopic climate and extremely rich water resources. Selective sweep analysis revealed candidate genes and pathways associated with environmental adaptation and homeostasis. Our findings provide a valuable source of information on the genetic diversity of Loudi cattle and ideas for population conservation and genome-associated breeding of local cattle in today’s extreme climate environment.

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“…A previous study demonstrated that worldwide cattle could be divided into five continental groups: European taurine, Eurasian taurine, East Asian taurine, Chinese indicine and Indian indicine (Chen et al, 2018). Nowadays, many reports of indigenous cattle in the Yunnan province have focused on whole-genome sequencing for precise analysis of their genetic features and traits, such as Lincang (Sun et al, 2022), Dengchuan (Jin et al, 2022) and Yunling cattle (Chen, Zhan, et al, 2020). Nevertheless, there is a paucity of literature on genome-wide studies of Zhaotong cattle in the inland regions of Yunnan province.…”

Section: Sc Usmentioning

confidence: 99%

A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province

Lyu,

Guan,

et al. 2023

Animal Genetics

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Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome‐wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.

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Whole-Genome Sequencing of Endangered Dengchuan Cattle Reveals Its Genomic Diversity and Selection Signatures

Cited by 10 publications

References 54 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

Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan

A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province

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