Whole-Genome Analyses Reveal Genomic Characteristics and Selection Signatures of Lincang Humped Cattle at the China–Myanmar Border

Sun, Luyang; Qu, Kaixing; Ma, Xiaoyan; Hanif, Quratulain; Zhang, Jicai; Liu, Jianyong; Chen, Ningbo; Quji, Suolang; Lei, Chuzhao; Huang, Bizhi

doi:10.3389/fgene.2022.833503

Cited by 10 publications

(7 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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“…The region identified on BTA5 was previously reported as having been under selection in several Indian B. indicus breeds ( Dixit et al, 2020 ) and in African zebu and B. indicus (Gir) cattle ( Tijjani et al, 2021 ). Naval-Sánchez et al (2020) and Sun et al (2022) recently compared the genome sequence of B. taurus and B. indicus cattle and reported missense mutations in HELB gene, located around 47.73 Mb on BTA5, that were specific to B. indicus cattle, which they suggested was an adaptation to hot environments, given that HELB is involved in DNA damage response. The BTA5 region also harbours DYRK2 and RAP1B genes with functions related to mammary gland development and lactation.…”

Section: Discussionmentioning

confidence: 99%

Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows

Kalaldeh

Swaminathan²,

Podtar³

et al. 2023

Front. Genet.

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Introduction: In India, crossbred cows incorporate the high production of B. taurus dairy breeds and the environmental adaptation of local B. indicus cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between B. indicus and B. taurus cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate B. indicus from B. taurus ancestry, as well as QTL that are segregating within the ancestral breeds.Methods: A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles.Results: At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of B. indicus versus B. taurus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98–49.44 Mbp) that differentiates B. indicus from B. taurus, with an estimated difference between homozygotes of approximately 10% of average yield, in favour of B. indicus origin.Discussion: Our results indicate that evolutionary differences between B. indicus and B. taurus cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.

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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 Analyses Reveal Genomic Characteristics and Selection Signatures of Lincang Humped Cattle at the China–Myanmar Border

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

Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows

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

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