Whole Genome Resequencing Helps Study Important Traits in Chickens

Xiong, Xinwei; Liu, Jianxiang; Rao, Yanghui

doi:10.3390/genes14061198

Cited by 11 publications

(5 citation statements)

References 54 publications

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“…The identification of genetic resources of new varieties should include comparisons at both the phenotypic and molecular levels (21). Genome resequencing technology is widely used for the detection of genetic variation in large breeds, given its greater coverage, accuracy, and efficiency compared with traditionally used methods (22)(23)(24). In this study, whole-genome resequencing was used for the validation of the MY breed as a novel genetic resource.…”

Section: Discussionmentioning

confidence: 99%

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Gu,

Wu,

Zheng

et al. 2024

Front. Vet. Sci.

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IntroductionThe Wuzhishan ant (MY) chicken exhibits significant differences from other chicken breeds. However, the molecular genetic relationship between the MY breed and other chicken breeds has not been assessed.MethodsWhole-genome resequencing was used to compare genetic diversity, nucleotide diversity, the fixation index, the linkage disequilibrium coefficient, and phylogenetic tree relationships between the MY breed and the Wenchang (WC), Danzhou (DZ), Bawangling (BW), and Longsheng Feng (LF) breeds.ResultsA total of 21,586,378 singlenucleotide polymorphisms and 4,253,341 insertions/deletions were screened out among the five breeds. The MY breed had the second highest genomic genetic diversity and nucleotide diversity and the lowest LD coefficient among the five breeds. Moreover, the phylogenetic tree analysis showed that individual birds of each breed clustered together with those of their respective breeds.DiscussionOur data indicated that the MY breed is distinct from the other breeds and can be considered a new genetic resource.

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Section: Discussionmentioning

confidence: 99%

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Gu,

Wu,

Zheng

et al. 2024

Front. Vet. Sci.

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“…Therefore, DPP6 gene can be suggested as one of good possible candidate gene for ADG variation in Hanwoo. While IL22RA1's role in muscle growth is not extensively studied, there is evidence suggesting its secondary involvement in muscle physiology [15][16][17] . IL22RA1 being identified as a candidate gene associated with health, adaptation and reproduction traits in cattle 18 .…”

Section: Discussionmentioning

confidence: 99%

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo Cattle

Sheet,

Jang,

Kim

et al. 2023

Preprint

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Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.78 kg) and high (≥ 0.88 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, distinct gene expression patterns were identified with 200, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as potential candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

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“…Hopefully, newly developed biotechnologies can greatly advance this field: (1) Omics analyses could help identify sex-associated genes and explore their regulation mechanism at various levels. (2) Genomewide association studies (GWASs) could establish the relationships between special traits (such as sex) and genes (or SNPs) through re-sequence analyses [43,44]. (3) The CRISPR system can contribute to gene function characterization through gene gain (or loss) of function [45].…”

Section: Future Investigations Of Gjsox9 In G Japonicusmentioning

confidence: 99%

gjSOX9 Cloning, Expression, and Comparison with gjSOXs Family Members in Gekko japonicus

Huang,

Zhao,

et al. 2023

CIMB

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SOX9 plays a crucial role in the male reproductive system, brain, and kidneys. In this study, we firstly analyzed the complete cDNA sequence and expression patterns for SOX9 from Gekko japonicus SOX9 (gjSOX9), carried out bioinformatic analyses of physiochemical properties, structure, and phylogenetic evolution, and compared these with other members of the gjSOX family. The results indicate that gjSOX9 cDNA comprises 1895 bp with a 1482 bp ORF encoding 494aa. gjSOX9 was not only expressed in various adult tissues but also exhibited a special spatiotemporal expression pattern in gonad tissues. gjSOX9 was predicted to be a hydrophilic nucleoprotein with a characteristic HMG-Box harboring a newly identified unique sequence, “YKYQPRRR”, only present in SOXE members. Among the 20 SOX9 orthologs, gjSOX9 shares the closest genetic relationships with Eublepharis macularius SOX9, Sphacrodactylus townsendi SOX9, and Hemicordylus capensis SOX9. gjSOX9 and gjSOX10 possessed identical physicochemical properties and subcellular locations and were tightly clustered with gjSOX8 in the SOXE group. Sixteen gjSOX family members were divided into six groups: SOXB, C, D, E, F, and H with gjSOX8, 9, and 10 in SOXE among 150 SOX homologs. Collectively, the available data in this study not only facilitate a deep exploration of the functions and molecular regulation mechanisms of the gjSOX9 and gjSOX families in G. japonicus but also contribute to basic research regarding the origin and evolution of SOX9 homologs or even sex-determination mode in reptiles.

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Whole Genome Resequencing Helps Study Important Traits in Chickens

Cited by 11 publications

References 54 publications

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo Cattle

gjSOX9 Cloning, Expression, and Comparison with gjSOXs Family Members in Gekko japonicus

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