Identification of genes involved in inbreeding depression of reproduction in Langshan chickens

Xue, Qian; Li, Guohui; Cao, Yuxia; Yin, Jianmei; Zhu, Yunji; Zhang, Huiyong; Zhou, Chixing; Shen, Haiyu; Dou, Xiaowei; YiJun, Su; Wang, Kehua; Zou, Jianmin; Wang, Han

doi:10.5713/ajas.20.0248

Cited by 9 publications

(7 citation statements)

References 37 publications

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“…SEMA5A (semaphorin 5A) is a strong candidate gene with selective sweep that is responsible for response to selection on antibody response to sheep red blood cells [ 73 ]. In the SRD5A1 (steroid-5-alpha-reductase, alpha polypeptide 1) gene, a differentially methylated region was found as the most likely biomarker of inbreeding depression of reproduction in Langshan chickens [ 89 , 90 ].…”

Section: Discussionmentioning

confidence: 99%

“…Two more closely located genes, PLRG1 (pleiotropic regulator 1) and SFRP2 (secreted frizzled related protein 2), also overlap with signals of selective sweeps and contribute to cell differentiation. SFRP2 is involved in inbreeding depression of reproduction [ 90 ] and embryogenesis (development of the neural system, eyes, muscles, and limbs) [ 123 ], and was described as a candidate gene for adaptation to solar radiation in North- and East-African chickens [ 106 ]. SPOCK3 (SPARC/osteonectin, cwcv, and kazal-like domains proteoglycan 3) is a candidate gene for abdominal fat within a CNV region overlapped with a QTL and a selective sweep [ 121 ].…”

Section: Discussionmentioning

confidence: 99%

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Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Abdelmanova

Dotsev

Romanov

et al. 2021

Biology

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“…In our previous research, we separated the hypothalamus and ovary of hens to study their roles in the FM process. However, it was reported that high rates of egg production of hens could be comprehensively regulated through the hypothalamic-pituitary-ovarian axis [76][77][78]. Furthermore, WGCNA has many distinct advantages over other methods because the analysis focuses on the association between coexpression modules and phenotypic traits, and the results have high reliability and biological significance [79].…”

Section: Aging-related Hub Genes Were Identified By Wgcnamentioning

confidence: 99%

Transcriptomic Analysis of Laying Hens Revealed the Role of Aging-Related Genes during Forced Molting

Zhang

Chen

Wen

et al. 2021

Genes

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Molting in birds provides us with an ideal genetic model for understanding aging and rejuvenation since birds present younger characteristics for reproduction and appearance after molting. Forced molting (FM) by fasting in chickens causes aging of their reproductive system and then promotes cell redevelopment by providing water and feed again. To reveal the genetic mechanism of rejuvenation, we detected blood hormone indexes and gene expression levels in the hypothalamus and ovary of hens from five different periods during FM. Three hormones were identified as participating in FM. Furthermore, the variation trends of gene expression levels in the hypothalamus and ovary at five different stages were found to be basically similar using transcriptome analysis. Among them, 45 genes were found to regulate cell aging during fasting stress and 12 genes were found to promote cell development during the recovery period in the hypothalamus. In addition, five hub genes (INO80D, HELZ, AGO4, ROCK2, and RFX7) were identified by WGCNA. FM can restart the reproductive function of aged hens by regulating expression levels of genes associated with aging and development. Our study not only enriches the theoretical basis of FM but also provides insights for the study of antiaging in humans and the conception mechanism in elderly women.

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“…In both variants of the assemblies, a large number of genes associated with reproductive processes were identified, demonstrating the intensification of selection. ABCD3, EHBP1L1, IDE, IP6K3, NSUN2, and MSH2 were potentially involved in spermatogenesis [69][70][71][72][73][74][75]; ASMT was involved in oocyte maturation [76,77]; and GGH was associated with the biosynthesis of folic acid regulation [78].…”

Section: Molecular Mechanisms Underlying Speciation Between Cryptic S...mentioning

confidence: 99%

Narrow-Headed Voles Species Complex (Cricetidae, Rodentia): Evidence for Species Differentiation Inferred from Transcriptome Data

et al. 2022

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The narrow-headed vole complex includes two cryptic species, Lasiopodomys raddei and L. gregalis, and three allopatrically-distributed lineages with obscure taxonomic ranks within the latter. Based on the RNA-seq data of 12 specimens, the current study aims to find the molecular mechanisms of intraspecies differentiation and, in particular, reproductive isolation between analyzed groups. According to the results of the GO-enrichment analysis, about a hundred biological processes associated with genes with contrasting SNPs for L. gregalis and L. raddei were identified. Among them, processes of interspecific interactions, defense responses, responses to external stimuli, and the perception of chemical stimuli and smell were identified, indicating the likely existence of pre-copulatory behavioral and physiological mechanisms that contribute to reproductive isolation between cryptic species. An evaluation of the ratio of non-synonymous substitutions to synonymous ones showed evidence of selection in L. raddei compared to L. gregalis for a large part of the analyzed genes. Among the analyzed genes, genes with both weakening and intensifying selection were found.

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Identification of genes involved in inbreeding depression of reproduction in Langshan chickens

Abstract: Title of the manuscript: Identification of genes involved in inbreeding depression of reproduction in Langshan chickens.

Cited by 9 publications

References 37 publications

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Transcriptomic Analysis of Laying Hens Revealed the Role of Aging-Related Genes during Forced Molting

Narrow-Headed Voles Species Complex (Cricetidae, Rodentia): Evidence for Species Differentiation Inferred from Transcriptome Data

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