Molecular Characterization and Expression of SPP1, LAP3 and LCORL and Their Association with Growth Traits in Sheep

La, Yongfu; Zhang, Xiaoxue; Li, Fadi; Zhang, Deyin; Li, Chong; Mo, Futao; Wang, Weimin

doi:10.3390/genes10080616

Cited by 30 publications

(21 citation statements)

References 26 publications

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“…Chromosome 6 also harboured SNPs with high incidence of common ROH across breeds. Some of the associated genes included the Secreted phosphoprotein 1 ( SPP1 ) and ligand dependent nuclear receptor corepressor-like ( LCORL ) which are on a domain of 36.15–38.56 Mb and play an essential role in tissue and embryonic growth [ 45 , 46 ]. LCORL was observed to be associated with height in cattle [ 47 , 48 ] and observed to be under selection in different sheep breeds [ 45 , 49 ] and in other species [ 50 – 54 ].…”

Section: Discussionmentioning

confidence: 99%

“…LCORL was observed to be associated with height in cattle [ 47 , 48 ] and observed to be under selection in different sheep breeds [ 45 , 49 ] and in other species [ 50 – 54 ]. La et al, [ 46 ] observed significantly high expression of SPP1 in the kidney of Hu sheep. The Prostaglandin f2-alpha synthase (PGFS) gene on chromosome 13 is associated with the Arachidonic acid metabolism and other metabolic pathways and were observed to be associated with wool growth regulation in Aohan fine wool sheep [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

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Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

et al. 2021

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Background Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. Results A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. Conclusions Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

et al. 2021

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“…LAP3 , MED28 , NCAPG , LCORL , and DCAF16 were identified within the significant genomic region (chr6: 37315342–42194093), captured by 24 candidate variants. LAP3 , as a member of LAPs family involved in cell maintenance and growth development, had been suggested that it has potential function on body weight in sheep ( La et al, 2019 ) and body measurements traits in cattle ( An et al, 2019 ). Moreover, previous studies also reported that LAP3 is the potential candidate gene for feed efficiency component traits ( Lindholm-Perry et al, 2011 ; Zhang et al, 2016 ), carcass merit, and internal organ traits including kidney weight and spleen weight ( Song et al, 2016 ; Xia et al, 2017 ; An et al, 2018 ; Miao et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle

Niu

Zhang

et al. 2021

Front. Genet.

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Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.

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“…The role of SPP1 is to interact with integrins and CD44 on the cell surface, regulating cell-cell and cell-matrix interactions. SPP1 can be used as a candidate gene for increasing body weight in sheep breeding [ 55 ]. OPN in myoblasts may be involved in regulating myogenesis and inflammation during the early stage of muscle regeneration promoting muscle repair.…”

Section: Discussionmentioning

confidence: 99%

Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq

Cao

et al. 2021

Animals

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Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5’ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3’ last exon (transcription terminal site)-the last exon splicing (TTS), indicating that TSS and TTS were the most common AS event in Pekin ducks, and these AS events were closely related to the regulation of muscle development at different growth stages. The results provided a valuable genomic resource for selective breeding and functional studies of genes. A total of 299 novel genes with ≥2 exons were obtained. There were 294 to 2806 differentially expressed genes (DEGs) in each pairwise comparison of Pekin duck. Notably, 90 DEGs in breast muscle and 9 DEGs in leg muscle were co-expressed at all developmental points. DEGs were validated by qPCR analysis, which confirmed the tendency of the expression. DEGs related to muscle development were involved in biological processes such as “endodermal cell differentiation”, “muscle cell cellular homeostasis”, “skeletal muscle tissue growth” and “skeletal muscle cell differentiation”, and were involved in pathways such as oxidative phosphorylation, ECM-receptor (extracellular matrix receptor) interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids. Some DEGs, including MYL4, IGF2BP1, CSRP3, SPP1 and KLHL31, as well as LAMB2, LAMA2, ITGB1 and OPN, played crucial roles in muscle growth and development. This study provides valuable information about the expression profile of mRNAs and pathways from duck skeletal muscle at different growth stages, and further functional study of these mRNAs and pathways could provide new ideas for studying the molecular networks of growth and development in duck skeletal muscle.

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Molecular Characterization and Expression of SPP1, LAP3 and LCORL and Their Association with Growth Traits in Sheep

Cited by 30 publications

References 26 publications

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle

Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq

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