A novel SNP of PLAG1 gene and its association with growth traits in Chinese cattle

Zhong, Jialin; Xu, Jie; Wang, Jian; Wen, Yifan; Niu, Hongyu; Li, Zheng; He, Hongbin; Peng, Kun; He, Pan; Shi, Shu-Yue; Huang, Yin-Qi; Lei, Chuzhao; Dang, Ruihua; Lan, Xianyong; Qi, Xinglei; Chen, Hong; Huang, Yongzhen

doi:10.1016/j.gene.2018.12.018

Cited by 26 publications

(25 citation statements)

References 18 publications

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“…SP1 has been demonstrated to co-express with other regulators to control early placental differentiation [42]. PLAG1, which was mapped in the most evident region of BTA14 for AFC and IFL, has been often reported to be associated with growth and reproduction traits in cattle [43][44][45]. The overlapping genomic regions between AFC and CR contained other growth-related genes such as SDC3 [46] and FABP3 [47].…”

Section: Candidate Genomic Regions For the Intercepts And Slopesmentioning

confidence: 99%

Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models

Shi

Brito

et al. 2021

BMC Genomics

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Background The effect of heat stress on livestock production is a worldwide issue. Animal performance is influenced by exposure to harsh environmental conditions potentially causing genotype-by-environment interactions (G × E), especially in highproducing animals. In this context, the main objectives of this study were to (1) detect the time periods in which heifer fertility traits are more sensitive to the exposure to high environmental temperature and/or humidity, (2) investigate G × E due to heat stress in heifer fertility traits, and, (3) identify genomic regions associated with heifer fertility and heat tolerance in Holstein cattle. Results Phenotypic records for three heifer fertility traits (i.e., age at first calving, interval from first to last service, and conception rate at the first service) were collected, from 2005 to 2018, for 56,998 Holstein heifers raised in 15 herds in the Beijing area (China). By integrating environmental data, including hourly air temperature and relative humidity, the critical periods in which the heifers are more sensitive to heat stress were located in more than 30 days before the first service for age at first calving and interval from first to last service, or 10 days before and less than 60 days after the first service for conception rate. Using reaction norm models, significant G × E was detected for all three traits regarding both environmental gradients, proportion of days exceeding heat threshold, and minimum temperature-humidity index. Through single-step genome-wide association studies, PLAG1, AMHR2, SP1, KRT8, KRT18, MLH1, and EOMES were suggested as candidate genes for heifer fertility. The genes HCRTR1, AGRP, PC, and GUCY1B1 are strong candidates for association with heat tolerance. Conclusions The critical periods in which the reproductive performance of heifers is more sensitive to heat stress are trait-dependent. Thus, detailed analysis should be conducted to determine this particular period for other fertility traits. The considerable magnitude of G × E and sire re-ranking indicates the necessity to consider G × E in dairy cattle breeding schemes. This will enable selection of more heat-tolerant animals with high reproductive efficiency under harsh climatic conditions. Lastly, the candidate genes identified to be linked with response to heat stress provide a better understanding of the underlying biological mechanisms of heat tolerance in dairy cattle.

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Section: Candidate Genomic Regions For the Intercepts And Slopesmentioning

confidence: 99%

Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models

Shi

Brito

et al. 2021

BMC Genomics

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“…PLAG1 инициирует транскрипцию инсулиноподобного фактора роста 2 (IGF2), митогенного гормона, важного для роста и развития плода, и участвует в генетической изменчивости роста как у человека, так и у КРС (25,(30)(31)(32). Опубликовано значительное число работ, в которых исследовалась связь гена PLAG1 с легкостью отела (33), размерами тела (25), живой массой в раннем возрасте (14), характеристиками туши (34), массой при рождении (35) и другими признаками КРС (36). Российские локальные породы представляют большой интерес в качестве резерва биоразнообразия (37,38), однако остаются неизученными в отношении гена PLAG1 несмотря на проведенные ранее полногеномные исследования (39,40).…”

Section: полногеномное исследование ассоциаций Snp с высотой в холке в популяциях локальных и трансграничных пород крупного рогатогоunclassified

Whole Genome Study of Single Nucleotide Polymorphisms’ Associations With Withers Height in Local and Transboundary Breeds in Russia

Abdelmanova¹

2021

S-h. biol.

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“…One of these regions is localized on BTA 14 and contains the XKR4, TMEM68, TGS1, LYN, RPS20, MOS, PLAG1, and CHCHD7 genes which are well-known candidates for growth, carcass-related traits [66][67][68], and feed intake [69][70][71]. The PLAG1 gene (or PLAG1-CHCHD7 region) is a strong candidate responsible for stature; body size, including height [72]; and weight in many cattle breeds [73][74][75][76][77][78]. Fink et al [79] found a strong association of the PLAG1 genotype with milk fat and protein yield.…”

Section: Functional Annotation Of Candidate Genes Localised Within Thmentioning

confidence: 99%

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

et al. 2020

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Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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A novel SNP of PLAG1 gene and its association with growth traits in Chinese cattle

Cited by 26 publications

References 18 publications

Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models

Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models

Whole Genome Study of Single Nucleotide Polymorphisms’ Associations With Withers Height in Local and Transboundary Breeds in Russia

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

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