Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

Shen, Jiafei; Hanif, Quratulain; Cao, Yang; Yu, Yong; Lei, Chuzhao; Zhang, Guoliang; Zhao, Yumin

doi:10.3389/fgene.2020.00094

Cited by 30 publications

(22 citation statements)

References 36 publications

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“…Moreover, we observed two genes (FGFR3 and FGFRL1), which were identified as negative regulators of endochondral ossification [57] and body size [58]. Several genes, including CTNNA1, LRRTM2, SIL1, and NMNAT1, have been implicated under the selection [59][60][61][62] and overlapped with the previously identified regions of ROH [49,63]. We also found two genes (CTNNBIP1 and NMNAT1) to be related to reproductive efficiency.…”

Section: Discussionsupporting

confidence: 58%

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Zhao

Zhang

Liu

et al. 2020

Animals

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Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.

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Section: Discussionsupporting

confidence: 58%

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Zhao

Zhang

Liu

et al. 2020

Animals

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“…Heat stress in northern China, such as in Hebei, Shandong, and Henan, reach emergency levels in July, and the loss of milk production has been calculated as 90-120 kg/cow/month [62]. The main breeds are Mongolian cattle, Chinese Holstein cattle, Inner-Mongolia Sanhe cattle, and Yanbian cattle, which have the characteristics of cold tolerance in this region [69][70][71][72]. The strategies recommended in the tropical region are applicable to alleviate heat stress during the summer, such as building sunshades, installing electric fans, reducing the number of heads in the mob, increasing the feeding times at night, adding more green materials in the diet, and increasing minerals and microelements to ensure the healthy growth of cattle [11,60,[73][74][75][76].…”

Section: Discussionmentioning

confidence: 99%

Temporal–Spatial Distribution of Risky Sites for Feeding Cattle in China Based on Temperature/Humidity Index

2020

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This study identifies risk areas for cattle husbandry based on temperature and a relative humidity index (THI) derived from climate data (1987 to 2016) at 839 meteorological stations in China using geostatistics (ordinary and indicator kriging) in the geographical information system (GIS). In general, monthly mean THI values were the highest in July and the lowest in January for all regions. The correlation analysis showed that there were negative relationships between THI values and latitude or elevation for the whole year (p < 0.01). The THI values were higher at low latitudes in coastal areas and at high latitudes in arid areas in summer. The healthy risk for cattle production varied depending on the time of the year and region. The study shows that cattle production is suitable throughout the whole year in the Qinghai-Tibet Plateau; from October to April for most areas, except the southern coastal areas; in May and September in Northeast China, North China, and parts of Northwest China; in June in Heilongjiang and Inner Mongolia. The information obtained in this study can provide a regional distribution of risk for the cattle industry in China.

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“…Based on whole-genome sequencing, many studies initially focused on the genetic architecture and economic traits under positive selection in commercial breeds (Bovine et al, 2009;Stothard et al, 2011), and then the focus gradually shifted to the adaptation of indigenous breeds, such as climate tolerance and disease resistance (Kim et al, 2017;Taye et al, 2017;Kim et al, 2020). With the development of next-generation sequencing technology and the enrichment of re-sequencing databases, genome-wide genetic analysis studies play an increasingly powerful role in the investigation of germplasm resources of landraces, such as cold tolerance of Yanbian cattle (Shen et al, 2020), excellent meat quality of Mongolian cattle (Chen et al, 2021), heat tolerance and parasite resistance of African cattle (Kim et al, 2017), and growth rate and feed conversion of Jiaxian red cattle (Xia et al, 2021). An earlier study on Dianzhong cattle using Illumina BovineHD BeadChip (777K) demonstrated that Dianzhong cattle contained mainly indicine ancestry mixed with taurine ancestry.…”

Section: Introductionmentioning

confidence: 99%

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning

Zhang

Jia

et al. 2021

Front. Genet.

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Dianzhong cattle is a classic Chinese indigenous cattle breed with historical records dating back to 200 BC. But with its genomic differences having not been clearly elucidated, the quest for genomic characterization will be an essential step towards understanding the genomic basis of productivity and adaptation to survival under Chinese farming systems. Here we compared 10 Dianzhong cattle (four newly sequenced and six downloaded) with 29 published genomes of three underlying ancestral populations (Chinese zebu, Indian zebu, and Yanbian cattle) to characterize the genomic variations of Dianzhong cattle. Dianzhong cattle has a high nucleotide diversity (0.0034), second only to Chinese zebu. Together with analyses of linkage disequilibrium decay and runs of homozygosity, Dianzhong cattle displayed higher genomic diversity and weaker artificial selection compared with Yanbian cattle. From a selective sweep analysis by four methods (Fst, π-ratio, XP-CLR, and XP-EHH), the positive selective signals were mainly manifested in candidate genes and pathways related to heat resistance, growth and development, fat deposition, and male reproduction. Missense mutations were detected in candidate genes, SDS (c.944C > A and p.Ala315Glu), PDGFD (c.473A > G and p.Lys158Arg), and DDX4 (rs460251486, rs722912933, and rs517668236), which related to heat resistance, fat deposition, and spermatogenesis, respectively. Our findings unravel, at the genome-wide level, the unique diversity of Dianzhong cattle while emphasizing the opportunities for improvement of livestock productivity in further breeding programs.

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Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

Cited by 30 publications

References 36 publications

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Temporal–Spatial Distribution of Risky Sites for Feeding Cattle in China Based on Temperature/Humidity Index

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning

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