scholarly journals Four Novel SNPs of MYO1A Gene Associated with Heat-Tolerance in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 964
Author(s):  
Peng Jia ◽  
Cuicui Cai ◽  
Kaixing Qu ◽  
Ningbo Chen ◽  
Yutang Jia ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Bovine Genome ◽  
Climatic Conditions ◽  
Candidate Snps ◽  
Phenotypic Effect ◽  
Indigenous Cattle ◽  
Synonymous Mutations ◽  
Chinese Cattle ◽  
Variation Database ◽  
Intron Mutation

Based on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a (MYO1A) gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. In our study, four novel candidate SNPs highly conserved in B. indicus breeds but barely existed in B. taurus were identified in MYO1A gene according to Bovine Genome Variation Database and Selective Signatures (BGVD). PCR and DNA sequencing were used to genotype 1072 individuals including 34 Chinese indigenous cattle breeds as well as Angus and Indian zebu. Two synonymous mutations (rs208210464 and rs110123931), one missense mutation (rs209999142; Phe172Ser), and one intron mutation (rs135771836) were detected. The frequencies of mutant alleles of the four SNPs gradually increased from northern groups to southern groups of Chinese cattle, which was consistent with the distribution of various climatic conditions of China. Additionally, four SNPs were significantly associated with four climatic conditions including annual mean temperature (T), relative humidity (H), temperature-humidity index (THI), and average annual sunshine hours (100-cloudiness) (SR). Among these, rs209999142 and Hap 1/1 had better performance than others. Our results suggested that rs209999142 was associated with heat-tolerance trait and rs208210464, rs110123931, and rs135771836 showed high phenotypic effect on heat-tolerance trait because of the strong linkage with rs209999142. These SNPs could be used as candidates for marker-assisted selection (MAS) in cattle breeding.

scholarly journals MTOR Variation Related to Heat Resistance of Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 915 ◽  
Author(s):  
Qingqing Ning ◽  
Kaixing Qu ◽  
Quratulain Hanif ◽  
Yutang Jia ◽  
Haijian Cheng ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Mean Annual Temperature ◽  
Opposite Pattern ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Chinese Cattle ◽  
Damage Repair ◽  
Temperature Heat ◽  
Humidity Index ◽  
Hot Environments

With the inexorable rise of global temperature, heat stress deserves more and more attention in livestock agriculture. Previous studies have shown that the mechanistic target of rapamycin (MTOR) (NC_037343.1:c.2062G>C) gene contributes to the repair of DNA damage repair and is associated with the adaptation of camels in dry and hot environments. However, it is unknown whether this mutation is related to the heat tolerance of Chinese cattle. In this study, PCR and sequencing were used to type the mutation locus in 1030 individuals of 37 cattle breeds. The analysis results showed that the frequency of G allele of the locus gradually diminished from the northern group to the southern group of native Chinese cattle, whereas the frequency of the C allele showed an opposite pattern, displaying a significant geographical difference across native Chinese cattle breeds. Additionally, an analysis of the locus in Chinese indigenous cattle revealed that this SNP was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < 0.01), suggesting that cattle with C allele was distributed in regions with higher T, RH and THI. In conclusion, this study proved that the mutation of MTOR gene in Chinese cattle could be associated with the heat tolerance.

scholarly journals A Novel SNP in EIF2AK4 Gene Is Associated with Thermal Tolerance Traits in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 375 ◽  
Author(s):  
Kaiyue Wang ◽  
Yanhong Cao ◽  
Yu Rong ◽  
Qingqing Ning ◽  
Peng Jia ◽  
...  
Keyword(s):  
Frequency Distribution ◽  
Association Analysis ◽  
Thermal Tolerance ◽  
Bovine Genome ◽  
Allelic Frequency ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Opposite Pattern ◽  
Indigenous Cattle ◽  
Chinese Cattle

Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4, also known as GCN2), which pertains to the family of serine–threonine kinase, is involved in oxidative stress and DNA damage repair. A missense single-nucleotide polymorphism (SNP) (NC_037337.1 g.35615224 T > G) in exon 6 of the EIF2AK4 gene which encodes a p.Ile205Ser substitution was observed in the Bovine Genome Variation Database and Selective Signatures (BGVD). The purpose of the current study is to determine the allelic frequency distribution of the locus and analyze its association with thermal tolerance in Chinese indigenous cattle. In our study, the allelic frequency distribution of the missense mutation (NC_037337.1 g.35615224 T > G) in Chinese cattle was analyzed by sequencing 1105 individuals of 37 breeds including 35 Chinese indigenous cattle breeds and two exotic breeds. In particular, association analysis was carried out between the genotypes and three environmental parameters including annual mean temperature (T), relative humidity (RH), and temperature–humidity index (THI). The frequency of the mutant allele G (NC_037337.1 g.35615224 T > G) gradually decreased from the southern cattle groups to the northern cattle groups, whereas the frequency of the wild-type allele T showed an opposite pattern, consistent with the distribution of indicine and taurine cattle in China. In accordance with the association analysis, genotypes were significantly associated with T (P < 0.01), RH (P < 0.01), and THI (P < 0.01), suggesting that the cattle with genotype GG were found in regions with higher T, RH, and THI. Thus, our results suggest that the mutation (NC_037337.1 g.35615224 T > G) of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.

scholarly journals The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures

2019 ◽  
Author(s):  
Ningbo Chen ◽  
Weiwei Fu ◽  
Jianbang Zhao ◽  
Jiafei Shen ◽  
Qiuming Chen ◽  
...  
Keyword(s):  
Bovine Genome ◽  
Distribution Patterns ◽  
Global Scale ◽  
Genomic Region ◽  
Genome Browser ◽  
Web Database ◽  
Genome Variation ◽  
Gene Search ◽  
Variation Database ◽  
Coordinate Conversion

AbstractNext-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.

Improving sustainable cotton production through enhanced resilience to climate change using mutation breeding.

2021 ◽  
pp. 145-156
Author(s):  
Manzoor Hussain ◽  
Ljupcho Jankuloski ◽  
M. Habib-ur-Rahman ◽  
Massoud Malek ◽  
Md. Kamrul Islam ◽  
...  
Keyword(s):  
Climate Change ◽  
Heat Stress ◽  
Heat Tolerance ◽  
Mutation Breeding ◽  
Climatic Conditions ◽  
Cotton Production ◽  
Climate Conditions ◽  
Growing Seasons ◽  
Major Factors ◽  
High Yields

Abstract Cotton, being a leading commercial fibre crop, is grown on 20.5 million hectares in three major cotton-producing countries: China, India and Pakistan. Wide differences in yield per hectare exist among these countries and these are being aggravated by changing climate conditions, i.e. higher temperatures and significant seasonal and regional fluctuation in rainfall. Pakistan is one of the countries most affected by climate change. The disastrous effects of extreme periods of heat stress in cotton were very prominent in Pakistan during the growing seasons 2013-2014 (40-50% fruit abortion) and 2016-2017 (33% shortfall), which posed an alarming threat to the cotton-based economy of Pakistan. Poor resilience of the most commonly grown cotton varieties against extreme periods of heat stress are considered to be major factors for this drastic downfall in cotton production in Pakistan. Using the approach of induced mutation breeding, the Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan, has demonstrated its capabilities in developing cotton mutants that can tolerate the changed climatic conditions and sustain high yields under contrasting environments. The results of studies on the phenological and physiological traits conferring heat tolerance are presented here for thermo-tolerant cotton mutants (NIAB-878, NIAB-545, NIAB-1048, NIAB-444, NIAB-1089, NIAB-1064, NIAB-1042) relative to FH-142 and FH-Lalazar. NIAB-878 excelled in heat tolerance by maintaining the highest anther dehiscence (82%) and minimum cell injury percentage (39%) along with maximum stomatal conductance (27.7 mmol CO2/m2/s), transpiration rate (6.89 μmol H2O/m2/s), net photosynthetic rate (44.6 mmol CO2/m2/s) and physiological water use efficiency (6.81 mmol CO2/μmol H2O) under the prevailing high temperatures.

PRLH and SOD1 gene variations associated with heat tolerance in Chinese cattle

2018 ◽  
Vol 49 (5) ◽  
pp. 447-451 ◽  
Author(s):  
L. Zeng ◽  
N. Chen ◽  
Q. Ning ◽  
Y. Yao ◽  
H. Chen ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Sod1 Gene ◽  
Chinese Cattle

A novel SNP of MYO1A gene associated with heat-tolerance in Chinese cattle

2020 ◽  
pp. 1-6
Author(s):  
Yanhong Cao ◽  
Peng Jia ◽  
Zhuyue Wu ◽  
Mingguang Huang ◽  
Shaomei Chen ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Chinese Cattle ◽  
Novel Snp

scholarly journals Detection of Bovine TMEM95 p.Cys161X Mutation in 13 Chinese Indigenous Cattle Breeds

Animals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 444 ◽  
Author(s):  
Sihuan Zhang ◽  
Kun Peng ◽  
Guoliang Zhang ◽  
Yang Cao ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Genetic Marker ◽  
Molecular Breeding ◽  
Transmembrane Protein ◽  
Amplification Refractory Mutation System ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Indel Mutation ◽  
Chinese Cattle ◽  
Mutation System

Chinese indigenous cattle breeds have abundant genetic resources, which are valuable for the molecular breeding of cattle around the world. Thus, identifying important candidate genes and their genetic markers is very important for cattle molecular breeding. A previous study found that a nonsense mutation (rs378652941, c.483C > A, p.Cys161X) in the bovine transmembrane protein 95 gene (TMEM95) seriously reduced the reproductive performance in bulls, but few studies have detected this mutation in Chinese indigenous cattle breeds. Since the mutation c.483C > A may serve as a potential genetic marker for selecting higher fertility bulls, in the present study, using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR), forced PCR restriction fragment length polymorphism (forced PCR-RFLP), and DNA sequencing methods, the mutation c.483C > A was detected in 765 individuals from 13 Chinese cattle breeds. However, the results showed that this mutation did not exist at this locus in our analyzed breeds. Interestingly, we identified a newly frameshift insertion/deletion (indel) mutation (NC_037346.1: g.27056998_27057000delCT) in the bovine TMEM95 gene in 11 cattle breeds, which changed the location of the termination codon and changed the 16 amino acids in the C-terminal to 21 amino acids. Combined with previous studies, our study provides evidence that in Chinese cattle breeds the mutation c.483C > A cannot be used as a genetic marker in molecular breeding.

A novel SNP of TECPR2 gene associated with heat tolerance in Chinese cattle

2021 ◽  
pp. 1-8
Author(s):  
Xiaohui Ma ◽  
Yangkai Liu ◽  
Luyang Sun ◽  
Quratulain Hanif ◽  
Kaixing Qu ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Chinese Cattle ◽  
Novel Snp

scholarly journals Polymorphisms in the bovine HSP90AB1 gene are associated with heat tolerance in Thai indigenous cattle

2011 ◽  
Vol 44 (4) ◽  
pp. 921-928 ◽  
Author(s):  
Rangsun Charoensook ◽  
Kesinee Gatphayak ◽  
Ahmad Reza Sharifi ◽  
Chavin Chaisongkram ◽  
Bertram Brenig ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Indigenous Cattle

scholarly journals Association of HSF1 Genetic Variation with Heat Tolerance in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1027
Author(s):  
Yu Rong ◽  
Mingfei Zeng ◽  
Xiwen Guan ◽  
Kaixing Qu ◽  
Jianyong Liu ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
North China ◽  
Bos Indicus ◽  
Heat Shock Factor 1 ◽  
Heat Stress Response ◽  
Chinese Cattle ◽  
Specific Allele ◽  
Native Cattle ◽  
Humidity Index ◽  
Hsf1 Gene

The heat shock factor 1 (HSF1) gene is a regulator of the heat stress response, maximizing HSP protein expression survival. In this research, we explored the frequency distribution of a missense mutation (NC_037341.1 g.616087A > G, rs135258919) in the HSF1 gene in Chinese cattle with amino acid substitution, valine to alanine. This mutation could be related to the heat tolerance in Bos indicus. A total of 941 individuals representing 35 Chinese native cattle breeds, combining pure taurine (Angus) and indicine cattle, were used to determine the genotypes of the mutation through PCR and partial DNA sequencing. The results showed significant differences in allele frequencies and their genotypes amongst Chinese cattle from different regions. Allele G or indicine-specific allele frequency diminished from south to north China, while allele A (genotype AA) or the taurine-specific allele had a contrary pattern, which agreed with the distribution of taurine and indicine cattle. According to the association analysis, the NC_037341.1 g.616087A > G (rs135258919) of the bovine HSF1 gene, annual temperature (T), relative humidity (RH), and the temperature humidity index (THI) (p < 0.01) were interrelated closely, which indicated that the NC_037341.1 g.616087A > G of the HSF1 gene is associated with heat tolerance in indicine cattle.

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