scholarly journals Genomic Patterns of Homozygosity in Chinese Local Cattle

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lingyang Xu ◽  
Guoyao Zhao ◽  
Liu Yang ◽  
Bo Zhu ◽  
Yan Chen ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Average Length ◽  
Nucleotide Polymorphism ◽  
Adaptive Traits ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Average Proportion ◽  
Genomic Patterns

AbstractGenome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5–1 Mb, Medium 1–5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.

scholarly journals Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds

Animals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 596 ◽  
Author(s):  
Fengwei Zhang ◽  
Kaixing Qu ◽  
Ningbo Chen ◽  
Quratulain Hanif ◽  
Yutang Jia ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genetic Characteristics ◽  
Cattle Breeds ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Whole Genome Resequencing ◽  
Immune Related Genes ◽  
Go Terms ◽  
Subtropical Environment

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

scholarly journals Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 705
Author(s):  
John Carlos I. Ignacio ◽  
Maricris Zaidem ◽  
Carlos Casal ◽  
Shalabh Dixit ◽  
Tobias Kretzschmar ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Genotyping Platform ◽  
Anaerobic Germination ◽  
Direct Seeded ◽  
Mapping By Sequencing ◽  
Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

scholarly journals Prevalence of ACSL (rs6552828) polymorphism among runners

2019 ◽  
Vol 24 ◽  
pp. 121-128
Author(s):  
Sigal Ben-Zaken ◽  
Yoav Meckel ◽  
Dan Nemet ◽  
Alon Eliakim
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Basis ◽  
Maximal Oxygen Consumption ◽  
Professional Athletes ◽  
Distance Runners ◽  
Nucleotide Polymorphism ◽  
Long Distance ◽  
Single Nucleotide ◽  
The Common

The ACSL A/G polymorphism is associated with endurance trainability. Previous studies have demonstrated that homozygotes of the minor AA allele had a reduced maximal oxygen consumption response to training compared to the common GG allele homozygotes, and that the ACSL A/G single nucleotide polymorphism explained 6.1% of the variance in the VO2max response to endurance training. The contribution of ACSL single nucleotide polymorphism to endurance trainability was shown in nonathletes, however, its potential role in professional athletes is not clear. Moreover, the genetic basis to anaerobic trainability is even less studied. Therefore, the aim of the present study was to examine the prevalence of ACSL single nucleotide polymorphism among professional Israeli long distance runners (n=59), middle distance runners (n=31), sprinters and jumpers (n=48) and non-athletic controls (n=60). The main finding of the present study was that the ACSL1 AA genotype, previously shown to be associated with reduced endurance trainability, was not higher among sprinters and jumpers (15%) compared to middle- (16%) and long-distance runners (15%). This suggests that in contrast to previous studies indicating that the ACSL1 single nucleotide polymorphism may influence endurance trainability among non-athletic individuals, the role of this polymorphism among professional athletes is still not clear.

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