scholarly journals Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1792
Author(s):  
Hongyang Wang ◽  
Yang Fu ◽  
Peng Gu ◽  
Yingying Zhang ◽  
Weilong Tu ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Growth And Development ◽  
Miniature Pig ◽  
Sequencing Data ◽  
Pig Breeds ◽  
Polymorphic Ssrs ◽  
Repeat Units ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Simple Sequence

Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.

scholarly journals Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)

2021 ◽  
Vol 104 (3) ◽  
pp. 003685042110355
Author(s):  
Hai-feng Tian ◽  
Qiao-mu Hu ◽  
Zhong Li
Keyword(s):  
Genetic Diversity ◽  
Capillary Electrophoresis ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Breeding Population ◽  
Monopterus Albus ◽  
Polymorphic Ssrs ◽  
Genome Wide ◽  
Swamp Eel ◽  
Simple Sequence

Objectives: Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. Methods: The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. Results: A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. Conclusions: The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes ( FIS = 0.155) in one breeding population provide baseline information for future breeding program.

scholarly journals Genome-wide analysis of DNA methylation in obese, lean and miniature pig breeds

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Yalan Yang ◽  
Rong Zhou ◽  
Yulian Mu ◽  
Xinhua Hou ◽  
Zhonglin Tang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Miniature Pig ◽  
Genome Wide Analysis ◽  
Pig Breeds ◽  
Genome Wide

scholarly journals Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

2020 ◽  
Author(s):  
Albert Maibam ◽  
Sunil Nigombam ◽  
Harinder Vishwakarma ◽  
Showkat Ahmad Lone ◽  
Kishor Gaikwad ◽  
...  
Keyword(s):  
Heat Stress ◽  
Pearl Millet ◽  
Stress Responses ◽  
Simple Sequence Repeats ◽  
Pennisetum Glaucum ◽  
Average Length ◽  
Gc Content ◽  
Functional Markers ◽  
Sequencing Data ◽  
Simple Sequence

Abstract Background Pennisetum glaucum (L.) R. Br. is mainly grown in arid and semi-arid regions. Being naturally tolerant to various adverse condtitions, it is a good biological resource for deciphering the molecular basis of abiotic stresses such as heat stress in plants but limited studies have been carried out till date to this effect. Here, we performed RNA-sequencing from the leaf of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42 °C for 6 h). Results Over 274 million high quality reads with an average length of 150 nt were generated. Assembly was carried out using trinity, obtaining 47,310 unigenes having an average length of 1254 nucleotides, N50 length of 1853 nucleotides and GC content of 53.11%. Blastx resulted in annotation of 35,628 unigenes and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms, 13,786 unigenes allocated to 23 Clusters of Orthologous Groups and 4,255 unigenes distributed into 132 functional KEGG pathways. 12,976 simple sequence repeats were identified from 10,294 unigenes for the development of functional markers. A total of 3,05,759 SNPs were observed in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidates genes were selected based on log2 fold change and adjusted p-value parameters for their differential gene expression by qRT-PCR. Conclusions The dynamic expression changes in two genotypes of P. glaucum reflect transcriptome regulation of signaling pathways in heat stress response. In order to develop genetic markers, 12,976 simple sequence repeats (SSRs) were identified. The sequencing data generated in this study shall serve as an important resource for further research in the area of crop biotechnology.

scholarly journals Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

2020 ◽  
Vol 8 (5) ◽  
pp. 662 ◽  
Author(s):  
Yuan Li ◽  
Xiao Chen ◽  
Kun Wu ◽  
Jiao Pan ◽  
Hongan Long ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Evolutionary History ◽  
Rapid Evolution ◽  
Genome Diversity ◽  
Unicellular Eukaryotes ◽  
Genome Wide ◽  
Species Analysis ◽  
Simple Sequence ◽  
High Diversity

Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1–100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.

scholarly journals Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e59562 ◽  
Author(s):  
Lidan Sun ◽  
Weiru Yang ◽  
Qixiang Zhang ◽  
Tangren Cheng ◽  
Huitang Pan ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Linkage Mapping ◽  
Prunus Mume ◽  
Genome Wide ◽  
Simple Sequence

scholarly journals Detection of simple sequence repeats in the chloroplast genome of Tetraphis pellucida Hedw.

2016 ◽  
Vol 3 (2) ◽  
pp. 207 ◽  
Author(s):  
Asheesh Shanker
Keyword(s):  
Chloroplast Genome ◽  
Simple Sequence Repeats ◽  
Average Length ◽  
Accession Number ◽  
Repeat Type ◽  
Perl Script ◽  
Repeat Units ◽  
Short Repeat ◽  
Diversity Studies ◽  
Simple Sequence

Simple sequence repeats (SSRs) consist of short repeat motifs of 1-6 nucleotides and are found in DNA sequences.The present study was conducted to detect SSRs in chloroplast genome of Tetraphis pellucida (Accession number: NC_024291), downloaded from the National Center for Biotechnology Information (NCBI). The sequence was mined with the help of MISA, a Perl script, to detect SSRs. The length of SSRs defined as ≥12 for mono, di, tri and tetranucleotide, ≥15 for pentanucleotide and ≥18 for hexanucleotide repeats. In total, 41 perfect microsatellites were identified in 127.489 kb sequence mined. An average length of 13.56 bp was calculated for mined SSRs with a density of 1 SSR/3.04 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 20 nt. Dinucleotides (14, 34.15%) were the most frequent repeat type, followed by tetranucleotides (10, 24.39%), trinucleotides (7, 17.07%), mononucleotides (6, 14.63%) and pentanucleotide (4, 9.76%) repeats. Hexanucleotide repeats were completely absent in chloroplast genome of Tetraphis pellucida. The mined SSRs can be used to develop molecular markers and genetic diversity studies in Tetraphis species.

scholarly journals Genome-wide characterization of simple sequence repeats in Palmae genomes

2020 ◽  
Vol 42 (5) ◽  
pp. 597-608
Author(s):  
Manee M. Manee ◽  
Badr M. Al-Shomrani ◽  
Mohamed B. Al-Fageeh
Keyword(s):  
Simple Sequence Repeats ◽  
Genome Wide ◽  
Simple Sequence

scholarly journals Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 537 ◽  
Author(s):  
Qiong Zhang ◽  
Baiquan Ma ◽  
Hui Li ◽  
Yuansheng Chang ◽  
Yuanyuan Han ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Genome Wide ◽  
Simple Sequence
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