scholarly journals Comparative transcriptome analysis of the ovary and testis of the lacustrine goby (Gobiopterus lacustris)

2019 ◽  
Author(s):  
Zhongdian Dong ◽  
Chengqin Huang ◽  
Hairui Zhang ◽  
Shunkai Huang ◽  
Ning Zhang ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Future Research ◽  
Coastal Environments ◽  
Comparative Transcriptome ◽  
Brackish Waters ◽  
Qpcr Analysis ◽  
First Time ◽  
Simple Sequence

ABSTRCTLacustrine goby (Gobiopterus lacustris) belongs to a genus of gobies that are small in size and endemic to freshwater, brackish waters or coastal environments around the Indian and Pacific oceans. To date, there are no genomic or transcriptomic studies on G. lacustris. Here, we constructed gonadal transcriptomes of G. lacustris for the first time and identified genes that may be involved in gonadal development and reproduction. In total, 60,657,644 and 52,016,136 clean reads were obtained from ovary and testis, respectively, using Illumina sequencing. Reads were assembled into 62,573 unigenes with N50 value of 3,082 bp and a mean length of 1,869 bp. A total of 47,891 (76.53%) unigenes were annotated in at least one of the seven databases that were used in this study. In addition, 38,550 SSRs (simple sequence repeat, microsatellite) were identified from 20,517 SSR containing sequences. Gene expression patterns in the testis and ovary were compared, and 10,954 DEGs (differentially expressed genes) were identified. Of these genes, 2,383 were up-regulated in the testis and 8,571 were up-regulated in the ovary. RT-qPCR analysis of 14 selected genes showed patterns consistent with the transcriptome results. Numerous DEGs involved in gonadal development and gametogenesis were identified, including foxl2, dmrt1, cyp19a1a, inha, inhb, sycp2, zglp1, tdrp, zps and esra. Using GO and KEGG enrichment analyses, pathways involving regulation of gonadal development and gametogenesis also identified. This work represents the first gonadal transcriptomic analysis of G. lacustris and provides a valuable dataset for future research on the genes involved in reproduction of G. lacustris.

scholarly journals Comparative Transcriptome Analysis of Female and Male Fine-Patterned Puffer: Identification of Candidate Genes Associated with Growth and Sex Differentiation

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 79
Author(s):  
Binbin Shan ◽  
Yan Liu ◽  
Changping Yang ◽  
Yuan Li ◽  
Liangming Wang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Sexual Size Dimorphism ◽  
Sex Differentiation ◽  
Complex Phenomenon ◽  
Common Phenomenon ◽  
Comparative Transcriptome ◽  
Comparison Analysis ◽  
Size Dimorphism ◽  
First Time ◽  
Simple Sequence

Sexual growth dimorphism is a common phenomenon in teleost fish. However, the mechanism of this complex phenomenon remains unclear. The fine-patterned puffer (Takifugu poecilonotus; Temminck and Schlegel, 1850) exhibits female-biased sexual size dimorphism similar to other pufferfish. In this study, the transcriptomes of female and male T. poecilonotus were sequenced, 285.95 million raw read pairs were generated from sequence libraries. After identification and assembly, a total of 149,814 nonredundant unigenes were obtained with an N50 length of 3538 bp. Of these candidates, 122,719 unigenes (81.91% of the total) were successfully annotated with multiple public databases. The comparison analysis revealed 10,385 unigenes (2034 in females and 8351 in males) were differentially expressed between different sexes of T. poecilonotus. Then, we identified many candidate growth- and sex-related genes, including Dmrt1, Sox3, Spatas, Prl/Prlr, fabps, Ghr, and Igf1r. In addition to these well-known genes, Fabp4 was identified for the first time in fish. Furthermore, 68,281 simple sequence repeats (SSRs) loci were screened and identified in the transcriptome sequence of T. poecilonotus. The results of our study could provide valuable information on growth- and sex-associated genes and facilitate further exploration of the molecular mechanism of sexual growth dimorphism.

scholarly journals INTER-SIMPLE SEQUENCE REPEAT ANALYSIS AND ALLELIC DIVERSITY AMONG GENOTYPES OF CULTIVATED Digitaria species

2018 ◽  
Vol 30 (2) ◽  
pp. 01-08
Author(s):  
D. A. Animasaun ◽  
K. F. Awujoola ◽  
R. Krishnamurthy ◽  
J. A. Morakinyo
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Similarity Index ◽  
Allelic Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Analysis ◽  
First Time ◽  
Simple Sequence

Acha (Digitaria exilis Kipps. and D. iburua Stapf.) are valuable indigenous food crops in West Africa, but despite several economic potentials of this crop, little or no attention is paid to its germplasm evaluation and improvement. In this study, we assessed genetic diversity and relationship among genotypes of cultivated acha in Nigeria using Inter-Simple Sequence Repeat (ISSR) markers for the first time. Genomic DNA were extracted from the genotypes and we performed fragment amplification by Polymerase Chain Reaction (PCR). A total of 95 loci consisting of 790 bands were amplified by 13 ISSR primers, out of which 53.37% were polymorphic. Loci amplification per primer ranged from 5-10, with an average of 7.30 loci per primer. Eight of the primers had above 50% polymorphism. Cluster analysis separated the genotypes into two major groups; a group consisting of two D. exilis genotypes and the other comprising a mixture of genotypes. The D. exilis in the latter group were distant members and was only similar at 0.72 similarity index. The polymorphism we obtained in the present study showed that the ISSR markers are effective for assessment of genetic diversity of the genotypes. Clustering of D. exilis and D. iburua together suggests a common progenitor but could have been separated by geographical isolation mechanism

scholarly journals Ecotype-Level Genetic Biodiversity of Five Italian Traditional Crops

Scientifica ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Francesco Guarino ◽  
Stefano Castiglione ◽  
Giovanni Improta ◽  
Maria Triassi ◽  
Angela Cicatelli
Keyword(s):  
Simple Sequence Repeat ◽  
Farming Systems ◽  
Farming Practices ◽  
High Mountains ◽  
Traditional Farming ◽  
Campania Region ◽  
Genetic Biodiversity ◽  
High Level ◽  
First Time ◽  
Simple Sequence

Italy displays a high level of agrobiodiversity due to its diversified pedoclimatic zones. The Administrative Region of Campania includes several and divergent biomes, occurring close to each other. In fact, the distance between a sea level environment and that of high mountains can be less than 20 km. These environmental conditions allow the cultivation of many different crops and vegetables, represented by diverse ecotypes and varieties that are well adapted to the distribution range where they have been selected and grown. Efforts to maintain and further increase biodiversity in farming systems require a better understanding of the existing diversity created by traditional farming practices. The aim of our study was to identify and molecularly characterize several ecotypes belonging to five horticultural species commonly cultivated in Campania. In particular, we analysed five ecotypes of maize, two of garlic, four of onion, one of escarole, and two of courgette by means of simple sequence repeat (SSR) markers in order to evaluate their level of genetic biodiversity. The results reveal, for the first time, the high genetic biodiversity of horticultural ecotypes of the Campania Region. This feature is very important to improve the quality and productivity of agroecosystems.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence

Mapping Unequal Crossing over Hotspot Region of Simple Sequence Repeat in Maize

2009 ◽  
Vol 35 (5) ◽  
pp. 958-961
Author(s):  
Ji-Hua TANG ◽  
Xi-Qing MA ◽  
Wen-Tao TENG ◽  
Jian-Bing YAN ◽  
Jing-Rui DAI ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Crossing Over ◽  
Sequence Repeat ◽  
Unequal Crossing Over ◽  
Simple Sequence

scholarly journals A Simple Sequence Repeat-Based Linkage Map of Barley

Genetics ◽  
2000 ◽  
Vol 156 (4) ◽  
pp. 1997-2005 ◽  
Author(s):  
L Ramsay ◽  
M Macaulay ◽  
S degli Ivanissevich ◽  
K MacLean ◽  
L Cardle ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Interspecific Cross ◽  
Hordeum Spontaneum ◽  
Doubled Haploid Population ◽  
Sequence Repeat ◽  
Genomic Libraries ◽  
Barley Cultivars ◽  
Multiple Loci ◽  
Marker Distribution ◽  
Simple Sequence

AbstractA total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F1 of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

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