Simple Sequence Mutations

2016 ◽  
pp. 217-230
Author(s):  
Christophe Béroud
Keyword(s):  
Simple Sequence

Polymorphism revealed by simple sequence repeats

1996 ◽  
Vol 1 (7) ◽  
pp. 215-222 ◽  
Author(s):  
W POWELL ◽  
G MACHRAY ◽  
J PROVAN
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence

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

LEGITIMACY OF PROGENIES USING SSR MARKERS AS CONTROLLING SYSTEM AND EARLIER SELECTION IN THE OIL PALM NURSERY (Elaeis guineensis JACQ.)

2018 ◽  
Vol 25 (1) ◽  
pp. 21-30
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Abdul Razak Purba
Keyword(s):  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oil Palm ◽  
Dna Markers ◽  
Elaeis Guineensis ◽  
Gene Marker ◽  
Controlling System ◽  
Crossing Probability ◽  
Simple Sequence

Information of legitimacy of oil palm progenies is important to guaranty the quality and to control commercial seeds procedures. A true and legitimate cross will produce progeny which has a combination of their parent's allele. The information could be obtained early in the nursery stage through DNA fingerprinting analysis. Simple Sequence Repeats (SSR) is one of DNA markers used for DNA fingerprinting, since the marker system has advantages to acquire information of allele per individual in population and efficiency diverse allele of progeny and their parents. The aim of the research is to obtain legitimacy of 12 progenies analyzing in the oil palm nursery stage. Thirteen SSR markers were used to analyze 12 crossings number of oil palm. The genotypes data by alleles of SSR inferred and quantified using Gene Marker® Software version 2.4.0 Soft Genetics® LLC and analyzed based on Mendel's Law of Segregation. The result showed based on heredity pattern of progeny and their parent's allele that progenies H were indicated genetically derived from their known parents while progenies from A and G indicated as illegitimate crossing. Probability value for legitimacy of progenies of 9 other crosses has 0.031 and 0.5. Legitimacy analysis of progeny using SSR markers could be used to control the quality of crossing material and earlier selection in the oil palm nursery.

The SUSPECT SYMPTOMS OF INBREEDING DEPRESSION AND THE HOMOZYGOSITY LEVEL OF FOURTH GENERATION OF SP450T AND FIFTH GENERATION OF DURA DELI OIL PALM SELFING POPULATION

2018 ◽  
Vol 24 (2) ◽  
pp. 55-66
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Hernawan Yuli Rahmadi ◽  
Abdul Razak Purba
Keyword(s):  
Inbreeding Depression ◽  
Oil Palm ◽  
Recurrent Selection ◽  
Fourth Generation ◽  
Depression Symptoms ◽  
Reciprocal Recurrent Selection ◽  
Chain Reaction ◽  
Fifth Generation ◽  
Polymerase Chain ◽  
Simple Sequence

Inbreeding is a common method used to reproduce candidate mother plant from selected parental lines for commercial seeds in Reciprocal Recurrent Selection (RRS) oil palm breeding program. However this practice may increased homozigosity level of selected population. This study concerned the level of homozygosity of SP540T fourth generations and Dura Deli Dolok Sinumbah fifth generations (3 crosses respectively) and their correlation with inbreeding depression symptoms. Polymerase Chain Reaction-Simple Sequence Repeat (PCR-SSR) with 16 markers developed for oil palm was used to analyze 327 samples. The result shows that the levels of homozigosity of SP540T fourth selfing generation were ranged between 0.44-0.84 or 0.61 in average. While the levels of homozygosity of Dura Deli fifth selfing generations were ranged between 0.60-0.93 or 0.78 in average. The homozygosity level in Dura Deli was 1.27% higher than SP540T populations. Correlation analysis showed that the higher the level of homozygosity, the higher of the inbreeding symptoms 2 observed (R =0.95).

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.

scholarly journals Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

Marine Drugs ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. 392
Author(s):  
Haomiao Cheng ◽  
Chris Bowler ◽  
Xiaohui Xing ◽  
Vincent Bulone ◽  
Zhanru Shao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Full Length ◽  
Biosynthetic Pathways ◽  
Glycosidic Linkage ◽  
Thalassiosira Weissflogii ◽  
Ecological Value ◽  
Pacbio Sequencing ◽  
Non Coding Rnas ◽  
Chitin And Chitosan ◽  
Simple Sequence

β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.

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