Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.Key words: rice, chloroplast, simple sequence repeat, microsatellites.

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Implementing molecular marker technology in forage improvement

Proceedings of the New Zealand Grassland Association ◽

10.33584/jnzg.2003.65.2498 ◽

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

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

Pakistan Journal of Botany ◽

10.30848/pjb2019-5(41) ◽

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

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

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2009.00958 ◽

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

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Genetic Diversity in Natural Populations of Abies chensiensis Based on Nuclear Simple Sequence Repeat Markers

CHINESE BULLETIN OF BOTANY ◽

10.3724/sp.j.1259.2012.00413 ◽

2013 ◽

Vol 47 (4) ◽

pp. 413-421

Author(s):

Li Weimin ◽

Li Sifeng ◽

Li Bin

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Natural Populations ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Abies Chensiensis ◽

Simple Sequence

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A Simple Sequence Repeat-Based Linkage Map of Barley

Genetics ◽

10.1093/genetics/156.4.1997 ◽

2000 ◽

Vol 156 (4) ◽

pp. 1997-2005 ◽

Cited By ~ 3

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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