Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation

2005 ◽  
Vol 3 (1) ◽  
pp. 45-57 ◽  
Author(s):  
M.L. Wang ◽  
N.A. Barkley ◽  
J.-K. Yu ◽  
R.E. Dean ◽  
M.L. Newman ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Transfer Rate ◽  
Genetic Relatedness ◽  
Expressed Sequence Tag ◽  
Cynodon Dactylon ◽  
Grass Species ◽  
Cereal Crops ◽  
Sequence Repeat ◽  
Simple Sequence

A major challenge for the molecular characterization and evaluation of minor grass species germplasm is the lack of sufficient DNA markers. A set of 210 simple sequence repeat (SSR) markers developed from major cereal crops (self-pollinated wheat and rice, mainly self-pollinated sorghum and out-crossing maize) were evaluated for their transferability to minor grass species (finger millet, Eleusine coracana; seashore paspalum, Paspalum vaginatum; and bermudagrass, Cynodon dactylon). In total, 412 cross-species polymorphic amplicons were identified. Over half of the primers generated reproducible cross-species or cross-genus amplicons. The transfer rate of SSR markers was correlated with the phylogenetic relationship (or genetic relatedness) of these species. The average transfer rate of genomic SSR markers was different from the average transfer rate of expressed sequence tag (EST)-SSR markers. The level of polymorphism was significantly higher among species (67%) than within species (34%), and was related to the degree of out-crossing for each species. The level of polymorphism detected within species was 57% from self-incompatible species, 39% from out-crossing species and 20% from self-pollinated species. Genomic SSRs detected a higher level of polymorphism than EST-SSRs. The use of transferred polymorphic SSR markers for the characterization and evaluation of germplasm is discussed.

scholarly journals Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

2016 ◽  
Vol 106 (4) ◽  
pp. 362-371 ◽  
Author(s):  
P. Cheng ◽  
X. M. Chen ◽  
D. R. See
Keyword(s):  
Ssr Markers ◽  
Stripe Rust ◽  
Simple Sequence Repeat ◽  
Puccinia Striiformis ◽  
The United States ◽  
Grass Species ◽  
Cereal Crops ◽  
Sequence Repeat ◽  
Grass Hosts ◽  
Simple Sequence

Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.

Simple sequence repeat (SSR) markers for Elymus, Pseudoroegneria and Pascopyrum species (Triticeae: Gramineae)

2011 ◽  
Vol 9 (4) ◽  
pp. 489-494 ◽  
Author(s):  
I. W. Mott ◽  
S. R. Larson ◽  
B. S. Bushman
Keyword(s):  
Ssr Markers ◽  
North American ◽  
Simple Sequence Repeat ◽  
Binary Data ◽  
Expressed Sequence Tag ◽  
Molecular Mapping ◽  
Perennial Grass ◽  
Grass Species ◽  
Sequence Repeat ◽  
Simple Sequence

The Triticeae tribe (Poaceae) includes several important cereal crops, cultivated forages, annual and perennial grass weeds and ecologically diverse native North American grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 polyploid perennial grass species occurring worldwide. The genomic constitutions of approximately 40% of the Elymus species are unknown. Molecular markers are needed to facilitate genetic analysis of diversity and functional traits in these species. We have developed simple sequence repeat (SSR) markers for use in Elymus based on Elymus expressed sequence tag sequences. To test the polymorphic content and transferability of these SSRs, 100 SSR primer pairs were tested on 84 plants representing seven North American Elymus, Pseudoroegneria and Pascopyrum species. The number of bands produced from each of the SSRs ranged from 1 to 11 with an average of 4.3 bands/SSR. A subset of the 23 most polymorphic SSRs produced 142 bands, an average of 6.2 bands/SSR. Binary data from the 100 SSRs successfully separated all individuals into their respective accessions in a neighbour-joining phylogram with a 100% confidence interval. Analysis of molecular variance showed that 29.9% of the total variation was within and 70.1% was among the accessions. These SSRs will be a useful tool for investigating genetic diversity, genome constitutions and molecular mapping in Elymus and other Triticeae grasses.

scholarly journals Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers

2008 ◽  
Vol 133 (6) ◽  
pp. 810-818 ◽  
Author(s):  
John McCallum ◽  
Susan Thomson ◽  
Meeghan Pither-Joyce ◽  
Fernand Kenel ◽  
Andrew Clarke ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bulb Onion ◽  
Expressed Sequence ◽  
Simple Sequence

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

scholarly journals Verification of Mandarin and Pummelo Somatic Hybrids by Expressed Sequence Tag–Simple Sequence Repeat Marker Analysis

2008 ◽  
Vol 133 (6) ◽  
pp. 794-800 ◽  
Author(s):  
Chunxian Chen ◽  
Jude W. Grosser ◽  
Milica Ćalović ◽  
Patricia Serrano ◽  
Gemma Pasquali ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Breeding System ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Somatic Hybrids ◽  
Poncirus Trifoliata ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence

Somatic hybridization is a powerful tool for the genetic improvement of citrus rootstocks, and it is part of an efficient in vitro-based breeding system described here. An essential component of the system is the requirement of confirming tetraploidy and the combination of the two donor genomes. Expressed sequence tag–simple sequence repeat (EST-SSR) markers provide a means to accomplish both of these objectives, and their application to a population of pummelo [Citrus grandis (L.) Osbeck] + mandarin (C. reticulata Blanco) somatic hybrids developed for the specific purpose of providing alternative rootstocks for sour orange (Citrus aurantium L.) is detailed. Nineteen new somatic hybrids were produced from various mandarin and pummelo parents, and their ploidy level and the complementation of their nuclear genomes were confirmed using four EST-SSR markers. These markers were selected from markers previously mapped in sweet orange [C. sinensis (L.) Osbeck] and trifoliate orange [Poncirus trifoliata (L.) Raf.] and prescreened for suitable allelic polymorphism within the mandarin and pummelo lines used. After polymerase chain reaction amplification of sequences from the parents and putative hybrids, the products were separated on a genetic sequencer and visualized electronically. Additionally, EST-SSR markers identified the unexpected zygotic origin of a presumed nucellar embryogenic callus line. Integration of EST-SSR techniques for high-throughput genotyping with previously developed approaches to somatic hybrid creation increases substantially the effectiveness and efficiency of this in vitro-based breeding system for citrus rootstock improvement.

Development of simple sequence repeat markers for bermudagrass from its expressed sequence tag sequences and preexisting sorghum SSR markers

2010 ◽  
Vol 29 (1) ◽  
pp. 23-30 ◽  
Author(s):  
Chengcheng Tan ◽  
Yanqi Wu ◽  
Charles M. Taliaferro ◽  
Michael P. Anderson ◽  
Chuck Tauer ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Expressed Sequence ◽  
Simple Sequence

scholarly journals Identification of Turf Bermudagrasses on the Oklahoma State University Baseball Field and Three Experimental Clones as Revealed with Simple Sequence Repeat Markers

2015 ◽  
Vol 25 (6) ◽  
pp. 714-724 ◽  
Author(s):  
Tilin Fang ◽  
Yanqi Wu ◽  
Shiva Makaju ◽  
Todd Tribble ◽  
Dennis L. Martin ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Cynodon Dactylon ◽  
State University ◽  
Oklahoma State University ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Cultural Requirements ◽  
Simple Sequence ◽  
Over Time

Turfgrass varietal identification is critical and allows turfgrass professionals to manage the turf based on the cultural requirements of the variety. On the Oklahoma State University (OSU) Baseball Field (OSUBF) in Stillwater, OK, some bermudagrass (Cynodon sp.) plants exhibited desirable traits but their exact identities were unknown due to the installation of multiple varieties over time. Accordingly, the major objective of this study was to identify if the desirable bermudagrass plants were from commercially available known varieties. Recently, the OSU turf bermudagrass breeding program developed and entered three fairway-type clonal bermudagrasses in the 2013 National Turfgrass Evaluation Program (NTEP) bermudagrass trial: OKC 1131, OKC 1163, and OKC 1302. The secondary objective was to create molecular marker profiles for these three experimental lines. Five OSUBF samples were analyzed using simple sequence repeat (SSR) markers, along with 24 clonal, commercially available turf bermudagrass varieties widely used in Oklahoma, the three OSU experimental clones, six randomly selected single plants from ‘Riviera’, and two controls for common bermudagrass (Cynodon dactylon) and african bermudagrass (Cynodon transvaalensis). SSR marker genotyping data indicated that the five OSUBF plants were clones of an identical bermudagrass. The OSUBF bermudagrass had the same fingerprint as ‘Astro-DLM’ bermudagrass for 14 out of 16 SSRs genotyped. Fifteen out of 30 additional SSR markers also showed differences between the OSUBF bermudagrass and ‘Astro-DLM’. The three OSU experimental clones were different from each other and had different fingerprints from the other tested varieties based on SSR profiles, indicating they are new breeding lines. These four distinct lines have potential to be released as new varieties if they demonstrate superior turf quality traits and adaptation over time.

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