108 research outputs found
Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus
BACKGROUND: Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. RESULTS: An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested. CONCLUSION: Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses
VNTR-based diversity analysis of 2x and 4x full-sib Musa hybrids
The triploid plantain landrace Obino l'Ewai (Musa spp., AAB genome) has
been crossed with a wild diploid banana (M. acuminata subsp. burmannica
var. 'Calcutta 4', AA genome) to generate full-sib diploid and
tetraploid hybrids combining good agronomic performance and disease
resistance. Microsatellite marker analysis of the parental genotypes
confirmed the highly heterozygous nature of both parental genotypes.
Comparative analysis of 2x and 4x full-sib hybrids with their parental
genotypes indicated that tetraploid hybrids are generally more closely
related to Obino l'Ewai than their diploid full-sibs. Based on VNTR
analysis it is possible to identify those hybrids, which may be most
useful in subsequent breeding of secondary triploid hybrids. There was
a significant (P<0.05) negative association between the VNTR-based
genetic similarity of hybrids to Obino l'Ewai and a phenotypic distance
index based on eight agronomic descriptors. However, there was no
association between the molecular genetic similarity of hybrids to
Calcutta 4 and the respective phenotypic distance index. Many
microsatellite markers generated an unexpectedly high number of
amplification products from AA and AAB genotypes plus their progeny
which may suggest the presence of a high frequency of loci duplication
in both A and B genomes, in addition to the detection of heterozygous
and/or homoeologous loci
Perspectives on the application of biotechnology to assist the genetic enhancement of plantain and banana ( Musa spp.)
Bananas and plantains ( Musa spp.) are the most important tropical
fruit crops. They form an integral component of the farming systems in
the humid agroecological zones of the tropics. A broad array of applied
cell and molecular techniques are increasingly being used worldwide to
facilitate and enhance the handling and improvement of plantain and
banana germplasm. Tissue culture is used for germplasm exchange,
conservation and rapid multiplication, while in vitro seed germination
(based on embryo culture or rescue) plays a critical role in generating
hybrid plants. DNA marker systems have been developed in Musa to assist
germplasm management, selection within the breeding pool or gene
introgression from wild species, and for disease diagnosis. Likewise,
genetic transformation using the particle gun method or through
Agrobacterium co-cultivation shows potential for the genetic
betterment of the crop. This article discusses the applications of
biotechnology for the genetic enhancement of banana and plantain. It
highlights current advances by research teams across the world and
reviews progress in molecular breeding of Musa by the International
Institute of Tropical Agriculture and its collaborators
A legume genomics resource: The Chickpea Root Expressed Sequence Tag Database
Chickpea, a lesser-studied grain legume, is being investigated due to
its taxonomic proximity with the model legume genome Medicago
truncatula and its ability to endure and grow in relatively low soil
water contents making it a model legume crop for the study of agronomic
response to drought stress. Public databases currently contain very few
sequences from chickpea associated with expression in root tissues.
However, root traits are likely to be one of the most important
components of drought tolerance in chickpea. Thus, we have generated a
set of over 2800 chickpea expressed sequence tags (ESTs) from a library
constructed after subtractive suppressive hybridization (SSH) of root
tissue from two closely related chickpea genotypes possessing different
sources of drought avoidance and tolerance (ICC4958 and Annigeri
respectively). This database provides researchers in legume genomics
with a major new resource for data mining associated with root traits
and drought tolerance. This report describes the development and
utilization of the database and provides the tools we have developed to
facilitate the bioinformatics pipeline used for analysis of the ESTs in
this database. We also discuss applications that have already been
achieved using this resource
Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)
<p>Abstract</p> <p>Background</p> <p>Cultivated peanut or groundnut (<it>Arachis hypogaea </it>L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut.</p> <p>Results</p> <p>A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies <it>hypogaea </it>were grouped together in one cluster, while the genotypes belonging to subspecies <it>fastigiata </it>were grouped mainly under two clusters.</p> <p>Conclusion</p> <p>Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as related <it>Arachis </it>species.</p
Analysis of genomic sequences from peanut ( Arachis hypogaea )
Peanut is an important legume crop across the world. However, in
contrast to most legume crops, groundnut lacks taxonomic proximity to
any major model genome. A relatively large number of genomic sequences
were generated from groundnut as part of a microsatellite marker
development project. In the current study, a total of 1312 sequences
were analyzed of which 448 contained microsatellite motifs. All
sequences (GenBank Accessions: BZ999351-CC000573) were analyzed after
clustering for possible similarity with publicly available sequences
from Arabidopsis, Lotus, soybean and Medicago. At least 39% of the
sequences analyzed had significant BLAST similarities with sequences
from the four databases searched, of which nearly half (47%) found
significant similarity with Lotus japonicus sequences. Over one
quarter (26.7%) of sequences found similarity with Arabidopsis thaliana
, while the remainder aligned with publicly available sequences from
the legumes soybean and Medicago truncatula . At least 17% of
microsatellite containing sequences could be assigned an identity. The
codon usage pattern for Arachis hypogaea most closely resembles that
of L. japonicus reflecting the similarly high sequence similarity
observed in BLAST searches at the protein level. The implications of
these findings for the taxonomy, and comparative genomics of groundnut
and its legume family relatives are discussed
- …