scholarly journals Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat

Genome ◽  
1995 ◽  
Vol 38 (1) ◽  
pp. 45-59 ◽  
Author(s):  
A. E. Van Deynze ◽  
J. Dubcovsky ◽  
K. S. Gill ◽  
J. C. Nelson ◽  
M. E. Sorrells ◽  
...  
Keyword(s):  
Dna Markers ◽  
Molecular Genetic ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Linkage Maps ◽  
Consensus Map ◽  
Triticeae Species ◽  
Group 1 Chromosomes ◽  
Homoeologous Chromosomes ◽  
Group 1

Group 1 chromosomes of the Triticeae tribe have been studied extensively because many important genes have been assigned to them. In this paper, chromosome 1 linkage maps of Triticum aestivum, T. tauschii, and T. monococcum are compared with existing barley and rye maps to develop a consensus map for Triticeae species and thus facilitate the mapping of agronomic genes in this tribe. The consensus map that was developed consists of 14 agronomically important genes, 17 DNA markers that were derived from known-function clones, and 76 DNA markers derived from anonymous clones. There are 12 inconsistencies in the order of markers among seven wheat, four barley, and two rye maps. A comparison of the Triticeae group 1 chromosome consensus map with linkage maps of homoeologous chromosomes in rice indicates that the linkage maps for the long arm and the proximal portion of the short arm of group 1 chromosomes are conserved among these species. Similarly, gene order is conserved between Triticeae chromosome 1 and its homoeologous chromosome in oat. The location of the centromere in rice and oat chromosomes is estimated from its position in homoeologous group 1 chromosomes of Triticeae.Key words: Triticeae, RFLP, consensus, comparative.

Molecular genetic identification of Avena chromosomes related to the group 1 chromosomes of the Triticeae

Genome ◽  
1995 ◽  
Vol 38 (1) ◽  
pp. 185-189 ◽  
Author(s):  
E. N. Jellen ◽  
R. L. Phillips ◽  
W. L. Rooney ◽  
H. W. Rines
Keyword(s):  
Molecular Genetic ◽  
Genetic Identification ◽  
Target Sequence ◽  
Homoeologous Group ◽  
Chinese Spring Wheat ◽  
Complete Series ◽  
Group 1 Chromosomes ◽  
Molecular Genetic Identification ◽  
Homoeologous Chromosomes ◽  
Group 1

A collection of 19 wheat (Triticum aestivum) probes, detecting sequences in the seven homoeologous groups of chromosomes, were hybridized to DNA from the 'Kanota' series of oat monosomic lines (Avena byzantina) to investigate their use for identifying groups of homoeologous oat chromosomes. Three probes from homoeologous group 1 of wheat, psr161, psr162, and psr121, mapped among the set of oat chromosomes 1C, 14, and 17. One homoeologous group 6 probe, psr167, mapped to oat chromosomes 1C and 17. Two oat probes that had previously been shown to map to oat chromosomes 1C, 14, and 17 were then hybridized to DNA from the 'Chinese Spring' wheat ditelosomics. They localized to homoeologous group 1 wheat chromosomes, one to the short arm and one to the long arm. These results reveal that in hexaploid oat there is a group of three chromosomes that correspond at least in part to homoeologous group 1 of wheat. The remaining wheat probes identifying other wheat homoeologous sets did not detect a complete series of homoeologous chromosomes in oat. This was presumably due to the incomplete status of the 'Kanota' monosomic series, chromosomal rearrangement in Avena, weak hybridization signals owing to low probe-target sequence homology, and (or) detection of only two hybridization bands by the wheat probe.Key words: oat, RFLPs, aneuploids, wheat, homoeologous groups.

scholarly journals A Consensus Map for Loblolly Pine (Pinus taeda L.). I. Construction and Integration of Individual Linkage Maps From Two Outbred Three-Generation Pedigrees

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 321-330 ◽  
Author(s):  
Mitchell M Sewell ◽  
Bradley K Sherman ◽  
David B Neale
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Fragment Length Polymorphism ◽  
Random Amplified Polymorphic Dna ◽  
Mapping Function ◽  
Genetic Maps ◽  
Linkage Data ◽  
Linkage Maps ◽  
Consensus Map ◽  
Pinus Taeda L

Abstract A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males {1983.7 cM [Kosambi mapping function (K)]} and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes (n = 12) of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers ∼1300 cM(K).

scholarly journals Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

2013 ◽  
Vol 40 (2) ◽  
pp. 95-106 ◽  
Author(s):  
Baozhu Guo ◽  
Manish K. Pandey ◽  
Guohao He ◽  
Xinyou Zhang ◽  
Boshou Liao ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
High Density ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Consensus Map ◽  
Genetic Linkage Maps ◽  
Marker Loci ◽  
Cultivated Peanut ◽  
Peanut Genome ◽  
Mapping Populations

ABSTRACT The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.

Interspecific nuclear–cytoplasmic compatibility controlled by genes on group 1 chromosomes in durum wheat

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 803-808 ◽  
Author(s):  
J. A. Anderson ◽  
S. S. Maan
Keyword(s):  
Dna Markers ◽  
Male Fertility ◽  
Spontaneous Mutation ◽  
Nuclear Genome ◽  
Rflp Markers ◽  
Seedling Vigor ◽  
Group 1 Chromosomes ◽  
Two Populations ◽  
Aneuploid Analysis ◽  
Group 1

Triticum longissimum cytoplasm is incompatible with the T. turgidum nuclear genome. Two nuclear genes, scs and Vi, derived from the nuclear genome of T. timopheevii and by a spontaneous mutation, respectively, restore nuclear–cytoplasmic compatibility, normal plant vigor, and male fertility in these alloplasmic genotypes. The objectives of this study were (i) to determine the chromosomal locations of scs and Vi; (ii) to identify DNA markers for scs and Vi; and (iii) to determine the interactions involving the dosage of scs and Vi. Two populations segregating for scs and Vi were produced and scored for seedling vigor (indicating presence of scs) and degree of self-fertility (indicating presence of Vi). Four RFLP markers were mapped near scs. Aneuploid analysis revealed that these markers, and hence the scs gene, are located on the long arm of chromosome 1A. Four RFLP markers were mapped near Vi on 1BS. Results indicated that other factors may be inhibiting the expression of Vi. We determined the dosage of scs and Vi in both populations with the aid of the linked RFLP markers. Individuals with two versus one dose of scs had reduced self-fertility, while individuals with two versus one dose of Vi had similar self-fertility.Key words: scs, Vi, Triticum, nucleocytoplasmic compatibility, RFLP.

scholarly journals Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice (Oryza sativa L.)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 716
Author(s):  
Nurhanis Selamat ◽  
Kalaivani K. Nadarajah
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Qtl Analysis ◽  
Oryza Sativa L ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Consensus Map ◽  
Breeding Programs ◽  
Stable Qtls

Rice is an important grain that is the staple food for most of the world’s population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.

scholarly journals Genetic maps of Saccharum officinarum L. and Saccharum robustum Brandes & Jew. ex grassl

1999 ◽  
Vol 22 (1) ◽  
pp. 125-132 ◽  
Author(s):  
Claudia T. Guimarães ◽  
Rhonda J. Honeycutt ◽  
Gavin R. Sills ◽  
Bruno W.S. Sobral
Keyword(s):  
Dna Markers ◽  
Genetic Model ◽  
Saccharum Officinarum ◽  
Genetic Maps ◽  
Breeding Ecology ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Arbitrarily Primed Pcr ◽  
Saccharum Robustum

Genetic analysis was performed in a population composed of 100 F1 individuals derived from a cross between a cultivated sugarcane (S. officinarum `LA Purple') and its proposed progenitor species (S. robustum `Mol 5829'). Various types (arbitrarily primed-PCR, RFLPs, and AFLPs) of single-dose DNA markers (SDMs) were used to construct genetic linkage maps for both species. The LA Purple map was composed of 341 SDMs, spanning 74 linkage groups and 1,881 cM, while the Mol 5829 map contained 301 SDMs, spanning 65 linkage groups and 1,189 cM. Transmission genetics in these two species showed incomplete polysomy based on the detection of 15% of SDMs linked in repulsion in LA Purple and 13% of these in Mol 5829. Because of this incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. Due to inclusion of RFLP anchor probes, conserved in related species, the resulting maps will serve as useful tools for breeding, ecology, evolution, and molecular biology studies within the Andropogoneae.

scholarly journals Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 1 of Wheat

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1883-1891 ◽  
Author(s):  
Kulvinder S Gill ◽  
Bikram S Gill ◽  
Takashi R Endo ◽  
Teri Taylor
Keyword(s):  
Genetic Map ◽  
Physical Map ◽  
Average Distance ◽  
High Density ◽  
Genetic Maps ◽  
Cdna Clones ◽  
Density Mapping ◽  
Physical Maps ◽  
Group 1 Chromosomes ◽  
Group 1

We studied the distribution of genes and recombination in wheat (Triticum aestivum) group 1 chromosomes by comparing high-density physical and genetic maps. Physical maps of chromosomes 1A, 1B, and 1D were generated by mapping 50 DNA markers on 56 single-break deletion lines. A consensus physical map was compared with the 1D genetic map of Triticum tauschii (68 markers) and a Triticeae group 1 consensus map (288 markers) to generate a cytogenetic ladder map (CLM). Most group 1 markers (86%) were present in five clusters that encompassed only 10% of the group 1 chromosome. This distribution may reflect that of genes because more than half of the probes were cDNA clones and 30% were PstI genomic. All 14 agronomically important genes in group 1 chromosomes were present in these clusters. Most recombination occurred in gene-cluster regions. Markers fell at an average distance of 244 kb in these regions. The CLM involving the Triticeae consensus genetic map revealed that the above distribution of genes and recombination is the same in other Triticeae species. Because of a significant number of common markers, our CLM can be used for comparative mapping and to estimate physical distances among markers in many Poaceae species including rice and maize.

Molecular genetic linkage maps for allotetraploid Leymus wildryes (Gramineae: Triticeae)

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 627-646 ◽  
Author(s):  
Xiaolei Wu ◽  
Steven R Larson ◽  
Zanmin Hu ◽  
Antonio J Palazzo ◽  
Thomas A Jones ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Perennial Grass ◽  
Perennial Grasses ◽  
Genetic Maps ◽  
Aflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Leymus Triticoides ◽  
Leymus Cinereus

Molecular genetic maps were constructed for two full-sib populations, TTC1 and TTC2, derived from two Leymus triticoides × Leymus cinereus hybrids and one common Leymus triticoides tester. Informative DNA markers were detected using 21 EcoRI–MseI and 17 PstI–MseI AFLP primer combinations, 36 anchored SSR or STS primer pairs, and 9 anchored RFLP probes. The 164-sib TTC1 map includes 1069 AFLP markers and 38 anchor loci in 14 linkage groups spanning 2001 cM. The 170-sib TTC2 map contains 1002 AFLP markers and 36 anchor loci in 14 linkage groups spanning 2066 cM. Some 488 homologous AFLP loci and 24 anchor markers detected in both populations showed similar map order. Thus, 1583 AFLP markers and 50 anchor loci were mapped into 14 linkage groups, which evidently correspond to the 14 chromosomes of allotetraploid Leymus (2n = 4x = 28). Synteny of two or more anchor markers from each of the seven homoeologous wheat and barley chromosomes was detected for 12 of the 14 Leymus linkage groups. Moreover, two distinct sets of genome-specific STS markers were identified in these allotetraploid Leymus species. These Leymus genetic maps and populations will provide a useful system to evaluate the inheritance of functionally important traits of two divergent perennial grass species.Key words: AFLP, perennial grasses, RFLP, STS, SSR.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

scholarly journals Constructing Large-Scale Genetic Maps Using an Evolutionary Strategy Algorithm

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2269-2282
Author(s):  
D Mester ◽  
Y Ronin ◽  
D Minkov ◽  
E Nevo ◽  
A Korol
Keyword(s):  
Discrete Optimization ◽  
High Performance ◽  
Large Scale ◽  
Simulated Data ◽  
Real Data ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Evolutionary Strategy ◽  
Group A ◽  
The One

Abstract This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with ∼50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

Sign in / Sign up

Export Citation Format

Share Document