The consensus rye microsatellite map with EST-SSRs transferred from wheat

Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped. The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R. With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.

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Application of SSR markers in the construction of Australian barley genetic maps

Australian Journal of Agricultural Research ◽

10.1071/ar02222 ◽

2003 ◽

Vol 54 (12) ◽

pp. 1187 ◽

Cited By ~ 7

Author(s):

G. A. Ablett ◽

A. Karakousis ◽

L. Banbury ◽

M. Cakir ◽

T. A. Holton ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Maps ◽

Sequence Repeat ◽

Consensus Map ◽

Allele Size ◽

Marker System ◽

Different Sources ◽

Simple Sequence ◽

Mapping Populations

Simple sequence repeat (SSR) or microsatellite markers were examined for polymorphisms among the parents of 12 barley mapping populations. Of 259 SSRs screened, 149 were mapped on 1 or more of the 12 doubled haploid populations studied. The relative genetic positions of the 149 mapped SSR markers on Australian varieties are presented in the form of a consensus map. A database was created based on the results of screenings of barley varieties with a series of SSR markers. Details of the markers are at: http://www.scu.edu.au/research/ cpcg/Barley/index.php. A procedure is suggested for mapping new populations with microsatellites using this information and information available on other databases. These 12 populations have been mapped with SSR markers that act as 'anchors' for other types of genetic markers and for traits of interest. Some challenges in mapping SSRs were detailed. Multi-locus markers can cause confusion since one marker can map at different locations. Polymorphisms should be confirmed in new mapping varieties since some variation of allele size is seen in different sources of varieties of the same name, possibly due to differences in sources of germplasm. Lack of standardisation between laboratories or between analytical systems may also lead to differences in called allele sizes. SSRs proved to be adaptable to several technologies and economical, providing a preferred marker system for mapping new barley populations and to 'anchor' other types of markers.

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Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

Peanut Science ◽

10.3146/ps13-03.1 ◽

2013 ◽

Vol 40 (2) ◽

pp. 95-106 ◽

Cited By ~ 12

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.

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A consensus map of rye integrating mapping data from five mapping populations

Theoretical and Applied Genetics ◽

10.1007/s00122-008-0939-4 ◽

2008 ◽

Vol 118 (4) ◽

pp. 793-800 ◽

Cited By ~ 36

Author(s):

J. Perry Gustafson ◽

Xue-Feng Ma ◽

Viktor Korzun ◽

John W. Snape

Keyword(s):

Consensus Map ◽

Mapping Data ◽

Mapping Populations

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Simple Sequence Repeat (SSR) Markers for Genetic Mapping of Raspberry and Blackberry

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.5.722 ◽

2005 ◽

Vol 130 (5) ◽

pp. 722-728 ◽

Cited By ~ 26

Author(s):

Eric T. Stafne ◽

John R. Clark ◽

Courtney A. Weber ◽

Julie Graham ◽

Kim S. Lewers

Keyword(s):

Molecular Markers ◽

Genetic Mapping ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Maps ◽

Black Raspberry ◽

Sequence Repeat ◽

Red Raspberry ◽

Simple Sequence ◽

Mapping Populations

Interest in molecular markers and genetic maps is growing among researchers developing new cultivars of Rubus L. (raspberry and blackberry). Several traits of interest fail to express in seedlings or reliably in some environments and are candidates for marker-assisted selection. A growing number of simple sequence repeat (SSR) molecular markers derived from Rubus and Fragaria L. (strawberry) are available for use with Rubus mapping populations. The objectives of this study were to test 142 of these SSR markers to screen raspberry and blackberry parental genotypes for potential use in existing mapping populations that segregate for traits of interest, determine the extent of inter-species and inter-genera transferability with amplification, and determine the level of polymorphism among the parents. Up to 32 of the SSR primer pairs tested may be useful for genetic mapping in both the blackberry population and at least one of the raspberry populations. The maximum number of SSR primer pairs found useable for mapping was 60 for the raspberry population and 45 for the blackberry population. Acquisition of many more nucleotide sequences from red raspberry, black raspberry, and blackberry are required to develop useful molecular markers and genetic maps for these species. Rubus, family Rosaceae, is a highly diverse genus that contains hundreds of heterozygous species. The family is one of the most agronomically important plant families in temperate regions of the world, although they also occur in tropical and arctic regions as well. The most important commercial subgenus of Rubus is Idaeobatus Focke, the raspberries, which are primarily diploids. This subgenus contains the european red raspberry R. idaeus ssp. idaeus L., as well as the american black raspberry R. occidentalis L. and the american red raspberry R. idaeus ssp. strigosus Michx. Interspecific hybridization of these, and other raspberry species, has led to greater genetic diversity and allowed for the introgression of superior traits such as large fruit size, fruit firmness and quality, disease resistance, and winter hardiness.

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QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽

10.3390/genes12040604 ◽

2021 ◽

Vol 12 (4) ◽

pp. 604

Author(s):

Paolo Vitale ◽

Fabio Fania ◽

Salvatore Esposito ◽

Ivano Pecorella ◽

Nicola Pecchioni ◽

...

Keyword(s):

Candidate Genes ◽

Recombinant Inbred Lines ◽

Snp Array ◽

Heading Date ◽

Tiller Number ◽

Genetic Maps ◽

Yield Potential ◽

Adaptation To Climate Change ◽

Map Resolution ◽

Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

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

Genetics ◽

10.1093/genetics/151.1.321 ◽

1999 ◽

Vol 151 (1) ◽

pp. 321-330 ◽

Cited By ~ 4

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).

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Quantitative Trait Loci for Resistance to Potato Dry Rot Caused by Fusarium sambucinum

Agronomy ◽

10.3390/agronomy12010203 ◽

2022 ◽

Vol 12 (1) ◽

pp. 203

Author(s):

Sylwester Sobkowiak ◽

Marta Janiszewska ◽

Emil Stefańczyk ◽

Iwona Wasilewicz-Flis ◽

Jadwiga Śliwka

Keyword(s):

Interval Mapping ◽

Potato Cultivars ◽

Genetic Maps ◽

Dry Rot ◽

Potato Genome ◽

Polygenic Control ◽

Efficient Breeding ◽

Chromosome I ◽

Mapping Populations ◽

Important Disease

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11-36 and 12-3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars.

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Marker-assisted Backcrossing for Identification of Salt Tolerant Rice Lines

International Journal of Agricultural Research Innovation and Technology ◽

10.3329/ijarit.v2i2.14008 ◽

2013 ◽

Vol 2 (2) ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

M Moniruzzaman ◽

MS Islam ◽

JA Rashid ◽

SN Begum ◽

MM Islam

Keyword(s):

Genetic Diversity ◽

Salt Tolerance ◽

Ssr Markers ◽

Marker Assisted Selection ◽

Genetic Maps ◽

Salt Tolerant ◽

High Yielding Variety ◽

Marker Assisted Backcrossing ◽

Tolerant Genotype ◽

New Cultivars

SSR or microsatellite markers are proved to be ideal for making genetic maps, assisting selection and studying genetic diversity in germplasm. SSR markers are playing important role to identify gene for salt tolerance that can be helpful for plant breeders to develop new cultivars. The experiment was conducted during the period from July 2009 to November 2010 in the experimental field and Biotechnology Laboratory of Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh to identify salt tolerant rice line of BC1F1 progenies of Binadhan-5 x FL-478 using SSR markers. Salt tolerant genotype, FL-478 was crossed with high yielding variety, Binadhan-5. Randomly selected 40 BC1F1 progenies along with their two parents (Binadhan-5, FL-478 and F1) were genotyped with microsatellite or SSR markers for identification of salt tolerant rice lines. Parental polymorphism survey was assayed by 10 SSR markers and three polymorphic SSR markers viz., RM 336, RM 510, and RM 585 were selected to evaluate BC1F1 rice lines for salt tolerance. In respect of Primer RM 336, 11 lines were found as salt tolerant and 25 lines were heterozygous and 3 lines were susceptible. Primer RM 510 identified two tolerant, 14 heterozygous and 22 susceptible lines. And primer RM 585 identified 4 lines as tolerant and 35 lines as susceptible. Thus, these markers could be efficiently used in tagging salt tolerant genes, in marker-assisted selection and quantitative trait loci (QTL) mapping. The selected BC1F1 could be used for developing BC2F1 and BC2F2 and mapping genes for salinity tolerance. DOI: http://dx.doi.org/10.3329/ijarit.v2i2.14008 Int. J. Agril. Res. Innov. & Tech. 2 (2): 1-8, December, 2012

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Correcting Pervasive Errors in Genotypic Datasets to Develop Genetic Maps

Agronomy ◽

10.3390/agronomy9040196 ◽

2019 ◽

Vol 9 (4) ◽

pp. 196

Author(s):

Sadal Hwang ◽

Tong Geon Lee

Keyword(s):

Genetic Variation ◽

Plant Species ◽

Genetic Linkage Map ◽

Gene Action ◽

Genetic Maps ◽

Potential Contribution ◽

Phenotypic Data ◽

Stepwise Procedure ◽

Mapping Populations

Genetic mapping studies provide improved estimates for novel genomic loci, allelic effects and gene action controlling important traits. Such mapping studies are regularly performed by using a combination of genotypic data (e.g., genotyping markers tagging genetic variation within populations) and phenotypic data of appropriately structured mapping populations. Randomly obtained DNA information and more recent high-throughput genome sequencing efforts have dramatically increased the ability to obtain genetic markers for any plant species. Despite the presence of constantly and rapidly increasing genotypic data, necessary steps to determine whether specific markers can be associated with genetic variation may often be initially neglected, meaning that ever-growing genotypic markers do not necessarily maximize the power of mapping studies and often generate false results. To address this issue, we present a framework for analyzing genotypic data while developing a genetic linkage map. Our goal is to raise awareness of a stepwise procedure in the development of genetic maps as well as to outline the current and potential contribution of this procedure to minimize bias caused by errors in genotypic datasets. Empirical results obtained from the R/qtl package for the statistical language/software R are prepared with details of how we handled genotypic data to develop the genetic map of a major plant species. This study provides a stepwise procedure to correct pervasive errors in genotypic data while developing genetic maps. For use in custom follow-up studies, we provide input files and written R codes.

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CONFIRMATION OF THE IDENTIFICATION OF THE RYE CHROMOSOME IN 1B/1R WHEAT-RYE CHROMOSOME SUBSTITUTION AND TRANSLOCATION LINES

Canadian Journal of Genetics and Cytology ◽

10.1139/g75-013 ◽

1975 ◽

Vol 17 (1) ◽

pp. 117-120 ◽

Cited By ~ 22

Author(s):

M. D. Bennett ◽

J. B. Smith

Keyword(s):

Hexaploid Wheat ◽

Major Part ◽

Root Tip ◽

Single Pair ◽

Chromosome Substitution ◽

Translocation Lines ◽

Chromosome 1R ◽

Antipodal Cells

Chromosome 1R is readily distinguished from all other rye chromosomes and from all the chromosomes of hexaploid wheat in both Giemsa stained root-tip metaphase cells and in Feulgen stained antipodal cells with highly endopolyploid nuclei. Studies of these cells, stained using the appropriate methods, show that the two varieties 'Weique' and 'Neuzucht' both contain a single pair of alien substituted chromosomes and confirm their identity as chromosome 1R. It is also shown that the two varieties 'Aurora' and 'Kavkaz' both possess a single pair of wheat-rye translocation chromosomes which contain at least the major part of the short arm of chromosome 1R.

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