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

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.

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Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽

10.1093/genetics/142.2.537 ◽

1996 ◽

Vol 142 (2) ◽

pp. 537-548 ◽

Cited By ~ 2

Author(s):

Michael W Nachman ◽

Gary A Churchill

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Large Scale ◽

Physical Map ◽

Genetic Maps ◽

Recombination Rates ◽

Physical Maps ◽

Genomic Patterns ◽

Mary Lyon ◽

Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

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Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat

Genetics ◽

10.1093/genetics/143.2.1001 ◽

1996 ◽

Vol 143 (2) ◽

pp. 1001-1012 ◽

Cited By ~ 6

Author(s):

Kulvinder S Gill ◽

Bikram S Gill ◽

Takashi R Endo ◽

Elena V Boyko

Keyword(s):

Chromosome Region ◽

Gene Clusters ◽

Small Chromosome ◽

Genetic Maps ◽

Cdna Clones ◽

Density Mapping ◽

Physical Maps ◽

Chromosome 5B ◽

Marker Distribution ◽

Group 5

Abstract The distribution of genes and recombination in the wheat genome was studied by comparing physical maps with the genetic linkage maps. The physical maps were generated by mapping 80 DNA and two phenotypic markers on an array of 65 deletion lines for homoeologous group 5 chromosomes. The genetic maps were constructed for chromosome 5B in wheat and 50 in Triticum tauschii. No marker mapped in the proximal 20% chromosome region surrounding the centromere. More than 60% of the long arm markers were present in three major clusters that physically encompassed <18% of the arm. Because 48% of the markers were cDNA clones and the distributions of the cDNA and genomic clones were similar, the marker distribution may represent the distribution of genes. The gene clusters were identified and allocated to very small chromosome regions because of a higher number of deletions in their surrounding regions. The recombination was suppressed in the centromeric regions and mainly occurred in the gene-rich regions. The bp/cM estimates varied from 118 kb for gene-rich regions to 22 Mb for gene-poor regions. The wheat genes present in these clusters are, therefore, amenable to molecular manipulations parallel to the plants with smaller genomes like rice.

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Identification of QTLs for Stripe Rust Resistance in a Recombinant Inbred Line Population

International Journal of Molecular Sciences ◽

10.3390/ijms20143410 ◽

2019 ◽

Vol 20 (14) ◽

pp. 3410 ◽

Cited By ~ 6

Author(s):

Manyu Yang ◽

Guangrong Li ◽

Hongshen Wan ◽

Liping Li ◽

Jun Li ◽

...

Keyword(s):

Genetic Map ◽

Stripe Rust ◽

Resistance Genes ◽

Phenotypic Variation ◽

Recombinant Inbred ◽

Rust Resistance ◽

High Density ◽

Genetic Maps ◽

Stripe Rust Resistance ◽

Resistance Locus

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating fungal diseases of wheat worldwide. It is essential to discover more sources of stripe rust resistance genes for wheat breeding programs. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for the construction of high-density genetic maps. In this study, a set of 200 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) was used to construct a high-density genetic map and to identify quantitative trait loci (QTLs) for stripe rust resistance using SLAF-seq technology. A genetic map of 2828.51 cM, including 21 linkage groups, contained 6732 single nucleotide polymorphism markers (SNP). Resistance QTLs were identified on chromosomes 1B, 2A, and 7B; Qyr.saas-7B was derived from CH42, whereas Qyr.saas-1B and Qyr.saas-2A were from CH55. The physical location of Qyr.saas-1B, which explained 6.24–34.22% of the phenotypic variation, overlapped with the resistance gene Yr29. Qyr.saas-7B accounted for up to 20.64% of the phenotypic variation. Qyr.saas-2A, a minor QTL, was found to be a likely new stripe rust resistance locus. A significant additive effect was observed when all three QTLs were combined. The combined resistance genes could be of value in breeding wheat for stripe rust resistance.

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Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.)

BMC Plant Biology ◽

10.1186/s12870-019-2004-7 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Zemao Yang ◽

Youxin Yang ◽

Zhigang Dai ◽

Dongwei Xie ◽

Qing Tang ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Qtl Mapping ◽

Genetic Map ◽

Quantitative Trait ◽

High Density ◽

Genetic Maps ◽

Interval Length ◽

Phenotypic Variance ◽

Qtls Mapping

Abstract Background Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. Results We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58–19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. Conclusions We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.

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Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)

Agronomy ◽

10.3390/agronomy9100653 ◽

2019 ◽

Vol 9 (10) ◽

pp. 653 ◽

Cited By ~ 1

Author(s):

Bartosz Kozak ◽

Renata Galek ◽

Dariusz Zalewski ◽

Ewa Sawicka-Sienkiewicz

Keyword(s):

Genetic Map ◽

Genome Wide Association Study ◽

Reference Genome ◽

High Density ◽

Genetic Maps ◽

New Variety ◽

Model Legume ◽

Speed Up ◽

Trait Locus ◽

Next Generation Sequencing Ngs

Genetic maps are an essential tool for investigating molecular markers’ linkage with traits of agronomic importance. Breeders put a lot of emphasis on this type of markers, which are used in breeding programs implementation and speed up the process of a new variety development. In this paper, we construct a new, high-density linkage genetic map for Polish material on narrow-leafed lupin. The mapping population originated from crossing the Polish variety ‘Emir’ and the Belarusian breeding line ‘LAE-1’. A new map was constructed based on DArTseq markers—a new type of marker generated with the next-generation sequencing (NGS) technique. The map was built with 4602 markers, which are divided into 20 linkage groups, corresponding with the number of gametic chromosomes in narrow-leafed lupin. On the new map there are 1174 unique loci. The total length of all linkage group is 3042 cM. This map was compared to the reference genome of narrow-leafed lupin and the CDS sequence for model legume species: emphMedicago truncatula, emphLotus japonicus and Glycine max. Analysis revealed the presence of the DArTseq marker common for all investigated species. We were able to map 38 new, unplaced scaffolds on the new genetic map of narrow-leafed lupin. The high-density genetic map we received can be used for quantitative trait locus (QTL) mapping, genome-wide association study analysis and assembly of the reference genome for the whole genome sequencing (WGS) method

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Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number

Frontiers in Plant Science ◽

10.3389/fpls.2020.600788 ◽

2020 ◽

Vol 11 ◽

Author(s):

Qiao Li ◽

Zhifen Pan ◽

Yuan Gao ◽

Tao Li ◽

Junjun Liang ◽

...

Keyword(s):

Genetic Map ◽

Quantitative Trait ◽

Recombinant Inbred Lines ◽

High Density ◽

Genetic Maps ◽

Phenotypic Variance ◽

Quality Traits ◽

Rna Seq ◽

Falling Number ◽

7S Globulin

Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31–47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58–25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.

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Molecular and physical mapping of a barley gene on chromosome arm 1HL that causes sterility in hybrids with wheat

Genome ◽

10.1139/g02-024 ◽

2002 ◽

Vol 45 (4) ◽

pp. 617-625 ◽

Cited By ~ 19

Author(s):

Shin Taketa ◽

Masayuki Choda ◽

Ryoko Ohashi ◽

Masahiko Ichii ◽

Kazuyoshi Takeda

Keyword(s):

Ssr Markers ◽

Physical Map ◽

Genetic Maps ◽

Barley Chromosome ◽

Addition Line ◽

Addition Lines ◽

Seed Fertility ◽

Chromosome Addition ◽

Sterility Gene ◽

Group 1 Chromosomes

Addition of the long arm of barley chromosome 1H (1HL) to wheat causes severe meiotic abnormalities and complete sterility of the plants. To map the barley gene responsible for the 1H-induced sterility of wheat, a series of addition lines of translocated 1H chromosomes were developed from the crosses between the wheat 'Shinchunaga' and five reciprocal translocation lines derived from the barley line St.13559. Examination of the seed fertility of the addition lines revealed that the sterility gene is located in the interstitial 25% region of the 1HL arm. The genetic location of the sterility gene was also estimated by physically mapping sequence-tagged site (STS) markers and simple-sequence repeat (SSR) markers with known map locations. The sterility gene is designated Shw (sterility in hybrids with wheat). Comparison of the present physical map of 1HL with two previously published genetic maps revealed a paucity of markers in the proximal 30% region and non-random distribution of SSR markers. Two inconsistencies in marker order were found between the present physical map and the consensus genetic map of group 1 chromosomes of Triticeae. On the basis of the effects on meiosis and chromosomal location, the relationship of the present sterility gene with other fertility-related genes of Triticeae is discussed.Key words: Hordeum vulgare, molecular markers, sterility, translocation, wheatbarley chromosome addition line.

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Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

DNA Research ◽

10.1093/dnares/dsu038 ◽

2014 ◽

Vol 22 (1) ◽

pp. 39-52 ◽

Cited By ~ 52

Author(s):

Y. Li ◽

S. Liu ◽

Z. Qin ◽

G. Waldbieser ◽

R. Wang ◽

...

Keyword(s):

High Resolution ◽

Genetic Map ◽

Channel Catfish ◽

Physical Map ◽

High Density

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

Genome ◽

10.1139/g95-006 ◽

1995 ◽

Vol 38 (1) ◽

pp. 45-59 ◽

Cited By ~ 168

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.

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Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.

Genetics ◽

10.1093/genetics/141.1.159 ◽

1995 ◽

Vol 141 (1) ◽

pp. 159-179 ◽

Cited By ~ 10

Author(s):

T M Barnes ◽

Y Kohara ◽

A Coulson ◽

S Hekimi

Keyword(s):

Caenorhabditis Elegans ◽

Genetic Map ◽

Recombination Rate ◽

Physical Map ◽

Gene Density ◽

Cdna Clones ◽

Recombination Rates ◽

Noncoding Dna ◽

Physical Size ◽

C Elegans

Abstract The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.

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