Magnaporthe grisea Genetic Map Description

Contents
See also Linkage Group Maps.

Genetic Maps

Description

Around 250 known genetic markers exist for Magnaporthe grisea. Some of these markers have been ordered on seven linkage group genetic maps. The genetic map information was obtained from Nitta N., M. L. Farman, S. A. Leong (1997) Genome organization of Magnaporthe grisea: Integration of genetic maps, clustering of transposable elements and identification of genome duplications and rearrangements. Theor. Appl. Genet. 95: 20-32.

Genetic Marker Data

Of the 254 known genetic markers for Magnaporthe grisea:
 
# % Description
200 79% placed on a genetic map linkage group
187 74% have associated BACs
133 52% placed and with associated BACs

Marker Venn Diagram

Correlation to Physical Map

Methodology

To construct the assembly-to-linkage-group mapping, the 133 markers that are both located on the genetic map and associated with one or more BACs were identified and their associated BACs were searched for in the assembly.
  • 126 of the 133 markers (95%) were successfully located in the current assembly via this method
  • 37 supercontigs, representing 35.9 Mb (93% of the assembly), are anchored and ordered on a linkage group map
  • 26 supercontigs have more than one marker and thus have been oriented on a linkage group map

Special Cases

Markers in more than one supercontig
In several cases a marker was located in more than one supercontig. The following markers have been split in this way:
    MarkerSupercontigs
    1131, 9
    13-9-A17, 6
    2-9-G19, 48
    22-2-D26, 7
    22-4-A18, 40
    23-4-D12, 25
    3-9-H11, 16
    33-2-B22, 37
    36-7-E13, 3
    38-7-A112, 23
    38-7-A212, 23
    4-144, 9
    4-15712, 23
    4-17818, 4
    4-223, 6
    4-481, 17, 2, 9
    44-8-B10, 27
    5-10-F17, 38
    5212, 8
    55-1-E15, 21, 3, 32
    7-3-B30, 6
    A11F95, 8
    A12B517, 9
    A14C41, 26
    CH2-29H12, 22, 8
    CH2-54H178, 9
    CH3-108H18, 21
    CH3-24H8, 9
    CH3-67H31, 9
    CH4-133H1, 14
    CH5-153H10, 25
    CH5-177H17, 19, 25
    CH5-97H1, 9
    G34R14, 2
    G39R10, 14
Markers with associated BACs, not placed in assembly
Seven markers with linkage group positions and associated BACs have not been located on any supercontigs, due to a failure to locate the BACs in the assembly. These markers are:
    MarkerLinkage Group
    21-3-EVII
    40-12-HI, VII
    46-12-CIII
    5-8-EIV
    64II
    CH3-12HV
    CH3-44HVI
Supercontigs in more than one linkage group
Many supercontigs contain markers that have been assigned to different linkage groups. This could indicate a problem with the assembly, a problem with the genetic map, or a problem assigning a marker a position in the assembly. Supercontigs containing markers from different linkage groups are displayed alongside the linkage group they have the most markers from. These supercontigs are:
    SupercontigMarkers in Different Linkage Groups
    119 in LGVI, 1 in LGI (A12D9), 1 in LGIV (A14C4)
    107 in LGIII, 1 in LGIV (4-194)
    126 in LGII, 1 in LGI (38-7-A1), 1 in LGIV (38-7-A2), 1 in LGVII (23-4-D)
    135 in LGI, 2 in LGII
    145 in LGIII, 1 in LGI (G34R), 1 in LGVI (CH4-133H)
    156 in LGIII, 1 in LGVII (55-1-E)
    173 in LGI, 2 in LGVI, 1 in LGII (A12B5), 1 in LGVII (CH5-177H)
    185 in LGV, 1 in LGIII (A16C12)
    191 in LGI (2-9-G), 1 in LGII (4-78), 1 in LGIV (4-181), 1 in LGVII (CH5-177H)
    24 in LGI, 2 in LGVI
    213 in LGVII, 1 in LGV (CH3-108H)
    221 in LGII (CH2-29H), 1 in LGVII (33-2-B)
    232 in LGIV, 1 in LGI (38-7-A1), 1 in LGII (4-157)
    253 in LGVII, 1 in LGIII (CH5-153H)
    261 in LGIV (A14C4), 1 in LGV (22-2-D)
    271 in LGIII (44-8-B), 1 in LGVI (CH3-122H)
    35 in LGII, 1 in LGVII (55-1-E)
    311 in LGI (11), 1 in LGIV (CH3-67H)
    342 in LGIV, 1 in LGVI (47-12-G)
    43 in LGVII, 1 in LGIV (4-14), 1 in LGV (4-178)
    63 in LGV, 1 in LGI (13-9-A), 1 in LGII (4-22), 1 in LGIV (42-10-C)
    76 in LGIV, 1 in LGV (22-2-D)
    85 in LGIII, 3 in LGII

Discrepancies

There are several cases where marker order on the linkage group map conflicts with the locations of markers in supercontigs. These differences are indicated visually by crossed lines on the Correspondence of Physical to Genetic Maps. The discrepancies may be due to:
  1. Errors in assembly of sequence into contigs or supercontigs
  2. Errors in order of markers on the linkage group map
  3. Correct but incomplete assembly data: for example, one supercontig may lie within a gap between contigs in another supercontig

Map Correlation Data

You can graphically view the correlation between the physical and genetic linkage maps from the Genetic Maps page.

You can download a comma-separated file listing all markers (including GI numbers for those with sequence, and contig positions for those located in our assembly): markers.csv (see Download Markers for data details).

A poster sized version of all of the physical & genetic maps is also available on the download page.