Construction of a genetic linkage map for Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage

Genome ◽  
2007 ◽  
Vol 50 (8) ◽  
pp. 742-756 ◽  
Author(s):  
K.S. Aitken ◽  
P.A. Jackson ◽  
C.L. McIntyre
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Saccharum Officinarum ◽  
Basic Chromosome Number ◽  
Genetic Maps ◽  
Sugarcane Cultivar ◽  
Repulsion Phase ◽  
Preferential Chromosome Pairing ◽  
Segregating Population

Saccharum officinarum L. is an octoploid with 80 chromosomes and a basic chromosome number of x = 10. It has high stem sucrose and contributes 80% of the chromosomes to the interspecific sugarcane cultivars that are grown commercially for sucrose. A genetic linkage map was developed for S. officinarum (clone IJ76-514) using a segregating population generated from a cross between Q165 (a commercial sugarcane cultivar) and IJ76-514. In total, 40 AFLP and 72 SSR primer pairs were screened across the population, revealing 595 polymorphic bands inherited from IJ76-514. These 595 markers displayed a frequency distribution different from all other sugarcane genetic maps produced, with only 40% being simplex markers (segregated 1:1). Of these 240 simplex markers, 178 were distributed on 47 linkage groups (LGs) and 62 remained unlinked. With the addition of 234 duplex markers and 80 biparental simplex markers (segregating 3:1), 534 markers formed 123 LGs. Using the multi-allelic SSR markers, repulsion phase linkage, and alignment with the Q165 linkage map, 105 of the 123 LGs could be grouped into 10 homology groups (HGs). These 10 HGs were further assigned to the 8 HGs observed in cultivated sugarcane and S. spontaneum . Analysis of repulsion phase linkage indicated that IJ76-514 is neither a complete autopolyploid nor an allopolyploid. Detection of 28 repulsion linkages that occurred between 6 pairs of LGs located in 4 HGs suggested the occurrence of limited preferential chromosome pairing in this species.

scholarly journals Construction of Genetic Map of Jute (Corchorus olitorius L.) Based on RAPD Markers

2009 ◽  
Vol 18 (2) ◽  
pp. 165-172 ◽  
Author(s):  
Samiul Haque ◽  
Nadim Ashraf ◽  
Selina Begum ◽  
R.H. Sarkar ◽  
Haseena Khan
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Group Analysis ◽  
Basic Chromosome Number ◽  
Marker Density ◽  
Linkage Groups ◽  
Average Marker Density ◽  
Rapd Polymorphism

The first and preliminary genetic linkage map of the jute genome was constructed with RAPD markers using two parents (variety O-9897 and accession no. 1805) and their F2 populations. Linkage analysis at a LOD (Log of odds base 10) score of 3.0 and a maximum distance 50 cM revealed 18 linkage groups. Among the 18 linkage groups, 15 contained single locus and the remaining three groups 16, 17 and 18 contained 2, 11 and 12 loci, respectively. The three multi locus linkage groups varying in length from 15.9 - 241.7 cM, snapped a total length of 463.7 cM with an average marker density of 19.6 cM between adjacent markers. The basic chromosome number of Corchorus spp. is seven (2n = 14), so in saturated map, seven linkage groups should have been obtained to represent the genome. But for linkage group analysis, the effort was very limited and the total number of loci (40) was also low.  Key words: Jute, Linkage map, RAPD, Polymorphism D.O.I 10.3329/ptcb.v18i2.3647 Plant Tissue Cult. & Biotech. 18(2): 165-172, 2008 (December)

scholarly journals 1. A genetic linkage map of Pinus massoniana based on SRAP, SSR and ESTP markers

2014 ◽  
Vol 63 (1-6) ◽  
pp. 1-8 ◽  
Author(s):  
Wenxia Chen ◽  
Mu Cao ◽  
Yuanxiu Wang ◽  
Zhichun Zhou ◽  
Li-An Xu
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Southern China ◽  
Pinus Massoniana ◽  
Genetic Maps ◽  
Masson Pine ◽  
F1 Progeny ◽  
Genomic Studies

Abstract Pinus massoniana (masson pine) is the most important native pine in southern China. High-density genetic maps have not been constructed for the species. In this study, a genetic linkage map with 251 markers (47 SSRs, 23 ESTPs and 181 SRAPs) was constructed using a F1 progeny mapping population derived from controlled pollination of two parents of different provenances. At LOD 7.0, a total of 17 linkage groups were constructed with twelve groups having nine or more markers and five other groups of two to four markers each. The total map length was 1,956 cM with an average of 8.4 cM among individual loci. The current linkage map represented 93% of the estimated genome length of 2,114 cM for masson pine. Such linkage map are useful for future genomic studies of masson pine including comparative mapping in Pinaceae and quantitative trait loci (QTL) mapping for economically important traits.

scholarly journals Genetic Linkage Map of Garlic (Allium sativum)

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 775A-775
Author(s):  
Yayeh Zewdie ◽  
Michael J. Havey ◽  
James P. Prince ◽  
Maria M. Jenderek*
Keyword(s):  
Linkage Map ◽  
Male Fertility ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Deleterious Alleles ◽  
Segregating Population

Garlic has been propagated exclusively by asexual means since time immemorial. The recent discovery of male fertile garlic accessions allowed studies on genetics and garlic improvement. Single nucleotide polymorphism (SNP) and random amplified polymorphic DNA (RAPD) based genetic linkage map was developed for garlic using a segregating population derived from one plant of PI 540316. Progenies segregated for male fertility and other morphological characters. Distortion of segregation was observed for most of the markers. This was expected due to the segregation of recessive deleterious alleles present in the garlic genome. The map contained 23 loci distributed on five linkage groups. It covered 319 cM with the average of 18 cM between loci. Linkage with the male fertility (Mf) locus was established with SNP marker AOB155 (26.7 cM).

A genetic linkage map in autotetraploid lucerne adapted to northern Australia, and use of the map to identify DNA markers linked to resistance to Phytophthora medicaginis

2005 ◽  
Vol 56 (4) ◽  
pp. 333 ◽  
Author(s):  
J. M. Musial ◽  
K. S. Aitken ◽  
J. M. Mackie ◽  
J. A. G. Irwin
Keyword(s):  
Linkage Map ◽  
Phenotypic Variation ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Linkage Groups ◽  
Resistance Qtls ◽  
Backcross Population ◽  
Resistant Parent ◽  
Repulsion Phase

Phytophthora root rot, caused by Phytophthora medicaginis, is a major limitation to lucerne (Medicago sativa L.) production in Australia and North America. Quantitative trait loci (QTLs) involved in resistance to P. medicaginis were identified in a lucerne backcross population of 120 individuals. A genetic linkage map was constructed for tetraploid lucerne using 50 RAPD (randomly amplified polymorphic DNA), 104 AFLP (amplified fragment length polymorphism) markers, and one SSR (simple sequence repeat or microsatellite) marker, which originated from the resistant parent (W116); 13 markers remain unlinked. The linkage map contains 18 linkage groups covering 2136.5 cM, with an average distance of 15.0 cM between markers. Four of the linkage groups contained only either 2 or 3 markers. Using duplex markers and repulsion phase linkages the map condensed to 7 homology groups and 2 unassigned linkage groups. Three regions located on linkage groups 2, 14, and 18, were identified as associated with root reaction and the QTLs explained 6–15% of the phenotypic variation. The research also indicates that different resistance QTLs are involved in conferring resistance in different organs. Two QTLs were identified as associated with disease resistance expressed after inoculation of detached leaves. The marker, W11-2 on group 18, identified as associated with root reaction, contributed 7% of the phenotypic variation in leaf response in our population. This marker appears to be linked to a QTL encoding a resistance factor contributing to both root and leaf reaction. One other QTL, not identified as associated with root reaction, was positioned on group 1 and contributed to 6% of the variation. This genetic linkage map provides an entry point for future molecular-based improvement of lucerne in Australia, and markers linked to the QTLs we have reported should be useful for marker-assisted selection for partial resistance to P. medicaginis in lucerne.

The construction of a preliminary genetic linkage map in the Japanese scallop Mizuhopecten yessoensis

2009 ◽  
Vol 31 (6) ◽  
pp. 629-637 ◽  
Author(s):  
Wei-Dong LIU ◽  
Xiang-Bo BAO ◽  
Wen-Tao SONG ◽  
Zun-Chun ZHOU ◽  
Chong-Bo HE ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Japanese Scallop ◽  
Mizuhopecten Yessoensis

An Integrated Genetic Linkage Map from Three F2 Populations of Cultivated Peanut(Arachis hypogaeaL.)

2016 ◽  
Vol 42 (2) ◽  
pp. 159 ◽  
Author(s):  
Jian-Bin GUO ◽  
Li HUANG ◽  
Liang-Qiang CHENG ◽  
Wei-Gang CHEN ◽  
Xiao-Ping REN ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Cultivated Peanut

Construction of genetic linkage map in Japannese flounder (Paralichthys olivaceus)

2013 ◽  
Vol 19 (6) ◽  
pp. 930-938 ◽  
Author(s):  
Renyi PANG ◽  
Wentao SONG ◽  
Fengtao GAO ◽  
Xiaolin LIAO ◽  
Yongwei ZHAO ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Paralichthys Olivaceus

Towards a Saturated Molecular Genetic Linkage Map for Cultivated Sunflower

Crop Science ◽  
2003 ◽  
Vol 43 (1) ◽  
pp. 367 ◽  
Author(s):  
Ju-Kyung Yu ◽  
Shunxue Tang ◽  
Mary B. Slabaugh ◽  
Adam Heesacker ◽  
Glenn Cole ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Molecular Genetic

scholarly journals AFLP-Based Genetic Linkage Map of the Colorado Potato Beetle Leptinotarsa decemlineata: Sex Chromosomes and a Pyrethroid-Resistance Candidate Gene

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 695-700 ◽  
Author(s):  
David J Hawthorne
Keyword(s):  
Candidate Gene ◽  
Linkage Map ◽  
Colorado Potato Beetle ◽  
Leptinotarsa Decemlineata ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Sex Chromosome ◽  
Pyrethroid Resistance ◽  
Codominant Markers ◽  
Potato Beetle

Abstract A genetic linkage map was constructed from an intraspecific cross of the Colorado potato beetle, Leptinotarsa decemlineata. This is an initial step toward mapping the loci that underlie important phenotypes associated with insect adaptation to an agroecosystem. The map was made with 172 AFLP and 10 anonymous codominant markers segregating among 74 backcross (BC1) individuals. Markers were mapped to 18 linkage groups and a subset of the markers with a mean intermarker distance of 11.1 cM is presented. A pyrethroid-resistance candidate gene, LdVssc1, was placed onto the map as well. The sex chromosome was identified by exploiting the XO nature of sex determination in this species using patterns of variation at LdVssc1 and the codominant markers.

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