A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping

Genome ◽  
2007 ◽  
Vol 50 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Lorenzo Barchi ◽  
Julien Bonnet ◽  
Christine Boudet ◽  
Patrick Signoret ◽  
István Nagy ◽  
...  
Keyword(s):  
High Resolution ◽  
Linkage Map ◽  
Capsicum Annuum ◽  
Fragment Length ◽  
Recombinant Inbred ◽  
Capsicum Annuum L ◽  
Sequence Tagged Sites ◽  
Length Polymorphisms ◽  
Number Of Individuals ◽  
Intermarker Distance

A high-resolution, intraspecific linkage map of pepper ( Capsicum annuum L.) was constructed from a population of 297 recombinant inbred lines. The parents were the large-fruited inbred cultivar ‘Yolo Wonder’ and the hot pepper line ‘Criollo de Morelos 334’, which is heavily used as a source of resistance to a number of diseases. A set of 587 markers (507 amplified fragment length polymorphisms, 40 simple sequence repeats, 19 restriction fragment length polymorphisms, 17 sequence-specific amplified polymorphisms, and 4 sequence tagged sites) were used to generate the map; of these, 489 were assembled into 49 linkage groups (LGs), including 14 LGs with 10 to 60 markers per LG and 35 with 2 to 9 markers per LG. The framework map covered 1857 cM with an average intermarker distance of 5.71 cM. Twenty-three LGs, composed of 69% of the markers and covering 1553 cM, were assigned to 1 of the 12 haploid pepper chromosomes, leaving 26 LGs (304 cM) unassigned. The chromosome framework map built with 250 markers led to a high level of mapping confidence and an average intermarker distance of 6.54 cM. By applying MapPop software, it was possible to select smaller subsets of 141 or 93 most informative individuals with a view to reducing the time and cost of further mapping and phenotyping. To define the smallest number of individuals sufficient for assigning any new marker to a chromosome, subsets from 12 to 45 individuals and a set of 13 markers distributed over all 12 chromosomes were screened. In most cases, the markers were correctly assigned to their expected chromosome, but the accuracy of the map position decreased as the number of individuals was reduced.

A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 249-265 ◽  
Author(s):  
V A Portyanko ◽  
D L Hoffman ◽  
M Lee ◽  
J B Holland
Keyword(s):  
Linkage Map ◽  
Fragment Length ◽  
Rflp Markers ◽  
Linkage Groups ◽  
Sequence Tagged Sites ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Incomplete Coverage ◽  
Marker Loci ◽  
Isozyme Loci

A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7 lines from the cross 'Ogle' × 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 2–43 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 16–34 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (89–95%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.Key words: Avena, linkage map, comparative mapping, homoeology.

scholarly journals A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms

1995 ◽  
Vol 66 (2) ◽  
pp. 109-126 ◽  
Author(s):  
Jinrui Shi ◽  
David G. Heckel ◽  
Marian R. Goldsmith
Keyword(s):  
Linkage Map ◽  
Bombyx Mori ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Fragment Length Polymorphisms ◽  
Genetic Maps ◽  
Crossing Over ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

SummaryWe present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori, based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.

A high-resolution genetic linkage map of soybean based on 357 recombinant inbred lines genotyped with BARCSoySNP6K

2015 ◽  
Vol 35 (2) ◽  
Author(s):  
Sungwoo Lee ◽  
Keith R. Freewalt ◽  
Leah K. McHale ◽  
Qijian Song ◽  
Tae-Hwan Jun ◽  
...  
Keyword(s):  
High Resolution ◽  
Linkage Map ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Recombinant Inbred Lines ◽  
Inbred Lines

Construction of a genetic map of barley (Hordeum vulgare L.) cross 'Azumamugi' × 'Kanto Nakate Gold' using a simple and efficient amplified fragment-length polymorphism system

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 284-292 ◽  
Author(s):  
Y Mano ◽  
S Kawasaki ◽  
F Takaiwa ◽  
T Komatsuda
Keyword(s):  
Hordeum Vulgare ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Recombinant Inbred ◽  
Fragment Length Polymorphism ◽  
Recombinant Inbred Lines ◽  
Amplified Fragment Length Polymorphism ◽  
Buffer System ◽  
Hordeum Vulgare L ◽  
Sequence Tagged Sites

We have devised a simple and efficient amplified fragment-length polymorphism (AFLP) system consisting of small slab gels, a discontinuous buffer system, and silver staining. Using this system, a single worker developed a barley map with 227 polymorphic fragments in 2 months. As a mapping population, 99 recombinant inbred lines of barley cultivars 'Azumamugi' × 'Kanto Nakate Gold' were used. Most of the 227 AFLP fragments showed a Mendelian segregation ratio of 1:1, and all were assigned to the seven barley chromosomes. Thus, these fragments are useful as molecular markers. They were integrated with 40 previously characterized sequence-tagged sites, 3 isozymes, and 2 morphological markers to construct an integrated map. The resulting map covered 925.6 cM with 272 markers (detecting 150 loci) at an average interval of 6.5 cM/locus. This system greatly simplifies map construction.Key words: amplified fragment length polymorphism (AFLP), Hordeum vulgare, linkage map, recombinant inbred line (RIL), sequence-tagged site (STS).

A restriction fragment length polymorphism based linkage map of a diploid Avena recombinant inbred line population

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 192-204 ◽  
Author(s):  
C A Kremer ◽  
M Lee ◽  
J B Holland
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Linkage Map ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Recombinant Inbred ◽  
Fragment Length Polymorphism ◽  
Grass Species ◽  
Disease Resistance Gene ◽  
Restriction Fragment Length

A population of 100 F6-derived recombinant inbred lines was developed from the cross of two diploid (2n = 14) Avena accessions, CI3815 (A. strigosa) and CI1994 (A. wiestii). Restriction fragment length polymorphism (RFLP) probes previously mapped in other grass species were used to develop a framework linkage map suitable for comparative genetics. Nine linkage groups were identified among the 181 loci mapped, with an average interlocus distance of 5 cM, and a total genetic map length of 880 cM. A cluster of five tightly linked crown rust resistance genes (Pca) was localized on the map, as were five loci identified by disease resistance gene analogs from maize, sorghum, and wheat. None of the five loci identified by the gene analogs were linked to the Pca locus. The linkage map was compared with previously published diploid and hexaploid linkage maps in an attempt to identify homologous or homoeologous chromosomes between populations. Locus orders and linkage relationships were poorly conserved between the A. strigosa × A. wiestii map and other Avena maps. In spite of mapping complications due to duplications within a basic genome as well as the allopolyploid constitution of many Avena species, such map comparisons within Avena provide further evidence of substantial chromosomal rearrangement between species within Avena.Key words: grasses, oat, genetic mapping, homoeology.

Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms

Nature ◽  
1988 ◽  
Vol 335 (6192) ◽  
pp. 721-726 ◽  
Author(s):  
Andrew H. Paterson ◽  
Eric S. Lander ◽  
John D. Hewitt ◽  
Susan Peterson ◽  
Stephen E. Lincoln ◽  
...  
Keyword(s):  
Linkage Map ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Quantitative Traits ◽  
Restriction Fragment Length Polymorphisms ◽  
Complete Linkage ◽  
Length Polymorphisms ◽  
Restriction Fragment Length
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