Characteristics and analysis of simple sequence repeats in the cotton genome based on a linkage map constructed from a BC1 population between Gossypium hirsutum and G. barbadense

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Abstract:

In the past decade, several molecular maps of cotton have been constructed using diverse DNA molecular markers and mapping populations. In this study, an interspecific linkage map of allotetraploid cotton was developed using a BC1 population ((Gossypium hirsutum × G. barbadense) × G. hirsutum). This map was genome-wide and was based entirely on simple sequence repeat (SSR) markers. Forty-four linkage groups were assigned to 26 chromosomes, with 917 loci spanning 5452.2 cM of the genome. The average distance between loci was 5.9 cM, providing uniform coverage of the A subgenome and D subgenome. Characteristics of this map were analyzed in detail, including the distributions of genomic SSRs, expressed sequence tag (EST)-SSRs, and distorted markers. Furthermore, the relationships between motif characteristics (size, type, length) and the level of polymorphism in EST-SSRs were also surveyed. The results showed that tetranucleotide and dinucleotide repeats had similar levels of polymorphism, and ACAT, AC, and ACT repeats had the highest polymorphism rates. Loci with lengths of 27 bp, 33 bp, and 24 bp were more likely to be polymorphic. This work will provide information to assist in designing future EST-SSRs.

Au cours de la dernière décennie, plusieurs cartes génétiques du cotonnier ont été produites à l’aide de divers types de marqueurs moléculaires et de différentes populations de cartographie. Dans ce travail, une carte génétique interspécifique du cotonnier allotétraploïde a été produite à l’aide d’une population BC1 ((Gossypium hirsutum × G. barbadense) × G. hirsutum). Cette carte est constituée entièrement de microsatellites (SSR) offrant une bonne couverture génomique avec 44 groupes de liaison assignés à 26 chromosomes et 917 locus couvrant 5452,2 cM. La distance moyenne entre les marqueurs est de 5,9 cM et offre une couverture uniforme des sous-génomes A et D. Cette carte est caractérisée et analysée en détail incluant la distribution des microsatellites génomiques, des EST-SSR et des marqueurs présentant une distorsion de la ségrégation. De plus, les relations entre les caractéristiques des motifs répétés (taille, type, longueur) et le degré de polymorphisme chez les EST-SSR sont également examinées. Les résultats montrent que les motifs tétra- et dinucléotidiques présentaient un degré comparable de polymorphisme et que les motifs ACAT, AC et ACT affichaient le plus de polymorphisme. Les locus mesurant 27, 33 ou 24 pb étaient plus polymorphes. Ce travail contribue une information permettant de faciliter le développement de futurs marqueurs EST-SSR.

Document Type: Research Article

Publication date: July 1, 2008

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  • From its inception in 1957, this international cytogenetics journal has catered to the research areas of the members of the Genetics Society of Canada; traditionally, these have included agriculture, entomology, genetics/cytogenetics, and evolutionary mechanisms. The contents of the journal have evolved as contributors developed new technologies and interests. A 20-member Editorial Board is composed of scientists from around the world. Reviews and commentary from respected experts are often featured.
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