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Genetic mapping of new cotton fiber loci using
EST-derived microsatellites in and recombinant inbred lines cotton population

there is an immediate need for a high density genetic map of cotton embedded
with fiber genes to facilitate marker assisted selection (MAS) for improved
fiber traits. With the goal in mind, genetic mapping with a new set of a
microsatellite markers was performed on 183 recombinant inbred lines developed
from the progeny of the interspecific cross Gossypium  hirsutum L. cv. TM1* Gossypium barbadense L.
Pima  3-79. Microsatellite developed
using 1557 ESTs containing SSRs and 5794 EST containing CSRs obtained from the
cultivated diploid species Gossypium arboreum L. ,  AKA8401. From a total of 1232 EST derived SSR
and CSR primer pairs, 1019 successfully amplified PCR products from a survey
panel of six Gossypium species; 202 were polymorphic between the G. hirsutum L.
and G. barbadense L. parents of the interspecific mapping population. Among
these polymorphic markers, only 86 showed significant sequence homology to
annotated genes with known functions. The chromosomal locations of 36
microsatellites were associated with 14 chromosomes or 13 chromosomes arms of
the cotton genome by hypoaneuploid deficiency analysis, enabling us to assign
genetic linkage groups to specific chromosomes. The resulting genetic map
consists of 193 loci, including 121 new fiber loci not previously mapped. These
fiber loci were mapped to 19 chromosomes and 11 LG spanning 1277 cM, providing
approximately trait loci analysis suggested that chromosomes 2, 3, 15, and 18
may harbor genes for trait related to fiber quality. These new PCR bases
microsatellite markers derived from cotton fiber ESTs will facilitate the
development of a high resolution integrated genetic map of cotton for
structural and functional study of fiber genes and MAS of genes that enhance
fiber quality.

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in more than 80, countries cotton is a major cropp and important renewable
resource, privoiding the world’s leading natural fiber for the manufacture of
textiles.    Cotton belongs to the genus
Gossypium, which consists of at least 45 diploid and five allo-tetraploid
species. Gossypium barbadense are modern allotetraploid cottons, which together
represent the most extensively cultivated species worldwide. While Gh is the
most widely cultivated species—prized for its higher yield and wider
environmental adaptation, Gb boasts vastly superior fiber quality. The
allotetraplloid species are thought to have formed about 1.1-1.9 million years
ago after polypoidization event that brought together the genomes of diploids
closely related to Gossypium herbaceum L. or Gossypium arboretum and Gossypium
raimondii and were domesticated through extensive human selection. A genome
diploid cottons produce spinnable fibers and have been cultivated. While D-genome
species produce very short and appressed fibers. However, many quantitative
trait loci for fiber traits have been associated with D-subgenome in
allotetraploid cottons indicating that the D genome contributes to fiber
morphogenesis and the determination of fiber properties.

main goals of cotton breeding programs wordwide are the genetic enhancement of
yield and, more recently, fiber quality. Improvement for fiber properties is
required to keep pace with the rapid changes taking place in the technology of
the manufacturing procedure. Key fiber quality traits, such as fiber elongation,
length, fitness and bundle strength are controlled by QTLs, which complicate
conventional breeding for fiber improvement. Molecular markers offer efficient
tools for dissecting QTLs affecting traits with complex genetic inheritance,
and facilitate marker-assisted selection and map based cloning.

cotton fiber quality while maintaining fiber yield is a challenging task for
conventional breeding, because of the negative association between these
two  traits and the genetic complexity of
fiber QTLs. The genetic enhancement of fiber traits can be facilitated by using
molecular approaches, such as the construction of a high density genetic map
based on functionally embedded fiber genes and by subsequent molecular tagging
of fiber QTLs for MAS. As a step

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