Cotton Breeding for Fiber Quality Improvement - Industrial Crops: Breeding for BioEnergy and Bioproducts - page 212

resolution genetic maps [ 23 , 114 ]. This includes the qFL-chr1 locus, which pro-
vides a valuable source of fiber length [ 115 ] and a number of QTLs for fiber
strength [ 116 , 117 ].
Stelly and colleagues [ 118 ] released a set of 17 disomic alien chromosome
substitution lines (CS-B lines), produced through hypoaneuploid-based
backcrossing in a near-isogenic genetic background of the G. hirsutum genetic
standard Texas Marker-1 (TM-1) line of G. barbadense chromosomes. They also
generated a set of chromosome-specific RIL populations from these substitution
lines which provide a novel source of germplasm for fine mapping of fiber and other
agronomic traits, with potential for introgressing those QTLs present on those
chromosomes or chromosome segments into elite G. hirsutum germplasm. Most
CS-B lines had different fiber quality properties to TM-1 so should be a better
source of well-characterized and additive fiber quality QTLs than using the
G. barbadense parent directly. Similar approaches are being explored with
unadapted G. tomentosum and G. mustelinum accessions. A total of 28 QTLs for
fiber elongation, length, fineness, fiber uniformity, boll weight, and boll number
[ 119 ] have been identified in G. tomentosum . Considered to be an unfavorable
parent to contribute to commercial targets, a number of QTLs contributed by this
species have resulted in the improvement of several G. hirsutum fiber characteris-
tics and potentially offers novel and valuable genetic diversity and needs to be
further exploited.
The classical genetic approach of QTL analysis has been combined with a
genomic approach. The expression levels of tens of thousands of genes or gene
clusters are analyzed within a segregating population, expression quantitative trait
loci (eQTL) are mapped like conventional QTLs, and their locations compared with
fiber quality QTLs from the same populations [ 120 , 121 ]. This genetic genomics
approach provides a novel way to close the gap between (structural) genetics and
(functional) genomics to discover chromosomal regions and eventually genes
important for fiber quality. This will ultimately facilitate the breeding of superior
genotypes through marker-assisted selection (MAS) or biotechnology [ 122 ].
Many mapping and genomic studies done to date have been in isolation from
operational breeding programs, and when associations between genomic regions
and fiber traits were identified, they were rarely picked up by breeders. Fiber traits
are complex; the QTL region detected are large (10-20 cM) and may contain
hundreds of genes, so identifying the underlying genes is not usually possible.
Other QTL studies have used too small a population, are cultivar-specific, and the
QTLs are too loosely defined to be of value in selection, particularly when there are
many of small effect [ 120 ]. Where QTLs are cultivar-specific, they are not appli-
cable beyond the populations originally studied.
Most public marker discovery and mapping efforts in cotton have involved using
SSR markers (e.g., the Cotton Marker Database at http://www.cottonmarker.org/ ,
also available through http://www.cottongen.org/ ), but SSR technology is tedious
and labor-intensive, and larger breeding programs have moved away from SSR to
SNP markers. Relatively few studies have been done on QTL mapping between
different G. hirsutum cultivars mainly because of the low levels of marker