Favorable alleles: Gh = G. hirsutum ; Gb = G. barbadense ;
Gt = G. tomentosum ; Gm = G. mustelinum[90,114–116].
The QTL detection in reciprocal backcross populations of G.
hirsutum x G. barbadense crosses
[117] using BC4F1 and BC4F2
populations under three environmental conditions by SNP genotyping
showed a small effect QTL made up 87% and 100% of QTL in G.
hirsutum and G. barbadense, respectively; favorable alleles
masked by unfavorable alleles, and there was higher potential forG. hirsutum improvement than G. barbadense. Three stable
QTLs—two for fiber micronaire and fiber elongation in G.
hirsutum and one for upper half mean length in G.
barbadense —were observed, while four QTLs related to fiber quality
exhibited opposite effects in reciprocal crosses, indicating the
epistasis effects there [117]. Chandnani et al. (2017) studied the
backcross population (BC3F1) of G. hirsutum × G.
mustelinum using 216SR markers on 3202 plants, revealing allelic
interactions, constraints on fixation, selection of donor alleles, and
challenges in the retention of introgressed chromatin for crop
improvement [118]. Waghmare et
al. (2016) analyzed the introgression pattern/heredity into G.
hirsutum from its sister G. tomentosum and found there were
similar rates of introgression into two subgenomes of G. hirsutum(AtDt) and one unusual region for preferential introgression, and
suggested genetic background profoundly preferential introgression,
while the complex heredity of wild genetic material introgression
imposed challenges to utilizing exotic genetic material crop
improvements there. However, Wang et al. (2017) performed QTL mapping
for fiber length in advanced backcross generations
(BC3F2,
BC3F2:3 and
BC3F2:4) of G. hirsutum xG. mustelinum and found the same complexity in exotic
introgression transmission but found the co-localization of many QRLs
for upper half-mean length and the uniformity index of short fiber
contents, indicating the co-selection potential of these QTLs for
improvements [119]. The QTL
mapping using the same population for fiber strength and fineness using
SSR markers identified QTLs for fiber strength and 27 for micronaire and
found that alleles from G. mustelinum increased fiber strength
for 8 of the 15 QTLs and reduced micronaire length for 15 of 27 of the
identified QTLs [120],
supporting the notion that the fiber quality can be improved by
utilizing genetic introgression from G. mustelinum. Transcriptome
analysis for fiber strength in G. hirsutum line IL9 having
introgression from G. mustelinum revealed there were 52
differentially expressed genes (DEGs) contributing to fiber strength
relating to introgression from G. mustelinum, and two genes with
known functions were identified within the fiber-strength quantitative
trait loci (QTL) regions [121].
Wang et al. reported 15 stable QTLs for fiber quality and later used
transcriptome analysis using same population; the integration of DEGs
and QTL identified 31 genes in 9 QTLs, of which 25 probably related to
fibers, suggesting candidate genes for fiber quality improvements
[122]. Using a chromosome
segment substitution line, Lu et al. (2021) identified six QTLs
associated with fiber length and two QTLs associated with fiber
strength, and through integrating transcriptome and qPCR data, they
identified four promising candidate genes for fiber length associated
with those QTLs [123]. A
SLAF-Seq-based approach to construct high-density genetic map for
Identifying fiber quality related QTL using RILs of with introgression
from G. barbadense identified 104 QTLs, comprising 67 for fiber
quality and 37 for yield-related traits, and identified six putative
candidate genes for stable QTL, including GhPEL6, GhCSLC6,and GhTBL5 for fiber length QTLs and GhCOBL4, GhMYB4 , andGhMYB85 for lint percentage QTLs
[124].
The number of QTLs found for each fiber quality trait, their
distributions in the genome, and the sources of favorable alleles from
the respective polyploid progenitors have revealed a number of
interesting findings about the genetic control of cotton fiber
properties and the potential benefit of interspecific introgression.
Introgressed alleles can improve Upland cotton fiber length, strength,
elongation, and fineness; however, this also includes alleles from
non-domesticated species with poor fiber quality as donor parents (Table
3). Nearly half of the QTLs were found in a small number of genomic
regions known as ‘fiber QTL hotspots’, and the majority of the loci have
predominantly additive gene action, confirming the long-held belief that
polyploid Gossypium species are a source of valuable alleles for
improving Upland cotton fiber quality. The high number of loci with
minor effects, low level of consistency across loci discovered in
various populations with the same pedigree, and absence of homoeologous
linkage, however, underscore the overall difficulty of modifying these
quantitatively inherited fiber properties. These findings show that lint
fiber formation may be mediated by a complex gene network and that the
evolution of spinnable fiber may have been mediated by coordinated
changes in the expression of functionally different cotton genes.
According to the enormous number of QTLs linked to the Dt-subgenome,
which comes from an ancestor that does not generate spinnable fiber, it
plays a substantial role in the genetic regulation of fiber growth and
development. Despite the challenges of controlling alien alleles during
introgressive breeding, a number of QTLs for fiber strength and length
have now been successfully introgressed into Upland cotton, and their
authenticity and improvement value has been confirmed using molecular
markers: these QTLs are promising candidates for breeding using markers.
Scientists from Nanjing Agricultural University in China, for example,
have discovered a large fiber strength QTL (QTLFS1) on chromosome 24 in
the germplasm line ‘Suyuan 7235,’ which is assumed to have been
introgressed from the diploid species G. anomalum [115]. F2,
F2: 3, backcross, and recombinant inbred mapping populations resulting
from the cross of line ‘Suyuan 7235’ ‘TM-1’ were used to find this QTL
[115,116]. QTLFS1 was shown to be stable in four test locations in
China and the United States over two growing seasons
[125], indicating that it might
be a promising option for increasing Upland cotton germplasm fiber
strength. Kumar et al. [109] tested this idea by introgressing this
QTL region into two upland genotypes from the United States (‘Sealand
542’ and ‘Sealand 883’) with varied fiber strengths and found that
segregating progenies bearing this QTL had enhanced fiber strength. This
locus has now been independently demonstrated to possess at least three
QTL clusters, with the allele from ‘Suyuan 7235’ imparting higher fiber
strength, by utilizing a high marker density bordering the 10 cm gap
inside the QTL region
[109,126]. Shen et al. verified
a fiber length QTL on Chromosome 1 (qFL-chr1) that was originally
introgressed from G. barbadense using an inbred backcross
technique [125]. The impacts of qFL-chr1 were identified in all
three populations when planted in Nanjing, China, and Georgia in the
United States over two years. The genetic effects of qFL-chr1 and QTLFS1
are small, with the donor alleles increasing fiber length and strength
by just 1.45 mm [109] and 22.8 kN m kg–1[125], respectively. However, the acquired genetic resources and DNA
marker toolkits represent two substantial contributions to Upland cotton
fiber quality enhancement. First, QTL-carrying near-isogenic lines
provide a novel genetic source for enhancing fiber length and strength
in Upland germplasm. As previously stated, Upland cotton has a limited
gene pool as a result of its evolutionary history, domestication, and
current plant breeding procedures. Because farmed germplasm is so
closely related, many beneficial genes, particularly those linked to
production and fiber quality, may have become fixed in the top gene
pool. While some transgressive segregation in fiber properties will
continue to be discovered through crossing among elite parents, the use
of interspecific gene combinations such as these QTLs provides an
important source of new genetic variation to ensure continued genetic
gain in Upland cotton fiber improvement.
Table 3. Resistant improvements against cotton’s disease and
insect pests by introgressive breeding.