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\begin{document}

\title{~Inter-Specific Hybridization in Cotton (Gossypium hirsutum) for Crop
Improvement~~~~}



\author[1]{Muhammad Zafar Iqbal}%
\affil[1]{Affiliation not available}%


\vspace{-1em}



  
  \date{June 13, 2024}


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Review

Inter-Specific Hybridization in Cotton (\emph{Gossypium hirsutum} ) for
Crop Improvement

Muhammad Zafar Iqbal \textsuperscript{1,} * Muhammad
Anwar\textsuperscript{2}\selectlanguage{english}
\begin{longtable}[]{@{}l@{}}
\toprule
\tabularnewline
\bottomrule
\end{longtable}

\textsuperscript{1} College of Grassland Science and Technology, Sichuan
Agricultural University, Wenjiang 611100, Chengdu China;
pengyanlee@163.com

\textsuperscript{2} Guangdong Technology Research Center for Marine
Algal Bioengineering, Guangdong Key, Laboratory of Plant Epigenetics,
College of Life Sciences and Oceanography, Shenzhen University, Shenzhen
518055, China; anwar\_uaar@yahoo.com

* Correspondence: m.zafarsindhu@hotmail.com (M.Z.I.)

\textbf{Abstract:} Interspecific hybridization has contributed
significantly to land diversity, species evolution, and crops'
domestication, including upland cotton, the cultivated form
of\emph{Gossypium hirsutum} . Being the world's most important fiber
crop species, \emph{Gossypium hirsutum} belongs to the allotetraploid
Gossypium consisting of six additional tetraploid species. The lint
fiber evolved once in diploid parent A-genome species in
the\emph{Gossypium} 's history and passed on during hybridization of the
A-genome with the D-genome and was maintained in subsequent evolution.
The domestication history of \emph{G. hirsutum} involved the collection
and use of lint fibers by indigenous people for the purpose of making
strings and other textile products; hence, spinnable lint fibers were
likely to have evolved under domestication. Crossing with \emph{G.
barbadense} has resulted in the development of multiple genetic lines in
contemporary upland cotton. However, in later-generation hybrids
between\emph{G. hirsutum} and other polyploid species, reproductive
barriers such as reduced fertility, segregation distortion, and hybrid
breakdown are frequently observed, complicating the task of
introgressing new, stably inherited allelic variation from
inter-specific hybridization. Recent efforts in molecular genetics
research have provided insights into the location and effects of QTLs
from wild species that are associated with traits important to cotton
production. These and future research efforts will undoubtedly provide
the tools that can be utilized by plant breeders to access novel genes
from wild and domesticated allotetraploid \emph{Gossypium} for upland
cotton improvement.

\textbf{Keywords:} interspecific hybridization; \emph{Gossypium
hirsutum;} crop improvement; fiber quality; polyploidization;
introgressive breeding

1. Introduction

Cotton is a food and fiber plant contributing to humanity's fundamental
requirements. Cotton fiber, in the form of textile objects, contributes
significantly to the comfort, style, and culture of human society.
Despite its lack of appeal as a food, cotton is a primary source of
vegetable oil, which is used extensively in meals such as baking and
frying fats, mayonnaise, margarine, and snack food. Following oil
extraction, the seed by-product is used as a raw material in animal
feed, fertilizer, and paper. Because of its flexibility, cotton is one
of the most important field crops in the world. According to the
International Cotton Advisory Committee (ICAC), which collects data on
global cotton production, consumption, and commerce, cotton is grown on
36 million hectares in over 100 countries {[}1{]}. The top five
cotton-producing countries are China, India, the United States,
Pakistan, and Brazil, which account for around two-thirds of worldwide
cotton production {[}2{]}. Cotton has become the most important natural
fiber in the textile industry, as well as a vital agricultural product
in the global economy. The annual value of the worldwide cotton crop is
estimated to be over USD 30 billion, with lint fiber accounting for 90\%
of that value {[}3{]}. Cotton farming and processing employ about 350
million people worldwide. Cotton's economic importance as a natural
fiber for the global textile industry has spurred a lot of interest in
improving the crop's inherent genetic potential by breeding cultivars
with higher biotic and abiotic tolerance, higher lint yield, and
enhanced fiber quality {[}4{]}.

Cotton's development and progress have benefited greatly from
interspecific hybridization. Cotton remarkable as a crop in that four
distinct species of the genus \emph{Gossypium} (Malvaceae) were
domesticated for lint fiber production on two separate continents
{[}5,6{]}. As a result, in the textile business, the two allotetraploid
species\emph{G. hirsutum} L. and \emph{G. barbadense} L., both native to
the Americas, and the two diploid species \emph{G. arboreum} L. and
\emph{G. herbaceum} L., both endemic to Africa and Asia, are referred to
as ``cotton.'' Allotetraploid \emph{Gossypium} has a single
polyploidization history, with progenitors that resemble \emph{G.
herbaceum} or \emph{G. arboreum} (A genome) and \emph{G. raimondii} (D
genome) merging together {[}6{]}. The two allotetraploids now provide
the great majority of the world's textile fiber, with \emph{G.
hirsutum}accounting for more than 90\% of worldwide cotton production
{[}7{]}. As a result, the focus of this review will be on \emph{G.
hirsutum} , popularly known as ``Upland'' cotton, a cultivated
allotetraploid species. Other domesticated and non-domesticated
allotetraploid species, on the other hand, will be included since they
represent a vast pool of untapped genetic resources for future genetic
advancement.

2. Taxonomy of \emph{Gossypium} and Origin of \emph{Gossypium hirsutum}

The genus Gossypium contains around 50 species, which are distributed in
tropics and subtropics regions. Diploid Gossypium species are
categorized into eight genome groups (A--G, K) based on chromosomal
pairing affinities {[}8{]}. Despite the fact that numerous important
diversification sites have been identified, these species collectively
have a large distribution. A-genome species are found both in Africa and
Asia; B- and F-genome species are mainly present in Africa; Arabia has
E-genome species; C-, G-, and K-genome species can be found in
Australia; whereas D-genome species can be found in Central and South
America. The detailed grouping and geographical distribution of
\emph{Gossypium} species are summarized in Table 1. Although molecular
phylogenetic investigations have established a phylogenetic framework
for the genus and its many genome types, a thorough understanding of the
evolutionary links between each species remains elusive {[}6{]}.
\emph{G. hirsutum} and \emph{G. barbadense} , two domesticated species,
plus \emph{G. tomentosum} Nutt ex Seem, \emph{G. darwinii} Watt, and
\emph{G. mustelinum} Miers ex G. Watt, are the five allotetraploid
Gossypium species that have been extensively recognized in the
past\emph{. G. ekmanianum} Wittmack, a sixth species, was recently
discovered, and a seventh was discovered (see below). Polyploid
Gossypium has a broad geographic distribution that includes several
seasonally dry subtropical and tropical parts of the North and South
American continents, mainly near coasts, as well as numerous Caribbean
and Pacific islands. As a result, these species are commonly referred to
as New World cotton. The fact that \emph{G. darwinii} (Galapagos
Islands), \emph{G. ekmanianum} (Hispaniola), and\emph{G. tomentosum}
(Hawaiian Islands) are all island endemics suggests that these species
evolved after long-distance dispersion episodes {[}6,9{]}. The native
Brazilian cotton (\emph{Gossypium mustelinum)} has never been
cultivated. It is tetraploid and may be crossed with cultivated cotton.
\emph{Gossypium mustelinum} is grown in semiarid region and expanded to
the coastal area of northeast Brazil in 2018. It is cultivated in
Paraiba and Pernambuco in Brazil {[}10{]}. \emph{G. hirsutum} is native
to Central America, whereas \emph{G. barbadense} is native to South
America, but their ranges overlap, notably in northwest South America
and across the Caribbean. Two new species have just been added to the
allopolyploid cotton group. Based on accessions obtained in the
Dominican Republic, the species \emph{G. ekmanianum} Wittm was recently
revived {[}11,12{]}. A seventh species, \emph{Gossypium
stephensii}{[}13{]}, has been recently discovered in the Wake Atoll in
the Pacific Ocean (Wake, Peale, and Wilkes Islands) {[}13,14{]}.\emph{G.
hirsutum} , \emph{G. tomentosum} , G. ekmanianum, and the newly found
species form one clade; \emph{G. barbadense} and \emph{G. darwinii} form
a second clade; and \emph{G. mustelinum} remains the allopolyploid
phylogeny's basal clade {[}6{]}. Because of their monophyletic origin,
all seven polyploid species have two sets of 13 homoeologous chromosomes
(2n = 4x = 52) and strict disomic chromosome pairing (Kimber 1961)
A-genome cytoplasm. Polyploidization occurred about 1--2 million years
ago by transoceanic migration of an Old World (A-genome) progenitor
followed by hybridization with a native New World (D-genome) progenitor
{[}6{]}. The At- and Dt-subgenomes of the tetraploids were provided by
diploid progenitors that resemble \emph{G. arboreum} or \emph{G.
herbaceum} , and \emph{G. raimondii} , respectively, according to
meiotic chromosomal pairing and comparative genome studies. The
progenitors of these species separated from a common ancestor 5--7
million years ago, according to DNA sequence evidence {[}6,15{]}.
Cotton's A- and D-genome progenitors have at least nine chromosomal
rearrangements in common {[}16{]}. Furthermore, the A-genome contains
around twice as much gametic DNA as the D-genome {[}17{]}, with the
increased genome size attributed mostly to the repetitive DNA fraction,
as the quantity of single-copy DNA in both genomes is nearly equal
{[}18{]}. Genetic mapping {[}19,20{]} identified the matching
homoeologous chromosomes of the At- and Dt-subgenomes, which were
recently confirmed by two draft genomes sequences {[}14{]}. In the At
sub genome, direct comparisons of gene order and synteny between the two
sub genomes revealed two reciprocal translocations between chromosomes
02/03 and 04/05, as well as multiple probable inversions {[}18,19{]}.
The tetraploid chromosomes have also been aligned with those of their
diploid progenitors, indicating that there has been more rearrangement
since polyploid development {[}20,21{]}. Nonetheless, these findings
suggest that gene collinearity between the two subgenomes is
substantial, and that chromosomal structural rearrangement has been
minimal after allopolyploid formation. A grouping of
\emph{Gossypium}species based on genomic diversity is shown in Table 1,
and the evolution of \emph{Gossypium} species, including
tetraploid\emph{Gossypium} species formation, is illustrated in Figure
1.

\textbf{Table 1.} Grouping and geographical distribution of the
genus\emph{Gossypium} species based on genomic diversity validated by
cytogenetic data and other means.\selectlanguage{english}
\begin{longtable}[]{@{}llll@{}}
\toprule
\textbf{Genome Group} & \textbf{Ploidy (No. of Species)} &
\textbf{Species Name} & \textbf{Geographical
Distribution}\tabularnewline
\midrule
\endhead
A & 2X (2) & \emph{G. herbaceum, G. arboreum,} & Asia,
Africa\tabularnewline
B & 2X (3--4) & &\tabularnewline
\emph{G. trifurcatum} & \emph{Cape Verde Island, Africa} &
&\tabularnewline
\emph{C} & \emph{2X (2)} & G. robinsonii, G. sturtianum &
\emph{Australia}\tabularnewline
\emph{D} & \emph{2X (13--14)} & &\tabularnewline
davidsonii, G. gossypioides, G. harknessii, G. klotzschianum, G. laxum,
G. lobatum, (Gossypium sp. Nov), G. raimondii, G. schwendimanii, G.
turneri, G. thurberi, G. trilobum & Mexico, Peru, Arizona, Galapagos
Islands & &\tabularnewline
E & 2X (5--9) & \emph{G. areysianum} Deflers\emph{,} (\emph{G.
benadirense})\emph{,} (\emph{G. bricchettii})\emph{, G. incanum, G.
stocksii, G. somalense, G. trifurcatum,} (\emph{G. trifurcatum})\emph{,}
(\emph{G. vollesenii}) & Southwest Asia, Northeast Africa, Arabian
Peninsula\tabularnewline
F & 2X (1) & \emph{G. longicalyx} & East Africa\tabularnewline
G & 2X (3) & \emph{G. australe, G. bickii, G. nelsonii} &
Australia\tabularnewline
K & 2X (12) & \emph{G. anapoides, G. cunninghamii, G. costulatum, G.
exiguum, G. enthyle}, \emph{G. londonderriense}, \emph{G. nobile},
\emph{G. marchantii, G. populifolium, G. pilosum, G. pulchellum, G.
rotundifolium}. & Australia, Northern Territory, Cobourg Peninsula,
Northwest Australia\tabularnewline
AD & 4X (7) & \emph{G. barbadense, G. darwinii, G. ekmanianum, G.
hirsutum, G. mustelinum, G. tomentosum, G. stephensii.} & New World
tropics and subtropics, including Hawaii, Galapagos Islands and the Wake
Atoll\tabularnewline
\bottomrule
\end{longtable}

\par\null

\textbf{Figure 1.} The evolution of \emph{Gossypium} genus and the
formation of tetraploid \emph{Gossypium} species. MB show genome size of
representative species.

3. Domestication of Upland Cotton

After polyploidization, \emph{G. hirsutum} evolved to produce
high-quality fiber and to best survive against adverse environments
{[}7{]}. The domestication history of \emph{G. hirsutum} is similar to
that of the other three domesticated cotton species; indigenous peoples
may have gathered and employed lint fibers for string and other textile
items. {[}7,20,21{]}. Domestication of cotton gave rise to long lint
fiber, which has a flat convoluted ribbon shape that allows it to be
spun into yarn {[}20,22{]}. Short `linters' or fuzz stick to the seed
coat tightly, whilst longer `lint' fibers cling to the seed coat
loosely. Fuzz fibers are an important source of raw material for paper
and other industrial products. Cotton is the world's most important
fiber crop due to its longer, spinnable lint fibers, and these novel
single-celled seed epidermal trichomes may have lured ancient peoples to
the cotton plant in the first place. Four separate Gossypium species
were domesticated independently by four civilizations on two continents,
as previously stated: A-genome diploids\emph{G. herbaceum} and \emph{G.
arboreum} were domesticated in Africa and Asia, and allopolyploids
\emph{G. hirsutum} and \emph{G. barbadense}were domesticated in Central
and South America {[}20,22,23{]}. Wild cotton feature short and coarse
lint \emph{fibers} that are very different from those seen in current
cultivar cottonseed. Although the elongated seed trichomes may operate
as a dispersion mechanism in some ecological circumstances and/or
function in maintaining an adequate microbiological and hydration
background for seed germination or early seedling development, the
biological function of lint fiber has not been determined {[}24{]}.
Early domesticators were likely drawn to primitive lint fiber, with
current germplasm's long lint fiber, resulting from the human selection
of genotypes with enhanced fiber quality attributes, as well as higher
lint output and other agronomic qualities {[}23,25{]}. Interestingly,
the elongation of fiber cells during development is directly linked to
the evolution of long spinnable lint fiber; particularly, developing
fiber cells in domesticated diploid and tetraploid cotton all exhibit a
protracted fiber-cell growth programmed. Only the F-genome/A-genome
lineages developed this developmental novelty, which may have aided the
domestication of A-genome cotton {[}26,27{]}. When the A-genome joined
the D-genome during polyploidization, this predisposition for extended
lint fiber growth was passed on to allopolyploids {[}28{]}. \emph{G.
hirsutum} is said to have been domesticated in Mesoamerica's Yucatan
Peninsula. According to Brubaker and {[}29{]}, race `punctatum' is the
earliest domesticated form of \emph{G. hirsutum} , having agronomic
characteristics that are transitional between the really wild race
`yucatanense' and races with more advanced attributes such as latifolium
and palmeri. Early attempts at domestication may have involved choosing
a more appealing plant from the wild population to generate door-yard
cultigens, which later evolved into large-scale field production as
civilization grew and agriculture became more specialized. Increased
lint output through choosing larger and more bolls per plant, lowering
plant size from the shrubby/small treelike habit of wild cotton to a
scale that people can utilize, and selecting for a more annual life
cycle are all qualities that early agriculturalists may have preferred.
Later decisions concentrated on finer, stronger, and consistently longer
fibers to improve the fiber's quality. Other fiber qualities such as
elongation and short fiber content have grown increasingly important as
the textile industry has become more automated. As agriculture and
agribusiness converge, the industrialization of production will continue
to define aspects that increase production efficiency. For example,
growing mechanization needed plant size selection, but monoculture's
vulnerability to pests and diseases necessitated enhanced selection for
resistance to these challenges. Ware {[}30{]} has published a thorough
historical account of the history of \emph{G. hirsutum} as Upland cotton
cultivars from the time of European arrival to the middle of the
twentieth century. The birth and development of Upland germplasm, the
current cultivated form of \emph{G. hirsutum} , occurred in the southern
United States of America, despite the fact that the specific location
of\emph{G. hirsutum} domestication is unclear. The `Cotton Belt' of the
United States was the epicenter of upland cotton's genetic development.
When a result, the cotton crop was brought to the eastern coastal areas
of North America as Europeans departed. While all four domesticated
Gossypium species were planted as crops in the United States from the
start, the allotetraploids outperformed the A genome diploids. As the
twentieth century progressed, a new categorization system based on
geographic areas and industrial techniques emerged, which is still in
use today: Acala type, Plains type, Delta type, and Eastern type
{[}31{]}. Asiatic diploid species\emph{G. arboreum} and \emph{G.
herbaceum} , with much shorter staple lengths than Upland or Sea Island
cotton, were produced in cotton-producing nations such as India, China,
and Russia prior to the establishment of the US cotton industry
{[}32{]}. The new spinning methods available at the time could not
handle the fiber produced by \emph{G. arboreum} and \emph{G. herbaceum}
. While there has been some success in breeding for longer fiber length
within the diploid species {[}33{]}, more Upland germplasm was
introduced to meet the need for new varieties with better fiber quality.
By the 1920s, practically all worldwide breeding efforts had shifted to
the allopolyploid \emph{G. hirsutum} , a short-fiber Asiatic species
{[}30{]}.

4. Cotton Improvement

Since Niles and Feaster's report, the great majority of cotton breeding
efforts have continued to use the same technique {[}9{]}. Cotton is
mostly a self-pollinated plant; hence most cotton growers use a modified
pedigree breeding approach to generate pure line cultivars. In general,
parents with different attributes or traits of interest are chosen for
cross hybridization, segregating populations are evaluated in the field
to identify individual plants with the desired trait combinations, seed
from the selected plants is evaluated in progeny rows, and inbred lines
that outperform ``check'' cultivars are evaluated in replicated tests
over multiple locations and years {[}34,35{]}. The procedures of cotton
breeding programs have been nicely laid out in literature {[}36--38{]}.
Current breeding operations make use of substantially more machinery,
allowing them to handle a bigger number of progeny rows with fewer
people and more sophisticated fertilization, plant growth control, and
pest management. Although the relative significance of these features
may have altered, the traits that are wanted in present cultivars are
not significantly different from those in earlier years of cotton
cultivation {[}37{]}. In every commercial cotton breeding program, lint
output remains the top objective {[}39--41{]}. Lint percent, which is a
component of lint output, was probably one of the first qualities to be
chosen throughout the domestication process and in early breeding, and
is still the most desired character {[}23,42--46{]}. Environmental
stability {[}47,48{]} and early maturity {[}49--51{]} are two more
agronomic features that have risen in relevance {[}37{]}. Despite the
fact that the advent of transgenic Bt cultivars has shifted the
attention away from insect resistance, host-plant resistance remains
significant for a variety of diseases and nematodes. Similarly, breeding
efforts used to priorities cotton genotypes with low vegetative growth
and erect stature, but plant height and compact growth habits may now be
readily regulated with plant growth regulators such as Mepiquat
{[}52{]}. The second most significant aim in early breeding attempts was
fiber quality, which is still the case in commercial cotton breeding
projects {[}53--55{]}. The replacement of manual spinning methods with
machine spinning and weaving technologies, which required adequate fiber
length and strength to work properly, provided the motivation for this
endeavor. Cotton fibers' quality is determined by their physical
characteristics. Lint fiber is frequently spun into yarn, which is
subsequently woven or knitted into a variety of textiles dependent on
the quality and desired end-product characteristics. The collection of
fiber characteristics that determine the efficiency of yarn spinning,
weaving, and other fabric-making activities, as well as the quality of
cotton textiles, is referred to as fiber quality. The key fiber factors
that are substantially linked with spinning performance and end product
quality are the length, strength, elongation, and fineness/maturity
(measured in micronaire) of the fiber. The relevance of fiber
characteristics and how they are quantified was nicely outlined by Chee
et al. (2009) {[}56{]}.

Lint production and fiber quality are both quantitatively inherited
characteristics. For yield and fiber quality variables, Campbell et al.
{[}57{]} reported the mean broad-sense and narrow-sense heritability.
Although yield components and fiber quality attributes are both
heritable and exhibit additive genetic variation and frequently exhibit
a negative correlation, it is suggested that this is due to linkage
rather than pleiotropy; however, Campbell et al. {[}58{]} found that the
negative connection in Pee Dee germplasm maintains after over 80 years
of breeding. As a result, improving yield and fiber quality
simultaneously is the most difficult problem in cotton breeding.

Meredith and Bridge (1973) tested the performance of four cottons
(\emph{G. hirsutum} L\emph{.} ) cultivars under four environmental
conditions and estimated seven yield components with seven fiber
properties using nine different harvests. Results revealed that the lint
index was lowest for early harvest and was highest for the middle
harvests, while cultivars were the most important source of variations
for fiber properties, indicating the importance of genetic variation for
fiber quality traits improvements {[}59{]}. Later they used a modified
recurrent selection method for improving lint percentage within a cotton
(\emph{G. hirsutum} L) cultivar `Deltapine 523,' through initially
plant-based selection, followed by progeny-row basis selection and
construction of S1, S2, and S3 selfed generations. They finally attained
eight progenies in S3 with 2.5\% higher span length {[}60{]}, thereby
significantly improving the cotton for lint yield, lint percentage,
fiber length, lint index, and Micronaire in the S3 generation population
compared to the S0 population {[}60{]}. Using \emph{G. barbadense} as a
donor parent, reciprocal backcross population of the S6 generation of
\emph{G. hirsutum} \selectlanguage{ngerman}× \emph{G. barbadense} crosses showed significant
genotypic variations, and improvements in fiber-quality-related traits,
including micronaire, fiber elongation, fiber strength, and upper half
mean length showed significant higher genotypic variance in \emph{G.
hirsutum}background than \emph{G. barbadense,} indicating cytoplasmic
effects on the genetic variations and heredity {[}61{]}. The growing
number of evidences has been reported to verifying the adoptive roles of
alien introgression for different quality traits, especially fiber
quality of\emph{G. hirsutum}{[}62--68{]}.

5. Development of Spinnable Fiber and Polyploidization

In terms of fiber quality improvement, it is worth noting that spinnable
fiber appeared just once in Gossypium's history, in an ancestor of the
two domesticated diploid A-genome species, after the F-genome lineage
split. This feature was handed down to allopolyploid cotton when the
A-genome fused with a D-genome from an ancestor that didn't make lint
fibers in a shared nucleus {[}27,69{]}. As previously stated, the
formation of long spinnable lint fiber is closely linked to a protracted
elongation phase during fiber cell development.

Applequist, Cronn and Wendel {[}26{]} used accessions from the AD-genome
allopolyploids \emph{G. hirsutum} and \emph{G. tomentosum} , as well as
diploid species \emph{G. herbaceum} (A-genome), \emph{G.
arboreum}(A-genome), \emph{G. raimondii} (D-genome), \emph{G.
davidsonii}(D-genome), \emph{G. anomalum} (B-genome), and \emph{G.
stur}(F-genome). Accessions from the AD-genome allopolyploids and the
A-genome diploids have a much higher rate of fiber elongation than the
other diploids, according to a comparison of growth curves across
species. Hovav et al. {[}27{]} came to a similar result after comparing
gene expression profiles over a developmental time-course of fiber
from\emph{G. herbaceum} and \emph{G. longicalyx} . In domesticated
A-genome\emph{G. herbaceum} , their findings revealed significant
changes in the expression of genes associated with stress responses and
cell elongation, as well as a longer developmental profile. Thus, the
evolution of lint fiber included a continuation of an ancient
developmental programmed that developed prior to polyploidization in the
ancestral A-genome. Polyploidization has another major meaning for the
evolution of spinnable fiber, in addition to supporting the evolution of
a protracted period of fiber elongation. The joining of the A- and
D-genomes in a single nucleus may have allowed D-genome alleles (genes)
to be recruited into fiber development, resulting in higher fiber
quality and production in polyploid cotton. Because only A-genome
diploid species generate spinnable fiber, the relevance of the D-genome
in polyploid cotton fiber quality genetic determination has long been
debated. Jiang et al. {[}70{]} presented the first evidence of the
extent to which loci on the Dt-subgenome cause genetic variation in
fiber quality attributes, showing that the majority of QTLs for fiber
quality mapping to the Dt-subgenome. Numerous genetic mapping analyses,
summarized by {[}56{]}, have now supported the observation that the
Dt-subgenome, from the ancestor that did not have spinnable fiber, plays
a large role in the genetic control of polyploid cotton fiber growth and
development. These findings show that Dt-subgenome genes have been
recruited to the genetic regulation of fiber quality attributes, leading
to polyploid cotton' transgressive fiber quality and yield compared to
diploid progenitors. Many advantageous alleles at important loci for
fiber qualities may have already been fixed as a result of natural
selection, according to {[}70{]}, because the At-subgenome has a
significantly longer history of selection for fiber formation. On the
other hand, fiber growth loci on the Dt-subgenome may not have been
subjected to strong selection until after polyploidization, and hence,
mutations that improved this feature may have only been advantageous
after polyploidization. As a result, the Dt-subgenome may have had
greater `room for improvement' of fiber qualities when the artificial
selection was recently enforced by domestication and breeding.
Recruitment of Dt-subgenome loci may provide polyploid cotton more
flexibility for artificial selection through breeding, explaining why
polyploid cotton has better fiber characteristics than farmed A-genome
diploids. The uneven pace of evolution in the polyploid AD-subgenome is
a secondary consequence of polyploidization for spinnable fiber and a
host of other characteristics that geneticists are only beginning to
understand through genome sequence analysis. The majority, if not all,
loci are duplicated in allopolyploid genomes by definition. Lynch and
Conery {[}71{]} addressed the different outcomes of duplicated genes,
claiming that most duplicated genes go through a brief period of relaxed
selection before being silenced or pseudogenized. However, a tiny
percentage of duplicated genes survive in duplicate and contribute to
developing phenotypic complexity through natural selection. A null
hypothesis is that homoeologous genes would develop independently and at
comparable rates following polyploid formation in recent allopolyploids
such as cotton, where the two subgenomes contain duplicated but somewhat
divergent copies of most genes. Allopolyploid cotton have gone through
bi-directional concerted evolution for some genes, resulting in
differing directional biases in different sections of the genome. In
situ hybridization revealed that distributed repetitive sequences that
are A-genome specific at the diploid level had expanded to the
Dt-subgenome in allopolyploids, which provided the first clues to this
occurrence {[}72,73{]}. Furthermore, multiple studies have found that
the Dt-subgenome has much greater allelic diversity of homoeologous
genes {[}74{]} and loci affecting quantitative features than the
At-subgenome {[}18,75{]}. Non-reciprocal DNA conversion favors genes in
the Dt-subgenome over genes in the At-subgenome, according to recent
genome sequence comparisons {[}76{]}: for example, the sequences of
around 40\% of the At and Dt genes in an elite cotton cultivar change
from their diploid ancestors. Most of these mutations are convergent,
with at least one gene being changed to the Dt state at a rate more than
double that of the reciprocal {[}9{]}. These findings show that
polyploidization allowed D-genome genes to take on new tasks in the
allopolyploid genome, potentially explaining why domesticated
allopolyploid cotton outperforms its diploid offspring in terms of
agronomic and fiber quality.

6. Gene Introgression and Inter-Specific Hybridization

Each phase in the domestication of cotton, from wild \emph{G.
hirsutum}to feral cultigens to the advent of Upland germplasm to current
better cultivars, imposed severe genetic bottlenecks, limiting allelic
diversity. Morphological {[}77{]}, and molecular characterization have
been used to record the amounts and patterns of genetic erosion involved
with the formation of early cultigens, landraces, and current cultivars
{[}78,79{]}. Too many genomic region and genes have reported to be
introgressed from wild relative of upland cotton contributed to the
improvements of upland cotton {[}8,65,80{]}.

The average genetic distance across 378 Upland accessions from the
United States examined with 120 SSR markers was only 0.195,
demonstrating that Upland cotton germplasm is quite limited {[}79{]}.
Lubbers and Chee {[}81{]} used 250 RFLPs to examine 320 Upland
cultivars/germplasm from the United States National Plant Germplasm
Collection and found cotton to have less genetic diversity than most
important crops. When top germplasm from various geographical origins
was assessed, the amount of genetic diversity did not improve. Indeed,
the average number of alleles discovered per locus in a survey of 157
elite cultivars from China, the United States, Africa, the Former Soviet
Union, and Australia utilizing 146 SSR loci was just 2.3 {[}82{]}.
Surprisingly, these genetic limitations were followed by sustained
improvements in several key cotton properties, particularly fiber
quality. Given the low allelic diversity in the Upland cotton gene pool,
it is reasonable to assume that the number of favorable alleles for
fiber quality (such as fiber length and strength) that have yet to reach
fixation is small, as these traits have been under intense selection
pressure since the early stages of domestication. As a result, it is not
unexpected that interspecific introgression has long been a topic of
discussion in the Upland cotton community {[}83,84{]}. Upland cotton
breeding has prioritized high production and adaptability, whereas
domesticated strains of \emph{G. barbadense} , often known as Pima,
Egyptian, or Sea Island cotton, have prioritized improved fiber quality.
As a result, farmed \emph{G. barbadense} fiber is substantially longer,
finer, and stronger than Upland cotton, which is more extensively grown.
However, both Pima and Egyptian cotton have a restricted range of
environmental adaptability in irrigated regions in dry zones of the
Western United States and Lower Egypt, respectively, of the \emph{G.
barbadense} that are still in production. Nonetheless, this species'
distinctive fiber qualities make it an attractive option for supplying
additional genetic variety to increase Upland cotton fiber quality. It
is no surprise, therefore, that studies of populations produced from
interspecific hybridization between wild and domesticated strains of
\emph{G. barbadense} and Upland cotton have investigated the genetic
basis and heritability of species fiber qualities {[}56,85{]}.
Interspecies genome merge provides an opportunity to the introduce a
foreign beneficial gene for crop improvements and genetic analysis. Saha
et al. (2006) developed monosomic and monotelodisomic substitution
hybrids between \emph{G. hirsutum} and \emph{G. tomentosum} and
identified several types of numerical and structural variations and
offered a valuable germplasm for localization of genomic markers and
development of backcross substitution line for cotton cultivars'
improvements {[}86{]}. Recently, Muthuraj et al. (2019) developed male
sterile triploid interspecific hybrids between tetraploid \emph{G.
hirsutum} and diploid \emph{G. armourianum,} which showed intermediate
phenotypes, and this germplasm is an important genetic source for
introducing sucking cotton pest ``jassid''-resistant genes into the
cultivated cotton cultivars through conventional breeding schemes
{[}87{]}. In order to barrier free wild gene introgression into
cultivated cotton, a tri-species hybrid ``(\emph{G. arboreum} × \emph{G.
anomalum} ) ×\emph{G. hirsutum} '' was produced. The cytomorphological
analysis of a tri-species hybrid and its backcross progenies to \emph{G.
hirsutum}showed the production of monovalent to hexavalent offspring and
allosyndetic chromosomes pairing, indicating the possibility of
intergenomic genetic exchanges and yet a homoeologous relationship among
these species {[}88{]}. As expected, the molecular marker data combined
with cytogenetic findings determined the multi-genome background in
monovalent to hexaploid progenies and provided an important intermediate
material for introducing exotic genetic introgression {[}88{]}. Draye et
al. (2005) used backcross-self-pollination population of a \emph{G.
hirsutum} and\emph{G. barbadense} cross and identified 32 and 9 QTLs for
fiber fineness and micronaire, respectively, and from nine micronaire
QTLs, seven were also associated with fiber fineness; however, the
majority of the members of the BC3F2 population showed inferior
phenotypes, thus imposing hurdles to utilize \emph{G. barbadense} in
conventional planting breeding programs {[}89{]}. The breeding
utilization of \emph{G. barbadense} -introgressed line
in\emph{G.hirsutum} showed high mid-parent heterosis for yield, and F1
to F3 hybrids outcompeted the high-yielding commercial cultivar
{[}90{]}, indicating the suitability of introgressed lines for being
outcompeting cultivars. Remarkable progress was made by Hulse-kemp et
al. (2015) by developing CottonSNP63K, an Illumina Infinium array with
45,104 intraspecific and 17,954 interspecific putative SNP markers, and
generating two high-density genetic maps, collectively providing new
cotton resources for cotton breeders {[}91{]}. Later, Hinze et al.
(2017) used this CottonSNP63K array and validated that it could
distinctly separate \emph{G. hirsutum} from other
\emph{Gossypium}species, distinguish the wild from cultivated types of
\emph{G. hirsutum} , and identify loci possibly linked to cotton seed
protein contents {[}92{]}. As chromosome segment substitution (CSSLs)
lines provide an ideal opportunity to map QTLs in interspecific hybrids,
a CSSL derived by hybridizing and backcrossing \emph{G. hirsutum} and
\emph{G. barbadense} genotyped by whole genome re-sequencing identified
64 QTLs for 14 agronomic traits, and many alleles of \emph{G.
barbadense} showed extremely high values for improving cotton seed pool
contents {[}93{]}. Recombinant inbred line populations produced between
the Chinese \emph{G. barbadense} cultivar 5917 and the American Pima S-7
were tested for lint yield and fiber quality traits, followed by GBS
sequencing, and there were 42 QTLs identified, including 24 QTLs on 12
linkage groups for fiber quality and 18 QTLs on 7 linkage groups for
lint yield, thereby proving an initial material for fine mapping of
QTLs, prediction of candidate genes, and development of molecular
markers.

The majority of these genetic investigations have shown that fiber
qualities are heritable {[}94--96{]}, implying that interspecific
introgression might increase specific Upland cotton fiber traits. In
addition to fiber quality, wild and domesticated allotetraploid
Gossypium is a significant source of disease and pest resistance genes
that might be transferred into Upland cotton {[}65,97--99{]}. Pathogens,
nematodes, and insects cause severe crop losses anywhere cotton is
grown, and crop protection expenditures account for a large percentage
of the high unit cost of cotton production, which is why transgenic
pest-management cultivars are so appealing. According to Meredith Jr
{[}100{]}, breeding for disease resistance is more important than
breeding for pest resistance in most breeding programs. This is
especially true with the development of Bt cotton varieties, which are
insect-resistant. Some wild species resistance characteristics are
simply inherited, and breeders have taken advantage of these features
since they are easy to select. However, many resistance qualities are
quantitatively inherited, and using DNA markers to manipulate them has
lately become considerably more successful. Disease resistance genes
found in wild and domesticated allopolyploid Gossypium are summarized in
Table 1. After polyploid development during the Mid-Pleistocene, around
1--2 Mya, \emph{G. hirsutum} , \emph{G. barbadense} , and the wild
allopolyploid species separated from a common ancestor. When introduced
into a diverse genetic background, mutations that have accumulated in
various allopolyploid lineages may or may not interact positively (Orr
1995). While allopolyploid species are sexually compatible,
later-generation hybrids sometimes exhibit partial reproductive
obstacles such as lower fertility, segregation distortion (non-Mendelian
inheritance), and hybrid breakdown {[}101{]}. Jiang et al. {[}102{]}
employed DNA markers to analyze the transmission genetics of an advanced
back cross generation interspecific hybrid population between \emph{G.
hirsutum} and \emph{G. barbadense} , demonstrating the effects of these
barriers to gene introgression across allotetraploid cotton. Individual
allele transmission patterns often promote the eradication of the donor
genotype, maintaining the recurrent genotype's integrity. Segregation
distortions were common, for example, and early generations of
hybridization resulted in the full eradication of certain donor alleles
as early as the BC3 generation due to under-representation of donor
alleles. Interestingly, the segregating ratios at identical loci
introgressed into different independently derived BC3 F2 families were
highly variable, with some families favoring recurrent parent alleles
while others favor donor parent alleles, implying that hybrid
incompatibility is best explained by multi-locus epistatic interactions
affecting gamete success and genotype fecundity. These findings
illustrate the challenge of using interspecific populations to generate
superior Upland cotton cultivars by pyramiding numerous beneficial
alleles for quantitative features, including lint production, fiber
length, fiber strength, and fiber fineness in a single genotype. Most
attempts to directly mix Upland cotton with Sea Island (\emph{G.
barbadense} ) varieties, as observed by Brown and Ware {[}103{]},
revealed that while the F1 generation is beautiful, the F2 and F3
generations are regarded as ``messy'' and are nearly usually abandoned
(Figure 2). While pedigree research revealed that several cultivars were
created through interspecific hybridization, a molecular study using
isozymes and DNA markers revealed that the Upland cotton gene pool is
rather uniform. Rare alleles are found in just a few closely related
cultivars within a germplasm group and are thought to have evolved by
introgression {[}6,104{]}. Furthermore, none of these \emph{G.
barbadense} -introgressed alleles were discovered in current cotton
cultivars, suggesting that the advantages of \emph{G. barbadense}
introgression in Upland cotton are still completely unmet. Conversely,
the introduction of Upland cotton genes into Pima cotton, a cultivated
variety of \emph{G. barbadense} , has substantially aided the production
and adaptability of current Pima cultivars {[}105,106{]}.

\par\null

\textbf{Figure 2.} Floral abnormality in later generation hybrids
between \emph{Gossypium hirsutum} and \emph{G. barbadense} : (\textbf{A}
) abnormal style, stigma, and anther formation; (\textbf{B} ,\textbf{C}
) abnormal bud development; and (\textbf{D} ) an abnormal flower of an
F2 generation of \emph{Gossypium hirsutum} × \emph{G. barbadense}
\textbf{.}

7. Introgressive Breeding

Interspecific populations derived from crossings between \emph{G.
hirsutum} and \emph{G. barbadense} solved the classic problem of limited
genetic diversity in Upland cotton genetic and QTL mapping in the early
days. These two grown species are sought for somewhat different traits
in addition to providing the DNA-level polymorphism required for genetic
map creation. As previously stated, \emph{G. hirsutum} breeding has
stressed maximal output and broad adaptability, whereas \emph{G.
barbadense} breeding has emphasized fiber quality. As a result, most
genetic mapping {[}15,107{]} and molecular quantitative genetic studies
of fiber properties have used populations derived from interspecific
hybridization involving wild and domesticated forms of \emph{G.
barbadense} crossed with Upland cotton. QTLs for numerous fiber quality
variables mapped in cotton were summarized by Chee and Campbell
{[}57{]}. Some important QTLs for fiber length, strength, and fineness
have now been found, and several have been verified {[}108,109{]}. This
knowledge gives cotton growers greater options to improve certain fiber
qualities in upland cotton by introducing genes from \emph{G.
barbadense} with minimal disruption to the favorable allelic
combinations developed over a century of selective selection. Inbred
backcross populations generated from crossing Upland varieties with the
allotetraploid species \emph{G. barbadense} , \emph{G. tomentosum} ,
and\emph{G. mustelinum} have been developed as part of a collaborative
effort to minimize Upland cotton's genetic susceptibility {[}110{]}.
Inbred backcrossing was used to reduce reproductive obstacles caused by
interspecific introgression between these species {[}111,112{]}. One can
examine very tiny pieces of introgressed DNA for agronomic or fiber
quality performance and analyze them for QTLs by establishing a
comprehensive set of Near Isogenic Introgression lines from the BC2 or
BC3 families. Because recombination and segregation have split the donor
genome into smaller components, the activity of specific genetic loci
may be more clearly defined than in previous generations. Table 2 shows
the number of QTLs detected in each of the inbred backcross groups.
Rong, Feltus, Waghmare, Pierce, Chee, Draye, Saranga, Wright, Wilkins
and May {[}18{]} reported the alignment of 432 fiber QTLs identified in
10 interspecific \emph{G. hirsutum} by \emph{G. barbadense} populations
into a consensus map, providing further information on the genetic
dissection of each of the fiber properties.

\textbf{Table 2.} Summary of QTL mapped in interspecific Gossypium
species.\selectlanguage{english}
\begin{longtable}[]{@{}lllllllll@{}}
\toprule
& G. barbadense & G. barbadense & G. barbadense & G. barbadense & G.
tomentosum & G. tomentosum & G. tomentosum & G.
tomentosum\tabularnewline
\midrule
\endhead
& \textbf{Gh} & \textbf{Gb} & \textbf{Total} & & \textbf{Gh} &
\textbf{Gt} & \textbf{Total} &\tabularnewline
Fiber length & 17 & 11 & 28 & {[}113{]} & 4 & 0 & 4 &
{[}76{]}\tabularnewline
Fiber strength & - & - & - & & 4 & 0 & 4 & {[}76{]}\tabularnewline
Micronaire & 1 & 8 & 9 & {[}89{]} & 1 & 3 & 4 & {[}76{]}\tabularnewline
Fiber elongation & 14 & 8 & 22 & {[}114{]} & 0 & 4 & 4 &
{[}76{]}\tabularnewline
\bottomrule
\end{longtable}

Favorable alleles: Gh = \emph{G. hirsutum} ; Gb = \emph{G. barbadense} ;
Gt = \emph{G. tomentosum} ; Gm = \emph{G. mustelinum}{[}90,114--116{]}.

The QTL detection in reciprocal backcross populations of \emph{G.
hirsutum} x \emph{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 \emph{G.
hirsutum} and \emph{G. barbadense,} respectively; favorable alleles
masked by unfavorable alleles, and there was higher potential
for\emph{G. hirsutum} improvement than \emph{G. barbadense.} Three
stable QTLs---two for fiber micronaire and fiber elongation in \emph{G.
hirsutum} and one for upper half mean length in \emph{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 \emph{G. hirsutum} \selectlanguage{ngerman}× \emph{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
\emph{G. hirsutum} from its sister \emph{G. tomentosum} and found there
were similar rates of introgression into two subgenomes of \emph{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
(BC\textsubscript{3}F\textsubscript{2},
BC\textsubscript{3}F\textsubscript{2:3} and
BC\textsubscript{3}F\textsubscript{2:4}) of \emph{G. hirsutum} x\emph{G.
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 \emph{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 \emph{G. mustelinum.} Transcriptome analysis for
fiber strength in \emph{G. hirsutum} line IL9 having introgression from
\emph{G. mustelinum} revealed there were 52 differentially expressed
genes (DEGs) contributing to fiber strength relating to introgression
from \emph{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 \emph{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 \emph{GhPEL6,}
\emph{GhCSLC6,}and \emph{GhTBL5} for fiber length QTLs and GhCOBL4,
\emph{GhMYB4} , and\emph{GhMYB85} 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 \emph{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 \emph{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\textsuperscript{--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.

\textbf{Table 3.} Resistant improvements against cotton's disease and
insect pests by introgressive breeding.\selectlanguage{english}
\begin{longtable}[]{@{}llll@{}}
\toprule
\textbf{Disease/Pest} & \textbf{Causal agents} &
\textbf{Source\textsuperscript{1}} & \textbf{Reference}\tabularnewline
\midrule
\endhead
Bacterial Blight & \emph{Xanthomonas campestris pathovar malvacearum} &
Ga, Gb & {[}127--130{]}\tabularnewline
Fusarium Wilt & Fusarium oxysporum f. sp. vasinfectum & Gb &
{[}97,131--134{]}\tabularnewline
Leaf curl virus & Begomoviruses & Gh & {[}135--139{]}\tabularnewline
Verticulum wilt root knot & Verticillium dahliae & Gb, Ga, &
{[}140--143{]}\tabularnewline
Nematodes & Meloidogyne incognita Rotylenchulus, Reniformis & Gh, Gd, Gb
& {[}144--149{]}\tabularnewline
Blue Viral Disease & Polerovirus & Gh & {[}150{]}\tabularnewline
Spider mites & Tetranychus urticae & Gb & {[}151--153{]}\tabularnewline
Suckig pest & Frankliniella occidentalis & Gb, Gm Gd, Gt &
{[}27,84,154,155{]}\tabularnewline
Root rot & Rhizoctonia bataticola & Gh & {[}156--158{]}\tabularnewline
\bottomrule
\end{longtable}

\textsuperscript{1}GB=G. barbadense, Gd=G. darwinii, Gh= G. hirsutum,
Gm= G. mustelinum, Gt= G. tomentosum.

8. Conclusions

Polyploidization offered the tetraploid genome an advantage over its
diploid forebears by allowing genes from the D-genome to be recruited to
improve allopolyploid cotton fiber output and quality. Interspecific
hybridization between an A-genome diploid species that produce spinnable
lint fiber and a D-genome diploid species that does not produced
allopolyploid cotton, which include the two species that provide the
bulk of the world's natural textile fiber. New genomic methods, such as
whole genome sequencing and re-sequencing, have substantially aided our
understanding of the Gossypium species' origins, diversity, genome
structure, and influence on human-directed evolution. More
significantly, the genomic technologies combined with traditional cotton
breeding will enable greater interspecific hybridization and gene
introgression to offer the requisite usable genetic variety for the
genetically depleted Upland cotton gene pool to continue to develop. The
use of interspecific gene combinations could help Upland cotton meet
current and future cotton production challenges, such as those posed by
environmental change, disease, and the need for yield stability and
specific combinations of desirable fiber traits to compete favorably
with synthetic textiles made from oil-based products.

\textbf{Author Contributions:} M.Z.I., M.A., and A.A.A. wrote the
manuscript; S.M, L.A.B. and S.A.M revised the article; Y.P. provided
conceptual framework, guided the authors, and provided funds for this
study. All authors have read and agreed to the published version of the
manuscript.

\textbf{Funding:} This article received no external funding

\textbf{Institutional Review Board Statement:} Not applicable.

\textbf{Informed Consent Statement:} Not applicable.

\textbf{Data Availability Statement:} The data presented in this study
are available in the article.

\textbf{Conflicts of Interest:} The authors declare no conflict of
interest.

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