Natural Variation in Wild Gossypium Species as a Tool to Broaden the Genetic Base of Cultivated Cotton

Modern plant breeding has profoundly impacted agricultural production through the development and deployment of varieties with increased yield and improved agronomic performance. However, intensive selection that accompanies contemporary breeding strategies has also introduced a very high degree of genetic uniformity in the field, making crops vulnerable to emerging biotic and abiotic challenges [1]. Crop failures due to the heavy dependence on only a few crop varieties have been documented throughout the history of agriculture. In 1845 for example, a strain of Phytophthora infestans ((Mont.) de Bary) that was accidentally introduced from North America to Ireland decimated the genetically uniform potato varieties cultivated by farmers, leading to the Irish potato famine [2]. In the 1950s, the Panama disease caused by Fusarium oxysporum wiped out the banana variety Gros Michel that was widely cultivated in Central America [3]. The widespread planting of a single corn hybrid variety in the southern US resulted in economic losses of more than a billion dollars in the 1970s due to an outbreak of a new race of the fungal pathogen, Bipolaris maydis [4,5]. In the 1980s, monocultures of a single type of grapevine root forced California grape growers to replant approximately two million acres of vines following an outbreak of a new race of the grape phylloxora, Daktulosphaira vitifoliae [6].

As in the case of most cultivated crops, the overriding emphasis on only a few agronomic traits (i.e., yield and fiber quality) during domestication has severely narrowed the genetic base of cotton. Generations of industry-scale cultivation of a relatively small number of genetically related varieties has further reduced the available genetic variation in this crop. In the US, 98% of cotton that is currently being grown is G. hirsutum [7] and 85% are genetically modified for improved herbicide and pest resistance [8]. The genetic uniformity in cultivated varieties put the cotton industry at a high risk of collapse in the likely event of a disease or pest outbreak or upsurge. 

Compounding the threats of disease and pest epidemics are abiotic challenges such as drought, heat and cold, as well as salinization of agricultural lands from years of intensified cultivation. While breeding objectives for cotton remain focused on improving baseline production and product quality, the emerging challenges in agriculture require that new cotton cultivars are developed with adaptation to extremes of temperature, reduced precipitation and saline soils, as well as resistance to new biotypes of pathogens and pests [9]. To this end, cotton breeders need to expand the cultivated germplasm base for the crop and consciously bring in genetic variation from diverse genetic resources that can provide tolerance to a multitude of environmental stresses as well as durable forms of resistance to pests and diseases.

Wild or exotic germplasm constitutes an important resource that can provide novel genetic diversity in cultivated crops that has been lost during domestication. Utilization of naturally occurring genetic variation from wild relatives of crops has been generally perceived as a better option (as opposed to artificial variation) in plant breeding because of the certain selective pressures that has already acted on the fitness of the organism [10]. Wild progenitors of domesticates are commonly found in marginal habitats that are unsuitable for agriculture and that are subject to severe biotic and abiotic stresses. Without human intervention, these wild relatives evolved adaptive mechanisms that allow them to survive harsh environments [10,11]. One such example is Solanum lycopersicoides , a tomato-like nightshade species that thrives in the western slopes of the main Andean cordillera in the Chile-Peru frontier. At 3800 m above sea level, S. lycopersicoides survives frosts and light freezes in well-exposed sites where the cold air from glaciers and snowfields drains. Field cultures of this wild species also exhibit resistance to viral diseases and Lepidopteran pests [12,13]. Yet another example is Hordeum spontaneum, a wild relative of barley. H. spontaneum shares a niche with halophytic vegetation in the Dead Sea coast which receives only a minimum average precipitation of 55 mm per year [14]. The autoecology of S. lycopersicoides and H. spontaneum suggests the presence of considerable genetic variation that lends phenotypic plasticity in both species, allowing them to withstand marginal environments.

The genus Gossypium to which cotton belongs has more than 50 well-established species, only 4 of which are cultivated. In terms of fiber production and quality, the wild cotton relatives are relatively inferior compared to the cultivated species. Despite this, the wild Gossypium germplasm serves as a rich reservoir of novel alleles that can be utilized to improve trait performance in cultivated cotton [7,15]. Interspecific hybridization to broaden the genetic base of the existing cultivars would be an important first step in utilizing the abundant genetic variation from the wild cotton relatives.

This review highlights the useful agronomic traits that have been reported for the different species of wild Gossypium during the past decade. Valuable genetic resources that incorporate the genome of wild Gossypium into the cultivated cotton by conventional breeding or with the aid of biotechnological techniques, as well as the potential application of these resources for trait improvement are discussed. Investigations toward unlocking the genetic and molecular basis of Verticillium wilt resistance and salt tolerance in different wild cotton relatives are presented in brief.

The genus Gossypium includes 46 diploid (2n = 26) and 7 allotetetraploid (2n = 52) species representing the AA, BB, CC, DD, EE, FF, GG, KK and AADD genomes (Table 1).

The genus diverged from its closest relatives, Kokia and Gossypioides, approximately 5-10 million years ago, whereas speciation was estimated to have occurred 1-5 million years ago. Long-distance, transoceanic dispersal was proposed to have driven the evolution of the diploid species, whereas wide hybridization between species having the A and D genomes and subsequent polyploidization gave rise to the allotetraploids (Figure 1) [7,51,52,53]. Species within the genus are geographically distributed in the arid and semi-arid regions of the tropics and sub-tropics, with new exotic species still being discovered in Australia and in the isolated islet chain in the West Pacific [7,28,50,54].

 

Wild Species	Useful Agronomic Traits	Origin	Genome
G. hirsutum	Widely cultivated	Central America	AD1
G. barbadense	Widely cultivated, long and high quality lint, resistance to Verticillium wilt [16]	South America	AD2
G. tomentosum	Tolerance to heat, source of the nectariless trait for resistance against tarnished plant bug, fleahoppers, boll rot and bollworm [17], resistance to jassids and thrips [18], high fiber quality, fiber length and fiber fineness [19]	Hawaiian Islands	AD3
G. mustelinum	Longer fibers [20,21]	NE Brazil	AD4
G. darwinii	Finer fibers, drought tolerance, resistance to Fusarium and Verticillium wilt [22]	Galapagos Islands	AD5
G. ekmanianum		Dominican Republic	AD6
G. stephensii		Wake Atoll	AD7
G. africanum	High fiber strength [23]	Southern Africa	A
G. herbaceumL	Resistance to hoppers, white flies, thrips, aphids, and leaf curl virus [24]	Southern Africa	A1
G. arboreumL	Resistance to hoppers, white flies, aphids, leaf curl virus [24], thrips [25], drought tolerance, resistance to black root rot, reniform nematodes [26] and spider-mites [27]	Indus valley, Madagascar	A2
G. anomalum	Resistance to cotton wilt, angular leaf spot, springtails and aphids, drought tolerance, high fiber quality, cytoplasmic male sterility [28]	Africa (Angola, Namibia)	B1
G. triphyllum	Flower color range from blue to purple [29]	Namibia in Africa	B2
G. capitis-viridis	High fiber quality, strong resistance to Verticillium and Fusarium wilt [30]	Cape Verde Islands	B3
G. trifurcatum		Somalia	B
G. sturtianum	Glandless-seed and glanded-plant [31] Resistance to Fusarium wilt [32]	Australia	C1
G. nandewarense		Australia	C1N
G. robinsonii		WA, Australia	C2
G. thurberi	Tolerance to mild frost via defoliation, high resistance to Verticilliumdahlia [29,33]	Mexico	D1
G. armourianum	Resistance to white flies, bacterial blight and jassids [18,29,34]	Mexico	D2-1
G. harknessii	Cytoplasmic male sterility and fertility restorer [35]	Mexico	D2-2
G. davidsonii	Salinity tolerance [36]	Mexico	D3-d
G. klotzschianum	Salinity tolerance [37]	Galapagos Islands	D3-k
G. aridum	Salinity tolerance [38] Resistance to reniform nematode [39]	Mexico	D4
G. raimondii	Resistance to jassids [34]	Peru	D5
G. gossypioides	Resistance to cotton leaf curl disease [40]	Mexico	D6
G. lobatum	Resistance to Verticillium wilt [41]	Mexico	D7
G. trilobum	Cytoplasmic male sterility and restorer factor. Drought tolerance, resistance to bollworm, pink worm, boll rot, Verticillium and Fusarium wilt [29,42]	Western Mexico	D8
G. laxum		Mexico	D9
G. turneri	Caduceus involucels [43]	Mexico	D10
G. schwendimanii		Mexico	D11
G. stocksii	Strong fibers, resistance to leaf curl virus [44], resistance to reniform nematode [45]	East Africa, Arabia	E1
G. somalense	Resistance to reniform nematode [45] Extra fiber strength, resistance to Egyptian bollworm and pink bollworm, arid tolerance [46]	Northeastern Africa	E2
G. areysianum		Arabia	E3
G. incanum		Arabia	E4
G. benadirense		Somalia, Ethiopia, Kenya	E
G. bricchettii		Somalia	E
G. vollesenii		Somalia	E
G. longicalyx	Resistance to reniform nematode [45,47]	Africa	F1
G. bickii	Glandless-seed and glanded-plant [48]	Central Australia	G1
G. australe	Glandless-seed and glanded-plant, resistance to aphids and spider-mites [49] Resistance to Fusarium and Verticillium wilts, drought tolerance [50]	Australia	G2
G. nelsonii		Australia	G3
G. costulatum		Australia	K1
G. populifolium		WA, Australia	K2
G. cunninghamii		Northern NT, Australia	K3
G. pulchellum		WA, Australia	K4
G. pilosum		WA, Australia	K5
G. anapoides		Australia	K6
G. enthyle		WA, Australia	K7
G. exiguum		WA, Australia	K8
G. londonderriense		Australia	K9
G. marchantii		Australia	K10
G. nobile		WA, Australia	K11
G. rotundifolium		WA, Australia	K12

Table 1: Origin, genome assignment and useful agronomic traits of Gossypium species.

 

Figure 1: Evolutionary relationship among the different cotton species that evolved after the divergence of Gossypium from the genus Kokia and Gossypioides 5-10 million years ago (adapted from 7,51-54). Letters in parenthesis indicate the genome assignment for each species. Red text indicates cultivated species belonging to the genus Gossypium.

 

Out of the more than 50 Gossypium species, only the allotetraploids G. hirsutum and G. barbadense, and the diploids G. arboreum and G. herbaceum are cultivated for their spinnable fibers. G. hirsutum, which is also known as Upland cotton, Long Staple cotton or Mexican cotton, occupy over 90% of the world cotton cultivation whereas G. barbadense, otherwise known as Sea Island cotton, Pima cotton or Egyptian cotton, contributes to 8% of the global cotton production. The cultivated diploid species provide approximately 2% of the world’s cotton and are cultivated in the more traditional growing areas of India, Pakistan, China, Bangladesh and Iran [24,51]. 

Based on genetic hybridization properties, Gossypium species are further grouped into the primary, secondary and tertiary gene pools. Both the cultivated (G. hirsutum and G. barbadense) and wild allotetraploids (G. tomentosum, G. mustelinum and G. darwinii) comprise the primary gene pool of cotton. The secondary gene pool includes the diploids having the A, B, D and F genomes, whereas the tertiary gene pool is composed of species with C, E, G and K genomes [7,55]. Genetic diversity studies using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR) and/or single nucleotide polymorphisms (SNPs) indicate the availability of a tremendous amount of genetic variation among the different wild species, as well as among exotic subspecies of Gossypium [9,56-60]. This genetic diversity is reflected in the extensive variation in the gross morphology, maturity, photoperiodicity, yield potential, fiber quality, environmental adaptability and tolerance to pests and diseases that has been reported for the wild species of Gossypium (Table 1) [55,61]. To efficiently utilize this natural variation in cotton improvement, the genetic and molecular basis of phenotypic variations observed across the wild Gossypium germplasm need to be unlocked.

The wild cotton germplasm has been recognized as a rich reservoir of genes underlying traits of agronomic importance and to some extent, has been tapped to improve the productivity and fiber quality of cultivated cotton. Wide hybridizations using exotic subspecies of G. hirsutum has successfully transferred Verticillium wilt resistance and salinity tolerance from G. hirsutum subsp. mexicanum var. nervosum to elite upland cotton cultivars [62]. Similarly, quantitative trait loci (QTLs) controlling fiber quality and yield potential have been identified from interspecific hybrids developed between G. hirsutumand the wild allotetraploids G. darwinii, G. mustelinum and G. tomentosum [15,20,63]. The use of genetic bridges to facilitate crossing between the two tri-species hybrids G. hirsutum x G. longicalyx x G. armourianum and G. hirsutum x G. longicalyx x G. herbaceum has successfully introgressed the reniform nematode (Rotylenchus reniformisi) resistance from G. longicalyx to G. hirsutum [64].

Despite the successful transfer of useful genes from a few wild species and subspecies into the cultivated cotton by conventional means, the extent of wide hybridizations within species of Gossypium has been limited. Inter- specific hybridization between the cultivated G. barbadense and G. hirsutum via conventional crosses has so far been unsuccessful [65,66]. Failure to develop interspecific hybrids between these two species may be attributed to the numerous genomic incompatibilities that result in sterility, cytological abnormalities, distorted segregation, hybrid breakdown, limited recombination between homologous chromosomes, and linkage drag that transfers undesirable traits along with the genes of interest in the wide hybrids [67-69].

As an alternative to conventional gene introgression, exotic libraries that provide opportunities to break up disadvantageous associations between traits so that beneficial genes can be moved across Gossypiumspecies from different gene pools have been generated. Chromosome segment substitution lines (CSSLs), monosomic alien addition lines (MAALs) and multi-parent advanced generation inter-crosses (MAGIC) are only few of the powerful genetic tools that can be used to identify and quantify the effects of specific alleles from wild relatives. 

CSSLs are developed by hybridizations between an elite or adapted crop cultivar with a wild donor parent. Chromosome introgressions from the wild donor to the cultivated parent genome are commonly monitored using molecular markers. Each CSSL is selected to carry only a single chromosome introgression in a known locus within the genome. The whole genome of a wild donor parent is typically represented in a set of CSSLs composed of several lines [70]. The uniform genetic background of CSSLs provides the advantage of easily associating a phenotype with the introgressed chromosome segment, as well as identifying genes/QTLs using only simple statistical analysis [71]. 

In cotton, CSSL sets representing the whole genome of G. barbadense in the background of G. hirsutumhave been developed by various groups of researchers and used to have been used to identify and map QTLs controlling fiber yield and quality [72-76]. To date however, no other Gossypium species has been used as a donor in the development of CSSLs.

MAALs are also important genetic stocks that are derived from crosses between a crop and its wild ancestor. Development of MAALs usually requires embryo rescue of the interspecific hybrid before it aborts. A distinct characteristic of MAALs is the presence of a single chromosome from the wild ancestor in addition to the normal chromosome complement of a given crop. MAALs not only provide a convenient way of dissecting wild genomes into individual chromosome in a functional genomics background but also serve as bridges to transfer favorable genes from the wild to the cultivated species [77]. 

Morphological, cytological and molecular analysis using microsatellite markers have aided in the development of MAALs for G. anomalum, G. australe, G. sturtianum and G. somalense in the background of the upland cotton. G. hirsutum ,G. australe and G. somalense have been reported to possess tolerance to drought, whereas all four wild species have been documented to have resistance to a range of pests (reniform nematode, Egyptian and pink bollworm, springtails, aphids and/or mites) and diseases (Fusarium, Verticillium, cotton wilt and/or angular leaf spot) [28,46,50,78,79]. Although these MAALs have already been characterized morphologically and to some extent, physiologically, screening of these exotic libraries under a range of biotic and abiotic pressures would allow the identification of lines that can be used for the improvement of disease resistance and drought tolerance in cotton.

In contrast to CSSLs and MAALs which are based on bi-parental crosses, MAGIC populations involve intercrossing a number of parental lines for several generations to combine the genomes of all parents in the progeny lines [80]. The use of multiple parents to develop the population effectively increases the genetic variation within the population as a result of greater mixing of diverse alleles. Because the population undergoes a greater number of recombination events, MAGIC populations can provide higher resolution for QTL mapping [81]. 

MAGIC populations have also been developed in cotton by intercrossing 10 cultivars and one non-commercial variety of G. hirsutum in a half-diallel design. Molecular characterization of the MAGIC population using SSRs and SNP markers showed introgressions coming from the 11 parents used in the crosses. Genome-wide association studies using this MAGIC population identified a QTL cluster controlling four fiber quality traits [82,83]. 

Despite the potential of MAGIC populations in moving genes from multiple wild cotton species into progeny lines, this type of genetic resource in cotton is still in its infancy. The value of utilizing wild MAGIC populations in the elucidation of genetic determinants underlying complex traits and in delivering solutions to current challenges in crop production is yet to be realized [80]. The potential use of wild MAGIC populations in actual breeding programs would also depend on the successful evaluation of the genetic diversity at the DNA level and linking these variations with observable phenotypic performances.

Aside from developing exotic libraries, biotechnological methods such as haploid induction, interspecific cell fusion and somatic hybridization have been proven effective in overcoming sexual incompatibilities between the wild and the cultivated cotton [42,84]. Symmetric electrofusions between the tetraploid G. hirsutum and the diploids G. trilobum, G. klotzschianum, G. bickii, G. davidsonii and G. stocksii have successfully generated viable somatic hybrids containing novel genetic combinations coming from the allotetraploid and the diploid parents [42,85-89]. The results of such studies indicate the feasibility and the efficiency of somatic hybridization in incorporating divergent genomes into breeding programs for cotton [42,44,45].