**1. Introduction**

The genetic diversity of cotton (*Gossypium* spp.) is exclusively wide with diverse geographic and ecological niches [1]. The *Gossypium* genus belongs to the *Malvaceae* family. This genus contains more than 45 diploid species and five well-documented allotetraploid species [2-4]. Species of this genus are grouped into nine genomic types (*x=n*=13, *2n*=26 diploid, and 4x=52 tetraploid) with the following designations: AD, A, B, C, D, E, F, G, and K [3]. Genomic designations are based on the similarities in chromosome size and structure, and the success of interspecific crosses. Based on their chromosomal uniformity, the diploid D genome species of the New World include 26 somatic chromosomes. Some hybrids within genomes are fertile and their chromosomes recombine during meiosis. However, hybrids across genomes are generally infertile and they have a few stable bivalents at meiosis as a result progeny-plant survival from interspecific crosses is sometime low [4]. The allotetraploid cottons [Upland, *G. hirsutum* (AD1) and *G. barbadense* (AD2)] of the New World dominate world natural-fiber production. And they can be described as large shrubs to trees [3,5]. An allotetraploid is a species that derived from the combination of two different genomes or doubling of genomes that are different. The At subgenome is probably best represented by a composite of two diploid genomes ([*G. herbaceum* L. (A1) and *G. arboreum* L. (A2)] from the Old World. These Asiatic species-progenitor cottons primarily produce fibers for non-industrial-textile con‐ sumption in India and Asia [4]. The Dt subgenome has a more complex genome (D) of the diploid species-progenitors from the New World. The D genome is comprised of formally reported 13 species [3,7-9] and several undescribed taxa e.g. US-72 [8-11]. Eleven of the 13 species of the New World reside in the country of Mexico (Fig. 1). Taxonomically, these species are recognized as the *Houzingenia* subgenus [5,7]. None of these D genome diploid species produce commercial fibers. These species of the D genome are not well known to public and

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private breeding programs around the world, and their utilization for cotton improvement has not been fully exploited. Some species of the D genome [*G. aridum* (D4), *G. lobatum* (D7), *G. laxum* (D9), etc] with arborescent growth habits express unique flowering and fruiting habits (following defoliation in the dry season). And even though none of the D diploid species produce commercial fibers, the diploid D genome species of the New World harbor important genes for improving fiber quality, pest and disease resistance, and drought and salt tolerance in the modern cultivated Upland and Pima cottons.

extinct or already extinct. If *in situ* diversity of the Mexican cottons is severely eroded, the germplasm collections all over the world and the USDA Cotton Germplasm Collection will assume a highly significant role in the preservation of the diversity previously residing in

The Diploid D Genome Cottons (*Gossypium* spp.) of the New World

http://dx.doi.org/10.5772/58387

205

Recently, the genome sequence of the best model, closest living ancestor relative of the allotetraploid cottons-of the Dt subgenome *(G. raimondii),* was published. This new informa‐ tion compiled with the ongoing next generation sequencing (NGS) projects around the world will provide insights into the evolution, population structure, genetic diversity, and utilization of this genetic resource. The next generation of genomic research will sequence characterize and locate genes that will help molecular breeders to identify differences among germplasm and breeding lines and to apply traditional genetic analyses to infer genes for marker assisted selection (MAS). In addition, the new sequence information obtained through NGS will be an

**2. Classification of the D diploid species, distribution, and dissemination**

The country of Mexico, besides being a part of the center of origin/diversity of *G. hirsutum,* also harbored 11 out of the 13 formally reported D species [3,7] and several non-described taxa of the New World diploid *Gossypium* species (one non-described taxon US-72,) [8-10]. The species of the *Houzingenia* subgenus are classified into six subsections: subsection *Houzingenia* Fryxell [*G. thurberi* Todaro (D1) and *G. trilobum* (Mociño & Sessé ex DC.) Skovsted (D8)]; subsection *Integrifolia* Todaro [*G. davidsonii* Kellogg (D3-d) and *G. klotzschianum* Andersson (D3-k)]; subsec‐ tion *Caducibracteolata* Mauer [*G*. *armourianum* Kearney (D2-1), *G*. *harknessii* Brandegee (D2-2), and *G*. *turneri* Fryxell (D10)]; subsection *Erioxylum* Rose & Standley [*G. aridum* (D4)*, G. lobatum* (D7)*, G. laxum* (D9)*,* and *G. schwendimanii* Fryx. & Koch (D11)]; subsection *Selera* (Ulbrich) Fryxell [*G*. *gossypioides* (D6)], and subsection *Austroamericana* Fryxell [*G. raimondii* Ulbrich (D5)] [3,4,7]. Eleven of the 13 species of the subgenus *Houzingenia* are distributed in Mexico and extend northward into Arizona (Fig. 1). The other two D species have disjointed distributions; *G. raimondii* is endemic to Peru, while *G. klotzschianum* is found in the Galápagos Islands. The species of the D genome are not well known and utilized in public and private breeding programs around the world. Additional information about morphological characteristics and distribution of the species can be found in Fryxell monograph [12] and several other publica‐ tions [8-9]. A supplemental information about recent collections [8-9] can be found at the USDA-ARS, SPA, CSRL, Plant Stress and Germplasm Development website (http:// www.lbk.ars.usda.gov/psgd/index-cotton.aspx). Also, the Mexican Instituto Nacional de Investigaciones Forestales Agricolas y Pecuarias (INIFAP), Iguala Gro. Mex. nursery has provided us with the opportunity to further study some of these species *ex situ*. Table 1 provides information on 12 of the species during their *ex situ* preservation at the Iguala nursery in Mexico. Data from *G. klotzschianum* is missing from this table. Species planted at the nursery flower from September to January, while *in situ*, some of the populations from these species

important resource to improve the cotton crop through transgenic technology.

Mexico's cotton species of the D genome.

flower through March-April..

**Figure 1.** The country of Mexico, states, and approximate areas-boundaries of the diploid species of the D genome endemic to this country. The location of new taxa with US-XX (XX=number – Table 2) is indicated representing possi‐ ble new species.

Even though Mexico's natural heritage of cotton genetic resources equals that of maize, until recently no national resources were dedicated to the preservation of this natural treasure [8]. The collection/exploration trips of these species have been difficult to document. Increasing human population and urbanization have severely reduced the survival of some of these species. *In situ* conservation of some of these species is threatened. New roads and population growth continue to increase. At this point, one species (*G. aridum* as formally reported) of the subsection *Erioxylum* appears not to be threatened, probably because of the great diversity (botanical and geographic) encompassed by this species. However, some of the most recent collected and non-described taxons (e.g., US-72) or ecotypes of the *G. aridum* species may be in the process of becoming extinct in the wild. In addition, the D8 *G. trilobum* species is almost extinct or already extinct. If *in situ* diversity of the Mexican cottons is severely eroded, the germplasm collections all over the world and the USDA Cotton Germplasm Collection will assume a highly significant role in the preservation of the diversity previously residing in Mexico's cotton species of the D genome.

private breeding programs around the world, and their utilization for cotton improvement has not been fully exploited. Some species of the D genome [*G. aridum* (D4), *G. lobatum* (D7), *G. laxum* (D9), etc] with arborescent growth habits express unique flowering and fruiting habits (following defoliation in the dry season). And even though none of the D diploid species produce commercial fibers, the diploid D genome species of the New World harbor important genes for improving fiber quality, pest and disease resistance, and drought and salt tolerance

**Figure 1.** The country of Mexico, states, and approximate areas-boundaries of the diploid species of the D genome endemic to this country. The location of new taxa with US-XX (XX=number – Table 2) is indicated representing possi‐

Even though Mexico's natural heritage of cotton genetic resources equals that of maize, until recently no national resources were dedicated to the preservation of this natural treasure [8]. The collection/exploration trips of these species have been difficult to document. Increasing human population and urbanization have severely reduced the survival of some of these species. *In situ* conservation of some of these species is threatened. New roads and population growth continue to increase. At this point, one species (*G. aridum* as formally reported) of the subsection *Erioxylum* appears not to be threatened, probably because of the great diversity (botanical and geographic) encompassed by this species. However, some of the most recent collected and non-described taxons (e.g., US-72) or ecotypes of the *G. aridum* species may be in the process of becoming extinct in the wild. In addition, the D8 *G. trilobum* species is almost

in the modern cultivated Upland and Pima cottons.

204 World Cotton Germplasm Resources

ble new species.

Recently, the genome sequence of the best model, closest living ancestor relative of the allotetraploid cottons-of the Dt subgenome *(G. raimondii),* was published. This new informa‐ tion compiled with the ongoing next generation sequencing (NGS) projects around the world will provide insights into the evolution, population structure, genetic diversity, and utilization of this genetic resource. The next generation of genomic research will sequence characterize and locate genes that will help molecular breeders to identify differences among germplasm and breeding lines and to apply traditional genetic analyses to infer genes for marker assisted selection (MAS). In addition, the new sequence information obtained through NGS will be an important resource to improve the cotton crop through transgenic technology.
