Project Summaries

12-221  Project Manager: D. C. Jones


Peng W. Chee, University of Georgia

It is widely accepted that Upland cotton, Gossypium hirsutum L., experienced a genetic bottleneck that has contributed to the low level of genetic diversity found within modern cotton cultivars. This low level of inherent diversity, coupled with the industry's practice of making crosses among closely related elite lines, (Bowman, 2000) has limited germplasm diversity. While public cotton breeders have focused on germplasm enhancement, very few of the enhanced germplasm lines that they have developed have actually been used within the pedigrees of commercially available cultivars (Van Esbroeck and Bowman, 1998). Similarly, a narrow focus by private sector cotton breeders to improve yield parameters without an equivalent emphasis on improving fiber has negatively impacted the fiber quality of extant cultivars. Low levels of diversity among elite cultivars have been reported in other major crops as well such as peanuts (Kochert et al., 1991), soybeans (Morgante et al., 1994), and wheat (Domini et al., 2000). The narrow germplasm base in Upland cotton has been substantiated by a body of work using pedigree-analysis to estimate coefficients of parentage (CP) (May et al., 1995), as well as molecular marker diversity studies to calculate CP (Becelaere et al., 2005; Gutierrez et al., 2002). This low level of genetic diversity is likely a contributing factor in the limited improvement of US cotton fiber quality. Improving genetic diversity is a major focus of the University of Georgia molecular cotton breeding program, especially as it pertains to fiber quality.

Molecular characterization is becoming increasingly more relied upon for accurate estimates of genetic diversity due to the assumptions used in calculating CP from pedigrees. Marker data provides for an estimate based on more tangible data and gives a more accurate comparison of the genomes between lines. We have assembled a panel of cultivars and germplasm to characterize using simple-sequence repeat (SSR) markers in an effort to determine the diversity of historically significant germplasm, currently important cultivars, or unique germplasm with exceptional fiber quality. In the process, we are also hoping to identify interspecific gene introgressions within G. hirsutum germplasm lines with extra-long staple (ELS) fiber quality or new potential regions to examine for quantitative trait loci (QTL).

The first panel of genotypes included 79 lines. Three G. barbadense lines and one G. palmeri line were included to identify rare alleles in the panel.  Private sector germplasm was represented by 17 lines, mostly from Delta Pine, Stoneville, and Fiber Max. Several publicly released cultivars and germplasm were also included, with 48 released and unreleased lines from Texas A&M University's (TAMU) cotton breeding program. Lines from TAMU included several G. hirsutum ELS lines (Smith, 2008), as well as some newer breeding lines with TAMU ELS lines in their pedigrees. A more thorough and diverse list of cultivars have been added to the list and are currently being analyzed in addition to those reported herein. DNA samples were extracted from the excised root tips of up to five germinating seeds per extraction. DNA extractions were done in a manner adapted from that described by Paterson et al. (1993). Polymerase chain reaction (PCR) amplification was similar to that described in (Chee et al., 2004). PCR products were visualized using 10% non-denaturing polyacrylamide gel electrophoresis followed by staining with silver nitrate (Zhang et al., 2002). Twenty-six of the SSR markers run thus far were score-able. From these 26 SSR markers, there were 57 informative, polymorphic bands. Cluster analysis was accomplished using NTSYS (Rohlf, 2002) to construct a dendrogram based on genetic distance.

As expected, the three G. barbadense lines Bleak Hall, Pima S-6, and K101, formed a cluster of their own with a dissimilarity coefficient of 1.18 from the rest of the test material. The next cluster included G. palmeri and all of the G. hirsutum lines. An evolutionarily recent progenitor of G. hirsutum, G. palmeri, formed a single offshoot by itself from the G. hirsutum lines.

The commercial and public lines showed some interesting relationships. Note that the vast majority of the commercial cultivars cluster with the upper half of the G. hirsutum material. Only two commercial cultivars, STV LA-887 and DP 45-867 are represented among the other cluster, and these are generally considered long-staple or ELS material. The data set used here is biased toward commercial cultivars that appear in the TAM pedigrees, so the clustering could potentially be misleading at this point in the study. That is, relationships among lines within this major cluster should not be applied or implied to reflect overall diversity of US germplasm. Ewings Long Staple x Tidewater (EWxT), SL 1, DP 45-867, and 04 SID 84-2, a TAMU breeding line, formed a cluster together. These 4 lines are each confirmed products of interspecific introgression from G. barbadense into G. hirsutum at some point in their pedigrees. This is interesting because in this data set, these germplasm show very little similarity to the G. barbadense lines tested, and more similarity to some of the commercial G. hirsutum cultivars, indicating that they might have G. barbadense introgression, but their genome is made up primarily of G. hirsutum genetic material. Also interesting to note is that the cluster of "introgression lines" shows greatest similarity to the cluster which includes TAM 94L-25 (Smith, 2003) and those genotypes produced from or essentially derived from this germplasm line including several of the TAMU ELS lines (Smith, 2008). This suggests the presence of introgressed segments from G. barbadense within some of the ELS lines.  Also worth speculating is these introgressed regions could harbor important fiber QTL.

The research goal of this project is to characterize the genetic diversity of American Upland cotton, and identify potential introgressed segments of G. barbadense in North American G. hirsutum germplasm and cultivars. While more work is necessary to more fully characterize the TAMU material and G. hirsutum cultivars, we are beginning to see interesting relationships among the materials tested. Thus far the data shows a great deal of similarity between the TAM ELS lines and introgression lines, EWxT, SL 1, DP 45-867, and 04 SID 84-2. Commercial cultivars included in the data set seem to be closely related, as suggested by previous research. The TAMU material also exhibits a great deal of genetic diversity as a microcosm of US germplasm. Analysis of additional markers as well as additional germplasm is ongoing, and will shed more light on the genetic diversity of American Upland cotton and potentially identify introgressed QTL from G. barbadense sources.

This project supports Cotton Incorporated Fellow Nino Brown.


Project Year: 2012

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