Crop Science Journal of Natural Resources and Life Sciences Education
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Abstract Freely available
Right arrow Figures Only
Right arrow Full Text (PDF) Free
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via ISI Web of Science (25)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Liu, S.
Right arrow Articles by Stewart, J.McD.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Liu, S.
Right arrow Articles by Stewart, J.McD.
Agricola
Right arrow Articles by Liu, S.
Right arrow Articles by Stewart, J.McD.
Crop Science 40:1459-1469 (2000)
© 2000 Crop Science Society of America

PLANT GENETIC RESOURCES

Simple Sequence Repeat–Based Assessment of Genetic Diversity in Cotton Race Stock Accessions

S. Liua, R.G. Cantrella, J.C. McCarty, Jr.b and J.McD. Stewartc

a Dep. of Agronomy and Horticulture, New Mexico State Univ., Las Cruces, NM 88003-8003 USA
b Jr., USDA-ARS Crop Sci. Lab., P.O. Box 5367, Mississippi State, MS 39762 USA
c Dep. Crop, Soil, and Environmental Sci., Univ. of Arkansas, Fayetteville, AR 72701 USA

rcantrel{at}nmsu.edu


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 Materials and methods
 Results and discussion
 Conclusions
 REFERENCES
 
Effective use of converted day-neutral Gossypium hirsutum L. race stocks in cotton genetic improvement programs depends on the extent of genetic variation for desirable alleles and the accurate characterization of the variability within and among germplasm accessions in the collection. This study was conducted to survey the molecular variation in the converted race stock collection by using simple sequence repeat (SSR) DNA markers and to determine the genetic distance of each race stock from a typical G. hirsutum cultigen. The molecular marker data will also provide a measure of the degree to which the recurrent photoperiodic parent has been recovered during backcross conversion to day-neutral stocks. Fifty-six flourescently labeled SSR primer pairs arranged in multiplex bins were used to genotype 97 day-neutral BC4F4 race stock accessions. The majority of the accessions had genetic distances <0.25 from the G. hirsutum standard TM1. There was strong evidence that the accessions were heterozygous or heterogeneous, so 10 plants were genotyped within the most diverse nine accessions, those with genetic distance from TM1 >0.25. In some families, the primitive photoperiodic parent was recovered, and in others there was extensive linkage drag from the day-neutral donor parent. The recovery of the primitive recurrent parent could be improved by marker-assisted backcrossing with SSR markers reported in this experiment. Careful genotyping with SSR markers prior to introgression into breeding programs is suggested to ensure maximum genetic diversity and integrity of the exotic race-stock donor germplasm.

Abbreviations: PCR, polymerase chain reaction • QTL, quantitative trait loci • SSR, simple sequence repeat


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
Materials and methods
 Results and discussion
 Conclusions
 REFERENCES
 
GENETIC DIVERSITY is desirable for long-term crop improvement and reduction of vulnerability to important crop pests. Many successful cotton cultivars have been developed from closely related parents, but limited yield gains in recent years have led some to advocate more extensive use of exotic germplasm (Meredith, 1991). Unless methods are improved to transfer useful allelic variation from diverse germplasm resources to primary cotton breeding gene pools, cotton germplasm resources will remain largely underutilized (Van Esbroeck and Bowman, 1998).

The collection of primitive Gossypium accessions is extensive (Percival and Kohel, 1990); however, their use in U.S. breeding programs is limited by their short-day flowering habit. Day-neutral genes have been introgressed into 97 primitive G. hirsutum race stock accessions by a large backcross breeding program (McCarty et al., 1979; McCarty and Jenkins, 1993). The converted primitive accessions are reservoirs of various genes for resistance to pests such as boll weevil (Anthonomus grandis grandis Boheman) (McCarty et al., 1986), fusarium wilt [Fusarium oxysporum Schlechtend.:Fr. f. sp. vasinfectum (Atk.) W.C. Snyder & H.N. Hans.], and tarnished plant bug (Lygus lineolaris Palisot de Beauvois) (Jenkins et al., 1979). Introgression can be achieved without serious losses in agronomic performance (McCarty et al., 1996).

Photoperiodic collections of other tetraploid Gossypium species exist. DeJoodie and Wendel (1992) characterized the diversity of G. tomentosum Nutt. ex Seem, G. mustelinum Miers ex Watt, and G. darwinii Watt relative to G. barbadense L. and G. hirsutum. Unfortunately, day-neutral versions of these tetraploid species are not available.

Tanksley and McCough (1997) proposed that wild, primitive accessions may harbor important novel quantitative trait loci (QTL) alleles that can significantly improve yield and other important traits when carefully introgressed into an elite genetic background with the use of DNA markers. The primitive converted cotton race stocks possess the potential for increasing the genetic diversity in cotton breeding programs and possibly are a reservoir of novel QTLs for important traits. The amount of genetic diversity at the molecular level in this germplasm is unknown, since they have not been systematically surveyed with DNA markers.

Limited pools of cotton germplasm have been characterized previously with random amplified polymorphic DNA (RAPDs) (Tatineni et al., 1996; Iqbal et al., 1997) and restriction fragment length polymorphisms (RFLPs) (Brubaker and Wendel, 1994; Meredith, 1995). However, the level of polymorphism detected was generally low. These marker types are difficult to scale up for genotyping large germplasm collections efficiently. DNA marker systems for germplasm genotyping must be accurate, highly informative, amendable to automation, and cost effective. The use of SSR markers coupled with fluorescence-based DNA fragment detection and semiautomated fragment size analysis can fulfill these requirements (Mitchell et al., 1997). Fluorescence-based SSR genotyping has been successfully used in Brassica spp. (Mitchell et al., 1997), tapioca (Manihot esculenta Crantz) (Chavarriaga-Aguirre et al., 1998), Arachis spp. (Hopkins et al., 1999), and sorghum [Sorghum bicolor (L.) Moench] (Dean et al., 1999). Multiplex polymerase chain reaction (PCR) bins of 55 SSR primer pairs have been optimized for use in cotton by Liu et al. (2000). Multiplex PCR is the simultaneous amplification of several target SSR sequences in a single reaction, rather than the pooling of PCR products from numerous individual reactions before electrophoretic separation on a gel (Mitchell et al., 1997). These SSRs can efficiently be used to genotype Gossypium germplasm accessions.

The objectives of our study were (i) to obtain a measure of the genotypic diversity among the day-neutral converted Gossypium accessions based on SSR markers, (ii) to estimate their genetic distance from a TM1, a typical G. hirsutum cultigen, and (iii) to determine the degree to which the genotype of the recurrent photoperiodic parent has been recovered, or conversely, the degree to which linkage drag or other factors have retained portions of the day-neutral donor parents.


   Materials and methods
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
Results and discussion
 Conclusions
 REFERENCES
 
Ninety-seven day-neutral converted G. hirsutum (AD)1 BC4F4 accessions (Table 1) derived from various wild race stocks were chosen for this experiment. Seventy-nine accessions have been released and assigned PI numbers (McCarty and Jenkins, 1993). Eighteen accessions have been released but not yet assigned PI numbers. Five plants of each germplasm accession, designated by DNA template ID number, were grown in a single pot (15-cm diam.) in the greenhouse in 1998 in Las Cruces, NM. Also included were G. tomentosum (AD)3 from an original seed collection (Hawaiian origin) by Dr. Margaret Menzel, G. mustelinum (AD)4 from Brazil (PI530735), G. darwinii (AD)5 (Galapagos Islands of unknown provenance), and G. hirsutum race yucatanense (PI501500) to represent daylength-sensitive unconverted wild tetraploid germplasm. These four were grown in the greenhouse at Fayetteville, AR, in 1998. The genetic standards were GB379 for G. barbadense (AD)2 and TM1 for G. hirsutum (AD)1. DPL61 is included because it was the day-neutral donor parent in the backcross derivation of the day-neutral race stocks.


View this table:
[in this window]
[in a new window]
  		Table 1 DNA template number, accession number, PI number, race designation, and origin of cotton accessions genotyped with simple sequence repeat (SSR) markers

 
Young leaves from five plants of the 97 BC4F4 converted accessions and DPL61 were bulk sampled for DNA extraction using the method of Paterson et al. (1994). DNA was extracted from an individual plant each of TM1, 3-79, G. tomentosum, G. mustelinum, G. darwinii, and G. hirsutum race yucatanense (TX2093). Purified DNA was placed in 1X TE buffer and quantified fluorometrically. The DNA solution was diluted to a working concentration of 10 ng µL-1 and stored at 4°C until PCR amplification.

Multiplex PCR conditions were used to develop high-throughput assays for SSR loci detection and scoring. Fifty-six fluorescent oligonucleotides (Table 2) were obtained from Perkin-Elmer/Applied Biosystems, Norwalk, CT. The 5' end of the forward primer was labeled with either 6-FAM (6-carboxyfluorescein), HEX (4,7,2',4',5',7'-hexachloro-6-carboxyfluorescein), or NED (7'8'-benzo-5'-fluoro-2',4,7-trichloro-5-carboxyfluorescein). These primers were chosen based on their ability to yield polymorphic products between TM1 and 3-79 DNA templates and ease of amplification in multiplex bins (Liu et al., 2000). Oligonucleotide primers with a CM designation were obtained from A.S. Reddy (Connell et al., 1998). The SSR primers were arranged into 13 multiplex bins (Table 2). Two SSR primer pairs were not placed into bins.


View this table:
[in this window]
[in a new window]
  		Table 2 Primers used for amplification of simple sequence repeat (SSR) loci in Gossypium germplasm and diversity data by loci

 
Both multiplex and single PCR reactions were performed in 10-µL volumes containing 10 ng of cotton template DNA, 1x Perkin Elmer PCR Buffer II (10x, 100mM Tris-HCl, pH 8.3, 500 mM KCl), 2.5-3.0 mM MgCl2, 0.2 mM dNTPs, 0.15 µM of each single primer, 0.4 unit of AmpliTaq Gold (Perkin-Elmer/Applied Biosystems). Dye-labeled forward and unlabeled reverse primers were used in all PCR reactions.

Temperature cycling was conducted on a GeneAmp PCR System 9600 (Perkin-Elmer/Applied Biosystems). The amplification profile consisted of an initial denaturation of DNA at 95°C for 12 min, followed by 40 cycles of 93°C (Step 1) for 15 s, 55°C (Step 2) for 30 s, and 72°C (Step 3) for 1 min. The ramp times were set at 42, 36, and 40 s to Step 1, Step 2, and Step 3, respectively. After 40 cycles, the extension temperature of 72°C was held for 6 min. The PCR products were diluted 5 to 10 times before preparing the loading samples.

Samples containing 1.0 µL of diluted PCR products and 1.0 µL of loading cocktail [60% formamide, 17% GeneScan 350 (ROX) internal lane size standard, 23% accompanied loading buffer] were heated at 92°C for 2 min, placed on ice, then loaded on a 5% Long Ranger (FMC Bioproducts, Rockland, ME) denaturing acrylamide gel (6 M urea). Each gel was used two times. Samples were electrophoresed on an automatic DNA sequencer (Perkin Elmer/Applied Biosystems, model 377) in 1X TBE buffer (89 mM Tris, 89 mM borate, 2 mM EDTA pH 8.3) at constant voltage (750 V) and temperature (45°C) for 1.5 h. Short gels (12 cm well-to-read) were used along with a square-tooth comb. Fragment size data were automatically collected with GeneScan Analysis software version 2.0.2 (Perkin Elmer/Applied Biosystem). The fragment with the highest fluorescent intensity was scored when SSR-primed products showed band stuttering. The local Southern algorithm (Elder and Southern, 1987) was used to automatically determine fragment size in base pairs to two decimal places.

The genotype of an accession is comprised of the allele sizes at all SSR loci. Only mapped SSR marker loci are included in this study. Liu (1999) mapped all the SSR loci to linkage groups in a 3-79/NM24016 F2 population. The linkage map of 63 SSRs comprised {approx}880 cM total map distance. Liu et al. (2000) assigned the same SSR marker loci to cotton chromosomes using aneuploid genetic stocks. The genetic distance (D) among genotypes was computed with the program Microsat (Minch et al., 1997). This distance estimate is based on the proportion (ps) of shared alleles and is derived as:

The proportion (ps) of shared alleles is defined as the mean of the minima of the relative frequencies of all alleles in the genotypes being compared; that is, ps = (sum over all alleles of MIN{P[A(i)], P[B(i)]})/n, where n is the total number of alleles for all loci (Bowcock et al., 1994). Cluster analysis of distance data used the neighbor-joining method and an unrooted dendrogram was generated using PAUP version 4b2 (Swofford, 1998).

Microsat was used to compute the diversity for each SSR marker. This is equivalent to polymorphism information content (PIC) at each SSR as described in the following equation by Anderson et al. (1992):

where Pij is the frequency of the jth SSR pattern for marker i and the summation covers n patterns. The SSR alleles that occurred only in a single accession were identified and produced by Microsat as taxon-specific alleles.

The nine most diverse day-neutral race stocks were selected based on genetic distance from TM1 of the bulk DNA samples from each accession as described above. Ten plants of each of the selected converted stocks, along with an equal number of the corresponding photoperiodic recurrent parent (denoted by the T number) were planted in the greenhouse for further sampling. The 10 BC4F4 plants of each day-neutral accession were sampled individually for DNA extraction and SSR genotyping on an individual plant–template basis. The primitive photoperiodic stocks were represented as a balanced DNA template bulk of 10 plants. Individual plant DNA samples were not analyzed for the recurrent parents. DNA extraction and all PCR protocols were identical to those described above for the plant bulks of each accession. The BC4F4 plants were identified by accession designation and sequentially as M numbers (M1–M100). Genetic distances from TM1 of each plant were determined using SSR markers identical to that of the bulk DNA samples.

Graphical genotype analysis was conducted on the plants from the single most diverse accession. The numerical SSR marker genotype for 17 marker loci spanning three linkage groups were imported into Supergene software (Boutin et al., 1995). Map data from Liu (1999) for these loci on chromosome 10, chromosome 20, and Linkage Group 6 were also imported. For graphical display of chromosome regions, numerical genotypes for bulk TM1 DNA and bulk of the photoperiodic recurrent parent DNA were used. TM1 was denoted as Parent 1 and the recurrent parent was denoted as Parent 2. The SSR numerical genotypes in the data set were coded as 1 for same as TM1, 2 for same as recurrent parent, and 3 for heterozygous. TM1 was used to represent the donor parent because of its genetic similarity to DPL16 and DPL61.


   Results and discussion
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
Conclusions
 REFERENCES
 
Allelic Diversity for SSR Markers
The 56 SSR primer pairs amplified 62 polymorphic marker loci in this experiment. Six primer pairs (BNL1317, BNL1414, BNL686, BNL3408, CM66, and BNL1440) amplified two loci each, which is in agreement with the results from Liu et al. (2000), where the SSR markers were mapped to chromosomes. The SSR primers amplified a total of 325 different alleles with an average of five SSR alleles per SSR marker in this germplasm set. The PIC value of each SSR marker is a measure of marker diversity. The average PIC value for all 62 SSR marker loci was 0.31, with a range from 0.05 to 0.82. The most informative SSR markers were BNL2572, BNL1053, BNL1721, and BNL3649. Multiplex PCR Bins 2A and 11 proved to be especially useful, with Bin 2A yielding eight polymorphic SSR markers and Bin 11 yielding 10 SSR markers (Table 2).

One hundred thirty-nine SSR allele fragments were classified as accession-specific (Table 3) , in that they occurred in a single accession and no other template in the experiment. As expected, the majority of these occurred within the wild tetraploid accessions of G. darwinii, G. mustelinum, and G. tomentosum. TX2093 (race yucatanense) selected as a truly wild accession of G. hirsutum, exhibited 20 unique alleles. This accession probably represents the highest level of diversity expected among the primitive G. hirsutum accessions prior to entering the conversion program. This is borne out in that all of the day-neutral converted accessions yielded a total of only eight accession-specific fragments.


View this table:
[in this window]
[in a new window]
  		Table 3 Simple sequence repeat (SSR) alleles specific to a particular cotton accession based on genotyping bulk template samples of each accession

 
Genetic Distances and Diversity
Genetic distance from the G. hirsutum standard TM1 was used as one measure of genetic diversity. The day-neutral converted accessions had genetic distances from TM1 that ranged from 0.11 to 0.33 based on the distance matrix. As a reference, the genetic distance estimated between TM1 and DPL61 is 0.10. The majority of the accessions were below 0.25, which means they shared more than 75% of the same SSR marker alleles with the TM1 standard. The dendrogram (Fig. 1) of all accessions shows that there are many small clusters, but the branch lengths are very short. Careful examination of the dendrogram (Fig. 1) and accession origin (Table 1) reveals that the most diverse day-neutral accessions originated from Guatemala and not from Mexico. Care should be taken not to infer this as a center of diversity, since these accessions are not random collections from the various geographic regions.



View larger version (27K):
[in this window]
[in a new window]
  		Fig. 1 Unrooted neighbor-joining dendogram based on genetic distance among all cotton accessions using simple sequence repeat (SSR) genotypes. Template ID numbers are referenced in Table 1. Branch lengths are shown

 
The diversity of the wild photoperiodic tetraploids was extensive. Although G. hirsutum race yucatanense is the same species as TM1, its wild origin is reflected in the large genetic distance (0.70) from the domesticated cultigen. All of the other race stocks represent various degrees of domestication from the original ancestral type; hence, they display less genetic diversity relative to TM1. The genetic distance from TM1 among the other tetraploid species was 0.80 for G. tomentosum, 0.81 for G. mustelinum, and 0.88 for G. darwinii (Table 4) . Gossypium tomentosum appeared to be moderately closer to G. hirsutum than the other species, while G. mustelinum was distantly associated with a cluster with G. barbadense GB379 and G. darwinii (Fig. 1).


View this table:
[in this window]
[in a new window]
  		Table 4 Genetic distance from TM1 of the most diverse cotton accessions

 
The low level of molecular marker diversity in the day-neutral accessions was disconcerting. The data for each day-neutral accession were collected from a bulk template sample (five-plant bulk). Close observation of the alleles amplified for many of the accessions revealed possible heterozygosity or heterogeneity. For instance, a single SSR marker locus would amplify three or more alleles within a single bulk template of an accession. This indicates that the plants comprising the template bulk contained several different genotypes for the particular SSR marker locus. In many cases, one of the alleles would be the same as TM1, which would markedly bias the genetic distance estimate that is based on the proportion of shared alleles. Only genotyping of individual plants within the accessions could accurately determine the true genetic distance.

The most diverse accessions were selected for further analysis (Table 4). These accessions all had genetic distances from TM1 of >0.25, based on the bulk template samples of each accession. When 10 individual plants of each day-neutral accession were genotyped with the 56 SSR primer pairs (62 loci), a more accurate measure of genetic diversity was revealed (Table 4). In all cases, the most diverse plant, relative to TM1, exceeded the genetic distance estimate derived from the bulk template sample of the accession (Table 4). As expected, no more than two alleles were detected for each SSR marker within any of the individual plants sampled. Five of the accessions contained day-neutral plants that were as genetically diverse from TM1 as the primitive recurrent parent. However, two day-neutral accessions (M-9644-0089 and M-9644-0116) did not contain BC4F4 individuals that approached the diversity of the primitive recurrent parent. In some cases, the recurrent parent has been recovered during the day-neutral conversion program, whereas in others, an unexpected loss of diversity has occurred.

Simple sequence repeat markers and existing linkage maps can be used to represent regions of the genome in a graphical genotype display where the donor or the recurrent-parent origins of chromosome regions are easily displayed. Using this method, the graphical genotypes for two chromosomes and one linkage group spanning 465 cM of the cotton genome of day-neutral plants from PI561950, T007 (the photoperiodic recurrent parent), and TM1 were constructed (Fig. 2) . TM1 is used because it is genetically very similar to DPL61, the donor parent. As expected, not all chromosome regions of T007 are unique relative to TM1 (genetic distance from TM1 = 0.58, Table 4). For one region on chromosome 6, T007 is heterozygous or heterogeneous for BNL2895. The variability for amount of T007 genome recovered among the day-neutral BC4F4 plants of PI561950 is extensive. Plant M8 has large regions similar in graphical genotype to TM1 (representative of the donor parent). For the 17 SSR markers located on the two chromosomes and one linkage group, M8 is homozygous for alleles only at BNL3792 from T007. The other regions are either heterozygous or homozygous for the TM1 allele. Plant M1 is also a good example of poor recovery of the recurrent parent T007. In contrast, plant M9 best represents recovery of the graphical genotype of T007 in a day-neutral BC4F4 plant. This is in agreement with the genetic distance (Table 4) where the diversity in M9 is high relative to TM1. Graphical genotypes (not shown) were constructed for 10 day-neutral plants of all nine BC4F4 populations (Table 4). The plant-to-plant variation was extensive in all accessions for the amount of recovery of the recurrent parent. In the case of M-9644-0089, the graphical genotype of all 10 plants displayed poor recovery of the recurrent parent, T0089.



View larger version (40K):
[in this window]
[in a new window]
  		Fig. 2 Graphical cotton genotypes of (a) chromosome 10 (142 cM), (b) chromosome 20 (159 cM), and (c) Linkage Group 6 (164 cM) for TM1, T007 (bulk of recurrent photoperiodic parent), and 10 plants of BC4F4 M9044-0007 (PI561950) day-neutral accession

 
It is possible to survey the graphical genotypes and determine which SSR marker regions are recovered by backcrossing at a higher rate than others (Fig. 2). The regions marked by BNL3279, BNL2960, and BNL252 appeared to be successfully recovered in most BC4F4 plants of PI561950. Markers BNL3563, BNL1665, and BNL3792 appear to be recovered at a very low rate after four backcrosses. These trends were maintained in other backcross family graphical genotypes.


   Conclusions
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 Conclusions
REFERENCES
 
Use of the day-neutral Gossypium race stocks in cotton improvement programs is contingent on the presence of genetic variability and the accurate characterization of that variability. The SSR markers provide an accurate way of determining genetic diversity at the molecular level. Many of the converted race stocks were found to have more than 75% shared alleles at the marker loci with typical G. hirsutum. This doesn't preclude them as reservoirs of novel alleles for qualitative traits, such as pest resistances. However many may be unlikely reservoirs of novel alleles for important QTLs.

The risk of indiscriminately using these as a source of QTL alleles is that one may introgress alleles that are already in the elite gene pool. This risk may be even greater if the race stock donor is selected as a parent based on performance per se. Based on the diversity found in the wild G. hirsutum, domestication of cotton has resulted in a more restricted genetic constituency that may be associated with the cultivated phenotype. The phenotypically superior race stock genotypes may be so because of the presence of alleles that are identical to those in the cultivated gene pool. Our results show that loss of diversity can be compounded in the converted race stocks because of linkage drag and or genetic drift even after several recurrent backcrosses.

The lack of recovery of the recurrent parent during the conversion program may be due to several events. Inadvertent selection for BCn plants that flower more profusely or exhibit earliness might retain donor gene segments at an unusually high frequency. Every attempt was made during backcross conversion to recover each recurrent photoperiodic accession without selection for other traits or uniformity within an accession (J.C. McCarty, 1999, personal communication). The recurrent parents are heterogeneous and possibly heterozygous collections of primitive germplasm. Thus, for each backcross, the use of a different recurrent parent plant could influence recovery of specific chromosome regions. Unfortunately, in this experiment, individual plants of the primitive recurrent parents were not genotyped, and therefore the degree of heterogeneity or heterozygosity could not be determined. There can be linkage drag adjacent to gene(s) controlling day-neutrality coming from the donor parent. Unfortunately, the gene(s) controlling photoperiod response in cotton have not been mapped. Inadvertent outcross contamination by other upland pollinators would also accelerate the retention of typical G. hirsutum marker alleles similar to that of the donor.

Clearly genetic variability exists in the converted race stock germplasm at the individual plant level. The key is to identify the plant(s) within each diverse accession that exhibit the most unique marker alleles relative to typical G. hirsutum. These diverse plants share <40% of the same marker alleles with typical G. hirsutum. These day-neutral plants are more likely reservoirs of novel QTL alleles, according to the criteria of Tanksley and McCough (1997). The challenge is to introgress these unique QTL alleles into elite cotton germplasm. The potential for exploiting this race stock germplasm via advanced backcross QTL analysis in a manner similar to that proposed by Tanksley et al. (1996) should be explored. Likely candidates as donors for such a program would be day-neutral selected plants M9, M18, M25, or M35 (Table 4). These day-neutral plants all have >40% unique alleles for these SSR markers compared with typical G. hirsutum.

The wild G. hirsutum race yucatanenese should be a good source of genetic diversity since it had 70% unique alleles relative to the modern cultivar. The wild tetraploids, G. mustelinum, G. tomentosum, and G. darwinii, should also provide excellent sources of genetic diversity. They exhibit >80% unique alleles at marker loci relative to typical G. hirsutum. These wild species are photoperiodic and difficult to use in germplasm enhancement programs. Efforts should be initiated to convert them to day-neutral germplasm to facilitate their use in breeding. The many accession-specific marker alleles identified in this experiment could be used to facilitate introgression into elite G. hirsutum germplasm.

Minimizing linkage drag, genetic drift, and genetic erosion is paramount in a backcross conversion program to recover the primitive germplasm base in a manageable day-neutral plant type. The degree to which the recurrent parent is not recovered represents a form of genetic erosion, since the genetic diversity will be unavailable in the race stock collection. The use of marker-facilitated backcrossing coupled with day-neutral conversion could help ensure that the recurrent parent is recovered to a higher degree. Ultimately, DNA markers should be used to select accessions and plants within an accession prior to costly introgression into cotton breeding programs. The SSR markers and high-throughput protocols in this study make this a feasible strategy.


   NOTES
TOP
 NOTES
ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 Conclusions
 REFERENCES
 
This work was supported in part by a grant from Cotton Incorporated, Raleigh, NC, to R.G. Cantrell.

Received for publication October 12, 1999.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 Conclusions
 REFERENCES
 




This article has been cited by other articles:


Home page
 Crop Sci.Home page
P. I. Ragsdale and C. W. Smith
Germplasm Potential for Trait Improvement in Upland Cotton: Diallel Analysis of Within-Boll Seed Yield Components
Crop Sci., May 31, 2007; 47(3): 1013 - 1017.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
I. Y. Abdurakhmonov, F. N. Kushanov, F. Djaniqulov, Z. T. Buriev, A. E. Pepper, N. Fayzieva, G. T. Mavlonov, S. Saha, J. N. Jenkins, and A. Abdukarimov
The Role of Induced Mutation in Conversion of Photoperiod Dependence in Cotton
J. Hered., May 1, 2007; 98(3): 258 - 266.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
G. Van Becelaere, E. L. Lubbers, A. H. Paterson, and P. W. Chee
Pedigree- vs. DNA Marker-Based Genetic Similarity Estimates in Cotton
Crop Sci., September 23, 2005; 45(6): 2281 - 2287.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
J. F. Zhang, Y. Lu, H. Adragna, and E. Hughs
Genetic Improvement of New Mexico Acala Cotton Germplasm and Their Genetic Diversity
Crop Sci., September 23, 2005; 45(6): 2363 - 2373.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
J. Zhang, Y. Lu, R. G. Cantrell, and E. Hughs
Molecular Marker Diversity and Field Performance in Commercial Cotton Cultivars Evaluated in the Southwestern USA
Crop Sci., June 24, 2005; 45(4): 1483 - 1490.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
M. Ulloa, S. Saha, J. N. Jenkins, W. R. Meredith Jr., J. C. McCarty Jr., and D. M. Stelly
Chromosomal Assignment of RFLP Linkage Groups Harboring Important QTLs on an Intraspecific Cotton (Gossypium hirsutum L.) Joinmap
J. Hered., March 1, 2005; 96(2): 132 - 144.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
H. Basal, P. Bebeli, C. W. Smith, and P. Thaxton
Root Growth Parameters of Converted Race Stocks of Upland Cotton and Two BC2F2 Populations
Crop Sci., November 1, 2003; 43(6): 1983 - 1988.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
S. A. Mohammadi and B. M. Prasanna
Analysis of Genetic Diversity in Crop Plants--Salient Statistical Tools and Considerations
Crop Sci., July 1, 2003; 43(4): 1235 - 1248.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
O. A. Gutierrez, S. Basu, S. Saha, J. N. Jenkins, D. B. Shoemaker, C. L. Cheatham, and J. C. McCarty Jr.
Genetic Distance among Selected Cotton Genotypes and Its Relationship with F2 Performance
Crop Sci., November 1, 2002; 42(6): 1841 - 1847.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
M. Karaca, S. Saha, J. N. Jenkins, A. Zipf, R. Kohel, and D. M. Stelly
Simple Sequence Repeat (SSR) Markers Linked to the Ligon Lintless (Li1) Mutant in Cotton
J. Hered., May 1, 2002; 93(3): 221 - 224.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Figures Only
Right arrow Full Text (PDF) Free
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via ISI Web of Science (25)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Liu, S.
Right arrow Articles by Stewart, J.McD.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Liu, S.
Right arrow Articles by Stewart, J.McD.
Agricola
Right arrow Articles by Liu, S.
Right arrow Articles by Stewart, J.McD.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
The SCI Journals Agronomy Journal Vadose Zone Journal
Journal of Natural Resources
and Life Sciences Education		 Soil Science Society of America Journal
Journal of Plant Registrations Journal of
Environmental Quality		 The Plant Genome