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QTL analysis of cotton fiber quality using multiple Gossypium hirsutum x Gossypium barbadense backcross generations.

AS THE LEADING NATURAL FIBER CROP, cotton is an important agricultural commodity, providing income to millions of farmers in both industrial and developing countries. Technological changes in the textile industry mean that priorities concerning fiber properties have also changed (May and Lege, 1999), and cotton breeders have concentrated efforts on different fiber properties as important predictors of yarn performance (May, 2002). Classical breeding studies have shown that these properties tend to be moderately to highly heritable (Meredith and Bridge, 1972). Upland cotton, G. hirsutum, dominates the world's cotton fiber production, representing 90% of the production. Compared with the Upland cotton, the second most cultivated species, G. barbadense, has superior fiber length, strength, and fineness, giving a higher spinning and manufacturing performance. Gossypium hirsutum varieties, however, are usually early maturing and higher yielding. Although bidirectional genome exchanges between the two species are well documented (reviewed in Brubaker and Wendel, 2001) attempts at utilizing deliberate interspecific recombination between G. hirsutum/G, barbadense by conventional breeding have had limited impact on cultivar development (Paterson and Smith, 1999). While the use of DNA markers for marker-assisted selection has received considerable attention among plant and animal breeders in the past 10 to 15 yr, published reports on QTL detection in cotton are recent. These include the mapping of disease resistance genes (Wright et al., 1998; B. Lyon, personal communication, 2001), genes or QTLs affecting leaf pubescence (Wright et al., 1999), fertility restoration (Lan et al., 1999), leaf morphology (Jiang et al., 2000a), stomatal conductance (Ulloa et al., 2000), and traits related to water stress response (Saranga et al., 2001). Studies have reported QTLs related to fiber quality derived both from populations of G. hirsutum (Shappley et al., 1998: Ulloa and Meredith, 2000), and populations from interspecific crosses between G. hirsutum x G. barbadense (Jiang et al., 1998; Yu et al., 1998; Kohel et al., 2001; Paterson et al., 2003; Zhang et al., 2003; Mei et al., 2004). Except for Mei et al. (2004), who detected 5 QTLs for four fiber-related traits, most of these studies showed that genetic control of fiber quality was highly complex, translating into high numbers of QTLs and moderate to low elementary additive QTL effects on trait value. In addition, comparisons between experiments and/or populations have so far been limited by the fact that bridge markers between mapping populations were scarce.

This paper reports on an analysis of cotton fiber QTLs undertaken as part of a marker-assisted backcross introgression scheme (Lacape et al., 2000) based on a combined RFLP-SSR-AFLP genetic map of a G. hirsutum/ G. barbadense backcross (Lacape et al., 2003). We choose a G. barbadense variety as the donor parent for superior fiber quality and a G. hirsutum variety as recurrent parent. The first (one set of phenotypic data) and second (two sets of data) backcrosses to the G. hirsutum recurrent parent were used for QTL detection.


Plant Material

The plant material included three populations, B[C.sub.1], B[C.sub.2], and B[C.sub.2][S.sub.1]. The initial cross involved "Guazuncho 2' (G. hirsutum) and 'VH8-4602' (G. barbadense) as the female and male parents, respectively. Guazuncho 2 is a modern pure-line G. hirsutum (Gh) variety created at INTA (Instituto Nacional de Technologia Agropecuaria) in Argentina. It was chosen for its good overall agronomic performance. VH8 originates from Antigua and was derived from a cross between two Sea Island G. barbadense (Gb) types. Compared with a G. hirsutum standard, it is characterized by superior values for fiber length (+10 mm in UHML as compared with Guazuncho 2), HVI-strength (+16 cN/tex), and standard fineness (-40 mtex). The first backcross generation involved the [F.sub.1] as the female and Guazuncho 2 as the male parent. Seventy-five B[C.sub.1] plants were grown in a greenhouse at Montpellier, France, during summer 1999 (May-October), and served as female parents for making the second backcross to Guazuncho 2. Fiber samples were taken from all B[C.sub.1]s after ginning the open-pollinated seed cotton on a laboratory roller gin. A set of 600 B[C.sub.2] plants originating from 60 different B[C.sub.1]s was grown under field conditions during summer 2000 (May October) at Montpellier. Among these, 200 individual B[C.sub.2] plants having shown a satisfactory production of B[C.sub.3] seeds and originating from 53 different B[C.sub.1]s were harvested. Open pollinated seeds of these B[C.sub.2] plants, constituting 200 B[C.sub.2][S.sub.1] progenies, were grown during the 2001 2002 (December-April) rainy season under field conditions at Primavera do Leste in Brazil. Each B[C.sub.2][S.sub.1] was planted in two fully randomized replications, each plot (one row) measuring 5 m. Each of the 400 plots was bulk harvested, the seed cotton ginned on a laboratory roller gin and the fiber sampled for analysis.

Analysis of Fiber Quality

All fiber samples were analyzed at the Cirad laboratory at Montpellier. Measurements were made with an HVI line (Zellweger Uster 900, Uster Technologies, Switzerland) including fiber length components (mean length, ML, upper half mean length. UHML, and uniformity index, UI), strength (STR), elongation (ELO), color components (reflectance, Rd. and yellowness index. +b). Maturimeter parameters (FMT3, Shirley Dev Ltd, England) included fiber maturity ratio (MR), micronaire reading (IM), linear fineness (H), and standard fineness (Hs).

SSR/AFLP Analysis of the B[C.sub.2] Population

The B[C.sub.1] population was used to construct a genetic map as described in Lacape et al. (2003). With the new microsatellite markers subsequently developed by Nguyen et al. (2004), the updated version of this map consists of 1160 loci mapped along 5520 cM. The 200 individual B[C.sub.2] plants were analyzed for a selected subset of SSR (81 primer pairs) and AFLP (45 EcoRI/ Msel primer pairs) loci chosen on the basis of their representative distribution across the 26 chromosomes. SSR and AFLP protocols are described in Lacape et al. (2003). The allelic constitution of the 200 B[C.sub.2] plants, either homozygous for G. hirsutum (Gh) alleles, Gh/Gh, or heterozygous for G. hirsutum and G. barhadense (Gh), Gh/Gb, was finally scored for 594 segregating loci.

Statistical Analysis

Heritability and Trait Correlation

Trait heritability was directly estimated from the parent/ offspring regressions of 200 B[C.sub.2]-B[C.sub.2][S.sub.1]. Pearson correlation coefficients were calculated for all trait combinations within each of the 3 phenotypic data sets.

Genetic Mapping

Additional markers scored only in the B[C.sub.2] population were positioned on the B[C.sub.1] map (Nguyen et al., 2004) after constructing a B[C.sub.2] genetic map and aligning the two maps by common loci. The Mapmaker "group," (LOD 5.0 and 30 maximal recombination frequency) "order," and "sequence" commands were used to generate the B[C.sub.2] linkage map from 594 segregating markers. Marker segregations in the B[C.sub.2] were tested for deviation from the expected 3:1 (Gh/Gh: Gh/Gb) ratio by a [chi square] test. All B[C.sub.2] linkage groups were assigned to a corresponding B[C.sub.1] group using loci in common between the 2 maps as bridges. Each additional B[C.sub.2] locus was positioned on the B[C.sub.1] map as a backbone reference map, by extrapolating its position from the positions of shared flanking loci. Hence. the same mapping data, i.e., those obtained in the B[C.sub.1] generation, were used for QTL analysis in the B[C.sub.1] and B[C.sub.2] populations.

QTL Analysis

Excluding the cosegregating markers, 595 B[C.sub.1] and 341 B[C.sub.2] markers were used to conduct three individual QTL analyses using one phenotypic data set in B[C.sub.1] and two phenotypic data sets (B[C.sub.2] and B[C.sub.2][S.sub.1]) in B[C.sub.2]. The association between phenotype and marker genotype was investigated through simple marker analysis (SMA), interval mapping (IM), and composite interval mapping (CIM) using the computer software QTL Cartographer 1.13 (Basten et al., 1999). For each variable, IM using multiple regression of phenotypic data on marker genotypic data over the whole genome was run with 1000 permutations to identify the minimum significant LOD score to be considered. For each individual test, permutation-based thresholds were considered at a 5% risk at the genome level. Composite interval mapping (Jansen and Stam, 1994: Zeng, 1994) was then performed by means of the markers preselected by stepwise regression as cofactors. The results of the QTL position, proportion of phenotypic variance explained (R2), and effect that are reported are those derived from CIM, after checking for their agreement with the SMA results. The QTL positions on the B[C.sub.1] or B[C.sub.2] map are reported on the B[C.sub.1]/B[C.sub.2] consensus map and drawn by MapChart software (Voorrips, 2002).

The effects of QTLs are considered from a product transformation perspective. Therefore, decreases in fiber fineness (H), standard fineness (Hs), micronaire reading (IM), and yellowness index, were indicative of a "positive" contribution conferred by either parent.


Phenotypic Variation

In the present study, the Gh and Gb accessions were characterized by their contrasting fiber properties with differences of 9.7 mm in UHML, 15.9 cN/tex in fiber strength, and 38 mtex in standard fineness, as averaged over three measurements (Fig. 1). The frequency distribution of each parameter in B[C.sub.1], B[C.sub.2], and B[C.sub.2][S.sub.1] populations showed typical quantitative variation (Fig. 1). All variables fitted a normal distribution and none were transformed in further analyses.


Combined AFLP/SSR B[C.sub.2] Map and B[C.sub.1]/B[C.sub.2] Consensus Map

Taken as a whole, and in the absence of any deliberate human selection pressure on the B[C.sub.1]s, the genetic transmission observed in the 200 B[C.sub.2] individuals met the expected 1:3 frequency, 25.4 to 74.6% of Gh/Gb and Gh/Gh allelic combinations, respectively. The segregation of 594 B[C.sub.2] markers revealed 511 loci mapped in 26 linkage groups (not shown). Each B[C.sub.2] group was bridged unambiguously to a corresponding chromosome or linkage group on the B[C.sub.1] map by 373 common markers. The number of bridge AFLP or SSR markers varied between seven for c16 and 26 for A03. Although some bias in the construction of the B[C.sub.2] map is expected from the fact that the B[C.sub.2] individuals were not independent and that B[C.sub.2] data were treated as a B[C.sub.1] in Mapmaker, the maps constructed from the two populations were in full agreement concerning locus orders. Distances between common loci were frequently reduced in the B[C.sub.2] map as compared with the B[C.sub.1] map (not shown). On the basis of the distance covered by the common markers, the B[C.sub.2] map was 15% shorter than the 3300 cM of B[C.sub.1]. A total of 138 loci (133 AFLPs and five SSRs) not scored in the B[C.sub.1], were mapped in the B[C.sub.2] population. From the extrapolated positions of these additional B[C.sub.2] loci onto the backbone B[C.sub.1] map, the B[C.sub.1]/B[C.sub.2] consensus map comprises 1306 loci and spans 5597 cM (Fig. 2). The average interval between two markers of the consensus map is 4.3 cM.


Trait Heritability and Correlation between Traits

On the basis of B[C.sub.2]/B[C.sub.2][S.sub.1] regression, the estimates of narrow sense heritability were highly significant for all individual fiber quality traits. These estimates fell within the range of [h.sup.2] values reviewed in May (1999). The highest [h.sup.2]s were for fiber length (UHML: 0.70: ML: 0.58) and fineness (H: 0.65; Hs: 0.57). The lowest [h.sup.2] estimates were for length uniformity (0.24) and color indices (0.29 for reflectance and yellowness index). In the case of length uniformity, some bias in the [h.sup.2] estimate might result from the fact that UI is calculated as a ratio (UHML/ML), while the lower [h.sup.2] for color indices clearly reflected the greater influence of nongenetic sources of variation as compared with other parameters. The moderate [h.sup.2] (0.40) value for fiber strength in our study was possibly related to the greater variability obtained from the HVI fiber strength measurement (May, 2002). compared with classical types of measurements.

Correlation coefficients between phenotypic traits calculated in each of the B[C.sub.1], B[C.sub.2] and B[C.sub.2][S.sub.1] populations are presented in Table 1. The strongest correlations consistently observed within the three data sets related ML to UHML (0.97 on average), IM to H (0.89) and to MR (0.83), and Rd to +b (-0.74), and (only in the B[C.sub.2][S.sub.1] data set) H to Hs (0.76). These were all expected as inherent to the measurement apparatus and/or physiological definitions of the trait concerned. Another group of correlations of lower magnitude relate length (ML or UHML), strength, and/or fineness components (IM or H), probably reflecting some genetic association of these characteristics as observed in the contrasting parents used (Fig. 1).

For simplicity, we will hereafter consider certain traits as groups of related or correlated traits: length components (LEN), grouping the two variables ME and UHML, maturity/fineness components (FIN), grouping the 4 variables IM, MR, H, and Hs, and color components (COL), grouping the two variables reflectance, Rd, and yellowness index, +b. Fiber strength (further noted STR), elongation (ELO), and length uniformity index (UNI) are considered individually,

QTL Analysis

The highest critical LOD thresholds after permutation tests varied between 3.2 and 4.0 for the various traits except for uniformity index in the B[C.sub.2], and B[C.sub.2][S.subb.1] generations (4.3 and 5.7, respectively) and for color indices in B[C.sub.2] generation (5.0 and 11.1 for Rd and +b respectively). Fifty QTLs met permutation-based LOD thresholds. The results are nevertheless reported for all the QTLs that showed a LOD superior to 2.5 in any of the generations, i.e., a total of 80 QTLs (Table 2). While QTLs detected above this LOD limit of 2.5 but below the permutation-based LOD threshold should be treated cautiously, i.e., putative QTLs, they enabled a more precise comparison of results between generations, between traits for a given chromosomal region, and between our data and other data sets for a given trait. For all but one (QTL for IM on c10) of the 50 QTLs meeting permutation-based threshold detected under CIM, and for 70 of the 80 putative QTL, we also obtained a significant marker-trait association (P > 0.001 of F statistics) using simple marker analysis.

Comparison of QTLs detected in the three populations indicated that, among the 50 significant QTLs, 11 were detected in both B[C.sub.2] and B[C.sub.2][S.sub.1], and six were detected in both B[C.sub.1] and either of B[C.sub.2] or B[C.sub.2][S.sub.1].

Percentages of phenotypic effects (Table 2) ranged between 4.8 and 14.8% for length, 3.1 and 17.9% for length uniformity, 4.4 and 21.3% for strength, 5.4 and 21.2% for elongation, 4.6 and 29.1% for fineness/maturity, and 4.8 and 15.6% for fiber color (yellowness index in B[C.sub.2] discarded from comparisons).

As expected, the respective contributions of the Gh and Gb parents to fiber quality (Table 2) indicated that a majority of Gb parent alleles had a positive influence on fiber length (12 versus 3), strength (8 versus 4), and fineness QTLs (13 versus 8), and a majority of Gh parent alleles had a positive influence on fiber color QTLs (13 versus 3).

Altogether, the 80 QTLs mapped over 22 of the 26 chromosomes (a single QTL on two unassigned linkage groups, NL5 and NL8), with chromosomes 1, 2, 7, and 12 lacking any QTLs (Fig. 2). The QTLs that were accounted for by a positive effect of the Gb alleles on either fiber length, strength, or fineness, mapped to 15 different chromosomes. Cases of colocalization of QTLs exceeded cases of isolated positioning. Such cases of colocalization of QTLs for different fiber properties were often detected in different population data sets. Cases of across-population and across-trait colocalization are illustrated for c17 with a colocalization of a fiber elongation QTL detected in the B[C.sub.1] population with a color QTL detected in the B[C.sub.2], on A02 (fineness QTL in the B[C.sub.1] and color QTL in the B[C.sub.2][S.sub.1]), on D03 (color QTL in the B[C.sub.1] and fineness QTL in the B[C.sub.2][S.sub.1]), and on A03 (uniformity QTL in the B[C.sub.1] and a strength QTL in the B[C.sub.2]).

Significant QTLs were identified for all six groups of fiber traits and in all three populations. After merging data from the three QTL analyses, the total of QTLs varied from six for length uniformity to 21 for the fineness-maturity complex.

For fiber length, nine QTLs met permutation-based thresholds, and six additional QTLs may be considered as putative. For 12 of these 15 QTLs, the positive allele contributing to increased fiber length derived from the Gb parent. The two length QTLs detected on c26 have peak LODs separated by 60 cM. The position and direction of three length QTLs on c5 (highest LOD in B[C.sub.1]), c26, and A01 (highest LOD in B[C.sub.2][S.sub.1]) agreed with QTLs reported in the literature (Table 2).

Three of the six QTLs reported for fiber length uniformity met permutation-based thresholds. Gb and Gh alleles contributed equally at three QTLs each. Two QTLs, on c14 and A03, were detected at positions that have been previously reported.

Six fiber strength QTLs met permutation-based thresholds, and six others were detected at lower LOD values. Eight QTLs resulted from a positive contribution of the Gb parent, five of which (on c3, c25, c23, A01, and A03) mapped at comparable positions in the literature. In addition, we detected two QTLs of a Gh positive contribution on c18, mapping at similar positions to two QTLs described by Paterson et al. (2003), near loci pAR788 and P5-11, but with opposite phenotypic effects.

From a total of 10 elongation QTLs, eight met permutation-based thresholds. Six resulted from a positive contribution of the Gb parent. Two QTLs on c20 are positioned 40 cM apart. The fiber elongation QTLs on c15, c9, c23, and c10 agreed with QTLs from the literature.

Fourteen of the 21 reported QTLs relating to the maturity or fineness complex met permutation-based thresholds of either IM, MR, H, or Hs parameter, and, for most of them, QTLs were detected simultaneously for several traits: (i) two traits: IM and MR on c22 and c6, IM and Hs on c9, Hs and MR on c5 and c18, H and Hs on c6 and c16; (ii) three traits: IM, MR and H on c3 and A02, IM, H, and Hs on D08; and (iii) four traits: IM, MR, H, and Hs on D03.

Thirteen cases were found in which the contribution of the Gb parent to each trait was positive (lower IM, H, and Hs values, and higher MR value). Interestingly, the map locations and effects for seven of the QTLs described in this way, including the strongest ones detected in B[C.sub.2] (c3) and B[C.sub.2][S.sub.1] (D03), corresponded to those for QTLs relating to IM values reported in the literature by Kohel et al. (2001) and Paterson et al. (2003). One QTL detected on D08 mapped at a similar position to a QTL reported in Paterson et al. (2003), near pGH225 (former c20 in the reference paper renamed to D08), but had the opposite effect.

In total, 16 QTLs were detected for the two color indexes, Rd and +b. Half of these QTLs explained variation observed for both indexes. In accordance with parental contributions (Fig. 1), 13 of the 16 detected QTLs resulted from a positive contribution of the Gh parent, conferring higher Rd and/or lower +b values. Five QTLs were reported in Paterson et al. (2003) for yellowness index, with similar map location and effect.

We observed a few cases of QTL-rich regions delimited along homeologous regions of the A- and D-subgenome chromosomes: fiber color QTLs on c6 and c25, both congruent with Paterson et al. (2003); fineness-maturity QTLs on the upper part of c6 and c25; fineness and elongation QTLs at central parts of cl0 and c20; and lastly on the c5-D08 homeologous pair a concentration of "negative" QTLs for length, elongation, fineness, and color.


In an attempt to overcome the limitations of conventional breeding for the improvement of cotton fiber quality through interspecific hybridization, we decided to use molecular markers in a marker-assisted selection scheme aimed at improving the efficiency of the introgression of fiber quality traits.

The quality of cotton fiber derives from several traits, the most important being length, fineness, and strength, each of which is the result of complex genetic architecture. This study confirmed the expected genetic complexity of individual cotton fiber components (Paterson et al., 2003; Shappley et al., 1998). Combining all the different traits, we detected a total of 80 QTLs using LOD2.5 as a threshold, of which 50 surpassed the permutation-based LOD thresholds (3.2-5.7). For most of the QTLs related to the most economically important traits, the favorable alleles came from the G. barbadense parent. However, the inferior parent, G. hirsutum, also contributed to fiber quality (Table 2): for length on c5 (length QTL of the highest LOD in B[C.sub.1]), strength on c18, and fineness/maturity on D08, c6, A02, and D03. Such observation supports the proposition that superior allele combinations may be obtained in interspecific progenies of mosaic genome constitution (Tanksley et al., 1996).

The distribution of QTLs between chromosomes or linkage groups assigned to A and D subgenomes shows a slight over-representation of QTLs mapping to the D-subgenome chromosomes (58%) as compared with the A-subgenome. This finding is in agreement with the idea that in AADD tetraploid cottons, the D-subgenome globally contributes to a higher level of trait variability than does the A-subgenome (reviewed by Paterson et al., 2003).

The cases of colocalization of QTLs for different traits (Fig. 2) confirmed the observed phenotypic correlations (Table 1); the presence of alleles of the Gb parent in some QTL-rich chromosome regions contributed simultaneously and positively to several properties among fiber strength, length, and fineness. Of significant interest are the localizations of "positive" QTLs related to traits of greater economic importance, i.e., fiber strength. length, and fineness. Chromosomes 3 and 23 are worth mentioning in this respect: c3 with the strongest length QTLs detected in B[C.sub.1] (LOD 4.43) and in B[C.sub.2][S.sub.1] (LOD 4.99), colocalized with the second strongest strength QTL detected in B[C.sub.1] (LOD 4.51), and -c23 with the strongest strength QTL detected in B[C.sub.2] (LOD 4.78) and B[C.sub.2][S.sub.1] (LOD 4.01) colocalized with a length QTL in B[C.sub.2] (LOD 2.80). Because fiber length, strength, and fineness may be considered as physiologically independent and relating to different spatial and temporal biological processes (Wilkins and Jernstedt, 1998), the colocalization of QTLs may be more indicative of linkage between different genes than of pleiotropy.

We observed a low consistency between the QTLs detected in the three populations (around 10% of QTLs in common between B[C.sub.2] and B[C.sub.2] and 20% between B[C.sub.2] and B[C.sub.2][S.sub.1]). Such apparent instability in QTLs detected under diverse environments is not uncommon (Ribaut et al., 1997: Saranga et al., 2001). In the present case, the factors that could explain such a difference between generations may involve the environmental conditions (greenhouse or field, Montpellier or Brazil), the genetic backgrounds of the B[C.sub.1] and B[C.sub.2] generation, or possible differences in the distribution of QTLs between the 75 plants constituting the B[C.sub.1] population and the subset of 53 B[C.sub.1] plants that effectively served as parents to the 200 B[C.sub.2]s. However, the colocalized QTLs also relate to various combinations of traits and data sets. Chromosomes 6 and 25, for example, contain a high density of QTLs corresponding to various trait or generation combinations: color in B[C.sub.2] and fineness in B[C.sub.1] on the upper part of c6; color in B[C.sub.1], fineness in B[C.sub.1] and/B[C.sub.2][S.sub.1], and length in B[C.sub.2] in the central part of c6; length in B[C.sub.2][S.sub.1] and fineness in B[C.sub.2] on the upper part of c25. Also noteworthy is the fact that the map position and sign of phenotypic effect for 26 (33%) of the 80 QTLs reported in this study confirm data reported from four other independent investigations reporting cotton fiber quality QTLs detected in interspecific G. hirsutum x G. barbadense populations (Jiang et al., 1998; Kohel et al., 2001: Paterson et al., 2003; Mei et al., 2004). To evaluate the consistency of QTLs across different populations, the genetic structure (backcross versus F2-derived populations) of these populations, their relationships (direct genetic relatedness in the case of our two populations), the range of molecular polymorphism (and therefore different genome coverage), as well as QTL x environment interactions must be taken into consideration (Melchinger et al., 1998; Paterson et al., 1991). Our observation that QTLs for cotton fiber quality show some stability across populations, however, provides the first insight on comparative QTL mapping in cotton. Knowledge of QTL-rich chromosome regions that are congruent between mapping population, generations, and locations is highly valuable from a breeding perspective. Such consistency in the detection of QTLs adds confidence in their reality and these QTL-rich chromosomes regions may serve as primary targets in future studies on cotton fiber quality. In particular, attention may be paid to the above-mentioned chromosomes 3 and 23: both are rich in strong QTLs in our study, Paterson et al. (2003) also found a fiber strength QTL in the lower part of c23, and chromosome 3 contained one of the four strength QTLs reported by Kohel et al. (2001) and a fineness QTL common between Kohel et al. (2001) and Paterson et al. (2003).

Among the 80 QTLs detected, the subset of "positive" fiber quality QTLs (i.e., of a G. barbadense positive allelic contribution) is distributed across 19 different chromosome segments, each bearing one of several QTLs, and is located on 15 different carrier chromosomes (Table 3). The 19 regions thus delimit a total length of 636 cM (20% of the carrier genome), or 11.5% of the total genome (Table 3, Fig. 3). In the process of our marker-assisted backcross strategy, these carrier chromosomes and chromosomal regions are now considered as G. barbadense target regions (foreground genome) to be manipulated through successive backcrosses for an introgression into a G. hirsutum background genome. Given such a high number of chromosome regions, we are now concentrating efforts on BC progenies containing subsets of introgressed chromosome segments (generally two to four), with the view toward further genetic fixation and intercrossing of advanced BC progenies for QTL pyramiding. The ongoing development of near isogenic lines, NILs, differing only by the introgression of G. barbadense alleles at a given QTL (QTL-NILs) will prove useful for studying the effect of a single given QTL on the phenotypic value of a plant harboring it. Such material will also be useful for expression studies and for map-based cloning.

Table 1. Intrapopulation correlations coefficients among fiber traits.
Significant (P < 0.01 correlations (r > 0.30 in the B[C.sub.1], and r
> 0.18 in the B[C.sub.2] and B[C.sub.2][S.sub.1]) are shown.

([dagger])   Population             ML     UHML     UI      STR

UHML         B[C.sub.1]             0.98
             B[C.sub.2]             0.96
             B[C.sub.2][S.sub.1]    0.98
UI           B[C.sub.1]             0.61    0.42
             B[C.sub.2]             0.66    0.43
             B[C.sub.2][S.sub.1]    0.49    0.31
STR          B[C.sub.1]             --      --      0.34
             B[C.sub.2]             0.80    0.75    0.59
             B[C.sub.2][S.sub.1]    0.56    0.51    0.44
ELO          B[C.sub.1]             --      --      0.40    --
             B[C.sub.2]             0.63    0.48    0.74    0.58
             B[C.sub.2][S.sub.1]    --      --      0.31    --
IM           B[C.sub.1]             0.31    --      0.48    --
             B[C.sub.2]            -0.33   -0.44    --      0.48
             B[C.sub.2][S.sub.1]   -0.53   -0.57    --     -0.27
MR           B[C.sub.1]             0.46    0.39    0.50    --
             B[C.sub.2]             --     -0.28    0.21   -0.39
             B[C.sub.2][S.sub.1]   -0.31   -0.33    --      --
H            B[C.sub.1]             --      --      0.33    --
             B[C.sub.2]            -0.43   -0.52    --     -0.51
             B[C.sub.2][S.sub.1]   -0.50   -0.54    --     -0.32
Hs           B[C.sub.1]            -0.58   -0.56   -0.40    --
             B[C.sub.2]            -0.26   -0.24   -0.20    --
             B[C.sub.2][S.sub.1]   -0.25   -0.29    --     -0.26
Rd           B[C.sub.1]             --      --      --      --
             B[C.sub.2]             0.23    --      0.36    --
             B[C.sub.2][S.sub.1]    --      --      --      --
+b           B[C.sub.1]             --      --      --      --
             B[C.sub.2]             --      --      --      --
             B[C.sub.2][S.sub.1]    --      --      --      --

([dagger])   Population             ELO     IM      MR

UHML         B[C.sub.1]
UI           B[C.sub.1]
STR          B[C.sub.1]
ELO          B[C.sub.1]
IM           B[C.sub.1]             0.52
             B[C.sub.2]             --
             B[C.sub.2][S.sub.1]    --
MR           B[C.sub.1]             0.39    0.94
             B[C.sub.2]             --      0.88
             B[C.sub.2][S.sub.1]    --      0.67
H            B[C.sub.1]             0.56    0.89    0.67
             B[C.sub.2]             --      0.91    0.62
             B[C.sub.2][S.sub.1]    0.21    0.88    0.24
Hs           B[C.sub.1]             --     -0.48   -0.75
             B[C.sub.2]             --      --     -0.46
             B[C.sub.2][S.sub.1]    0.18    0.37   -0.44
Rd           B[C.sub.1]             --      --      --
             B[C.sub.2]             --      --      --
             B[C.sub.2][S.sub.1]   -0.19    --      --
+b           B[C.sub.1]             --      --      --
             B[C.sub.2]             --     -0.27   -0.27
             B[C.sub.2][S.sub.1]    --      --      --

([dagger])   Population              H      Hs      Rd

UHML         B[C.sub.1]
UI           B[C.sub.1]
STR          B[C.sub.1]
ELO          B[C.sub.1]
IM           B[C.sub.1]
MR           B[C.sub.1]
H            B[C.sub.1]
Hs           B[C.sub.1]             --
             B[C.sub.2]             0.40
             B[C.sub.2][S.sub.1]    0.76
Rd           B[C.sub.1]             --      --
             B[C.sub.2]             --     -0.34
             B[C.sub.2][S.sub.1]   -0.20    --
+b           B[C.sub.1]             --      --     -0.84
             B[C.sub.2]             --      --     -0.77
             B[C.sub.2][S.sub.1]    --      --     -0.60

([dagger]) Traits are: UHML, upper half mean length; ML, mean length;
UI, uniformity index; STR, strength; ELO, elongation; IM, micronaire
reading; MR, maturity ratio; H, linear fineness; [H.sub.s], standard
fineness; Rd, reflectance; +b, yellowness index.

Table 2. Synthesis of the QTLs influencing properties related
to fiber quality, as detected by composite interval mapping of
B[C.sub.1], B[C.sub.2] or B[C.sub.2][S.sub.1], populations.
LOD and [R.sup.2] that are underlined are values meeting
permutation-based thresholds.

                                          LOD max in population

            Nearest    cM from top in
QTL-chrom    locus     consensus map            B[C.sub.1]


LEN-c14     E7M1_307         44
LEN-1-c3    E8M1_400         55
LEN-2-c3    CIR084b         129          4.43 ([double dagger])
LEN-c5      A1135b           31          4.49 ([double dagger])
LEN-c6      E3M4_410        141
LEN-1-c25   E4M3_268          0
LEN-2-c25   E3M5_162         51
LEN-c23     BNL1414a        125
LEN-c10     ElM3_370        113
LEN-c20     E4M3_108        256
LEN-1-c26   E4M4_230         76
LEN-2-c26   E8M2_173        138
LEN-A01     E5M8_400         41
LEN-c18     BNL193          142
LEN-D02     BNL3171         193

Uniformity Index

UNI-c14     E7M4_360         85
UNI-DO8     BNL2448a        111
UNI-c20     EIM6_149        117
UNI-c18     E3M8_400         62
UNI-AO3     CIR416          217          3.96 ([double dagger])
UNI-NL5     E7M7_184         43          5.36 ([double dagger])


STR-c3      BNL3989          90          4.51 ([double dagger])
STR-1-c5    BNL852b         101          5.61 ([double dagger])
STR-2-c5    E6M6_430        334
STR-c25     E3M5_162         51
STR-c16     E4M6_312         65
STR-1-c23   E8M8_350         57
STR-2-c23   BNL1414a        125          3.61 ([double dagger])
STR-AO1     E4M6_232        191
STR-1-c18   ElM5_410         53
STR-2-c18   E3M4_350        108
STR-A03     BNL3442         217
STR-D02     BNL3171         193


ELO-c15     BNL3090b        103          3.10 ([double dagger])
ELO-c17     pAR172b          32          4.91 ([double dagger])
ELO-c22     G1058a           24          3.94 ([double dagger])
ELO-DO8     E8M8_124        189
ELO-c9      BNL1414b        208
ELO-c23     BNL1161a         30
ELO-c10     EIM3_370        113
ELO-1-c20   BNL2570          97
ELO-2-c20   BNL3948         132
ELO-NL8     A1826             0          5.42 ([double dagger])

Micronaire (IM), maturity ratio (MR) and fineness (H/[H.sub.s])

FIN-1-c3    E5M7_218         30
FIN-2-c3    CIR084b         129          2.80 Hs
FIN-c4      E3M4_210        106
FIN-c22     BNL4030a        112
FIN-1-c5    CIR102           29          3.91 ([double dagger]) Hs
FIN-2-c5    E6M8_237        271
FIN-1-D08   BNL3452          32
                                         2.73 ([double dagger]) Hs
FIN-2-D08   CIR398u         107          3.62 ([double dagger]) IM
FIN-3-D08   E8M8_124        189
FIN-1-c6    CIR298            0          5.87 ([double dagger]) IM
                                         4.18 MR
FIN-2-c6    E6M5_145        154
                                         4.44 H
FINc-c6     CIR179          278          5.31 ([double dagger]) H
FIN-c25     E4M3_268          0
FIN-c16     E7M1_167         81
FIN-c9      E5M5_158        295
FIN-1-c10   A1158a            3          4.31 IM
FIN-2-c10   BNL3895          78
FIN-c20     BNL946          143
FIN-c18     pAR788a          33          4.68 ([double dagger]) MR
                                         3.47 ([double dagger]) Hs
FIN-A02     E1M7_219        183          4.26 ([double dagger]) MR
                                        41.08 ([double dagger]) IM
FIN-D03     BNL3860           0

Color (reflectance, Rd, and yellowness, +b)

COL-c3      BNL3408b          0
COL-c17     E3M5_134         37
COL-1-D08   BNL852a          84
COL-2-D08   E8M8_124        189
COL-1-c6    BNL3359b         11
COL-2-c6    E2M2_158        126          4.84 ([double dagger]) +b
                                         2.99 ([double dagger]) Rd
COL-c25     E2M7_89          73          4.37 ([double dagger]) Rd
                                         4.57 ([double dagger]) +b
COL-c16     BNL2986          57
COL-c9      E5M5_158        295          2.95 ([double dagger]) Rd
                                         3.61 ([double dagger]) +b
COL-c23     E8M8_350         57
COL-c10     E8M8_490         90
COL-c26     E4M4_230         76
COL-A01     E7M1_186        162
COL-c18     BNL193          142
COL-A02     E6M6_550        187
COL-D03     BNL3860           0          4.19 ([double dagger]) Rd
                                         3.04 ([double dagger]) +b

                         LOD max in population

QTL-chrom          B[C.sub.2]              B[C.sub.2][S.sub.1]


LEN-c14                                 3.22 ([double dagger])
LEN-1-c3                                4.99 ([double dagger])
LEN-c6      2.89 ([double dagger])
LEN-1-c25                               3.12 ([double dagger])
LEN-2-c25   3.38 ([double dagger])
LEN-c23     2.80 ([double dagger])
LEN-c10     2.72 ([double dagger])
LEN-c20     2.77 ([double dagger])
LEN-1-c26   4.00 ([double dagger])      2.86 ([double dagger])
LEN-2-c26                               3.58 ([double dagger])
LEN-A01     4.86 ([double dagger])      4.19 ([double dagger])
LEN-c18     4.28 ([double dagger])
LEN-D02     3.02 ([double dagger])

Uniformity Index

UNI-c14                                 2.52 ([double dagger])
UNI-DO8     2.79
UNI-c20     3.73 ([double dagger])      3.97 ([double dagger])
UNI-c18     5.68 ([double dagger])      7.75 ([double dagger])


STR-2-c5                                2.53
STR-c25     2.56 ([double dagger])
STR-c16                                 3.40 ([double dagger])
STR-1-c23   2.63 ([double dagger])
STR-2-c23   4.78 ([double dagger])      4.01 ([double dagger])
STR-AO1                                 2.86 ([double dagger])
STR-1-c18                               3.43 ([double dagger])
STR-2-c18   3.20 ([double dagger])
STR-A03     3.19 ([double dagger])
STR-D02     3.75 ([double dagger])


ELO-DO8     3.63 ([double dagger])      9.72 ([double dagger])
ELO-c9                                  2.81 ([double dagger])
ELO-c23     4.83 ([double dagger])
ELO-c10     4.75 ([double dagger])
ELO-1-c20                               4.31 ([double dagger])
ELO-2-c20   5.69 ([double dagger])

Micronaire (IM), maturity ratio (MR) and fineness (H/[H.sub.s])

FIN-1-c3    5.17 ([double dagger]) MR
            3.76 ([double dagger]) IM   3.95 ([double dagger]) IM
                                        3.52 ([double dagger]) H
FIN-c4      3.39 ([double dagger]) Hs
FIN-c22     3.24 ([double dagger]) IM
            3.27 MR
FIN-2-c5                                5.51 ([double dagger]) Hs
FIN-1-D08                               3.99 ([double dagger]) H
                                        2.67 ([double dagger]) IM
FIN-3-D08                               3.11 ([double dagger]) HS
FIN-2-c6                                4.46 ([double dagger]) Hs
                                        2.68 ([double dagger]) H
FIN-c25     2.96 ([double dagger]) Hs
FIN-c16                                 3.64 ([double dagger]) H
                                        2.86 ([double dagger]) Hs
FIN-c9      2.99 Hs
FIN-2-c10                               2.52 ([double dagger]) Hs
FIN-c20                                 3.42 ([double dagger]) H
FIN-c18                                 3.19 ([double dagger]) MR
FIN-D03                                 7.72 ([double dagger]) H
                                        6.06 ([double dagger]) IM
                                        4.92 ([double dagger]) Hs

Color (reflectance, Rd, and yellowness, +b)

COL-c3                                  2.84 ([double dagger]) +b
COL-c17     5.44 ([double dagger]) Rd
COL-1-D08   4.63 Rd
COL-2-D08                               4.13 ([double dagger]) Rd
COL-1-c6    6.99 +b
COL-c25                                 4.63 ([double dagger]) Rd
            3.49 ([double dagger]) +b   7.02 ([double dagger]) +b
COL-c16     2.57 Rd
COL-c9                                  4.35 ([double dagger]) Rd
            6.33 +b
COL-c23                                 4.56 ([double dagger]) Rd
                                        2.91 ([double dagger]) +b
COL-c10                                 3.61 ([double dagger]) +b
COL-c26     4.11 ([double dagger]) +b   3.25 ([double dagger]) +b
COL-A01     2.93 ([double dagger]) Rd
COL-c18     4.91 ([double dagger]) Rd   3.37 ([double dagger]) Rd
            6.20 +b
COL-A02                                 5.29 ([double dagger]) Rd
                                        3.47 ([double dagger]) +b

                      [R.sup.2] % var explained

QTL-chrom   B[C.sub.1]   B[C.sub.2]   B[C.sub.2][S.sub.1]


LEN-c14                                       6.3
LEN-1-c3                                     10.5
LEN-2-c3       14.8
LEN-c5         14.4
LEN-c6                       5.3
LEN-1-c25                                     6.1
LEN-2-c25                    7.6
LEN-c23                      5.4
LEN-c10                      5.8
LEN-c20                      4.8
LEN-1-c26                   13.4              7.9
LEN-2-c26                                     6.7
LEN-A01                     12.0             10.9
LEN-c18                      9.7
LEN-D02                      3.8

Uniformity Index

UNI-c14                                       4.8
UNI-DO8                      3.1
UNI-c20                      8.7             10.6
UNI-c18                     10.7             17.3
UNI-AO3        12.5
UNI-NL5        17.9


STR-c3         16.2
STR-1-c5       21.3
STR-2-c5                                      4.4
STR-c25                      6.4
STR-c16                                       7.6
STR-1-c23                    5.4
STR-2-c23      12.2         10.0              7.8
STR-AO1                                       5.0
STR-1-c18                                     6.7
STR-2-c18                   11.8
STR-A03                      5.6
STR-D02                      8.0


ELO-c15        10.0
ELO-c17        16.7
ELO-c22        13.0
ELO-DO8                      5.8             17.2
ELO-c9                                       12.5
ELO-c23                      8.8
ELO-c10                      9.2
ELO-1-c20                                     8.3
ELO-2-c20                   12.1
ELO-NL8        21.2

Micronaire (IM), maturity ratio (MR) and fineness (H/[H.sub.s])

FIN-1-c3                    11.3
                             7.0             10.5
FIN-2-c3        8.9
FIN-c4                       8.2
FIN-c22                      6.9
FIN-1-c5       12.5
FIN-2-c5                                     22.2
FIN-1-D08                                     7.9
FIN-2-D08      11.7
FIN-3-D08                                     5.9
FIN-1-c6       20.5
FIN-2-c6                                     15.1
               17.4                           8.8
FINc-c6        21.5
FIN-c25                      7.6
FIN-c16                                      16.5
FIN-c9                      29.1
FIN-1-c10      14.3
FIN-2-c10                                     4.6
FIN-c20                                       5.8
FIN-c18        16.9                           7.5
FIN-A02        15.8
FIN-D03                                      17.6

Color (reflectance, Rd, and yellowness, +b)

COL-c3                                        5.6
COL-c17                     12.8
COL-1-D08                    8.1
COL-2-D08                                     6.3
COL-1-c6                    39.9
COL-2-c6       15.7
COL-c25        13.7                           8.5
               14.9          9.4             14.1
COL-c16                      4.8
COL-c9          8.7                          15.6
               10.3         38.2
COL-c23                                       7.9
COL-c10                                       8.3
COL-c26                     40.4              7.0
COL-A01                      4.9
COL-c18                     10.4              6.7
COL-A02                                       8.2
COL-D03        12.7

            Genetic effect
QTL-chrom     Gh parent                Ref              Note ([dagger])


LEN-c14         -0.70
LEN-1-c3        -0.90
LEN-2-c3        -1.50
LEN-c5           1.60        ([section])                       1
LEN-c6          -1.20
LEN-1-c25       -0.80
LEN-2-c25       -1.42
LEN-c23         -1.30
LEN-c10         -1.20
LEN-c20         -1.10
LEN-1-c26       -2.10
LEN-2-c26       -0.70        ([section])                       2
LEN-A01         -1.80        ([paragraph])                     3
LEN-c18          1.80
LEN-D02          1.70

Uniformity Index

UNI-c14         -0.50        ([paragraph])                     4
UNI-DO8          3.30
UNI-c20         -1.50
UNI-c18          2.10
UNI-AO3         -1.00        ([section])                       5
UNI-NL5          1.13


STR-c3          -2.20        ([section])                       6
STR-1-c5        -2.80
STR-2-c5         0.90
STR-c25         -2.30        ([paragraph])(#)                  7
STR-c16         -1.10
STR-1-c23       -2.20
STR-2-c23       -2.90        ([paragraph])                     8
STR-AO1         -0.76        ([paragraph])                     9
STR-1-c18        0.97
STR-2-c18        3.43
STR-A03         -1.97        ([paragraph])                    10
STR-D02          2.85


ELO-c15          0.25        ([paragraph])                    11
ELO-c17         -0.33
ELO-c22         -0.29
ELO-DO8          0.41
ELO-c9           0.28        ([double dagger])                12
ELO-c23          0.60        ([paragraph])                    13
ELO-c10         -0.50        ([paragraph])                    14
ELO-1-c20       -0.22
ELO-2-c20       -0.51
ELO-NL8         -0.35

Micronaire (IM), maturity ratio (MR) and fineness (H/[H.sub.s])

FIN-1-c3         0.07        ([section])([paragraph])         15
FIN-2-c3        17.8
FIN-c4          20.3         ([paragraph]                     16
FIN-c22          0.41        ([paragraph]                     17
FIN-1-c5       -21.6
FIN-2-c5       -25.6
FIN-1-D08       -8.6
FIN-2-D08       -0.37
FIN-3-D08       12.9
FIN-1-c6         0.49
FIN-2-c6        19.7
FINc-c6        -15.2
FIN-c25         21.3
FIN-c16         15.0         ([paragraph]                     18
FIN-c9         -46.5         ([paragraph]                     19
FIN-1-c10        0.40
FIN-2-c10       10.2
FIN-c20          6.9         ([paragraph]                     20
FIN-c18         -0.09
FIN-A02         -0.08
FIN-D03        -14.0         ([paragraph]                     21

Color (reflectance, Rd, and yellowness, +b)

COL-c3          -0.29
COL-c17          3.03        ([paragraph]                     22
COL-1-D08        2.88
COL-2-D08        0.91
COL-1-c6        -2.51
COL-2-c6        -0.88        ([paragraph]                     23
COL-c25          2.60
                -0.86        ([paragraph]                     24
COL-c16         -2.25
COL-c9           1.57
COL-c23          1.04
COL-c10          0.36
COL-c26         -2.44
COL-A01         -1.83        ([paragraph]                     25
COL-c18          3.52
COL-A02          0.90        ([paragraph]                     26
COL-D03          2.46

([dagger]) QTL denomination, marker locus, and position
reference relatively (= when similar) to corresponding QTL:
1-Lf-2(t)-BNL3029 (+50 cM), 2-Lf-3(t)-C59E1 (=), 3-LGA01-pAR338 (=),
4-Chr14G1147 (+25 cM), 5-LGA03-pAR570a (=), 6-Sf-1(t)-BNL3259
(+20 cM), 7-Chr25-pGH309 (+10 cM), 8-Chr23-pAR209 (=),
9-LGA01-pAR238 (+50 cM), 10-LGA03-pAR570a (=), 11-Chr15-pAR400b
(=), 12-Chr9-accacc6 (+40 cM), 13-Chr23-P12-12 (+20 cM),
14-Chr10-pVNC163b (-30 cM), 15-Ff-3(t)-P09-53 LGA06-pGH364 (=),
16-Chr04-pAR138 (-40 cM), 17-LGD07-A1152 (=), 18-LGD01-G1158a (=),
19-Chr09-P10-62 (-80 cM), 20-LGD04-pAR430 (+30 cM), 21-LGD03-pAR248
(=), 22-Chr17-pGH861 (-40 cM), 23-Chr06-A1208b (=), 24-Chr25-pGH309
(=), 25-LGA01-G1125b (=), 26-LGA02-pGH232b (-40 cM).

([double dagger]) Refers to QTLs also detected by simple
marker analysis (P < 0.01)

([section]) Kobel et al. (2001).

([paragraph]) Paterson et al. (2003).

(#) Jiang et al. (1998).

([double dagger])  Mei et al. (2004)

Table 3. Synthesis of 19 targeted regions mapped on 15 different
chromosomes. The targeted intervals are defined as situated between
the two loci flanking the QTL peak LOD position at a 1 LOD confidence
interval and thus identify the segment of the G. barbadense
donor genome for possible introgression into a G. hirsutum genetic
background. All QTLs for fiber quality traits are of a "positive"
contribution from the G. barbadense allele, except for "negative"
cases indicated in parentheses.

                            Chromosome          Target
Chromosome                    length           interval


C14                             197             28-57
c3                              153             32-67
c4                              190            102-118
c22                             139            112-139
c5                              360             78-101
c6                              296            137-144
c25                             183             44-73
c16                             168             65-117
c23                             173             45-66
c10                             192              0-21
c20                             268             88-161
c26                             195             67-143
A01                             233             16-54
c18                             158             32-46
A03                             271            209-234
Total carrier chromosomes      3176      Total target regions

Chromosome                   size    Trait


C14                           29     Length
c3                            35     Length, fineness
                              48     Length, strength, fineness
c4                            16     Fineness
c22                           27     Fineness
c5                            23     Strength
c6                             7     Length, fineness
c25                           29     Length, strength
c16                           52     Strength, fineness, color
c23                           21     Strength (elongation-, color-)
                              22     Length, strength
c10                           21     Fineness
                              42     Length, fineness, color
c20                           73     Elongation, fineness
c26                           76     Length (color-)
A01                           38     Length
                              38     Strength
c18                           14     Fineness
A03                           25     Strength, uniformity
Total carrier chromosomes    636


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Jean-Marc Lacape, * Trung-Bieu Nguyen, Brigitte Courtois, Jean-Louis Belot, Marc Giband, Jean-Paul Gourlot, Gerard Gawryziak, Sandrine Roques, and Bernard Hau

J.-M. Lacape, T.-B. Nguyen, B. Courtois, M. Giband, J.-P. Gourlot, G. Gawryziak, S. Roques and B. Hau, CIRAD, Avenue Agropolis, 34398 Montpellier, Cedex 5, France: J.-L. Belot, CIRAD, Projet Cone Sud, SHIS/QI15, Conjunto 15. Casa 3, Lago Sul, 71635-350, Brasilia DF, Brazil. Received 26 Feb. 2004. * Corresponding author (
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Title Annotation:Crop Breeding, Genetics & Cytology
Author:Lacape, Jean-Marc; Nguyen, Trung-Bieu; Courtois, Brigitte; Belot, Jean-Louis; Giband, Marc; Gourlot,
Publication:Crop Science
Geographic Code:1USA
Date:Jan 1, 2005
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