Journal of Heredity Advance Access originally published online on April 13, 2005
Journal of Heredity 2005 96(4):441-444; doi:10.1093/jhered/esi052
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Brief Communication |
Mapping Quantitative Trait Loci Associated with Leaf and Stem Pubescence in Cotton
From CIRAD (UMR1096), TA 70/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
Address correspondence to J.-M. Lacape at the address above, or e-mail: marc.lacape{at}cirad.fr.
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Abstract |
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Leaf pubescence in cotton have a potential for insect pest management. Varying degrees of leaf trichome density in Gossypium species and cultivars have been associated to a series of five genes, referred to as t1–t5. We used two segregating interspecific G. hirsutum x G. barbadense backcross populations developed in our laboratory to assess qualitatively and quantitatively leaf and stem pubescence. QTL analyses were performed using simple and composite interval mapping. Based on both types of measurements and under both types of QTL analyses, nine QTLs met permutation-based thresholds. The nine QTLs mapped to four different chromosome regions. Highest LOD values corresponded to the QTLs detected on c6 (four colocalized QTLs) and on D03 (two QTLs) for which the higher pubescence in the progeny derived from the pubescent G. hirsutum parent alleles. Conversely, on c17 (one QTL) and A01 (two QTLs), the G. hirsutum parental alleles affected negatively pubescence. These results combined with another published study confirm (1) the location in a center region of chromosome 6 of the t1 locus as a major locus/gene determining leaf pubescence, and (2) additional genes located on seven additional chromosomes have been shown to impart trichome density either positively or negatively. The existence of a high density of PCR-based loci in most of the regions identified as harboring leaf pubescence QTLs, particularly that on chromosome 6, will facilitate future efforts for map-based cloning.
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Introduction |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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Several plant characters in cotton (Gossypium hirsutum L.) have a potential for insect pest management. The degree of hair or trichome density on the leaves of Gossypium species and cultivars is related to varying degrees of resistance/susceptibility to sucking pests, like whiteflies (Meagher et al. 1997), aphids, and jassids, or to the boll weevil (reviewed in Thomson and Lee 1980; Percy and Kohel 1999). Leaf pubescence may be measured either qualitatively (ratings) or quantitatively (trichome counts) (Bourland et al. 2003; Wright et al. 1999). Though Bourland et al. (2003) emphasized some within-plant variation of leaf pubescence, cotton cultivars are usually described as either smooth, lightly hairy, hairy, very hairy, or pilose.
Prior to 1985, a series of major genes (H1, H2, H6, Sm2, Sm1-smooth stem, 
-smooth leaf, Sm3) and modifier genes (H3-stem, H4-lower leaf surface, H5-length) of diverse origins (G. hirsutum, G. barbadense, G. raimondii, G. tomentosum, G. armourianum) influencing pubescence had been identified (Endrizzi et al. 1984). Because of the presumable allelic relationships between some of these loci, genes affecting plant trichome density and pattern were grouped into five major loci, namely t1 to t5. Corresponding allelic series were also renamed, T1, 
and 
as in the example of t1 (Lee 1985). The t1 locus is known to be part of cytological group IV on chromosome 6 (Percy and Kohel 1999), as originally described by Knight (1952).
Wright et al. (1999) studied different F2 populations derived from crosses between G. hirsutum (cultivars Empire B2, Empire B3, Empire B2b6, S295) and G. barbadense (Pima S7) with RFLP markers. The parents, initially chosen because they carried different bacterial resistance genes, also showed contrasted pubescence. Wright et al. (1999) detected four QTLs that impart leaf and stem pubescence. Apart from a leaf pubescence QTL with a strong phenotypic effect (positive contribution of the G. hirsutum allele for pubescence) that mapped on chromosome 6 and was inferred to correspond to the t1 locus, three other leaf pubescence QTLs were detected on chromosomes 1, 7, and 25. A supplementary QTL on c23 was associated with trichome density on the stem. These authors hypothesized that the four latter additional QTLs corresponded to the t2 to t5 loci.
Using a combined RFLP-SSR-AFLP linkage map (Nguyen et al. 2004) and different backcross populations stemming from an interspecific G. hirsutum x G. barbadense cross, we studied and mapped QTLs for fiber-related traits (Lacape et al. 2005). Based on complementary observations of pubescence made on the same plant material, we hereby describe the mapping of QTLs for leaf and stem pubescence.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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The plant material has been described in Lacape et al. (2003). It was grown in Montpellier and consists of 75 BC1 plants studied in 1999 under greenhouse conditions and 200 BC2 plants studied in 2000 under field conditions. The two backcross populations stem from an interspecific cross between G. hirsutum cv. Guazuncho 2 and G. barbadense cv. VH8-4602, followed by backcrossing using G. hirsutum as the recurrent parent.
Leaf (in 1999 and 2000) and stem (in 1999) pubescence of individual BC1 and BC2 plants were assessed by two methods. In 1999 (BC1 population), a qualitative visual scoring of the pubescence of the lower surface of the leaves (LS1) or of the stem (SS1), was conducted using a five-grade (0–4) scale and an averaged value over two persons. Leaf trichome density was quantitatively measured in 1999 and 2000 by counting the number of trichomes per unit area of the lower surface of a leaf (LD1 and LD2 for BC1 and BC2, respectively). Trichomes present on the lower surface of circular leaf punches of 28.27 mm2 (6 mm diameter) were counted using a magnifying glass. Two samples per plant were taken from the right and left sides of the midvein (near the confluence of the two subtending large veins) of two young fully expanded leaves, that is, subtending the fourth or fifth node initiated on the main stem or on a vegetative branch.
Pearson correlations coefficients were calculated for all combinations of the three traits measured in 1999. Genomic DNA extraction, molecular analysis, and linkage map construction were undertaken as described in Lacape et al. (2003). The BC1 and BC2 maps comprised 1160 and 511 loci respectively, of which we used 595 and 341 well-distributed loci (Lacape et al. 2005) for the two series of individual QTL analyses, after excluding clustered loci. QTL analysis was performed using the computer software QTL Cartographer 1.13 (Basten et al. 1999) through simple marker analysis (SMA), interval mapping, and composite interval mapping (CIM). Permutation-based LOD thresholds were calculated (1000 permutations). LOD thresholds were 3.9, 4.0, and 3.2 for SS1, LS1, and LD1, respectively, and 3.5 for LD2. QTL positions as determined from CIM were checked for agreement with the SMA results. For ease of the representations, LOD graphs drawn with the MapChart software (Voorrips 2002) were reported on the BC1 map as a backbone map, after projecting additional BC2 loci (Lacape et al. 2005).
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Results and Discussion |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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Figure 1 represents the frequency distribution of the phenotypic values over the 75 BC1 and 200 BC2 plants. The two parents, G. hirsutum and G. barbadense, are clearly differentiated for all pubescence-related measurements. Trichome density displays a normal distribution in both the BC1 and BC2 populations. Qualitative scores (leaf and stem in BC1, LS1, and SS1) show distributions with a trend to bimodality. The average trichome density in the BC1 population (LD1) is 1.29 trichomes per mm2 (range 0.02–3.17), and 30% of the BC1 plants have a higher trichome density than that of the pubescent parent (Guazuncho 2), that is, 1.56 trichomes per mm2. The average trichome density of the BC2 plants is 1.34 (range 0.07–3.08), and 40% of the BC2 plants have a higher density than that of Guazuncho 2.
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The correlations between the three traits measured in 1999 (BC1) were all highly significant (LS1/SS1 r2 = 0.77**, LS1/LD1 0.56**, SS1/LD1 0.50**), thus confirming the validity of qualitative visual scorings as a fast mean for the estimation of leaf pubescence of cotton cultivars (Bourland et al. 2003).
Seven QTLs (Table 1, Figure 2) met permutation-based thresholds in the BC1 population, and two in the BC2 population. The nine QTLs mapped on four different chromosomes, c6 (four QTLs, one for each trait studied), c17 (one QTL for LS1), A01 (two QTLs: one for LD1 and one for LD2), and D03 (two QTLs: SS1 and LS1).
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The two strongest QTLs (LD2 on c6 of LOD 11.89 and SS1 on D03 of LOD 13.52), each explaining 43% of the phenotypic variance, were related to a decrease in pubescence caused by the G. barbadense (glabrous parent) alleles. In addition, the QTL on chromosome 6 was consistently detected using both the qualitative and quantitative types of measurements, and in both generations analyzed: for leaf score in BC1 (LOD 9.14), leaf density in BC1 and BC2 (LOD 11.89 and 6.30, respectively), whereas a QTL for stem score, with a below-threshold LOD of 3.37, was detected in the same region (Figure 2). The location of the QTLs within a central region of chromosome 6 (near the AFLP locus E2M5_182 and SSR locus BNL4108), at the same place as a QTL reported by Wright et al. (1999), fits the description of the t1 locus, which is situated near the centromeric region of the c6 (linkage group IV) cytomorphological linkage map (Percy and Kohel 1999). Two dense genetic maps of tetraploid cotton were recently developed (Nguyen et al. 2004; Rong et al. 2004). In Rong et al. (2004), the corresponding region of c6 is flanked by the locus BNL1153, as locus pGH312 cited in Wright et al. (1999) is reported on a different chromosome in Rong et al. (2004), and locus P1-34; it encompasses 32 cM and is rich of 35 loci. In Nguyen et al. (2004), a region of 38 cM, between markers BNL1440 and BNL4108, comprises 24 loci. A marker density of over 1 locus/cM could facilitate the fine mapping and eventual cloning of this locus. The strong QTL for SS1 (LOD 13.52), corresponding to a decrease in stem pubescence brought by the G. barbadense allele and measured in the BC1 was located at the bottom of linkage group D03 near locus A1197. A nearly significant QTL (LOD 3.5) for LS in the BC1 was also detected at the same location.
Two other significant QTLs were associated with an "unexpected" increase in pubescence caused by the presence of the G. barbadense (glabrous parent) alleles. A QTL for leaf trichome density was detected at the same location on linkage group A01 in both the BC1 (LOD 4.5) and BC2 (LOD 4.91) populations (Table 1). This region of linkage group A01 (140–170 cM) is covered with 35 loci, including 14 SSRs, on our map (Nguyen et al. 2004; and http://tropgenedb.cirad.fr). The QTL for LS in the BC1 detected at the top of chromosome 17 (LOD 3.91) has an LOD slightly inferior to the permutation-based threshold (LOD 4.03). Finally, a QTL of lower LOD value (LOD 2.54) was detected for LD (decrease in pubescence by the G. hirsutum allele) in the BC2 population at the bottom of chromosome 1. This location is in agreement with that of a QTL (named chr1-QLP2) reported by Wright et al. (1999) for mature leaf trichome density. Nevertheless, the effect of the G. hirsutum allele is in opposition in the two studies.
Combining our QTL mapping data with those of Wright et al. (1999), both studies being based on interspecific G. hirsutum x G. barbadense populations, eight pubescence QTLs have been identified on eight different chromosomes, c1, c6, c7, A01, c17, c23, c25, and D03. Four QTLs are inferred to map on each of the A and D subgenomes. The only QTL in common, mapped on chromosome 6, is the strongest one in both studies. For three of the eight QTLs (c1, c6, and D03) the high pubescence derives from the presence of G. hirsutum (pubescent parent) alleles, and for five of them from the presence of G. barbadense (glabrous parent) alleles. This observation supports the possibility that new allele combinations may be obtained in interspecific progenies of mosaic genome constitution (Tanksley et al. 1996) and is illustrated by the fact that the range of phenotypic variation within BC1 and BC2 populations overpasses that of the parental range (Figure 1) in our study. Genetic hypotheses of epistasis and/or complementary actions could cause the phenotypic variation of the offspring to exceed the parental range. The pubescence of the aerial parts of cotton plants confirms a complex genetic control, probably involving more than the five t1–t5 loci. Of these five loci, only t1 on c6 and its homoeologous t2 (not detected in our study) on c25, have strong candidate QTLs positioned on a reasonably dense genetic map. Similarly multilocus or multi-QTL models were proposed in Gossypium for the fiberless phenotype (Turley and Kloth 2002), or in Arabidopsis thaliana for leaf trichome number (Larkin et al. 1996).
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Footnotes |
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Corresponding Editor: Prem Jauhar
Received June 29, 2004
Accepted January 5, 2005
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References |
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TopAbstractIntroductionMaterials and MethodsResults and DiscussionReferences |
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