Genetica (2010) 138:1171–1179 DOI 10.1007/s10709-010-9507-3

Genetic effects of individual in cotton cultivars detected by using substitution lines as genetic probes

Jixiang Wu • Johnie N. Jenkins • Jack C. McCarty • Sukumar Saha

Received: 8 October 2009 / Accepted: 29 September 2010 / Published online: 26 October 2010 Ó US Government 2010

Abstract Determination of chromosomes or chromo- Keywords Cotton Á Chromosome substitution line Á some arms with desirable in different inbred lines Genetic effects and/or crosses should provide useful genetic information for crop improvement. In this study, we applied a modified additive-dominance model to analyze a data set of 13 cotton chromosome substitution lines and their recurrent Introduction parent TM-1, five commercial cultivars, and their 70 F2 hybrids. The chromosome additive and dominance vari- Chromosome substitution (CS) lines are developed through ance components for eight agronomic and fiber traits were the replacement of a whole chromosome or chromosome determined. On average, each chromosome or chromosome arm in the recurrent parent by the corresponding chromo- arm was associated with 6.5 traits in terms of additive and/ some or chromosome arm from the donor parent. There- or dominance effects. The chromosomes or chromosome fore, CS lines, which are divergent for one chromosome or arms, which contributed significant additive variances for chromosome arm from the recurrent parent and are the the traits investigated, included 2, 16, 18, 25, 5sh (short same for the remaining chromosomes, are valuable for arm), 14sh, 15sh, 22sh, and 22Lo (long arm). Chromosome detecting desirable chromosomes associated with quanti- additive effects were also predicted in this study. The tative traits of importance. results showed that CS-B 25 was favorably associated with The CS lines in wheat have been used to detect alleles several fiber traits, while FM966 was favorably associated on specific chromosomes responsible for grain yield and with both yield and fiber traits with alleles on multiple quality (Law 1966; Zemetra et al. 1986; Al-Quadhy et al. chromosomes or chromosome arms. Thus, this study 1988; Zemetra and Morris 1988; Mansur et al. 1990; Berke should provide valuable genetic information on pure line et al. 1992a, b; Yen and Baenziger 1992; Yen et al. 1997; development for several improved traits such as yield and Shah et al. 1999; Campbell et al. 2003, 2004). For example, fiber quality. chromosomes 3 and 6A from cultivar ‘Wichita’ were determined to have major quantitative trait loci (QTLs) associated with increased grain yield and kernel weight J. Wu Department of Plant and Soil Sciences, Mississippi State when present in the ‘Cheyenne’ background, while University, Mississippi State, MS 39762, USA ‘Cheyenne’ had major QTLs on 3 and 6A associated with decreased grain yield and kernel weight when present in & J. N. Jenkins Á J. C. McCarty ( ) Á S. Saha the ‘Wichita’ background (Berke et al. 1992a). The USDA-ARS, Crop Science Research Laboratory, P. O. Box 5367, Mississippi State, MS 39762, USA approach regarding development of interspecific chromo- e-mail: [email protected] some substitution in cotton Gossypium hirsutum L. was outlined by Endrezzi (1963) and several cotton chromo- Present Address: some substitution lines were developed and evaluated J. Wu Plant Science Department, South Dakota State University, (Endrezzi 1963; Kohel et al. 1977; Ma and Kohel 1983). Brookings, SD 57007, USA Seventeen cotton chromosome substitution lines were 123 1172 Genetica (2010) 138:1171–1179 recently developed and released through replacement of a certain chromosomes or chromosome arms of five elite chromosome or a chromosome arm in TM-1 (G. hirsutum, cultivars which were from different cotton breeding com- the recurrent parent) by the respective chromosome or panies. A new chromosome genetic model (Wu et al. 2006) chromosome arm from 3–79 (G. barbadence L.) (Stelly was employed and the results from this study should pro- et al. 2005). Since each of these chromosome substitution vide valuable genetic information to help breeders in the lines contained chromosome or chromosome arm from improvement of economically important traits. G. barbadence, they were called CS-B lines. Each CS-B line is iso-genetic to the recurrent parent TM-1 with only one chromosome or chromosome arm divergent. With such Materials and methods a high level of uniformity in the recurrent genetic back- ground, chromosomes associated with traits of importance Experiments and data collection in cotton have been detected through the comparative analyses. For example, chromosomes 16 and 18 from 3–79 Five elite cultivars, ‘Deltapine 90’ (DP90); ‘Sure-Grow in TM-1 background were associated with reduction in 747’ (SG747); ‘Phytogen 355’(PSC355); ‘Stoneville 474’ cotton yield, chromosome 25 with reduced micronaire and (ST474); and ‘FiberMax 966’(FM966), representing increased fiber length and strength compared with TM-1, germplasm of the major cotton seed breeding companies in chromosome arms 22sh and 22Lo with increased lint per- the USA, were crossed as females with 13 CS-B lines centage; and chromosome arm 5sh with high flowering rate (Stelly et al. 2005), and TM-1(Jenkins et al. 2006). These during the primary growing season (Saha et al. 2004, 2006; chromosome substitution lines include 5 subgenome A and Jenkins et al. 2006, 2007; McCarty et al. 2006). Investi- 8 subgenome D chromosomes or chromosome arms from gation of these cotton lines when crossed with commercial 3–79 substituted into TM-1, the recurrent parent. cultivars is another interesting issue so that the merit of The 70 crosses were made at Mississippi State, MS, in these CS-B lines can be determined for future cotton summer 2002. The F1 seeds were sent to a winter nursery in genetic and breeding studies (Jenkins et al. 2006, 2007). Tecoman, Mexico, and self pollinated to produce F2 seeds. The development of a set of CS lines was very time- The resulting 70 F2 hybrids, five cultivars, 13 CS-B lines, consuming both in wheat and cotton. As reported in many and the recurrent parent, TM-1, were grown with a ran- previous studies mentioned above, the CS lines have been domized complete block design in four environments in widely used to dissect genetic associations of traits of 2003 and 2004 at the Plant Science Research Center at importance with the substituted chromosomes; however, Mississippi State, MS (33.4 N, 88.8 W). For detailed these results were mainly focused on the genetic expres- information, readers may refer to the reports by Jenkins sions of substituted chromosomes in the recurrent parent et al. (2006, 2007). Traits analyzed in this study included background. Additional ways to use the CS lines in lint yield (LY, kg/ha), seed cotton yield (YLD, kg/ha), boll genetics and breeding studies should add more values to weight (BW, g), lint percentage (LP, %), micronaire the CS lines that have been developed. A modified addi- (MIC), elongation (EL, %), 2.5% fiber span length (SL, tive-dominance (AD) genetic model proposed by Wu et al. mm), and fiber strength (T1, kNm/kg). (2006) offers an opportunity to detect desirable genetic factors associated with chromosome in specific inbred lines Genetic models and data analyses (cultivars) when they are crossed to a CS line and the current parent. For example, chromosome 25 of FM966 Our previous modified AD model (Wu et al. 2006) was was associated with improved fiber strength and fiber developed with the intention to detect individual chromo- length (Wu et al. 2006). This modified AD model has been some effects in lines crossed with CS-B lines, which were employed to dissect QTLs in transgenic cotton (Wang et al. considered genetic probes. Since this modified model (Wu 2007; Zhang et al. 2008). Thus, the CS lines can be et al. 2006) requires a data set including a CS-B line, extensively utilized as ‘‘probes’’ in the detection of favor- recurrent parent, several cultivars (lines), and the F2 able alleles associated with traits of importance in different hybrids between the cultivar and a CS-B line and TM-1, inbred lines. thirteen data sets were separately analyzed because there In previous studies (Jenkins et al. 2006, 2007), the were 13 CS-B lines in our study. Thus, each of our data sets classic AD genetic model was employed to investigate involved a specific CS-B parent line, the TM-1 parent line, general and specific combining ability when 13 CS-B lines 5 cultivars, and 10 F2 hybrids between the 5 cultivars and were crossed with five elite cultivars. However, specific CS-B line and TM-1. Two types of genetic models were chromosome effects of these elite cultivars could not be used to analyze each of 13 data sets. First the modified AD detected by the classic AD genetic model. In the present genetic model with G 9 E interaction (Wu et al. 2006) was study, a focus on determining the specific effects related to used. Nine variance components are included in this model 123 Genetica (2010) 138:1171–1179 1173 and the corresponding proportions of variance components contributions for seed cotton yield, lint cotton yield, mi- to the phenotypic variance were calculated based on F1 cronaire, and fiber length (31, 13, 17, and 11%, respec- 2 2 2 generation: VA1 = 2rA1,VD1 = rD1,VA2 = 2rA2,VD2 = tively). Chromosome 18 had additive contributions for 2 2 2 2 rD2;VAE1 = 2rAE1,VDE1 = rDE1,VAE2 = 2rAE2, micronaire (30%); 25 for boll weight, micronaire, elonga- 2 2 VDE2 =rDE2,Ve = re, and VP = VA1 ? VD1 ? VA2 ? tion, length, and strength (22, 26, 18, 17, and 47%, VD2 ? VAE1 ? VDE1 ? VAE2 ? VDE2 ? Ve, where, A1 respectively). Chromosome arm 5sh had additive contri- and D1 are additive and dominance effects of the target butions for boll weight, micronaire, and fiber length (29, chromosomes or chromosome arms; A2 and D2 are addi- 24, and 15%, respectively). Chromosome 14sh had additive tive and dominance effects from the remaining 25 chro- contributions for boll weight, fiber elongation, and fiber mosomes; and AE1, DE1, AE2, and DE2 are the G 9 E length (47, 24, and 16%, respectively). Chromosome 15sh effects regarding A1, D1, A2, and D2 effects (Wu et al. 2006). had additive contributions for fiber length and fiber Second the classic AD genetic model (Wu et al. 1995; strength (24 and 16%, respectively); 22sh for lint per- Jenkins et al. 2006; McCarty et al. 2006; Saha et al. 2006) centage, micronaire, elongation, and fiber length (59, 38, was used. 16, and 55%, respectively). Chromosome 22Lo had addi- The variance components for both genetic models were tive contributions for lint percentage, boll weight, micro- obtained by the minimum norm quadratic unbiased esti- naire, elongation, and fiber length (42, 42, 44, 31, and 24%, mation (MINQUE) (Rao 1971; Searle et al. 1992) with respectively). each prior value set as 1.0 (Zhu 1994). Genetic effects were Compared to the proportional additive and dominance predicted by the adjusted unbiased prediction (AUP) variance components by the classic AD genetic model approach (Zhu 1993). A jackknife, a re-sampling tech- (data not shown), the proportional chromosome additive nique, was applied to calculate the standard error (SE) for and dominance variance components (Table 1) by the each parameter by removal of each block within each of modified AD genetic model were generally lower. It is not four environments. In this study, non-pseudo-value based surprising because the remaining chromosomes could also estimated values rather than pseudo-value based estimates make additive and/or dominance contributions to each trait. (Miller 1974) were used to calculate the standard error (SE) for each parameter (Wu et al. 2008). The reason was that Chromosome additive effects for agronomic and fiber non-pseudo-value based jackknife method has a higher traits power over the other method with comparable Type I error. There were four replications in each of four environments, Chromosome additive and dominance variance compo- thus the degrees of freedom were 15. Approximate t-tests nents in Table 1 both contributed to the overall genetic then were applied for detecting the significance of each variance. Cotton breeders may also be interested in chro- parameter. One- and two-tailed t-tests were used to test the mosome additive effects in specific parents and/or domi- significance of the variance components and the genetic nance effects in specific crosses. Using the modified AD effects, respectively. All data analyses were conducted by model allowed us to predict the additive and dominance using programs written in C ?? (Wu et al. 2003, 2006). effects related to 13 chromosomes or chromosome arms in the five cultivars, TM-1 and a specific CS-B line and their crosses. However, due to a large volume of results, only the Results additive effects for specific chromosomes or chromosome arms that made a large contribution to the phenotypic Variance components for 13 chromosomes variance for each trait are presented (Tables 2 and 3) or chromosome arms because pedigree breeding attempts to accumulate additive effects. Nine variance components for each of eight quantitative Significant positive additive effects for lint percentage traits were determined for each of 13 data sets; however, from alleles on arms 22sh and 22Lo were detected in only additive and dominance variance components con- cultivars SG747, PSC355, ST474, FM966, and CS-B22sh tributed by 13 chromosomes or chromosome arms for eight and CS-B22Lo. However, negative additive effects from agronomic and fiber traits are described in Table 1.On alleles on the same two chromosome arms were detected in average, each chromosome or chromosome arm was TM-1 and DP90 (Table 2). Significant additive effects for associated with two agronomic and a total of five traits in boll weight from alleles on chromosome 25 and 5sh, 14sh, terms of additive effects and dominance effects, respec- and 22Lo were present. In these four CS-B lines, and tively (Table 1). had additive contributions cultivars DP90, PSC355 and ST474 the chromosome for micronaire, elongation, and fiber strength (28, 36, effects were negative. However, alleles on these same and 21%, respectively). Chromosome 16 had additive chromosomes or arms were significant and positive for 123 1174 Genetica (2010) 138:1171–1179

Table 1 The proportional additive (A1) and dominance (D1) components due to each chromosome or chromosome arms for eight quantitative traits when 13 CS-B lines and TM-1 were crossed with five diverse cultivars Chromosome/arm LP BW YLD LY MIC EL SL T1

02 A1 0.00 0.00 0.00 0.00 0.28** 0.36** 0.07** 0.21** D1 0.00 0.02 0.05 0.03 0.05 0.05** 0.00 0.12** 04 A1 0.00 0.00 0.00 0.00 0.05* 0.04* 0.05** 0.01 D1 0.08** 0.06* 0.00 0.00 0.18** 0.16** 0.07** 0.07 06 A1 0.00 0.00 0.00 0.00 0.00 0.02** 0.00 0.00 D1 0.10** 0.00 0.00 0.00 0.08 0.14** 0.18** 0.15** 07 A1 0.00 0.00 0.00 0.00 0.13** 0.07** 0.00 0.00 D1 0.08** 0.19** 0.00 0.00 0.22** 0.01 0.15** 0.26** 16 A1 0.02 0.00 0.31** 0.13** 0.17** 0.06** 0.11** 0.02 D1 0.01 0.00 0.01 0.02 0.00 0.15** 0.00 0.02 17 A1 0.00 0.00 0.00 0.00 0.00 0.04* 0.06** 0.02* D1 0.14** 0.06* 0.00 0.00 0.12** 0.12** 0.01** 0.06** 18 A1 0.00 0.08** 0.08** 0.00 0.30** 0.09** 0.05** 0.03 D1 0.09** 0.00 0.00 0.00 0.01 0.00 0.00 0.16** 25 A1 0.00 0.22** 0.00 0.00 0.26** 0.18** 0.17** 0.47** D1 0.00 0.11** 0.00 0.00 0.07* 0.01 0.31** 0.03 05sh A1 0.00 0.29** 0.00 0.00 0.24** 0.09** 0.15** 0.02* D1 0.14** 0.00 0.00 0.00 0.06 0.00 0.32** 0.03 14sh A1 0.00 0.47** 0.00 0.00 0.02** 0.24** 0.16** 0.07** D1 0.01 0.01 0.01 0.01 0.00 0.00 0.05* 0.11** 15sh A1 0.00 0.00 0.00 0.00 0.00 0.03** 0.25** 0.12** D1 0.04** 0.07* 0.01 0.00 0.04 0.10** 0.00 0.07* 22sh A1 0.59** 0.06** 0.00 0.00 0.38** 0.16** 0.55** 0.01* D1 0.09** 0.17** 0.04 0.02** 0.02 0.02 0.05 0.03 22Lo A1 0.42** 0.42** 0.00 0.00 0.44** 0.31** 0.24** 0.00 D1 0.01 0.00 0.00 0.00 0.04 0.02 0.03 0.17** * Probability level B 0.05 and ** Probability level B 0.01 LP = lint percentage, BW = boll weight, YLD = seed cotton yield, LY = lint yield, MIC = micronaire, EL = elongation, SL = 2.5% span length, and T1 = fiber strength

TM-1 and FM966 (Table 2). Chromosome 16 in CS-B16 arms except 25 all increased micronaire. Alleles on specific had a negative additive effect on seed cotton yield chromosomes or arms in cultivars DP90, FM966, and TM- (-925 kg/ha); whereas, chromosome 16 in TM-1, SG747, 1 reduced micronaire where these same chromosomes in PSC 355, and FM966 had positive effects for seed cotton SG474, PSC355 (except 22Lo), and ST474 increased mi- yield (333, 197, 130, and 280 kg/ha, respectively) cronaire (Table 3). Chromosomes 2 and 25 and arms 14sh (Table 2). Chromosome 16 in CS-B16 also had a very and 22Lo in CS-B lines, DP90, and FM966 were associated negative additive effect on lint yield (-230 kg/ha); with additive effects to reduce elongation. These same whereas, chromosome 16 in TM-1, SG747, PS355, ST474, chromosomes and arms in TM-1, SG747, PSC355, and and FM966 had positive effects for lint yield (29, 61, 36, ST474 were associated with increased additive effects for 21, and 91 kg/ha, respectively). This indicated that chro- elongation (Table 3). Chromosome 25, 15sh, 22sh, and mosome 16 should have had a large positive or negative 22Lo affected fiber 2.5% span length. In CS-B25 and 15sh effect on lint percentage and boll weight because it had a fiber length was increased, whereas in CS-B22sh and 22Lo large positive or negative effect on seed cotton and lint fiber length was decreased. These four chromosomes or yield. Lint percentage and boll weight are important factors arms in PSC355 and FM966 contained alleles to increase for lint yield. fiber length. These same chromosomes or arms in SG747 For micronaire additive effects for three chromosomes and ST474 carried alleles which reduced fiber length. (2, 18, and 25) and three arms (05sh, 22sh and 22Lo) are Chromosome 25 and 15sh alleles from TM-1 carried alleles presented (Table 3). Alleles on individual chromosomes or which reduced fiber length; whereas, 22sh and 22Lo in

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Table 2 Selected chromosome based GCA (additive) effects for four agronomic traits by the modified AD model CS-B TM-1 DP90 SG747 PSC355 ST474 FM966

Lint percentage (%) 22sh 0.92** -3.14** -0.24** 0.53** 0.18** 1.02** 0.74** 22Lo 0.42** -2.33** -0.19** 0.40** 0.08** 0.97** 0.65** Boll weight (g) 25 -0.13** 0.26** -0.14** 0.00 -0.12** -0.12** 0.26** 05sh -0.16** 0.29** -0.18** 0.00 -0.10** -0.15** 0.29** 14sh -0.49** 0.53** -0.17** 0.03 -0.08** -0.23** 0.40** 22Lo -0.43** 0.5** -0.22** 0.01 -0.05** -0.18** 0.36** Seed cotton yield (kg/ha) 16 -924.9** 332.9** -7.9 196.9** 129.5** -6.4 279.8** Lint yield (kg/ha) 16 -230.4** 29.1** -8.1* 61.3** 36.4** 21.1** 90.5** * Probability level B 0.05 ** Probability level B 0.01 CS-B specifies specific chromosome or arm of 3–79 in TM-1 as listed in the first columns

Table 3 Selected chromosome based GCA (additive) effects for four fiber traits by the modified AD model CS-B TM-1 DP90 SG747 PSC355 ST474 FM966

Micronaire 02 0.16** -0.19** -0.13** 0.03** 0.05** 0.11** -0.03** 18 0.25** -0.25** -0.13** 0.00 0.08** 0.13** -0.07** 25 -0.32** 0.12** -0.08** 0.05** 0.11** 0.12** 0.00 05sh 0.19** -0.23** -0.13** 0.02* 0.08** 0.11** -0.05** 22sh 0.32** -0.31** -0.14** 0.01* 0.04** 0.13** -0.05** 22Lo 0.32** -0.30** -0.14** 0.03** 0.01 0.15** -0.07** Elongation (%) 02 -0.66** 0.51** -0.25** 0.52** 0.52** 0.09** -0.74** 25 -0.30** 0.28** -0.24** 0.41** 0.41** 0.06** -0.61** 14sh -0.37** 0.34** -0.32** 0.46** 0.44** 0.05** -0.60** 22Lo -0.55** 0.46** -0.29** 0.56** 0.46** 0.06** -0.70** 2.5% span length(mm) 25 0.56** -0.30** -0.03 -0.24** 0.00 -0.37** 0.38** 15sh 0.56** -0.33** -0.05 -0.24** 0.01 -0.51** 0.55** 22sh -1.36** 0.90** 0.10** -0.24** 0.17** -0.49** 0.92** 22Lo -0.55** 0.36** 0.04 -0.19** 0.16** -0.41** 0.59** Fiber strength (kNm/kg) 02 3.47** -6.09** 2.52** -6.07** 0.60** -3.42** 8.99** 25 12.42** -13.47** 3.44** -11.19** 0.46 -3.82** 12.15** * Probability level B 0.05 ** Probability level B 0.01 CS-B specifies specific chromosome or arm of 3–79 in TM-1 as listed in the first columns

TM-1 carried alleles which increased fiber length TM-1, SG747, and ST474 reduced fiber strength. The (Table 3). CS-B lines 2 and 25, and chromosomes 2 and 25 greatest increase in fiber strength was from chromosome 25 from DP90, PSC355, and FM966 carried alleles for in CS-B25 and FM966 with an increase of over 12 kNm/kg increased fiber strength. These same chromosomes from (Table 3).

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The additive effects were also predicted by the classic genetic factors associated with different chromosomes or AD genetic model for each of the 13 data sets. Selected chromosome arms regarding these agronomic and fiber additive effects comparable to Tables 2 and 3 are reported traits. in Tables 4 and 5, respectively. The additive effects pre- dicted by the classic AD model were whole genome based. Thus, it may be interesting to compare chromosome spe- Discussion cific additive effects and whole genome based additive effects. Chromosome arm 22sh in CS-B22sh and chromo- The use of chromosome substitution lines to dissect genetic some arm 22Lo in CS-B22Lo showed positive additive factors controlling quantitative traits of interest associated effects for lint percentage (Table 2), comparable to the with substituted chromosomes has long been investigated. same chromosome arms in cultivar ST474 and FM966. On Using the comparative method with the mixed model the other hand, CS-B22sh and CS-B22Lo showed whole approach, cotton CS-B lines have been investigated for genome negative additive effects for lint percentage, indi- different traits in the both parental lines and hybrids (Saha cating that other chromosomes in CS-B22sh and CS- et al. 2004, 2006; Jenkins et al. 2006, 2007; McCarty et al. B22Lo may also contribute additive effects to this trait. On 2006). Previous study was conducted with these CS-B lines the other hand, chromosome arm 22sh in TM-1 had similar crossed with different cultivars for both agronomic and additive effect to the whole genome based additive effect fiber traits (Jenkins et al. 2006, 2007). Herein we used the of TM-1 for lint percentage, indicating that the accumu- modified AD genetic model (Wu et al. 2006) with these lated additive effect contributed by the other chromosomes chromosome substitution lines as testers (‘‘probes’’) to was close to zero. Similar results could be observed for detect favorable genetic factors associated with a target other agronomic and fiber traits (Tables 2, 3, 4, and 5). chromosome or chromosome arm in different cultivars. In summary, both arms 22sh and 22Lo in FM966 had Based on our previous simulation study, we found that each additive effects associated with increased lint percentage; variance component was estimated without significant bias, chromosome 25 and arms 5sh, 14sh, and 22Lo in FM966 with the same genetic design used in this study. Also, the were associated with improved additive effects for boll predicted chromosome additive effects were correlated weight. Chromosome 16 in SG747 and FM966 was with the preset values (C0.90) although they were highly associated with improved additive effects for lint yield. related to the difference between a CS line and the recur- Chromosome 25, and arms 15sh, 22sh, and 22Lo in rent parent (Wu et al. 2006). Thus, this present study is not FM966 were associated with improved additive effects for only a further investigation for the data we have collected fiber length. Chromosomes 2 and 25 in FM966 were (Jenkins et al. 2006, 2007), but it is also a useful extension associated with improved additive effects for fiber for the utilization of CS lines to gain further information strength. Thus, cultivar FM966 has many favorable useful in cotton breeding and genetic studies.

Table 4 Selected whole genome based GCA (additive) effects for four agronomic traits by the classic AD model CS-B TM-1 DP90 SG747 PSC355 ST474 FM966

Lint percentage (%) 22sh -0.59** -2.99** -0.06 0.80** 0.40** 1.32** 1.11** 22Lo -0.83** -2.82** -0.05* 0.73** 0.25** 1.54** 1.19** Boll weight(g) 25 -0.04** 0.22** -0.19** 0.00 -0.17** -0.17** 0.35** 5sh -0.05** 0.21** -0.22** 0.00 -0.12** -0.19** 0.36** 14sh -0.23** 0.23** -0.14** 0.03** -0.05** -0.22** 0.38** 22Lo -0.19** 0.22** -0.20** 0.01 -0.02** -0.16** 0.33** Seed cotton yield 16 -758.5** -102.9** 17.6 288.3** 177.2** 17.7 360.6** LY 16 -343.2** -122.3** 2.1 142.5** 82.9** 49.0** 189.0** * Probability level B 0.05 ** Probability level B 0.01 LP = lint percentage (%), BW = boll weight (g), YLD = seed cotton yield (kg/ha), and LY = lint cotton yield (kg/ha) CS-B specifies a CS-B line where a specific chromosome or arm of 3–79 replaced TM-1 as listed in the first columns

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Table 5 Selected whole genome based GCA (additive) effects for four fiber traits by the classic AD model CS-B TM-1 DP90 SG747 PSC355 ST474 FM966

Micronaire 02 0.08** -0.12** -0.15** 0.03** 0.06** 0.13** -0.03** 18 0.13** -0.13** -0.14** -0.01 0.10** 0.14** -0.08** 25 -0.29** -0.03** -0.09** 0.07** 0.16** 0.16** 0.02* 5sh 0.08** -0.14** -0.14** 0.02* 0.09** 0.13** -0.05** 22sh 0.15** -0.14** -0.14** 0.01 0.04** 0.13** -0.04** 22Lo 0.16** -0.13** -0.14** 0.03** 0.00 0.15** -0.07** Elongation (%) 02 -0.53** 0.26** -0.32** 0.70** 0.70** 0.18** -0.99** 25 -0.27** 0.22** -0.41** 0.70** 0.68** 0.13** -1.05** 14sh -0.31** 0.25** -0.52** 0.73** 0.69** 0.10** -0.94** 22Lo -0.43** 0.28** -0.41** 0.80** 0.63** 0.12** -1.00** 2.5% span length(mm) 25 0.46** -0.08** -0.06 -0.32** 0.00 -0.47** 0.46** 15sh 0.40** -0.12** -0.07* -0.29** 0.03 -0.63** 0.68** 22sh -0.88** 0.24** 0.12** -0.24** 0.22** -0.50** 1.03** 22Lo -0.45** 0.09** 0.06* -0.21** 0.25** -0.50** 0.76** Fiber strength (kNm/kg) 02 1.19** -6.07** 3.37** -8.73** 1.73** -5.10** 13.61** 25 6.45** -7.70** 3.22** -12.37** 1.22** -3.74** 12.93** * Probability level B 0.05 ** Probability level B 0.01 CS-B specifies a CS-B line where a specific chromosome or arm of 3–79 replaced TM-1 as listed in the first columns

Our results showed that arms 22sh and 22Lo harbored FM966 were associated with longer fibers. Chromosomes 2 additive alleles for lint percentage. Chromosome 25 and and 25 of FM966 were associated with stronger fibers. arms 5sh, 14sh, and 22Lo were important contributors to Thus, it appears that cultivar FM966 has multiple chro- boll weight. Chromosome 16 was important for both seed mosomes favorably associated with several agronomic and cotton and lint yield. Chromosomes 2, 18, and 25, and arms fiber traits. 5sh, 22sh, and 22Lo were strongly associated with additive Although the CS-B lines, that are genetically different effects for micronaire. Chromosomes 2 and 25, and arms from TM-1 by one chromosome or chromosome arm, can 14sh, 22sh, and 22Lo had important factors associated with be used to detect the effects of specific chromosomes in additive effects for fiber elongation. Chromosome 25 and other germplasm lines or cultivars as showed in this study, arms 5sh, 14sh, 25sh, 22sh, and 22Lo had important we found that the predicted chromosome additive effects genetic factors associated with additive effects for fiber between some chromosomes or chromosome arms were length. Chromosomes 2 and 25 were two important con- correlated (Tables 2 and 3). For example, additive effects tributors to the additive variation in fiber strength. These for boll weight between chromosome 25 and chromosome results were in an agreement with our previous reports arm 5sh in seven parental lines were correlated (Table 2). (Saha et al. 2004, 2006; Jenkins et al. 2006, 2007). Similar results were found for micronaire and fiber elon- Cotton breeders are also interested in discovering gation (Table 3). Numerically, we observed that some of desirable chromosome additive effects in specific cultivars these CS-B lines although different from TM-1 by one for important traits. Thus, specific chromosome additive chromosome or arm, were similar, see Table 1 reported by effects for five cultivars, TM-1, and each CS-B line were Jenkins et al. (2006, 2007) and Table 1 reported by Saha predicted in this study. Chromosome arms 22sh and 22Lo et al. (2006) for both agronomic and fiber traits. These CS- of FM966 had additive effects associated with increased B line effects also showed similar patterns for traits in F2 lint percentage; chromosome 25, arms 5sh, 14sh, and 22Lo hybrids with both TM-1 (see Table 2, Saha et al. 2006) and of FM966 were associated with larger bolls. Chromosome F2 hybrids with five commercial cultivars (see Tables 2, 3, 16 of SG747 and FM966 was associated with improved lint 4, 5, Jenkins et al. 2006, 2007). Furthermore, these CS-B yield. Chromosome 25 and arms 15sh, 22sh, and 22Lo of lines showed similar additive effects for some traits with 123 1178 Genetica (2010) 138:1171–1179 the classic AD genetic model for the complete data set (see Jenkins JN, Wu J, McCarty JC, Saha S, Gutierrez OA, Hayes R, Stelly Table 6, Jenkins et al. 2006, 2007; see Table 4, Saha et al. DM (2006) Genetic Effects of thirteen Gossypium barbadense L chromosome substitution lines in topcrosses with Upland 2006). We also used the classic AD genetic model to cultivars: I. Yield and yield components. Crop Sci 46:1169–1178 analyze each of the 13 data sets. The results (Tables 4 and Jenkins JN, McCarty JC, Wu J, Saha S, Gutierrez OA, Hayes R, Stelly 5) showed the same patterns as the results showed in DM (2007) Genetic evaluation for thirteen chromosome substi- Tables 2 and 3. Therefore, it was not surprising that high tution lines crossed with five commercial cultivars: fiber traits. Crop Sci 47:561–572 correlations for additive effects among some chromosomes Kohel RJ, Endrizzi JE, White TG (1977) An evaluation of Gossypium or chromosome arms for some traits were observed in this barbadense L. chromosome 6 and 17 in the G. hirsutum L. study (Tables 2 and 3). genome. Crop Sci 17:404–406 It is still unclear how different genes within a genome Lacape JM, Nguyen TB, Courtois B, Belot JL, Gibnad M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton work together to affect a particular trait. Thus, our sepa- fiber quality using multiple Gossypium hirsutum 9 Gossypium ration of additive and dominance effects under both the barbadense backcross generations. Crop Sci 45:123–140 modified AD model and the classic AD model may not be Law CN (1966) The location of genetic factors affecting a quanti- completely achieved with our simple models. The expres- tative character in wheat. 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