Abstract
Key message
Background-independent (BI) and stably expressed (SE) quantitative trait loci (QTLs) were identified using two sets of introgression lines across multiple environments. Genetic background more greatly affected fiber quality traits than environmental factors. Sixty-one SE-QTLs, including two BI-QTLs, were novel and 48 SE-QTLs, including seven BI-QTLs, were previously reported.
Abstract
Cotton fiber quality traits are controlled by QTLs and are susceptible to environmental influence. Fiber quality improvement is an essential goal in cotton breeding but is hindered by limited knowledge of the genetic basis of fiber quality traits. In this study, two sets of introgression lines of Gossypium hirsutum × G. barbadense were used to dissect the QTL stability of three fiber quality traits (fiber length, strength and micronaire) across environments using 551 simple sequence repeat markers selected from our high-density genetic map. A total of 76 and 120 QTLs were detected in the CCRI36 and CCRI45 backgrounds, respectively. Nine BI-QTLs were found, and 78 (41.71%) of the detected QTLs were reported previously. Thirty-nine and 79 QTLs were SE-QTLs in at least two environments in the CCRI36 and CCRI45 backgrounds, respectively. Forty-eight SE-QTLs, including seven BI-QTLs, were confirmed in previous reports, and 61 SE-QTLs, including two BI-QTLs, were considered novel. These results indicate that genetic background more strongly impacts on fiber quality traits than environmental factors. Twenty-three clusters with BI- and/or SE-QTLs were identified, 19 of which harbored favorable alleles from G. barbadense for two or three fiber quality traits. This study is the first report using two sets of introgression lines to identify fiber quality QTLs across environments in cotton, providing insights into the effect of genetic backgrounds and environments on the QTL expression of fiber quality and important information for the genetic basis underlying fiber quality traits toward QTL cloning and molecular breeding.
Similar content being viewed by others
Avoid common mistakes on your manuscript.
Introduction
Cotton is an important economic crop worldwide that produces natural fibers used in the textile industry. It is essential that fiber quality is improved in order to keep pace with the development of spinning technology and cotton harvesting mechanization. However, the narrow genetic variation in Upland cotton limits the improvement in cotton varieties (Qin et al. 2008). It has been a long-term challenge for cotton breeders to improve fiber quality and yield to meet the needs of cotton producers and the textile industry. Cotton (Gossypium spp.) contains 52 species (Li et al. 2014), including two important cultivated tetraploid species: G. hirsutum (Upland cotton), with a high fiber yield, wide adaptability and medium fiber quality, and G. barbadense (Sea-Island, Egyptian or Pima cotton), with a low fiber yield, and narrow adaptability but high fiber quality (Lu et al. 2018). Therefore, the use of traditional breeding methods alone for fiber quality breeding is neither accurate nor efficient. Molecular marker-assisted selection (MAS) is a fast and effective method for improving Upland cotton fiber quality.
In the past 20 years, researchers have identified a large number of QTLs related to fiber quality in G. barbadense using interspecific segregating populations of G. hirsutum×G. barbadense or natural populations of G. barbadense (Abdullaev et al. 2017; Said et al. 2015a), but most of the map** populations are early segregating populations of G. hirsutum×G. barbadense such as F2 populations (Jiang et al. 1998; Kohel et al. 2001; Lin et al. 2005; Mei et al. 2004; Paterson et al. 2003), F2:3 populations (He et al. 2007) and early backcross generation populations (BC1, BC2, BC2S1) (Lacape et al. 2005; Shi et al. 2015, 2016). A few map** populations are recombinant inbred line (RIL) populations (Lacape et al. 2009, 2010) or backcross introgression line (BIL) populations (Nie et al. 2015; Yu et al. 2013), as well as natural populations of G. barbadense (Abdullaev et al. 2017; Wang et al. 2013a). Due to the complex background of these map** populations, it is difficult to accurately identify and precisely locate QTLs (Islam et al. 2016). Therefore, most of the QTL map** results cannot be applied to the genetic improvement in Upland cotton (Sun et al. 2017). Introgression lines (ILs), also known as chromosome segment introgression lines (CSILs) or chromosome segment substitution lines (CSSLs), are constructed by hybridization, backcrossing, self-pollination and MAS. Only the introgressed segment differs between a CSSL and its recipient parent. As the same set of CSSLs has the same or a similar genetic background but differs only in a specific genetic region on one chromosome (thus eliminating the influence of complex genetic backgrounds), CSSLs are ideal materials for studying quantitative traits and QTL map** in crops. The construction and utilization of CSSLs have been widely reported in tomato, rice, maize and other crops (Balakrishnan et al. 2019; Bouchez et al. 2002; Monforte and Tanksley 2000; Okada et al. 2018; Qi et al. 2013; Qiu et al. 2013), and a QTL for FL, qFL-chr1, was fine mapped and analyzed using near-isogenic introgression lines (NIILs) of Upland Tamcot 2111 (G. hirsutum, the recurrent parent) × Pima S-6 (G. barbadense, the donor parent) (Xu et al. 2017). Some QTLs related to fiber quality in G. barbadense were identified based on segregating populations of derived progenies of one IL (Chen et al. 2018; Wang et al. 2011, 2016). To date, most of the CSLs, ILs or CSSLs reported in cotton have been detected in the obsolete TM-1 genetic background. Although many QTLs for fiber quality traits have been detected in cotton, few of them have been used in MAS in breeding (Cao et al. 2014). This may be due to inaccurate QTL map** in populations with complex genetic backgrounds, the use of different environments or the use of different genetic backgrounds in QTL map** populations and breeding populations. In addition, using the QTLs identified in map** populations in breeding populations is a challenge. To date, the genetic background effects on QTL expression have not been reported.
To transfer beneficial genes from G. barbadense into Upland cotton cultivars, we constructed two sets of CSSLs with two different Upland cotton genetic backgrounds in which Hai1 (G. barbadense) was the donor parent and CCRI36 and CCRI45 (G. hirsutum) were the recipient parents (Li et al. 2016, 2019a; Lu et al. 2009). Some of the CSSLs were genetically evaluated, and some QTLs for yield and fiber quality were identified using secondary segregating populations derived from one, two or four CSSLs as parents (Guo et al. 2015, 2018; Li et al. 2019b; Song et al. 2016). With the rapid development of biotechnology, multiple cotton genomes have been sequenced, providing a foundation for further cotton gene identification and molecular breeding at the genome level (Hu et al. 2019; Li et al. Two sets of CSSLs were derived from two interspecific crosses with Hai1 (G. barbadense) as the donor parent and CCRI36 or CCRI45 (G. hirsutum) as the recipient parent. CCRI45 (also called CCRI221) is a late-maturing Upland cotton (G. hirsutum) cultivar, and CCRI36 is an early-maturing Upland cotton cultivar; both cultivars have high yield and were bred by the Institute of Cotton Research (ICR), the Chinese Academy of Agricultural Sciences (CAAS), Anyang, Henan Province. Hai1 is a cultivated line of G. barbadense with very high fiber quality. First, two crosses (resulting in two F1 populations) were performed, with Hai1 as the male parent and CCRI36 or CCRI45 (G. hirsutum) as the female parent. Subsequently, BC5F3 populations with the CCRI36 background were obtained by five generations of successive backcrossing (with CCRI36 as the recurrent parent) and two generations of self-pollination and MAS (Li et al. 2016, 2019a). Similarly, BC4F3 populations with the CCRI45 background were also obtained by four generations of backcrossing (with CCRI45 as the recurrent parent) and two generations of self-pollination and MAS (Yang et al. 2009; Li et al. 2016). In 2009, 2660 CCRI36 × Hai1 BC5F3 individuals and 2328 CCRI45 × Hai1 BC4F3 individuals were grown in the field in Anyang in Henan Province (Anyang Experiment Farm, ICR, CAAS). In 2010, BC5F3:4 individuals of CCRI36 × Hai1 and BC4F3:4 individuals of CCRI45 × Hai1 were planted in progeny rows. The single-row length was 5 m and the row width was 0.8 m in the 2009 Anyang (09HNA) and 2010 Anyang (10HNA) experiments. On the basis of the above design, two subpopulations in each genetic background were randomly selected, including 408 CSSLs in the CCRI36 background, named 36Pop, and 332 CSSLs in the CCRI45 background, named 45Pop. Subsequently, 36Pop was evaluated in a total of five environments as follows. In 2011, individual CSSLs in 36Pop (BC5F3:5) and their recurrent parent were grown in three environments at three different locations: Anyang in Henan Province (11HNA), Liaoyang in Liaoning Province (11LNL) and Shihezi in ** for fiber quality traits across multiple generations and environments in upland cotton. Mol Breed 30:569–582" href="/article/10.1007/s00122-020-03578-0#ref-CR54" id="ref-link-section-d94658705e1023">2012). Based on the genetic linkage map comprising 2292 marker loci distributed on 26 chromosomes and covering almost the whole cotton AD genome (5115.16 cM) with an average marker interval of 2.23 cM, 551 simple sequence repeat (SSR) markers with an average interval of 10 cM between two markers were selected for the screening of genotypes in two sets of CSSLs (Shi et al. 2015). Chromosome (C) 4 had the least number of markers (11 SSRs), while C11, C19 and C21 had the largest (30 SSRs). The longest genetic distance between two markers was 25.99 cM, and the shortest was 0.45 cM. The details of selected markers and their adjacent markers on the genetic map are in Table S1. The sequences of each primer used in this report can be downloaded at http://www.cottonmarker.org and were synthesized by Bioethics Engineering Co., Ltd (Shanghai). The phenotypic data from the CSSLs with the CCRI36 background in seven environments (09HNA, 10HNA, 11HNA, 11LNL, 11XJS, 14XJN, 14XJS) and with the CCRI45 background in nine environments (09HNA, 10HNA, 11HNA, 11XJK, 14XJA, 14XJK, 14HNZ, 15HNZ, 15HNA) were used for analysis. Descriptive statistical analysis, correlation analysis and analysis of variance (ANOVA) were performed using SPSS 20.0 software (SPSS, Chicago, IL, America). Genotypic analysis of populations and analysis of chromosome introgressed segments calculations (including background recovery rate of the CSSLs, the number and length of introgressed segments) were performed using GGT 2.0 software developed by van Berloo (http://www.plantbreeding.wur.nl/UK/software_ggt.html) (van Berloo 2008). QTL map** was performed with QTL IciMap** (version 4.0), and the RSETP-LRTADD map** method was applied with a logarithm of odds (LOD) threshold of 2.5 (Li et al. 2007; Wang et al. 2019). The QTLs were named as follows: (q + trait abbreviation) + chromosome/linkage group + QTL number. QTLs for the same trait in different environments and populations were considered stable when their confidence intervals overlapped (Shi et al. 2015, 2016; Sun et al. 2012). The resulting linkage map and QTLs were drawn using MapChart ver.2.2 software (Voorrips 2002). The results of the descriptive statistical analysis of each trait in the different populations are shown in Table 1. The average FL, FS and FM values of the recurrent parent were generally consistent with those of the corresponding population in all environments. The FL of the populations in all environments was slightly greater than that of the recurrent parents, except in 14XJN; the FS of the populations in the other environments was slightly higher than that of the recurrent parents, except in 10AY; and the FM value of the populations in all environments was slightly lower than that of the recurrent parents. The average FL, FS and FM values of 36 and 45 recurrent parents were similar in all environments, with medium fiber quality. The descriptions of the statistical analysis of quality for 45Pop in 09HNA, 10HNA, 11HNA and 11XJK follow those reported by Ma et al. (2013). In all environments, the range and coefficient of variation of each trait in all the populations were large. For the same population in all environments, the variation in FM was the greatest among the three traits, and the variation in FS was greater than that in FL. These results indicate abundant genetic variation in the CSSL populations produced by advanced backcrossing and continuous self-crossing. The absolute skewness of all traits in all populations and environments was less than 1, thus following a normal distribution (Table 1, Fig. S1). The correlation coefficients of each trait between different environments were significant (Table S2), indicating that these materials were stable across multiple environments. Most of the correlation coefficients among environments for FL and FM were larger than 0.5, whereas those for FS were smaller than 0.5, indicating that FS was more greatly affected by the environment than FL and FM. ANOVA revealed highly significant effects of genotype (G), the environment (E) and the interaction between genotype and the environment (G × E interaction) on all three traits in the populations (Table 2). The broad-sense heritability values, calculated by partitioning the variance into genetic and G × E effects, were above 85% for all three traits. Through the evaluation and analysis of multiple environments, some of the CSSLs with excellent and stable CSSLs were screened out (Li et al. 2017; Lu et al. 2012; Said et al. 2015a, b; Zhai et al. 2016). A total of 23 QTL clusters were found in this paper, with at least two stable or common QTLs affecting at least two or more different traits. These clusters were distributed on 13 chromosomes (C2, C7, C10, C12, C13, C14, C15, C16, C17, C19, C20, C21 and C22) (Table 4, Table S4). BI- and SE-QTL regions (BISERs) are those containing BI- and SE-QTLs affecting two or more different traits. SE-QTL regions (SERs) are those containing at least two SE-QTLs affecting at least two different traits. Twenty-three QTL clusters included six BISERs and 17 SERs. Six BISERs were involved in the control of two or three traits. BISER-C7-1 was located near the NAU1085 marker (92.24 cM) on C7, which harbored two BI-QTLs (qFL-C7-3 and qFS-C7-4 with a positive additive effect) and one SE-QTL (qFM-C7-3 with a negative additive effect). BISER-C15-1 was located near the NAU3177 marker (43.61 cM) on C15, with two BI-QTLs (qFL-C15-1 and qFS-C15-3, with positive additive effects). BISER-C16-1 was located near the BNL2634 marker (65.97 cM) on C16, with two BI-QTLs (qFL-C16-2 and qFS-C16-3, with positive additive effects). BISER-C17-1 was located near the NAU2909 marker (47.26 cM) on C17, containing one BI-QTL (qFM-C17-2 with a negative additive effect) and two SE-QTLs (qFL-C17-3 and qFS-C17-1 with a positive additive effect). BISER-C17-2 was located near the HAU0195a marker (122.79 cM) on C17, containing one BI-QTL (qFS-C17-3 with a positive additive effect) and two SE-QTLs (qFL-C17-5 with a positive additive effect and qFM-C17-4 with a negative additive effect). BISER-C2-1 was located near the NAU2277 marker (178.82 cM) on C2, which contained one BI-QTL (qFL-C2-6 with a positive additive effect) and one SE-QTL (qFS-C2-2 with a positive additive effect). The Hai1 alleles in the three BISERs (BISER-C7-1, BISER-C17-1 and BISER-C17-2) simultaneously increased FL and FS and decreased FM, and those in the other three BISERs simultaneously increased FL and FS. Among the 17 SERs, 15 affected both FL and FS. These 15 SERs (SER-C2-1, SER-C7-1, SER-C10-1, SER-C12-1, SER-C12-2, SER-C13-1, SER-C13-2, SER-C14-1, SER-C14-2, SER-C16-2, SER-C19-1, SER-C20-1, SER-C21-1, SER-C21-2 and SER-C22-1) were located near HAU1980b (54.78 cM) on C2; near PGML01950 (53.19 cM) on C7; near BNL3563 (178.11 cM) on C10; near HAU1361 (84.57 cM) and NAU4889 (110.86 cM) on C12; near BNL1707 (8.68 cM) and CGR5242 (164.25 cM) on C13; near NAU3648 (40.73 cM) and HAU1219a (206.88 cM) on C14; near BNL3065 (176.71 cM) on C16; near NAU3405 (17.39 cM) on C19; near HAU1491a (139.9 cM) on C20; near PGML00972 (238.32 cM) and Gh132 (241.43 cM) on C21; and near NAU1325 (152.64 cM) on C22. The Hai1 alleles in two regions (SER-C14-2 and SER-C16-2) simultaneously decreased FL and FS, and those in the other 13 SERs simultaneously increased FL and FS. The other two SERs (SER-C15-1 and SER-C16-1) affected FS and FM, and they were located near HAU1058a (26.9 cM) on C15 and near CGR5149 (16.79 cM) on C16. The Hai1 alleles in the two regions simultaneously increased FS and FM (Table 4, Table S4). CSSLs are valuable genetic resources for basic and applied research on the improvement in complex traits (Balakrishnan et al. 2019). The materials used in this paper were CSSLs with the Upland cotton background and one or more introgressed segments from G. barbadense. Only the introgressed segments differed between the CSSLs and their recipient parents. A set of CSSLs, which had the same or a similar genetic background and differed only in a specific genetic region, can eliminate the influence of a complex genetic background, making CSSLs ideal materials for researching quantitative trait inheritance and gene identification in crops and advantageous in the identification of QTLs. The CSSLs are similar to their recurrent parents in terms of field-observed phenotypes but with one or more specific traits of G. barbadense (Ma et al. 2013; Li et al. 2019b). In this paper, the CSSLs exhibited high genetic diversity in fiber quality traits (Table 1, Fig. S1). Through multiple environmental evaluation, some stable and high-quality lines were obtained (Li et al. 2017; Lu et al. QTLs for fiber quality traits Cotton fiber quality traits are very important traits that are largely affected by both genetic backgrounds and environmental factors. In the present study, a total of 76 QTLs (29 FL-QTLs, 26 FS-QTLs and 21 FM-QTLs) and 120 QTLs (49 FL-QTLs, 52 FS-QTLs and 19 FM-QTLs) were detected in the two sets of CSSLs of the CCRI36 and CCRI45 backgrounds, respectively (Fig. 2, Table S3). Nine QTLs (four FL-QTLs, four FS-QTLs and one FM-QTL) were simultaneously detected in both backgrounds (the CCRI36 background and the CCRI45 background) (Table 3, Table S3). Thus, a total of 187 QTLs were identified in this study, including 74 FL-QTLs, 39 FM-QTLs and 74 FS-QTLs. By comparison, 36 of the 76 QTLs detected in the CCRI36 background and 49 of the 120 QTLs detected in the CCRI45 background were identical or similar to previously reported QTLs (Table S3) as they shared common markers in the confidence interval on the same chromosome. In the CCRI36 background: 11 FL-QTLs (qFL-C1-1, qFL-C2-4, qFL-C5-2, qFL-C7-3, qFL-C16-2, qFL-C16-3, qFL-C19-5, qFL-C20-1, qFL-C20-4, qFL-C21-3 and qFL-C22-1), 12 FM-QTLs (qFM-C1-1, qFM-C1-2, qFM-C3-1, qFM-C3-2, qFM-C7-3, qFM-C12-1, qFM-C14-1, qFM-C16-1, qFM-C17-2, qFM-C17-4, qFM-C20-1 and qFM-C25-5) and 13 FS-QTLs (qFS-C7-4, qFS-C11-1, qFS-C13-3, qFS-C15-3, qFS-C15-5, qFS-C16-3, qFS-C16-4, qFS-C17-3, qFS-C20-1, qFS-C20-2, qFS-C20-4, qFS-C20-5 and qFS-C25-3) were previously reported (Deng et al. 2019; Fang et al. 2014; Guo et al. 2018; Jamshed et al. 2016; Li et al. 2019b; Ma et al. 2017; Said et al. 2015b; Shao et al. 2014; Shen et al. 2005; Shi et al. 2012; Wang et al. 2016, 2017a, b; Yang et al. 2015; Zhai et al. 2016; Zhang et al. 2012, 2016). In the CCRI 45 background: 16 FL-QTLs (qFL-C2-1, qFL-C2-3, qFL-C7-3, qFL-C10-1, qFL-C10-2, qFL-C14-1, qFL-C14-2, qFL-C14-3, qFL-C14-5, qFL-C15-4, qFL-C16-2, qFL-C17-4, qFL-C19-1, qFL-C19-2, qFL-C25-1 and qFL-C26-3) were previously reported, 10 FM-QTLs (qFM-C5-2, qFM-C5-3, qFM-C7-1, qFM-C7-2, qFM-C15-1, qFM-C17-2, qFM-C24-2, qFM-C25-1, qFM-C25-2 and qFM-C25-3) and 23 FS-QTLs (qFS-C7-3, qFS-C7-4, qFS-C9-1,qFS-C10-1, qFS-C10-2, qFS-C11-5, qFS-C11-6, qFS-C12-1, qFS-C14-1, qFS-C15-2, qFS-C15-3, qFS-C15-6, qFS-C16-3, qFS-C17-1, qFS-C17-3, qFS-C19-2, qFS-C21-1, qFS-C21-2, qFS-C21-4, qFS-C22-1, qFS-C24-1, qFS-C25-1 and qFS-C25-2) were previously reported (Chen et al. 2018; Deng et al. 2019; Fang et al. 2014; Guo et al. 2015; He et al. 2007; Huang et al. 2018; Jamshed et al. 2016; Li et al. 2019b; Lin et al. 2005; Ning et al. 2014; Said et al. 2015b; Shao et al. 2014; Shen et al. 2005; Shi et al. 2012; Tang et al. 2015; Wang et al. 2011, 2012, 2015, 2016; Zhai et al. 2016; Zhang et al. 2012). Notably, seven of QTLs (qFL-C7-3, qFL-C16-2, qFM-C17-2, qFS-C7-4, qFS-C15-3, qFS-C16-3 and qFS-C17-3) were BI-QTLs. Therefore, 77 (41.17%) of the QTLs detected in this study were previously reported, and the other 110 QTLs were considered novel. It is worth mentioning that 49 of the QTLs were confirmed in our earlier-generation interspecific backcross populations (Shi et al. 2019b; Song et al. 2016; Guo et al. 2015, 2018). These QTLs included 14 QTLs (qFL-C2-4, qFL-C10-2, qFL-C16-3, qFL-C20-1, qFM-C1-2, qFM-C24-2, qFS-C11-1, qFS-C11-6, qFS-C12-1, qFS-C13-3, qFS-C16-4, qFS-C20-1, qFS-C21-1 and qFS-C21-4) confirmed in our earlier-generation interspecific backcross populations (Shi et al. 2019b), seven QTLs (qFL-C7-3, qFL-C20-4, qFL-C22-1, qFS-C7-4, qFS-C20-2, qFS-C20-4 and qFS-C20-5) reported by Song et al. (2016), two QTLs (qFS-C15-5 and qFS-C22-1) reported by Guo et al. (2018) and two QTLs (qFS-C19-2 and qFS-C21-2) reported by Guo et al. (2015). Of them, seven (qFL-C7-3, qFL-C16-2, qFM-C17-2, qFS-C7-4, qFS-C15-3, qFS-C16-3 and qFS-C17-3) were BI-QTLs (Table S3). In the CCRI36 background, a total of 39 SE-QTLs (20 FL-QTLs, six FS-QTLs and 13 FM-QTLs) were stably expressed in at least two environments, 23 of which were previously reported, including nine FL-QTLs (qFL-C1-1, qFL-C2-4, qFL-C5-2, qFL-C7-3, qFL-C16-3, qFL-C19-5, qFL-C20-1, qFL-C20-4 and qFL-C22-1), nine FM-QTLs (qFM-C1-1, qFM-C3-1, qFM-C7-3, qFM-C12-1, qFM-C14-1, qFM-C16-1, qFM-C17-2, qFM-C17-4 and qFM-C25-5) and five FS-QTLs (qFS-C7-4, qFS-C16-3, qFS-C16-4, qFS-C17-3 and qFS-C20-5) (Table S3). In the CCRI45 background, a total of 79 SE-QTLs (31 FL-QTLs, 39 FS-QTLs and nine FM-QTLs) were stably expressed in multiple environments, 32 of which were previously reported, including nine FL-QTLs (qFL-C2-1, qFL-C2-3, qFL-C7-3, qFL-C10-2, qFL-C14-1, qFL-C14-5, qFL-C16-2, qFL-C19-1 and qFL-C19-2), eight FM-QTLs (qFM-C5-3, qFM-C7-2, qFM-C15-1, qFM-C17-2, qFM-C24-2, qFM-C25-1, qFM-C25-2 and qFM-C25-3) and 15 FS-QTLs (qFS-C7-3, qFS-C7-4, qFS-C9-1, qFS-C11-6, qFS-C12-1, qFS-C14-1, qFS-C15-2, qFS-C15-3, qFS-C16-3, qFS-C17-1, qFS-C17-3, qFS-C21-2, qFS-C21-4, qFS-C22-1 and qFS-C24-1) (Table S3). Among them, seven QTLs (qFL-C7-3, qFL-C16-2, qFM-C17-2, qFS-C7-4, qFS-C15-3, qFS-C16-3 and qFS-C17-3) were BI-QTLs and stably expressed in multiple environments of each of both backgrounds (Table 3, Table S3). Therefore, among the 109 SE-QTLs, 48 were confirmed in previous reports and 61 were considered novel. These QTLs are likely to exhibit genetic stability and warrant further clarification by QTL fine map** and cloning to better understand the genetics and molecular mechanisms underlying fiber development. In the present study, more QTLs were located on the D subgenome than the A subgenome (29 on the A subgenome and 47 on the D subgenome in the CCRI36 background, and 50 on the A subgenome and 70 on the D subgenome in the CCRI45 background), which was consistent with most previous reports (Fang et al. 2014; Jiang et al. 1998; Lacape et al. 2010; Paterson et al. 2003; Said et al. 2013; Yang et al. 2015). Fiber quality traits in cotton are complex quantitative traits. One of the difficulties in improving complex traits is the environmental sensitivity of the identified QTLs. The percentages of SE-QTLs for the three traits (FL, FS and FM) were 60.00% and 49.00% in previous papers reported by Sun et al. (2012) and Jamshed et al. (2016), respectively. In the present paper, the overall percentage of SE-QTLs was 62.50%. These results were consistent with the results of previous reports (Sun et al. 2012; Jamshed et al. 2016), indicating that environmental factors have a large influence on fiber quality traits (Tan et al. 2018). To date, there has been no report on the effect of genetic background on the QTL expression of fiber quality in cotton. In the present study, among the 187 QTLs detected overall, only nine (4.81%) were BI-QTLs, which indicated that genetic background has a strong influence on fiber quality traits in cotton. In rice, some studies show that the expressions of the QTLs for complex traits are strongly affected by genetic background (Qiu et al. 2019b). These provide a material foundation for further gene cloning and fiber quality improvement. This study represents the first report using two sets of CSSLs with different genetic backgrounds but with the same donor parent to dissect the stability of QTLs of fiber quality traits across multiple environments in cotton. A total of 76 and 120 QTLs were identified in the CSSLs with the CCRI36 and CCRI45 backgrounds, respectively. Among them, nine BI-QTLs were found, and 78 (41.71%) of the detected QTLs were reported previously. Thirty-nine and 79 were SE-QTLs in at least two environments in the CCRI36 and CCRI45 backgrounds, respectively. Forty-eight SE-QTLs, including seven BI-QTLs, were confirmed in previous reports and 61 SE-QTLs, including two BI-QTLs, were considered novel. Twenty-three clusters with BI- and/or SE-QTLs were identified, 19 of which harbored favorable alleles from G. barbadense for two or three fiber quality traits. In summary, these results revealed the BI- and/or SE-QTL regions, indicated that genetic background has a stronger effect on fiber quality traits than environmental factors and provided insights into the effects of genetic background and environment on the expression of fiber quality QTLs in cotton. This study provides valuable information and new stable QTL regions for further QTL cloning and improvement in fiber quality by MAS in cotton breeding.Materials and methods
Development of two sets of cotton CSSLs and multi-environment field experiments
Data analysis and QTL map**
Results
Evaluation of CSSLs and fiber quality
Discussion
Characteristics of the materials used in this study
Effects of genetic backgrounds and environments on the expression of QTLs
Conclusion
References
Abdullaev AA, Salakhutdinov IB, Egamberdiev SS, Khurshut EE, Rizaeva SM, Ulloa M, Abdurakhmonov IY (2017) Genetic diversity, linkage disequilibrium, and association map** analyses of Gossypium barbadense L. germplasm. PLoS ONE 12:e0188125
Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S (2019) Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theor Appl Genet 132:1–25
Bouchez A, Hospital F, Causse M, Gallais A, Charcosset A (2002) Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics 162:1945–1959
Cao Z, Wang P, Zhu X, Chen H, Zhang T (2014) SSR marker-assisted improvement of fiber qualities in Gossypium hirsutum using G. barbadense introgression lines. Theor Appl Genet 127:587–594
Chen Y, Liu G, Ma H, Song Z, Zhang C, Zhang J, Zhang J, Wang F, Zhang J (2018) Identification of introgressed alleles conferring high fiber quality derived from Gossypium barbadense L. in secondary map** populations of G. hirsutum L. Front Plant Sci 9:1023
Cheng L, Wang Y, Meng L, Hu X, Cui Y, Sun Y, Zhu L, Ali J, Xu J, Li Z (2012) Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice. Genome 55:45–55
Deng X, Gong J, Liu A, Shi Y, Gong W, Ge Q, Li J, Shang H, Wu Y, Yuan Y (2019) QTL map** for fiber quality and yield-related traits across multiple generations in segregating population of CCRI 70. J Cotton Res 2:13
Fang DD, Jenkins JN, Deng DD, McCarty JC, Li P, Wu JX (2014) Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.). BMC Genom 15:397
Guo L, Shi Y, Li J, Gong J, Liu A, Shang H, Gong W, Chen T, Qun Ge, Sun J, Yuan Y (2015) Map** QTL of fiber yield and quality traits in F2 populations of chromosome segment substitution lines from Gossypium hirsutum × Gossypium barbadense. Cotton Sci 27(6):550–560
Guo LX, Shi YZ, Gong JW, Liu AY, Tan YN, Gong WK, Li JW, Chen TT, Shang HH, Ge Q, Lu QW, Sun J, Yuan YL (2018) Genetic analysis of the fiber quality and yield traits in G-hirsutum background using chromosome segments substitution lines (CSSLs) from Gossypium barbadense. Euphytica 214:82
He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W (2007) QTL map** for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica 153:181–197
Hu Y, Chen J, Fang L et al (2019) Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet 51:739–748
Huang C, Shen C, Wen T, Gao B, Zhu Li X, Ahmed MM, Li D, Lin Z (2018) SSR-based association map** of fiber quality in upland cotton using an eight-way MAGIC population. Mol Genet Genom 293:793–805
Islam MS, Fang DD, Thyssen GN, Delhom CD, Liu YL, Kim HJ (2016) Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne. BMC Plant Biol 16:36
Jamshed M, Jia F, Gong J et al (2016) Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population. BMC Genom 17:197
Jenkins JN, Wu JX, McCarty JC, Saha S, Gutierrez O, Hayes R, Stelly DM (2006) Genetic effects of thirteen Gossypium barbadense L. chromosome substitution lines in topcrosses with upland cotton cultivars: I.Yield and yield components. Crop Sci 46:1169–1178
Jiang C, Wright RJ, El-Zik KM, Paterson AH (1998) Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci USA 95:4419–4424
Kohel RJ, Yu J, Park YH, Lazo GR (2001) Molecular map** and characterization of traits controlling fiber quality in cotton. Euphytica 121:163–172
Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum × Gossypium barbadense backcross generations. Crop Sci 45:123–140
Lacape JM, Jacobs J, Arioli T, Derijcker R, Forestier-Chiron N, Llewellyn D, Jean J, Thomas E, Viot C (2009) A new interspecific, Gossypium hirsutum × G. barbadense, RIL population: towards a unified consensus linkage map of tetraploid cotton. Theor Appl Genet 119:281–292
Lacape JM, Llewellyn D, Jacobs J, Arioli T, Becker D, Calhoun S, Al-Ghazi Y, Liu S, Palai O, Georges S, Giband M, de Assuncao H, Barroso PA, Claverie M, Gawryziak G, Jean J, Vialle M, Viot C (2010) Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum × G. barbadense RIL population. BMC Plant Biol 10:132
Li H, Ye G, Wang J (2007) A modified algorithm for the improvement of composite interval map**. Genetics 175:361–374
Li FG, Fan GY, Wang KB, Sun FM et al (2014) Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet 46:567–572
Li F, Fan G, Lu C, **ao G et al (2015) Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33:524–530
Li B, Shi Y, Gong J, Li J, Liu A, Shang H, Gong W, Chen T, Ge Q, Jia C, Lei Y, Hu Y, Yuan Y (2016) Genetic effects and heterosis of yield and yield component traits based on Gossypium barbadense chromosome segment substitution lines in two Gossypium hirsutum backgrounds. PLoS ONE 11:e0157978
Li PT, Wang M, Lu QW et al (2017) Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and chromosome segment substitution lines from G. hirsutum × G. barbadense. BMC Genom 18:705
Li PT, Rashid MHO, Chen TT et al (2019a) Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum × G. barbadense in response to Verticillium dahliae infection. BMC Plant Biol 19:19
Li SQ, Liu AY, Kong LL, Gong JW, Li JW, Gong WK, Lu QW, Li PT, Ge Q, Shang HH, ** and genetic effect of chromosome segment substitution lines with excellent fiber quality from Gossypium hirsutum × Gossypium barbadense. Mol Genet Genom 294:1123–1136
Lin Z, He D, Zhang X, Nie Y, Guo X, Feng C, Stewart JM (2005) Linkage map construction and map** QTL for cotton fibre quality using SRAP, SSR and RAPD. Plant Breed 124:180–187
Lu Q, Shi Y, **ao X, Li P, Gong J, Gong W, Liu A, Shang H, Li J, Ge Q, Song W, Li S, Zhang Z, Rashid MHO, Peng R, Yuan Y, Huang J (2017) Transcriptome analysis suggests that chromosome introgression fragments from Sea Island cotton (Gossypium barbadense) increase fiber strength in Upland cotton (Gossypium hirsutum). G3 (Bethesda) 7:3469
Ma L, Shi Y, Lan M, Yang Z, Zhang J, Zhang B, Li J, Wang T, Gong J, Liu A, Shang H, Gong W, Yuan Y (2013) Evaluation of chromosome segment substitution lines related to fiber yield and quality traits from Gossypium hirsutum × Gossypium Barbadense. Cotton Sci 25(6):486–495
Ma LL, Zhao YP, Wang YM, Shang LG, Hua JP (2017) QTLs analysis and validation for fiber quality traits using maternal backcross population in Upland cotton. Front Plant Sci 8:2168
Mei M, Syed NH, Gao W, Thaxton PM, Smith CW, Stelly DM, Chen ZJ (2004) Genetic map** and QTL analysis of fiber-related traits in cotton (Gossypium). Theor Appl Genet 108:280–291
Monforte AJ, Tanksley SD (2000) Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: a tool for gene map** and gene discovery. Genome 43:803–813
Nie X, Tu J, Wang B, Zhou X, Lin Z (2015) A BIL population derived from G. hirsutum and G. barbadense provides a resource for cotton genetics and breeding. PLoS ONE 10:e0141064
Ning ZY, Chen H, Mei HX, Zhang TZ (2014) Molecular tagging of QTLs for fiber quality and yield in the upland cotton cultivar Acala-Prema. Euphytica 195:143–156
Okada S, Onogi A, Iijima K, Hori K, Iwata H, Yokoyama W, Suehiro M, Yamasaki M (2018) Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. Breed Sci 68:210–218
Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11(2):122–127
Paterson AH, Saranga Y, Menz M, Jiang CX, Wright RJ (2003) QTL analysis of genotype× environment interactions affecting cotton fiber quality. Theor Appl Genet 106:384–396
Qi H, Huang J, Zheng Q, Huang Y, Shao R, Zhu L, Zhang Z, Qiu F, Zhou G, Zheng Y, Yue B (2013) Identification of combining ability loci for five yield-related traits in maize using a set of testcrosses with introgression lines. Theor Appl Genet 126:369–377
Qin H, Guo W, Zhang YM, Zhang T (2008) QTL map** of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theor Appl Genet 117:883–894
Qiu X, Chen K, Lv W, Ou X, Zhu Y, **ng D, Yang L, Fan F, Yang J, Xu J, Zheng T, Li Z (2017) Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.). Theor Appl Genet 130:951–967
Saha S, Wu J, Jenkins JN, McCarty JC, Stelly DM (2013) Interspecific chromosomal effects on agronomic traits in Gossypium hirsutum by AD analysis using intermated G. barbadense chromosome substitution lines. Theor Appl Genet 126:109–117
Said JI, Lin Z, Zhang X, Song M, Zhang J (2013) A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton. BMC Genom 14:776
Said JI, Knapka JA, Song M, Zhang J (2015a) Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations. Mol Genet Genom 290:1615–1625
Said JI, Song M, Wang H, Lin Z, Zhang X, Fang DD, Zhang J (2015b) A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. Mol Genet Genom 290:1003–1025
Shao QS, Zhang FJ, Tang SY, Liu Y, Fang XM, Liu DX, Liu DJ, Zhang J, Teng ZH, Paterson AH, Zhang ZS (2014) Identifying QTL for fiber quality traits with three upland cotton (Gossypium hirsutum L.) populations. Euphytica 198:43–58
Shen XL, Guo WZ, Zhu XF, Yuan YL, Yu JZ, Kohel RJ, Zhang TZ (2005) Molecular map** of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed 15:169–181
Shi Y, Li W, Li A et al (2015) Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage. J Integr Plant Biol 57:450–467
Shi Y, Zhang B, Liu A, Li W, Li J, Lu Q, Zhang Z, Li S, Gong W, Shang H, Gong J, Chen T, Ge Q, Wang T, Zhu H, Liu Z, Yuan Y (2016) Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense. BMC Genom 17:877
Shi Y, Liu A, Li J, Zhang J, Zhang B, Ge Q, Jamshed M, Lu Q, Li S, **ang X, Gong J, Gong W, Shang H, Deng X, Pan J, Yuan Y (2019) Dissecting the genetic basis of fiber quality and yield traits in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense. Mol Genet Genom 294:1385–1402
Song W, Wang M, Su W, Lu Q, **ao X, Cai J, Zhang Z, Li S, Li P, Gong J, Gong W, Shang H, Liu A, Li J, Chen T, Ge Q, Shi Y, Yuan Y (2017) Genetic and phenotypic effects of chromosome segments introgressed from Gossypium barbadense into Gossypium hirsutum. PLoS ONE 12:e0184882
Stelly DM, Saha S, Raska DA, Jenkins JN, McCarty JC, Gutierrez OA (2005) Registration of 17 upland (Gossypium hirsutum) cotton germplasm lines disomic for different G. barbadense chromosome or arm substitutions. Crop Sci 45:2663–2665
Su CF, Wang W, Qiu XM, Yang L, Li S, Wang MX, Pan QB (2013) Fine-map** a fibre strength QTL qFS-D11-1 on cotton chromosome 21 using introgressed lines. Plant Breed 132:725–730
Sun FD, Zhang JH, Wang SF, Gong WK, Shi YZ, Liu AY, Li JW, Gong JW, Shang HH, Yuan YL (2012) QTL map** for fiber quality traits across multiple generations and environments in upland cotton. Mol Breed 30:569–582
Sun Z, Wang X, Liu Z, Gu Q, Zhang Y, Li Z, Ke H, Yang J, Wu J, Wu L, Zhang G, Zhang C, Ma Z (2017) Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnol J 15:982–996
Tan ZY, Zhang ZQ, Sun XJ, Li QQ, Sun Y, Yang P, Wang WW, Liu XY, Chen CL, Liu DX, Teng ZH, Guo K, Zhang J, Liu DJ, Zhang ZS (2018) Genetic map construction and fiber quality QTL map** using the CottonSNP80K array in Upland cotton. Front Plant Sci 9:225
Tang SY, Teng ZH, Zhai TF, Fang XM, Liu F, Liu DJ, Zhang J, Liu DX, Wang SF, Zhang K, Shao QS, Tan ZY, Paterson AH, Zhang ZS (2015) Construction of genetic map and QTL analysis of fiber quality traits for Upland cotton (Gossypium hirsutum L.). Euphytica 201:195–213
van Berloo R (2008) GGT 2.0: versatile software for visualization and analysis of genetic data. J Hered 99:232–236
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
Wan XY, Wan JM, Weng JF, Jiang L, Bi JC, Wang CM, Zhai HQ (2005) Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor Appl Genet 110:1334–1346
Wang P, Ding YZ, Lu QX, Guo WZ, Zhang TZ (2008) Development of Gossypium barbadense chromosome segment substitution lines in the genetic standard line TM-1 of Gossypium hirsutum. Chin Sci Bull 53:1512–1517
Wang FR, Gong YC, Zhang CY, Liu GD, Wang LM, Xu ZZ, Zhang J (2011) Genetic effects of introgression genomic components from Sea Island cotton (Gossypium barbadense L.) on fiber related traits in upland cotton (G. hirsutum L.). Euphytica 181:41–53
Wang P, Zhu Y, Song X, Cao Z, Ding Y, Liu B, Zhu X, Wang S, Guo W, Zhang T (2012) Inheritance of long staple fiber quality traits of Gossypium barbadense in G. hirsutum background using CSILs. Theor Appl Genet 124:1415–1428
Wang XQ, Yu Y, Li W, Guo HL, Lin ZX, Zhang XL (2013a) Association analysis of yield and fiber quality traits in Gossypium barbadense with SSRs and SRAPs. Genet Mol Res 12:3353–3362
Wang Y, Zang JP, Sun Y, Ali J, Xu JL, Li ZK (2013b) Background-independent quantitative trait loci for drought tolerance identified using advanced backcross introgression lines in rice. Crop Sci 53:430–441
Wang Y, Ning Z, Hu Y, Chen J, Zhao R, Chen H, Ai N, Guo W, Zhang T (2015) Molecular map** of restriction-site associated DNA markers in allotetraploid Upland cotton. PLoS One 10:e0124781
Wang FR, Zhang CY, Liu GD, Chen Y, Zhang JX, Qiao QH, Yuan ZC, Fan SJ, Zhang J (2016) Phenotypic variation analysis and QTL map** for cotton (Gossypium hirsutum L.) fiber quality grown in different cotton-producing regions. Euphytica 211:169–183
Wang BH, Draye X, Zhuang ZM, Zhang ZS, Liu M, Lubbers EL, Jones D, May OL, Paterson AH, Chee PW (2017a) QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between Gossypium hirsutum and G-mustelinum. Theor Appl Genet 130:1297–1308
Wang BH, Zhuang ZM, Zhang ZS, Draye X, Shuang LS, Shehzad T, Lubbers EL, Jones D, May OL, Paterson AH, Chee PW (2017b) Advanced backcross QTL analysis of fiber strength and fineness in a cross between Gossypium hirsutum and G. mustelinum. Front Plant Sci 8:1848
Wang M, Tu L, Yuan D et al (2019) Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet 51:224–229
Wu J, Jenkins JN, McCarty JC, Saha S, Stelly DM (2006) An additive-dominance model to determine chromosomal effects in chromosome substitution lines and other gemplasms. Theor Appl Genet 112:391–399
Xu P, Gao J, Cao Z, Chee PW, Guo Q, Xu Z, Paterson AH, Zhang X, Shen X (2017) Fine map** and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton. Theor Appl Genet 130:1309–1319
Yang Z, Li J, Li A, Zhang B, Liu G, Li J, Shi Y, Liu A, Jiang J, Tao Wang, Yuan Y (2009) Develo** chromosome segment substitution lines (CSSLs) in cotton (Gossypium) using advanced backcross and MAS. Mol Plant Breed 7(2):233–241
Yang XL, Zhou XD, Wang XF, Li ZK, Zhang Y, Liu HW, Wu LQ, Zhang GY, Yan GJ, Ma ZY (2015) Map** QTL for cotton fiber quality traits using simple sequence repeat markers, conserved intron-scanning primers, and transcript-derived fragments. Euphytica 201:215–230
Yu JW, Zhang K, Li SY, Yu SX, Zhai HH, Wu M, Li XL, Fan SL, Song MZ, Yang DG, Li YH, Zhang JF (2013) Map** quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population. Theor Appl Genet 126:275–287
Zhai H, Gong W, Tan Y, Liu A, Song W, Li J, Deng Z, Kong L, Gong J, Shang H, Chen T, Ge Q, Shi Y, Yuan Y (2016) Identification of chromosome segment substitution lines of Gossypium barbadense introgressed in G. hirsutum and quantitative trait locus map** for fiber quality and yield traits. PLoS One 11:e0159101
Zhang K, Zhang J, Ma J, Tang SY, Liu DJ, Teng ZH, Liu DX, Zhang ZS (2012) Genetic map** and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.). Mol Breed 29:335–348
Zhang SW, Zhu XF, Feng LC, Gao X, Yang B, Zhang TZ, Zhou BL (2016) Map** of fiber quality QTLs reveals useful variation and footprints of cotton domestication using introgression lines. Sci Rep 6:31954
Zhao X, Daygon VD, McNally KL, Hamilton RS, **e F, Reinke RF, Fitzgerald MA (2016) Identification of stable QTLs causing chalk in rice grains in nine environments. Theor Appl Genet 129:141–153
Zheng TQ, Wang Y, Ali AJ, Zhu LH, Sun Y, Zhai HQ, Mei HW, Xu ZJ, Xu JL, Li ZK (2011) Genetic effects of background-independent loci for grain weight and shape identified using advanced reciprocal introgression lines from Lemont × Teqing in rice. Crop Sci 51:2525–2534
Acknowledgements
This work was funded by the National Key R & D Program for Crop Breeding (2016YFD0100306), the Natural Science Foundation of China (31101188), the National Agricultural Science and Technology Innovation Project of the CAAS and the fund project of Director.
Author information
Authors and Affiliations
Contributions
YY and YS conceived and designed the experiments. JZ, LM, RH, LG and WS performed the molecular experiments. AL, JL, JZ, LM, QL, XX, GQ, WG, JG, HH, XD and JP conducted the phenotypic evaluations and collected the data from the field. YS and SL performed the analysis, and YS drafted the manuscript. YY and JZ revised the manuscript. All authors have read and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Communicated by Brent Hulke.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Fig. S1
Frequency distribution of fiber quality traits in the two CSSL populations. (PDF 393 kb)
Fig. S2
Introgressed Hai1 chromosome segments in the 36Pop population of CSSLs with the CCRI36 genetic background. (PDF 905 kb)
Fig. S3
Introgressed Hai1 chromosome segments in the 45Pop population of CSSLs with the CCRI45 genetic background. (PDF 758 kb)
Table S1
Details of selected markers from the genetic linkage map of the CCRI36 × Hai1 BC1F1 population. (PDF 754 kb)
Table S2
Correlation analysis of three traits in two populations of two sets of CSSLs with different genetic backgrounds across multiple environments. (PDF 55 kb)
Table S4
Details of QTL clusters for fiber quality in CSSL populations. (PDF 171 kb)
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Shi, Y., Liu, A., Li, J. et al. Examining two sets of introgression lines across multiple environments reveals background-independent and stably expressed quantitative trait loci of fiber quality in cotton. Theor Appl Genet 133, 2075–2093 (2020). https://doi.org/10.1007/s00122-020-03578-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-020-03578-0