Unconditional and conditional QTL underlying the genetic interrelationships between soybean seed isoflavone,and protein or oil contents

Selection for soybean (Glycine max L. Merr.) rich in isoflavones, protein and oil has been difficult due to negative genetic interrelationships. In this study, genetic interrelationships among seed isoflavones and protein and oil contents were evaluated using both unconditional and conditional QTL mapping. Daidzein (DZ), genistein (GT), glycitein (GC) and total isoflavone (TI) contents were analysed in F_5:6, F_5:7 and F_5:8 recombinant inbred lines (RILs) derived from a cross between ‘Zhongdou 27’(TI 3791 μg/g; protein content 42.84%; oil content 18.73%) and ‘Jiunong 20’ (TI 2061 μg/g; protein content 34.05%; oil content 21.42%). When DZ, GT, GC and TI were analysed for their genetic relationships with protein or oil contents, eight conditional QTL were detected, which included DZ|pro, GC|pro, GT|pro, TI|pro, DZ|oil, GC|oil, GT|oil and TI|oil. Seventeen QTL that had significant genetic associations between seed isoflavone, and seed protein or oil contents were found, including two for DZ conditioned on protein (qDZ|proK‐1, qDZ|proF‐2); one for GC conditioned on protein (qGC|proM‐1); three for GT conditioned on protein (qGT|proM‐1, qGT|proA2‐1, qGT|proL‐1); three for TI conditioned on protein (qTI|proM‐1, qTI|proA2‐1, qTI|proF‐2); one for DZ conditioned on oil (qDZ∣oil K_1); one for GC conditioned on oil (qGC∣oilI_1); four for GT conditioned on oil (qGT∣oil A2_1, qGT∣oil F_1, qGTF_2, qGT∣oilD2_1); three for TI conditioned on oil (qTI∣oilA2‐1, qTI∣oilE‐1, qTI∣oilL‐1). Few epistatic interactions among loci were detected. These loci may be valuable for improving seed isoflavone, protein and oil contents.     

Dynamic quantitative trait loci underlies isoflavone accumulation in soybean seed

Most of quantitative trait loci (QTL) underlying soybean seed isoflavone contents were derived from the harvest stage of plant development, which uncover the genetic effects that were expressed in earlier seed developmental stages. The aim of this study was to detect conditional QTL associated with isoflavone accumulation during the entire seed development. A total of 112 recombinant inbred lines developed from the cross between ‘Zhongdou 27’ (higher seed isoflavone content) and ‘Jiunong 20’ (lower seed isoflavone content) were used for the conditional QTL analysis of daidzein (DZ), genistein (GT), glycitein (GC) and total isoflavone (TI) accumulations through composite interval mapping with mixed genetic model. The results indicated that the number and type of QTL and their additive effects for individual and total isoflavone accumulations were different among R3 to R8 developmental stages. Three unconditional QTL and six conditional QTL for DZ, four unconditional QTL and five conditional QTL for GT, six unconditional QTL and five conditional QTL for GC, six unconditional QTL and seven conditional QTL for TI were identified at different developmental stages, respectively. Unconditional and conditional QTL that affect individual and total isoflavone accumulations exhibited multiple expression patterns, implying that some QTL are active for long period and others are transient. Two genomic regions, Satt144‐Satt569 in linkage group F (LG F; chromosome 13, chr 13) for DZ, GC, GT and TI accumulations and Satt540‐Sat_240 in LG M (chr 07) for TI and GC accumulations, were found to significantly affect individual and total isoflavone accumulations in multiple developmental stages, suggesting that the accumulation of soybean seed isoflavones is governed by time‐dependent gene expression.     

Genetics of fertility restoration of ‘Wild Abortive’ cytoplasmic male sterility in rice,Oryza sativa L.

Summary Genetics of fertility restoration in six varieties and breeding lines of rice was studied in Wild Abortive cytoplasmic genetic male sterility system using cytoplasmic male sterile lines V 20 A and IR 54752 A. Fertility evaluation of the plants in F₂ and testcross populations of the crosses of V 20 A with PR 103, PR 106 and PAU 502-94-1, and IR 54752 A with PAU 1124-36-1 and PAU 1126-1-1 revealed that fertility restoration in PR 103, PR 106, PAU 502-94-1, PAU 1124-36-1 and PAU 1126-1-1 was controlled by two independently segregating dominant genes. The two genes appeared to have additive effects; one of them being stronger than the other in imparting fertility restoration. Data on spikelet fertility of the plants in F₂ and testcross populations of V 20 A/UPR 82-1-1 cross showed that fertility restoration in UPR 82-1-1 was controlled by two independently segregating dominant genes which exhibited recessive epistatic interaction.

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Genetic impacts of fiber sugar content on fiber characters in Sea Island cotton, Gossypium barbadense L.

A genetic model with additive effect, dominant effect, additive × additive effect, and their interaction with environment effect (GE) was employed to analyze the 2-year data of F₁ and F₂ hybrids from 5 × 4 diallel cross, whose parents were Sea Island cotton with different fruit branch types. Unconditional and conditional genetic variances were analyzed to demonstrate genetic impacts of fiber sugar content on fiber characters. Results of unconditional genetic variances showed that dominance × environment interaction effect and additive × additive epistatic effects mainly controlled the genetic variation of fiber sugar content, and environment influenced the inheritance of fiber sugar content. Fiber uniformity, fiber elongation, and fiber micronaire were mainly controlled by dominance × environment effects. Fiber strength was mainly controlled by the interaction of additive × additive epistatic effects and the environment. Analysis of correlation coefficients indicated that the varieties or hybrids with high-fiber sugar content had short fiber, low-fiber uniformity, strength, and fineness, which indicated the close co-variation between fiber quality traits and fiber sugar content. Relatively better fiber quality traits could be obtained effectively through selecting parents with low-fiber sugar. Fiber sugar content of different parents had different genetic effect on fiber quality traits.     

Inheritance of quality traits in processing tomato (Lycopersicon esculentum Mill.)

Summary The genetic basis of pH, colour and soluble solids in processing tomato is examined. In a first experiment, aimed at identifying the base populations with which to start selection, parents, F₁ and F₂ progenies of an 8 × 8 diallel cross without reciprocals were tested.The results indicate that additive, dominance and additive x additive epistatic effects were noticeable for the three characters. Higher order interlocus interactions were also detected.As to the soluble solids, a trait for which higher order epistatic effects were less marked, the breeding potential of the cross combinations was assessed by calculating the expected mean values at the F generation. Some cross populations having C33 or C35 as parent appeared to be superior.A second experiment was conducted to collect data on the heritability of the foregoing qualitative traits by utilizing the regressions of F₃ offspring on F₂ parents. The low heritability coefficients observed would suggest the ineffectiveness of individual selection in early generations.In both the F₂ and F₃ generations rather low correlation coefficients among the three quality traits were observed.     

大豆籽粒异黄酮含量的遗传效应研究

大豆异黄酮含量差异较大的6个大豆品种为亲本，通过双列杂交配置杂交组合，测定了两个环境条件下亲本、F₁和F₂种子的异黄酮含量。采用双子叶植物种子数量性状遗传模型和统计分析方法, 分析了胚、细胞质和母体植株等不同遗传体系的基因效应以及环境互作效应。结果发现大豆籽粒异黄酮含量的表现主要受制于母体遗传效应, 其次为胚(子叶)基因效应,细胞质效应影响较小。不同遗传体系的基因主效应明显大于环境互作效应。异黄酮含量的机误方差较大,说明异黄酮含量更易受到环境条件变化影响。亲本遗传效应分析表明, 选用豫豆29或郑90007亲本有利于增加杂种后代大豆籽粒异黄酮含量,提高品质改良的效果。胚显性方差和母体显性方差均极显著，表明种子杂种优势和母体杂种优势会同时存在，而且是不受环境影响的主效应基因。     

Genetics of stem elongation ability in rice (Oryza sativa L.)

Summary The genetics of stem elongation ability in rice was studied in parents, F₁, F₂ and backcross generations of six crosses. Segregation analysis indicated dominance for stem elongation ability. Estimation of genetic parameters under epistatic model indicated more than one locus control stem elongation ability and both additive and nonadditive gene effects were important. Epistatic effects were predominant over additive and dominance effects with an important role of duplicate type of epistasis. The occurrence of significant additive and additive x additive types of genetic variation and the moderately high broad sense heritability indicated the possibility of selection for an increased manifestation of stem elongation ability.     

Molecular loci associated with seed isoflavone content may underlie resistance to soybean pod borer (Leguminivora glycinivorella)

Soybean pod borer (SPB) (Leguminivora glycinivorella (Mats.) Obraztsov) causes severe loss of soybean (Glycine max L. Merr.) seed yield and quality in some regions of the world, especially in north‐eastern China, Japan and Russia. Isoflavones in soybean seed play a crucial role in plant resistance to diseases and pests. The aim of this study was to find whether SPB resistance QTL are associated with soybean seed isoflavone content. A cross was made between ‘Zhongdou 27’ (higher isoflavone content) and ‘Jiunong 20’ (lower isoflavone content). One hundred and twelve F_5:10 recombinant inbred lines were derived through single‐seed descent. A plastic‐net cabinet was used to cover the plants in early August, and thirty SPB moths per square metre were put in to infest the soybean green pods. The results indicated that the percentage of seeds damaged by SPB was positively correlated with glycitein content (GC), whereas it was negatively correlated with genistein (GT), daidzein (DZ) and total isoflavone content (TI). Four QTL underlying SPB damage to seeds were identified and the phenotypic variation for SPB resistance explained by the four QTL ranged from 2% to 14% on chromosomes Gm7, 10, 13 and 17. Moreover, eleven QTL underlying isoflavone content were identified, and ten of them were encompassed within the same four marker intervals as the SPB QTL (BARC‐Satt208‐Sat292, Satt144‐Sat074, Satt540‐Sat244 and Satt345‐Satt592). These QTL could be useful in marker‐assisted selection for breeding soybean cultivars with both SPB resistance and high seed isoflavone content.     

Dissection of genetic architecture for oil content in soybean seed using two backcross populations

Soybean seed oil was valued in foods, animal feed and some industrial applications. Molecular marker‐assisted selection (MAS) for high‐oil‐content cultivars was an important method for soybean breeders. The objective of this study was to identify quantitative trait loci (QTL) and epistatic QTL underlying the seed oil content of soybeans across two backcross (BC) populations (with one common male parent ‘Dongnong47’) and two different environments. Two molecular genetic maps were constructed. They encompassed 1046.8 cM [with an average distance of 6.75 cM in the ‘Dongnong47’  ×  ‘Jiyu89’ (DJ) population] and 846.10 cM [with an average distance of 5.76 cM in the ‘Dongnong47’  ×  ‘Zaoshu18’ (DZ) population]. Nine and seven QTL were identified to be associated with oil content in the DJ and DZ populations, respectively. The phenotypic variation explained by most of the QTL was usually less than 10%. Among the identified QTL, those stable ones across multiple environments and populations often had stronger additive effects. In addition, three stable QTL in the DZ populations were identified in the similar genomic region of the three QTL in the DJ population [qDJE and qDZE‐1 were located near Satt151 of Chromosome 15 (Chr15), qDJA1 and qDZA1 were located near Satt200 of Chr15 (LG A1), and qDJD2‐1 and qDZD2‐1 were located near Sat365 of Chr17]. In conclusion, MAS will be able more effectively to combine beneficial alleles of the different donors to design new genotypes with higher soybean seed oil content using the BC populations.     

Genetic analysis on oil content in rapeseed (Brassica napus L.)

High oil content is one of the most important characteristics of rapeseed (Brassica napus L.) breeding. In order to understand the genetic basis of seed oil content, a series of reciprocal crosses between rapeseed parents with high oil content (53110, 61616 and 6F313), medium-oil content (Zhongshuang 9) and low oil content (51070 and 93275) were conducted. It was found that the oil content of F₁ hybrid seeds in rapeseed was mainly controlled by the maternal genotype. The maternal effect value of oil content was estimated to be 0.86. The pollen parent had a xenia effect on oil content, estimated to be 0.14 which changed the mean value by 1.86 percent. The inheritance of oil content was studied in a set of 8 × 8 diallel crosses of different varieties. The results indicated that the inheritance of oil content could be explained by an additive-dominant-epistasis model. Although the dominant and additive effects played major roles and accounted for more than 70% of the total variance, there was also a small epistatic effect. The broad and narrow sense heritability of oil content was 83.88 and 36.94%, respectively. Based on the oil content differences between the reciprocal crosses in the same offspring generation (F₁ and F₂) in rapeseed, it could be concluded that there were significant cytoplasmic effects on oil content. In this study, two lines with significantly cytoplasmic effects, either positive or negative, were selected.     

Genetic analysis of male sterility in rice mutants with environmentally influenced levels of fertility

Summary Twenty-six male sterile plants grown in the field were recovered in the M7 generation from ethyl methane sulfonate-treated material of the rice cultivar M-201. Fertility increased five-fold when ratooned plants from the field were grown in a growth chamber with a 12 hour daylength. Crosses between mutant and normal fertile cultivars produced fertile F₁ plants. Female fertility was normal as judged by percent seed set from unbagged panicles of parental and recombinant lines. Transgressive segregation for fertility was observed for all crosses in the F₂ and F₃ generations. Five of 37 F₃ male sterile plants showed moderate levels of seed fertility under winter greenhouse conditions and reduced seed set when transplanted to summer field plots. Fertility data from reciprocal crosses suggested cytoplasmic factors had little or no effect on levels of male sterility in the mutant lines. Chi-squared analyses of F₂ and F₃ generation results indicated male sterility of the mutants is conditioned by two nuclear genes with epistatic effects.     

Quantitative and molecular characterization of heat tolerance in hexaploid wheat

Understanding the genetic basis of tolerance to high temperature is important for improving the productivity of wheat (Triticum aestivum L.) in regions where the stress occurs. The objective of this study was to estimate inheritance of heat tolerance and the minimum number of genes for the trait in bread wheat by combining quantitative genetic estimates and molecular marker analyses. Two cultivars, Ventnor (heat-tolerant) and Karl92 (heat-susceptible), were crossed to produce F₁, F₂, and F₃populations, and their grain-filling duration (GFD) at 30/25 ^°C 16/8 h day/night was determined as a measure of heat tolerance. Distribution of GFD in the F₁ and F₂ populations followed the normal model (χ², p > 0.10). A minimum of 1.4 genes with both additive and dominance effects, broad-sense heritability of 80%, and realized heritability of 96%for GFD were determined from F₂ and F₃ populations. Products from 59primer pairs among 232 simple sequence repeat (SSR) pairs were polymorphic between the parents. Two markers, Xgwm11 andXgwm293, were linked to GFD by quantitative trait loci (QTL) analysis of the F₂ population. The Xgwm11-linked QTL had only additive gene action and contributed 11% to the total phenotypic variation in GFD in the F₂population, whereas the Xgwm293-linked QTL had both additive and dominance action and contributed 12% to the total variation in GFD. The results demonstrated that heat tolerance of common wheat is controlled by multiple genes and suggested that marker-assisted selection with microsatellite primers might be useful for developing improved cultivars. This revised version was published online in August 2006 with corrections to the Cover Date.     

Estimation of genetic parameters for in vitro traits in wheat immature embryo cultures involving high X low regeneration capacity genotypes

Summary Estimates of gene actions were obtained for five in vitro traits of immature wheat (Triticum aestivum L.) embryo cultures from a cross of two wheat cultivars and the resulting reciprocal, F₁, F₂ and backcross populations. The contribution of additive gene effects to in vitro traits was not as important as the dominance gene effects. Epistatic gene effects were relatively more important than either additive or dominance gene effects. Of the individual types of digenic epistatic effects, the dominance x dominance estimates were relatively larger in magnitude for all in vitro culture traits measured. The maternal effect played a minor role in the inheritance of the in vitro studied traits since the difference among the reciprocal values was not significant. It is shown from the generation mean method that epistasis played a major role in the inheritance of most of the traits under study. The negative values of additive and dominance genetic variance were estimates of zero. Heritability estimates, in broad sense, were relatively high for the in vitro studied traits. In some cases, heritability estimates in broad and narrow senses are almost equal since the estimation of dominance genetic variance led to negative values. According to the results of the gene effects, dominance and epistasis were important for the shoot formation trait. Selection would be effective among the isolated genotypes on individual basis.     

Impacts of erucic acid and glucosinolate content on genetic relationships between protein content and fatty acids of rape seed across environments

Impacts of erucic acid content (EAC) and glucosinolate content (GSLC) on the genetic correlations between protein content (PC) and oil content (OC) or PC and fatty acid contents (FAC) in rape seed (Brassica napus L.) was analyzed by using unconditional and conditional methods related to genetic effects from the diploid embryo nuclear genes, cytoplasm genes and diploid maternal plant nuclear genes. A diallel mating design in two environments was conducted by using eight varieties along with their F₁ and F₂. It was found that there were significant relationships between PC and EAC or PC and GSLC of rape seed, and the conditional analysis method could be used to exclude the influences of EAC or GSLC for further revealing the actual genetic relationships between PC and OC or PC and FAC. The results from conditional analysis showed that when PC was conditioned on EAC or GSLC the conditional phenotypic and genotypic relationships between PC|EAC and oleic acid content or PC|GSLC and OC were changed to significantly positive, while those between PC|EAC and eicosenoic acid content or PC|GSLC and linolenic acid content became significantly negative. Thus, the levels of EAC and GSLC of rape seed could affect the correlations between PC and OC or PC and FAC. For the conditional genetic relationship analysis of different genetic systems, visible changes were found for many genetic correlation components from the embryo, cytoplasm and maternal plant between PC and OC or PC and FAC after eliminating the influences of EAC or GSLC, especially for conditional embryo dominance, cytoplasmic, maternal additive main covariances and conditional embryo dominance interaction covariance.     

新疆高品质陆地棉纤维品质性状遗传分析研究

 以9-1696×CCRI 35配置单交组合及其衍生世代,利用该组合的P₁、P₂、F₁、F₂、B₁和B₂ 6世代群体的纤维品质性状,采用世代平均值法、主-多基因混合遗传模型分离分析法对该组合纤维长度、整齐度、比强度和伸长率4个纤维品质性状做遗传分析。结果表明：（1）4个纤维品质性状均以加性遗传为主,同时检测出显著的上位性效应。经模型适合性检验,纤维长度和伸长率两个纤维品质性状符合加性－显性－上位性遗传模型。比强度和整齐度性状符合加性－上位性遗传模型。（2）比强度和伸长率符合两对加性－显性－上位性主基因＋多基因混合遗传模型,其主基因遗传率分别为：比强度（47.80%）、伸长率（20.07%）。纤维长度和整齐度遗传受主基因和多基因共同控制。     

Genetic effects on Fe, Zn, Mn and P contents in Indica black pericarp rice and their genetic correlations with grain characteristics

Complete diallel crosses with 6 varieties of black pericarp rice and 1 variety of aromatic white rice were conducted to analyze the seed, maternal and cytoplasmic genetic effects on Fe, Zn, Mn and P contents in kernels by using a genetic model for quantitative traits of seeds in parents and their F₁s and F₂s. Seed, maternal as well as cytoplasmic genetic effects controlled the contents of all the mineral elements studied. The seed genetic effects were found to be more influential than the maternal genetic effects on Fe, Zn, Mn contents. Seed additive effects constituted a major component of the genetic effects whereas the seed additive along with maternal additive and dominant effects formed the main part in the inheritance of P content. The heritabilities of seed effects on all the mineral contents were highly significant (p< 0.01). The estimated values of narrow-sense heritabilites of seed genetic effects on Fe, Zn and Mn contents were high, while those of seed and maternal effects on P content were intermediate. Single plant selection and single grain selection based on the seed mineral element contents were advocated to improve the hybrid progeny. Genetic correlations showed that there existed significant genetic correlations of seed additive, seed dominance, cytoplasm, maternal additive and maternal dominance between grain characteristics such as 100-grain weight,grain length, grain width, grain shape and mineral elements Fe, Zn, Mn and P contents. Indirect selection of grain characteristics may be one of the breeding methods to select for higher contents of Fe, Zn, Mn and P in black pericarp indica rice. This revised version was published online in July 2006 with corrections to the Cover Date.     

大豆叶片性状和叶绿素含量QTL间的上位性和环境互作效应

以丰产性好、抗旱力强的栽培大豆晋豆23为母本,山西农家品种半野生大豆灰布支黑豆为父本杂交衍生的447个RIL作为供试群体。将亲本及447个家系分别于2011、2012和2013年采用随机试验种植,按照标准测量叶长、叶宽和叶柄长3个性状,并于2012年8月1日和8月8日和2013年8月2日和8月9日各测量1次叶绿素含量。采用QTLNETwork 2.0混合线性模型分析方法和主基因+多基因混合遗传分离分析法,对大豆叶片性状和叶绿素含量进行遗传分析和QTL间的上位性和环境互作效应研究。结果表明,叶长受2对加性-加性×加性上位性混合主基因控制,叶宽受3对等效主基因控制,叶柄长受4对加性-加性×加性上位性主基因控制,叶绿素含量受4对加性主基因控制;检测到10个与叶长、叶宽、叶柄长和叶绿素含量相关的QTL,分别位于A1、A2、C2、H_1、L和O染色体。其中2个叶长QTL分别位于C2和L染色体,是2对加性×加性上位互作效应及环境互作效应QTL;3个叶宽加性与环境互作QTL分别位于A2、C2和O染色体;2个叶柄长QTL分别位于L和O染色体;3个叶绿素含量QTL分别位于A1、C2和H_1染色体。叶片性状和叶绿素含量的遗传机制较复杂,加性效应、加性×加性上位互作效应及环境互作效应是大豆叶片性状和叶绿素含量的重要遗传基础。建议大豆分子标记辅助育种中,一方面要考虑起主要作用的QTL,另一方面要注重上位性QTL的影响,这对于性状的遗传和稳定表达具有积极的意义。     

Analysis of the genetic control of β-carotene and <Emphasis Type="SmallCaps">l</Emphasis>-ascorbic acid accumulation in an orange-brownish wild cherry tomato accession

An additive-dominance, additive × additive (ADAA) and genotype × environment interaction mix model was used to study the genetic control of β-carotene and l-ascorbic acid in six basic generations (P₁, P₂, F₁, F₂, BC₁P₁ and BC₁P₂) of tomato derived from the cross CDP8779 accession (Solanum lycopersicum L.) × CDP4777 accession (S. lycopersicum var. cerasiforme). The study was performed in two environments: (1) open field; (2) protected environment, consisting of hydroponic cultivation in a glasshouse. The results indicate that β-carotene accumulation was mainly additive (32.2% of the genetic component), with a small dominant component (4.2%) and an important additive × environment interaction contribution (63.6%). In target environments with moderate to high temperatures and no limiting radiation, this the expression additive × environment interaction could substantially enhance the β-carotene content. This trait showed also a high narrow-sense heritability (h ² = 0.62). Ascorbic acid accumulation was also mainly additive (61.7% of the genetic component), with a minor additive epistatic component (21.5%). This epistatic effect caused a negative heterosis that reduced the positive main additive effect. Nevertheless, in the described target environments, the additive × environment interaction contribution (16.8%) may enhance the ascorbic acid content and compensate for the negative heterosis effect. The total narrow-sense heritability of this trait can be considered useful (h ² = 0.52). In conclusion, the CDP4777 accession is a very interesting donor parent for the joint improvement of β-carotene (without diminishing lycopene content) and ascorbic acid content in commercial nutraceutical tomato breeding programmes; the F₁ hybrids derived from this accession showed nearly 450% of the commonly reported average β-carotene content and close to 130% of the ascorbic acid content of the female parent.     

中国南瓜可溶性固形物含量的主基因+多基因遗传分析

为明确中国南瓜可溶性固形物含量的遗传规律,选用中国南瓜杂交获得的6世代群体(P1、P2、F1、F2、BCP1、BCP2)为材料,应用植物数量性状的主基因+多基因遗传模型研究其遗传规律。结果表明,该群体可溶性固形物含量的遗传符合2对加性-显性-上位性主基因+加性-显性多基因混合遗传模型,2对主基因的加性效应均为-0.7077,均使可溶性固形物含量降低;显性效应分别为3.5034和1.3586,均使可溶性固形物含量升高。多基因的加性效应和显性效应分别为2.3066和-0.6679。其主基因遗传率在BCP1、BCP2、F2分别为17.06%、56.01%、95%,多基因遗传率在BCP1、BCP2、F2分别为47.16%、18.78%、0;说明主基因表现出较高的遗传力,可以在早期世代对可溶性固形物含量进行选择。研究为中国南瓜育种品质性状选择和分子标记辅助选择提供了理论依据。     

Identification of quantitative trait loci with main and epistatic effects for plant architecture traits in Upland cotton (Gossypium hirsutum L.)

Plant architecture is important for cotton cultivation and breeding. In this study, two mapping generations/populations F₂ and F_2:3 in Upland cotton (Gossypium hirsutum L.), derived from ‘Baimian1’ and TM‐1, were used to identify quantitative trait loci (QTLs) for 10 plant architecture traits. A total of 55 main‐effect QTLs (M‐QTLs) were detected. Four common M‐QTLs, qTFB‐10(F₂/F_2:3) for total fruit branches, qFBL‐26b(F₂)/qFBL‐26(F_2:3) for fruit branch length, qFBA‐5(F₂/F_2:3) for fruit branch angle and qFBN‐26b(F₂)/qFBN‐26(F_2:3) for fruit branch nodes, were found. The synergistic alleles and the negative alleles can be utilized in cotton plant architecture breeding programmes according to specific breeding objectives. Altogether 54 pairs of epistatic QTLs (E‐QTLs) exhibiting the interactions of additive‐by‐additive (AA), additive‐by‐dominant (AD), dominant‐by‐additive (DA) and dominant‐by‐dominant (DD) were detected. The epistasis appeared to be an important contributor to genetic variation in cotton plant architecture traits. Therefore, the identified markers associated with E‐QTLs as well as M‐QTLs will be of importance in future breeding programmes to develop cotton cultivars exhibiting desirable plant architecture.