Genetic analysis of kernel oil content in tropical maize with design III and QTL mapping

Oil content and grain yield in maize are negatively correlated, and so far the development of high-oil high-yielding hybrids has not been accomplished. Then a fully understand of the inheritance of the kernel oil content is necessary to implement a breeding program to improve both traits simultaneously. Conventional and molecular marker analyses of the design III were carried out from a reference population developed from two tropical inbred lines divergent for kernel oil content. The results showed that additive variance was quite larger than the dominance variance, and the heritability coefficient was very high. Sixteen QTL were mapped, they were not evenly distributed along the chromosomes, and accounted for 30.91% of the genetic variance. The average level of dominance computed from both conventional and QTL analysis was partial dominance. The overall results indicated that the additive effects were more important than the dominance effects, the latter were not unidirectional and then heterosis could not be exploited in crosses. Most of the favorable alleles of the QTL were in the high-oil parental inbred, which could be transferred to other inbreds via marker-assisted backcross selection. Our results coupled with reported information indicated that the development of high-oil hybrids with acceptable yields could be accomplished by using marker-assisted selection involving oil content, grain yield and its components. Finally, to exploit the xenia effect to increase even more the oil content, these hybrids should be used in the Top Cross^™ procedure.     

QTL mapping of maize (Zea mays) stay-green traits and their relationship to yield

A maize genetic linkage map derived from 115 simple sequence repeat (SSR) markers was constructed from an F₂ population. The F₂ was generated from a cross between a stay-green inbred line (Q319) and a normal inbred line (Mo17). The map resolved 10 linkage groups and spanned 1431.0 cM in length with an average genetic distance of 12.44 cM between two neighbouring loci. A total of 14 quantitative trait loci (QTL) were detected for stay-green traits at different postflowering time intervals and identified by composite interval mapping. The respective QTL contribution to phenotypic variance ranged from 5.40% to 11.49%, with trait synergistic action from Q319. Moreover, maize stay-green traits were closely correlated to grain yield. Additional QTL analyses indicated that multiple intervals of stay-green QTL overlapped with yield QTL.     

Genetic analysis of plant height using two immortalized populations of “CRI12 × J8891” in Gossypium hirsutum L.

Plant height is an important plant architecture trait that determines the canopy structure, photosynthetic capacity and lodging resistance of upland cotton populations. To understand the genetic basis of plant height for marker-assisted breeding, quantitative trait loci (QTL) analysis was conducted based on the genetic map of recombinant inbred lines (RILs) derived from the cross “CRI12 × J8891” (Gossypium hirsutum L.). Three methods, including composite interval mapping, multiple interval mapping and multi-marker joint analysis, were used to detect QTL across multiple environments in the RILs and in the immortalized F₂ population developed through intermating between RILs. A total of 19 QTL with genetic main effects and/or genetic × environment interaction effects were identified on 15 chromosomes or linkage groups, each explaining 5.8–14.3 % of the phenotypic variation. Five digenic epistatic QTL pairs, mainly involving additive × additive and/or dominance × dominance, were detected in different environments. Seven out of eight interacting loci were main-effect QTL, suggesting that these loci act as major genes as well as modifying genes in the expression of plant height. The results demonstrate that additive effects, dominance and epistasis are all important for the genetic constitution of plant height, with additive effects playing a more important role in reducing plant height. QTL showing stability across environments that were repeatedly detected by different methods can be used in marker-assisted breeding.     

玉米抗穗粒腐病QTL定位

用已构建的包括88个AFLP标记和151个SSR标记的遗传图谱和230个F₂植株用于抗病QTL定位研究,在四川雅安、绵阳对F2株系进行抗病性鉴定,采用复合区间定位法进行抗病QTL检测。在雅安检测到位于第2、3、4、6和9染色体上的抗病QTL 6个,解释表型变异的8.3%~25.7%;在绵阳检测到位于第1、6、7和9染色体上的抗病QTL 4个,解释表型变异的11.3%~26.4%。在10个抗病QTL中,位于第6和第9染色体上的2个同时在两点被检测到,贡献率均超过15%,表明玉米穗粒腐病确实存在遗传抗病性。利用2个环境抗病指数的平均值进行抗性QTL检测,共检测到位于第1、6和7连锁群上的3个抗性QTL,单个QTL的贡献率在8.9%~17.2%之间。结果有助于了解玉米穗粒腐病的抗性机制,并为分子标记辅助选择提供理论支撑。     

Molecular mapping of QTL for southwestern corn borer resistance, plant height and flowering in tropical maize

Development of multiple insect resistance in tropical maize represents a major effort of the maize breeding programme at CIMMYT. Resistance to the southwestern corn borer (SWCB) is polygenically controlled with primarily additive gene action. Our main objective was to identify quantitative trait loci (QTL) involved in resistance to SWCB. Other objectives were to detect QTL in the same population for plant height, female flowering, and the anthesis-silking interval (ASI). A population of 472 F₂ individuals derived from a cross between the susceptible line Ki3 and the resistant inbred CML139, was restriction fragment length polymorphism (RFLP) genotyped using 110 maize probes. F₃ families were rated for leaf-feeding damage after artificial infestation at one location in three consecutive years. Height and flowering were measured in protected trials in two locations. QTL analyses were conducted using joint composite interval mapping. Seven QTL on chromosomes 3, 5, 6, 8, and 9 explained 30% of the phenotypic variance (σ²_p) for SWCB damage. Most QTL alleles conferring resistance were contributed from CML139. QTL showed dominance, partial dominance and additive gene action. Eleven QTL dispersed across the genome were determined to affect plant height and explained 43% of σ²_p. Four of these were in close proximity to loci with qualitative effects on plant height. Thirteen QTL (50% of sigma;²_p) were identified for days to female flowering and nine (30% of σ²_p) for ASI. Our results, along with those from other mapping studies at CIMMYT, are allowing us to formulate marker-assisted selection schemes to complement the breeding efforts for such complex traits as borer resistance.     

QTL analysis of Cercospora leaf spot resistance in sugar beet

The inheritance of Cercospora leaf spot resistance in sugar beet was investigated by means of quantitative trait loci (QTL) analysis of a segregating population of 193 individuals, using 110 AFLP and 35 restriction fragment length polymorphism (RFLP) markers. Five QTL were found through composite interval mapping on linkage groups 1, 2, 3, and 9, respectively, two of which were linked on linkage group 3. The significance of these QTL was tested by permutation analysis The QTL had mostly additive, but also certain negative dominance effects; all the resistance alleles came from the Cercospora-resistant parent. Each quantitative trait locus accounted for 7-18% of the phenotypic variation, leaving 37% of the variation unexplained. The results are discussed in relation to the potential use of marker-assisted breeding for Cercospora leaf spot resistance in sugar beet.     

Mode of inheritance of common bean (Phaseolus vulgaris L.) traits for tolerance to low soil phosphorus (P)

Low soil phosphorus (P) has been singled out as a major constraint leading to perpetually low bean (Phaseolus vulgaris L.) grain yield far below the expected yield potential. In developing countries beans are mainly produced by small-scale farmers who have little capacity to use inorganic fertilizers to replenish their soils. Yet bean production contributes significantly to their income and provides a cheap source of protein to rural and urban populations. The genetics of inheritance of the traits conferring low soil P tolerance is not well understood. The identification and understanding of the mode of inheritance of the traits for P-efficiency in bean will go along way in boosting bean yields through development of varieties adapted to low soil P. The objective of this study was to determine the inheritance of the traits conferring adaptation to low soil P, for the important large seeded red mottled bean market class. Three parents with known tolerance to low soil P were crossed with five adapted but non-tolerant genotypes in an 8 × 8 half diallel mating scheme. The resulting F₁ seeds were evaluated under medium and low soil P conditions at two locations. Both general combining ability (GCA) and specific combining ability (SCA) variances were highly significant (P ≤ 0.01) for all five characters studied except SCA variance for root dry weight at one location. The magnitude of GCA variance was up to twelve times higher than the SCA variance. The GCA:SCA ratio varied from 0.62 to 0.96 for the characters studied. The additive genetic variance was more important than the dominance variance for tolerance to low soil P.     

Identification of QTL for stalk sugar-related traits in a population of recombinant inbred lines of maize

Increasing sugar content in silage maize stalk improves its forage quality and palatability. The genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement, yet little information on QTL for stalk sugar content in maize has been reported. To this end, we investigated QTLs associated with stalk sugar traits including Brix, plant height (PHT), three ear leaves area (TELA), and days to silking (DTS) in two environments using a population of 202 recombinant inbred lines from a cross between YXD053, which has a high stalk sugar content, and Y6-1, which has a low stalk sugar content. A genetic map with 180 SSR and 10 AFLP markers was constructed, which spanned 1,648.6 cM of the maize genome with an average marker distance of 8.68 cM, and QTLs were detected using composite interval mapping. Seven QTLs controlling Brix were mapped on chromosomes 1, 2, 6 and 9 in the combined environments. These QTLs could explain 2.69–13.08 % of the phenotypic variance. One major QTL for Brix on chromosome 2 located between the markers bnlg1909 and umc1635 explained 13.08 % of the phenotypic variance. Y6-1 also contributed QTL allele for increased Brix on chromosome 6. One major QTLs controlling PHT on chromosome 1 and TELA on chromosome 4 were also identified and accounted for 13.68 and 12.49 % of the phenotypic variance, respectively. QTL alleles for increased DTS were located on chromosomes 1 and 5 of YXD053. Significant epistatic effects were identified in four traits, but no significant QTL × environment interactions were observed. The information presented here may be valuable for stalk sugar content improvement via marker-assisted selection in silage maize breeding programs.     

Fine mapping of major QTLs for alkaline tolerance at the seedling stage in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) through genetic linkage analysis combined with high-throughput DNA sequencing

Exploiting genes and quantitative trait loci (QTLs) related to maize (Zea mays L.) alkaline tolerance is helpful for improving alkaline resistance. To explore the inheritance of maize alkaline tolerance at the seedling stage, a mapping population comprising 151 F_2:3 lines derived from the maize cross between Zheng58, tolerant to alkaline, and Chang7-2, sensitive to alkaline, was used to establish a genetic linkage map with 200 SSR loci across the 10 maize linkage groups, with an average interval of 6.5 cM between adjacent markers. QTLs for alkaline resistant traits of alkaline tolerance rating (ATR), germination rate (GR), relative conductivity (RC), weight per plant (WPP) and proline content (PC) were detected. The obtained results were as follows: Five QTLs on chromosomes 2, 5 and 6 (GR and WPP: chr. 2; PC and ATR: chr. 5; and RC: chr. 6) were mapped. For precise mapping of the QTLs related to alkaline resistance, two bulked deoxyribonucleic acid (DNA) pools were constructed using individual DNAs from the most tolerant 30 F₂ individuals and the most sensitive 30 F₂ individuals according to the ATR and used to establish a high density map of SLAF markers strongly associated with the ATR by specific locus amplified fragment sequencing (SLAF-Seq) combined with super bulked segregant analysis (superBSA). One marker-intensive region involved three SLAFs at 296,000–6,203,000 bp on chromosome 5 that were closely related to the ATR. Combined with preliminary QTL mapping with superBSA, two major QTLs on chromosome 5 associated with alkaline tolerance at the maize seedling stage were mapped to marker intervals of dCap-SLAF31521 and dCap-SLAF31535 and phi024 and dCap-SLAF31521, respectively. These QTL regions involved 9 and 75 annotated genes, respectively. These results will be helpful for improving maize alkaline tolerance at the seedling stage by marker-assisted selection programs and will be useful for fine mapping QTLs for maize breeding.     

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.     

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.     

不同发育时期玉米叶片保绿度遗传主效应及其与环境互作效应分析

采用包括基因型×环境互作效应的加性-显性遗传模型及非条件和条件的分析方法,研究多环境下玉米吐丝后不同发育时期叶片保绿度性状的遗传主效应及其与环境互作效应。结果表明:非条件遗传分析表明控制玉米叶片保绿度在发育不同时期的各遗传效应均受到环境条件的影响并存在着表达水平上的差异;条件遗传方差分量分析表明,控制玉米吐丝后不同时期叶片保绿度表现的净遗传效应在各个发育时期均有新的不同程度的表达,对玉米由抽丝期到成熟期发育进程基因表达净效应的选择越来越受到环境条件的影响。     

Quantitative trait analysis of flowering time in spring rapeseed (B. napus L.)

The inheritance of flowering time trait in spring-type rapeseed (Brassica napus L.) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for the trait are only few. We identified QTL underlying variation for flowering time in a doubled haploid (DH) mapping population of nonvernalization-responsive canola (B. napus L.) cultivar 465 and line 86 containing introgressions from Houyou11, a Chinese early-flowering cultivar in Brassica rapa L. Significant genetic variation in flowering time and response to photoperiod were observed among the DH lines from 465/86. A molecular linkage map was generated comprising three types of markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 4 major loci, localized on four different linkage groups A6, A7, C8 and C9. These loci each accounted for between 9.2 and 12.56 % of the total genotypic variation for first flowering. The published high-density maps for flowering time mapping used different marker systems, and the parents of our crosses have different genetic origins, with either spring-type B. napus or B. rapa. So we cannot determine whether the QTL on the same linkage groups were in the same region or not. There was evidence of additive × additive epistatic effects for flowering time in the DH population. Epistasis existed not only between main-effect QTLs, but also between QTLs with minor effects. Four pair of epistasis effects between minor QTLs explained about 20 % of the genetic variance observed in the DH population. The results indicated that minor QTLs for flowering time should not be ignored. Significant genotypes × environment interactions were also found for the quantitative traits, and with significant change in the ranking of the DH lines in different environments. The results implied that FQ3 was a non-environment-specific QTL and may control flowering time by autonomous pathway. FQ4 were winter-environment-specific QTL and may control flowering time by photoperiod-pathway. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for high altitude areas, via marker-assisted selection.     

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

Wheat (Triticum aestivum L.) yield is directly proportional to physio-morphological traits. A high-density genetic map consisting of 2575 markers was used for mapping QTL controlling stay-green and agronomic traits in wheat grown under four diverse water regimes. A total of 108 additive QTL were identified in target traits. Among them, 28 QTL for chlorophyll content (CC) were detected on 11 chromosomes, 43 for normalized difference vegetation index (NDVI) on all chromosomes except 5B, 5D, and 7D, five for spikes per plant (NSP) on different chromosomes, nine for plant height (PH) on four chromosomes, and 23 for thousand-kernel weight (TKW) on 11 chromosomes. Considering all traits, the phenotypic variation explained (PVE) ranged from 3.61 to 41.62%. A major QTL, QNDVI.cgb-5A.7, for NDVI with a maximum PVE of 20.21%, was located on chromosome 5A. A stable and major PH QTL was observed on chromosome 4D with a PVE close to 40%. Most distances between QTL and corresponding flanking markers were less than 1 cM, and approximately one-third of the QTL coincided with markers. Each of 16 QTL clusters on 10 chromosomes controlled more than one trait and therefore could be regarded as pleiotropic regions in response to different water regimes. Forty-one epistatic QTL were identified for all traits having PVE of 6.00 to 25.07%. Validated QTL closely linked to flanking markers will be beneficial for marker-assisted selection in improving drought-tolerance in wheat.     

Meta-analysis of constitutive and adaptive QTL for drought tolerance in maize

The response of plants to drought stress is very complex and involves expression of a lot of genes and pathways for diverse mechanisms and interactions with environments. Many quantitative trait loci(QTL) mapping experiments have given heterogeneous results due to use of different genotypes and populations tested in various environments. Our purpose was to identify some important constitutive and adaptive QTL using meta-analysis and to find specific genes and their families for speculating on drought tolerance networks. A total of 239 QTL detected under water-stressed conditions and 160 detected under control conditions from 12 populations tested in 22 experiments were compiled and compared, resulting in identification of 39 consensus QTL under water stress, and 36 under control conditions. Of them, 32 consensus QTL were supposed to be adaptive while others were constitutive QTL. The consensus QTL on chromosomes 1, 2, 3, 5, 6 and 9 were highly overlapped with several different traits and could be identified under multiple environments, most of which were related to traits of high phenotypic variance. Moreover, 48 candidate genes related to stress tolerance were located in silico in these consensus QTL regions what should facilitate the construction of QTL networks and help to understand the mechanisms related to drought tolerance.     

Stay-green expression in early generation sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench] QTL introgression lines

Reduced leaf senescence (stay-green) has been demonstrated to improve tolerance of post-flowering moisture stress in grain sorghum. A number of quantitative trait loci (QTLs) associated with stay-green have been identified in sorghum, to facilitate transfer of this trait into adapted genetic backgrounds. This study reports initial evaluations, in both well watered and post-flowering stress environments, following partial introgression (BC₂F₃/BC₁F₄ generations) of four stable stay-green QTLs (StgB, Stg1, Stg3 and Stg4) from donor parent B35 to senescent variety R 16. The majority of the introgression lines had higher leaf chlorophyll levels at flowering (a distinctive trait of the donor parent) and a greater percentage green leaf area during the latter part of grain filling, than did R 16, indicating that the stay-green QTLs were expressed phenotypically in the R 16 background. None of the QTL introgression lines achieved the same level of stay-green as B35, however. Maintenance of a greater relative green leaf area during the latter half of grain filling was related to a greater relative grain yield in two of three post-flowering moisture deficit environments in which the materials were evaluated (r ² = 0.34 in 2004–2005 and r ² = 0.76 in 2005–2006), as was a direct measure of leaf chlorophyll in one of the post-flowering stress environments in which this was measured (r ² = 0.42, P < 0.05). Thus the study provided useful evidence that the marker-assisted backcross transfer of stay-green QTLs from B35 into an adapted, but senescent background has the potential to enhance tolerance of post-flowering drought stress in sorghum.     

Molecular mapping of quantitative trait loci (QTLs) controlling aluminium tolerance in bread wheat

Aluminium (Al) toxicity is a major constraint to crop productivity in acidic soils. A quantitative trait locus (QTL) analysis was performed to identify the genetic basis of Al tolerance in the wheat cultivar ‘Chinese Spring’. A nutrient solution culture approach was undertaken with the root tolerance index (RTI) and hematoxylin staining method as parameters to assess the Al tolerance. Using a set of D genome introgression lines, a major Al tolerance QTL was located on chromosome arm 4DL, explaining 31% of the phenotypic variance present in the population. A doubled haploid population was used to map a second major Al tolerance QTL to chromosome arm 3BL. This major QTL (Qalt _CS .ipk-3B) in ‘Chinese Spring’ accounted for 49% of the phenotypic variation. Linkage of this latter QTL to SSR markers opens the possibility to apply marker-assisted selection (MAS) and pyramiding of this new QTL to improve the Al tolerance of wheat cultivars in breeding programmes.     

Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

Drought is a major abiotic constraint for rice production worldwide. The quantitative trait loci (QTLs) for drought tolerance traits identified in earlier studies have large confidence intervals due to low density linkage maps. Further, these studies largely focused on the above ground traits. Therefore, this study aims to identify QTLs for root and shoot traits at the vegetative growth stage using a genotyping by sequencing (GBS) based saturated SNP linkage map. A recombinant inbred line (RIL) population from a cross between Cocodrie and N-22 was evaluated for eight morphological traits under drought stress. Drought was imposed to plants grown in 75 cm long plastic pots at the vegetative growth stage. Using a saturated SNP linkage map, 14 additive QTLs were identified for root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. Majority of the drought responsive QTLs were located on chromosome 1. The expression of QTLs varied under stress and irrigated condition. Shoot length QTLs qSL1.38 and qSL1.11 were congruent to dry shoot mass QTL qDSM1.38 and dry root mass QTL qDRM1.11, respectively. Analysis of genes present within QTL confidence intervals revealed many potential candidate genes such as laccase, Calvin cycle protein, serine threonine protein kinase, heat shock protein, and WRKY protein. Another important gene, Brevis radix, present in the root length QTL region, was known to modulate root growth through cell proliferation and elongation. The candidate genes and the QTL information will be helpful for marker-assisted pyramiding to improve drought tolerance in rice.     

玉米抗丝黑穗病QTL分析

以Mo17（抗）×黄早四（感）的F₂分离群体（191个单株）为作图群体,构建了含有84个SSR位点和48个AFLP位点的遗传连锁图谱,全长1 542.9 cM,平均图距11.7 cM。在吉林省公主岭和黑龙江省哈尔滨2个地点通过人工接种方法对184个相应的F₃家系（缺失7个）进行抗病鉴定。采用复合区间作图法对抗丝黑穗病数量性状位点（QTL）进行定位及遗传效应分析。在吉林公主岭地区检测到5个QTL,分别位于第1、2、3、8、9染色体上,解释的表型方差为10.0%~16.3%。在黑龙江哈尔滨地区也检测到5个QTL,分别位于第1、2、3、4、7染色体上,解释的表型方差为4.6%~13.4%。比较分析发现,两地一致在第2、3染色体上各检测到1个QTL,其中第2染色体上的表现为超显性效应,第3染色体上的表现为加性效应。研究结果为玉米抗丝黑穗病种质改良提供了重要信息。     

QTL for popping characteristics in popcorn

Popping volume (PV), flake size (FS) and popping rate (PR) are three important popping characteristics in popcorn ( Zea mays L.). We developed 259 F_2:3 lines from a cross between a dent corn inbred 'Dan232' and a popcorn inbred 'N04' that were grown during spring and summer to evaluate the three popping characteristics. Fifteen quantitative trait loci (QTL) were detected on chromosomes 1, 2, 5, 6, 7 and 8 using composite interval mapping. The numbers of QTL were 6, 4 and 5 for PV, FS and PR, respectively, with phenotypic variance explained ranging from 4.9% to 15.6% for a single QTL, accounting for a total of 54.0%, 34.5% and 39.1% of the total phenotypic variance respectively. Partially dominance and overdominance effects played an important role in popping characteristics. Only 13 pairs of digenic interactions were detected. The QTL on chromosome bin 1.05–1.06 for PV and PR, and 5.07 for FS were in accordance with previous reports and could be good candidate QTL for marker-assisted selection. There was a significant correlation amongst QTL on chromosomes 1, 6 and 8 for PV and PR.