Rice Cross Research Articles

Mapping of Quantitative Trait Loci for Contents of Macro- and Microelements in Milled Rice (Oryza sativa L.).

Macro- and microelement contents are important traits for nutritional quality in rice. In this study, quantitative trait loci (QTLs) for the contents of seven mineral elements in milled rice were detected using recombinant inbred lines (RILs) of the indica rice cross Zhenshan 97/Milyang 46, followed by the validation and fine mapping of a QTL region on the short arm of chromosome 6. A total of 20 QTLs distributed on chromosomes 1, 3, 5, 6, 10, and 11 were detected in the RIL population. Co-localizations of QTLs for multiple traits were observed, of which the qP3/qMg3/qZn3 region was shown to have the largest effects for the contents of phosphorus, magnesium, and zinc, and the qK6.1/qCa6/qZn6/qMn6/qCu6 region was found to be responsible for five of the seven traits. Using near isogenic lines having sequential segregating region, the target QTL on chromosome 6 was delimitated to a 29.9 kb region flanked by RM19410 and Si2944. This QTL showed major effects for all seven traits, with the enhancing alleles derived from the male parent Milyang 46.

Quantitative Trait Locus Mapping and Candidate Gene Analysis for Functional Stay-Green Trait in Rice

Functional stay-green (FSG) delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green (NFSG) retains only leaf greenness without sustaining photosynthetic activity. Retention of chlorophylls and photosynthetic capacity is important for increasing crop yield. We determined the main-effect quantitative trait loci (QTLs) for FSG traits in the japonica rice SNU-SG1 and isolated candidate genes. To identify QTLs influencing FSG, we analyzed eight traits: (1) 1 day after heading-degree of chlorophyll content of flag leaf, (2) 1 day after heading-degree of chlorophyll content of second leaf, (3) 1 day after heading-degree of chlorophyll content of flag and second leaves, (4) 50 day after heading-degree of chlorophyll content of flag leaf, (5) 50 day after heading-degree of chlorophyll content of second leaf, (6) 50 day after heading-degree of chlorophyll content of flag and second leaves, (7) relative decline degree of chlorophyll content of flag and second leaves, and (8) flowering time. We carried out QTL analysis with F7 RIL from a cross of japonica rice ‘SNU-SG1’ and indica rice ‘Milyang23 (M23)’. Using 131 molecular markers, we identified 18 QTLs for the eight traits with a threshold LOD value > 2.8. Sequence analysis identified 16 candidate genes for 10 main-effect QTLs. Of these, we have chosen seven strong candidate genes for the 10 main-effect QTLs. These genetic resources will be useful for breeding high-yielding rice cultivars.

Genetic dissection of hybrid breakdown in an indica/japonica cross and fine mapping of a quantitative trait locus qSF-12 in rice (Oryza sativa L.)

Hybrid breakdown is an important form of post-zygotic reproductive barriers, often arising from hybrid progeny between two varietal groups of Asian cultivated rice (Oryza sativa L.), indica and japonica. However, the genetic mechanism underlying the hybrid breakdown remains unclear. In the present study, a chromosomal segment substitute line (CSSL) population together with a backcross inbred line population, derived from the same cross of Sasanishiki/Habataki, were employed for genetic analysis of rice hybrid breakdown (spikelet fertility as index). Quantitative trait locus mapping results showed that, in both populations, qSF-12 was stably detected across different locations and growing seasons, which was found to interact with qSF-8. Subsequently, a CSSL line SL438 with low spikelet fertility was used to cross with Sasanishiki to generate the secondary F2 population for the mapping of qSF-12. The results showed that qSF-12 was restricted to a 137-kb long region on BAC clone AL928774, containing 11 predicted ORFs in total. The DNA sequencing revealed that a 3-bp insertion/deletion exists between two parents in the coding region of LOC_Os12g38850. Together with the RNA-seq data, it is suggested that LOC_Os12g38850is the putative candidate of qSF-12, which encodes a DUF1336 domain containing protein. These results provide an important clue to further dissect the mechanism of hybrid breakdown in rice and the linked markers will be useful in rice cross breeding.

Development and cytogenetic characterization of some interspecific crosses in rice (Oryza sativa L. × Oryza rufipogon Griff.)

Development and cytogenetic characterization of some interspecific crosses in rice (Oryza sativa L. × Oryza rufipogon Griff.)

Studies on the effects of pericarp pigmentation on grain development and yield of black rice

Black rice was characterized by dark purple pericarp and much lower yield than that of white rice varieties. We investigated the factors responsible for the lower yields of black rice by conducting crosses of rice with purple pericarp mutant and white pericarp cultivars. The seed weight of black rice was lower than that of brown or white rice progeny within the crosses. The F2 segregants showed increased anthocyanin deposition with simultaneous reduction of chlorophyll in the seed pericarp. These results revealed that an unknown metabolic alteration exists in the chlorophyll synthesis due to the high level of cyanindin-3-0-glucoside deposition in the purple pericarp rice, indicating that anthocyanin deposition in the pericarp of black rice hindered the photosynthetic rate, leading to low yield. These findings suggest that the low yield of black rice is closely related to physiological factors other than the genetic yield traits.

Mapping of qTGW1.1, a Quantitative Trait Locus for 1000-Grain Weight in Rice (Oryza sativa L.)

1000-grain weight (TGW) is one of the three component traits of the grain yield in rice (Oryza sativa L). This study was conducted to validate and fine-map qTGW1.1, a minor QTL for TGW which was previously located in a 3.7-Mb region on the long arm of rice chromosome 1. Five sets of near isogenic lines (NILs) were developed from two BC2F4 populations of the indica rice cross Zhenshan 973/Milyang 46. The NIL sets consisted of two homozygous genotypic groups differing in the regions RM11448−RM11522, RM11448−RM11549, RM1232−RM11615, RM11543−RM11554 and RM11569−RM11621, respectively. Four traits, including TGW, grain length, grain width and heading date, were measured. Phenotypic difference between the two genotypic groups in each NIL population was analyzed using SAS procedure GLM. Significant QTL effects were detected on TGW with the Zhenshan 97 allele increasing grain weight by 0.12g to 0.14g and explaining 8.30% to 15.19% of the phenotypic variance. Significant effects were also observed for grain length and width, whereas no significant effect was found for heading date. Based on comparison among the five NILs on the segregating regions and the results of QTL analysis, qTGW1.1 was delimited to a 376.9-kb region flanked by DNA markers Wn28382 and RM11554. Our results indicate that the effects of minor QTLs could be steadily detected in a highly isogenic background and suggest that such QTLs could be utilized in the breeding of high-yielding rice varieties.

Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.).

Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F1s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.

Optimization of Media and Cold Pretreatment for Anther Culture Using Japonica/Indica and Indica/Indica Hybrids and their Callus Induction Comparisons in Different Rice Crosses

Rice ( Oryza sativa ) is pivotal to the lives of a large number of people around the world. Nowadays, anther culture is widely used in rice improvement as it can increase the selection efficiency. By optimizing the induction media and preservation time for cold pre-treatment, a significant improvement of embryogenic potential of the callus has been obtained in 3 different crosses of indica and japonica rice cultivars. It was observed that medium 2A was the best among the others as it was capable to induce a great number of calli while the addition of silver nitrate to the N6 medium doubled up the production of embryogenic calli. Analysis of variance indicated that there was a significant interaction between medium and cold pre-treatment. Seven days of preservation time showed much better callus production in N6 medium compared to MS medium. Significant differences of the callus induction were observed among indica cultivars. Therefore, seven days cold pre-treatment in the combination of silver nitrate in N6 medium can be used in practicing anther culture technique in indica rice. Anther culture technique was also used in twelve rice genotypes that consisted of three different rice crosses namely indica aromatic × japonica aromatic, indica aromatic × indica aromatic, and indica non-aromatic × indica aromatic to produce and comparisons of callus induction. It was found that MRQ50×Rambir Basmati genotype grew faster than other genotypes. Meanwhile, MR219×Rato Basmati took longest time to grow up and MR219×Sadri produced more callus than other genotypes. In addition, the indica non-aromatic× indica aromatic cross had the highest frequency in callus formation. Finally, the genotypes that produced more callus could be used as potential breeding material.

Genetic Analysis of F1 Hybrids Derived from Aromatic (Exotic) × Aromatic (Malaysian) Rice Crosses and Their Callus Induction Performance for Haploid Production

The aim of this study was basically to develop new aromatic rice lines through integrated breeding approaches. After screening and selection of superior parental materials, F1s were raised from four different crosses (MRQ50×Gharib, MRQ50×RMB, MRQ50×RTB and MRQ50×E13) and used for haploid production through Anther culture. Phenotypic coefficient of variation % (PCV), genotypic coefficient of variation % (GCV), heritability % (h2), genetic advance (GA) were estimated for yield and yield contributing traits such as for panicle length, grain per panicle, 1000 grain weight and yield per plant. In the cross MRQ50×RMB, the highest PCV was observed in grain per panicle (34.29) followed by yield per plant (31.73), 1000 grain weight (18.44), and panicle length (12.30). The same trends were occurred in cross MRQ50×RTB. The highest GCV was detected in grain per panicle (32.15) followed by yield per plant (30.90), 1000 grain weight (16.67) and panicle length (10.13). However, in the cross MRQ50×RTB, the highest GCV was obtained in yield per plant (37.89) followed by grain per panicle (30.54) and panicle length (9.33). Yield per plant was distinguished as the highest heritable trait in the cross MRQ50×RMB followed by grain per panicle (87.9), 1000 grain weight (81.7), and panicle length (67.8). On the contrary, in the cross MRQ50×RTB, this scenario was a bit different in which yield per plant was detected a highly heritable trait but the trends were different in grain per panicle, 1000 grain weight, and panicle length. Finally, the highest genetic advance was occurred in yield per plant followed by 1000 grain weight, grain per panicle, and panicle length. These trends were equal in both crosses. Study of callus induction ability of all hybrids studies showed that the best performance of callus induction was MRQ50×Gharib and N6 medium was found to be adequate for callus induction.

Registration of a Rice Gene Mapping Population of Lemont × Jasmine 85 Recombinant Inbred Lines

A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar Lemont and indica cultivar Jasmine 85 was developed to facilitate genetic studies for important agronomic traits. The indica- and tropical japonica-based rice recombinant inbred line (RIL) mapping population has been used to identify genomic regions associated with resistance to sheath blight (caused by Rhizoctonia solani) and rice blast (caused by Magnaporthe oryzae). The Lemont × Jasmine 85 mapping population, also referred to as SB5 (Reg. No. MP-7, NSL 506950), was developed under the Rice Coordinated Agricultural Project (RiceCAP) and released on 31 Aug. 2009 by the USDA–ARS and University of Arkansas, Division of Agriculture. The mapping population has 572 F2:8 RILs, 256 of which were used to construct a linkage map using simple sequence repeat markers to identify quantitative trait loci for sheath blight and blast resistance. This mapping population and related datasets represent a valuable resource for basic rice genomic research and applied marker-assisted breeding efforts in disease resistance and other agronomic traits.

Identification of Quantitative Trait Loci for Agronomic Traits in Two Rice Populations Derived from a Cross with a Wide Compatibility Line

Hybrid sterility is the major obstacle that can act as a barrier to genetic recombination and limits favorable gene transfer during inter-subspecific crosses in rice. However, hybrid sterility can be overcome by utilization of wide-compatible varieties (WCV). In the present study, two F2 populations generated from crosses between a wide-compatibility line (HWC-line) and two Korean varieties, Dasan and Hwacheong were evaluated for eight agronomic traits. A total of 157 molecular markers consisted of 116 STS, 40 SSR and 1 FNP were used to create genetic linkage maps spanning all 12 chromosomes. Twenty-one main-effect QTLs (M-QTLs) were identified in HWC-line/Dasan (HD) population. These loci are populated with two QTLs for culm length, one for spikelet per panicle, one for spikelet fertility, four for grain length, five for grain width, five for grain shape, and three for 100 grain-weight. In HWC-line/Hwacheong (HH) population, 17 QTLs were detected including two QTLs for culm length, one for panicle length, one for spikelet fertility, five for grain length, three for grain width, three for grain shape, and two for 100-grain weight. Of the total 34 QTLs found in the two F2 populations, 9 QTLs associated with culm length, grain length, grain width and grain shape were newly identified in this study. These QTLs will be useful for further understanding the genetic basis of agronomic traits and for developing markers for selection in rice breeding. In addition, HWC-line could be used as a bridge for inter-subspecies crosses overcoming hybrid sterility.

Fine mapping of qHd1, a minor heading date QTL with pleiotropism for yield traits in rice (Oryza sativa L.).

Key message A minor QTL for heading date located on the long arm of rice chromosome 1 was delimitated to a 95.0-kb region using near isogenic lines with sequential segregating regions. Heading date and grain yield are two key factors determining the commercial potential of a rice variety. In this study, rice populations with sequential segregating regions were developed and used for mapping a minor QTL for heading date, qHd1. A total of 18 populations in six advanced generations through BC2F6 to BC2F11 were derived from a single BC2F3 plant of the indica rice cross Zhenshan 97 (ZS97)///ZS97//ZS97/Milyang 46. The QTL was delimitated to a 95.0-kb region flanked by RM12102 and RM12108 in the terminal region of the long arm of chromosome 1. Results also showed that qHd1 was not involved in the photoperiodic response, having an additive effect ranging from 2.4 d to 2.9 d observed in near isogenic lines grown in the paddy field and under the controlled conditions of either short day or long day. The QTL had pleiotropic effects on yield traits, with the ZS97 allele delaying heading and increasing the number of spikelets per panicle, the number of grains per panicle and grain yield per plant. The candidate region contains ten annotated genes including two genes with functional information related to the control of heading date. These results lay a foundation for the cloning of qHd1. In addition, this kind of minor QTLs could be of great significance in rice breeding for allowing minor adjustment of heading date and yield traits.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2395-7) contains supplementary material, which is available to authorized users.

Dissection of qTGW1.2 to three QTLs for grain weight and grain size in rice (Oryza sativa L.)

Dissection of qTGW1.2, a minor quantitative trait locus (QTL) for 1,000-grain weight located on the long arm of rice chromosome 1, was reported here. Six sets of near isogenic lines (NILs) were developed from six BC2F9 plants of the indica rice cross Zhenshan 973/Milyang 46, respectively, segregated in a sequential order covering the region for qTGW1.2. They were tested for 1,000-grain weight, grain length, grain width and heading date. The SAS procedure GLM was used to analyze the phenotype differences among three genotypic groups in each NIL set. The qTGW1.2 was separated into three QTLs, including qTGW1.2a located in the 933.6 kb interval RM11730–RM11762, qTGW1.2b in the 418.8 kb interval RM11781–RM11800, and qTGW1.2c in the 2.1 Mb interval RM11800–RM11885. While qTGW1.2a and qTGW1.2c displayed the genetic action mode of negatively partial dominance, qTGW1.2b appeared to have a positively dominance effect as large as its additive effect. In addition, the effects of the three QTLs were consistently detected in different NIL sets. It was also shown that the effects of qTGW1.2a and qTGW1.2b on grain weight were related more to grain length than grain width, and qTGW1.2c related more to grain width than grain length. Our results indicate that the effects of minor QTLs could be steadily detected in a highly isogenic background and suggest that dominance effects of minor QTLs might play an important role in the genetic control of heterosis in rice.

Analysis of segregation distortion and its relationship to hybrid barriers in rice.

BackgroundSegregation distortion (SD) is a frequently observed occurrence in mapping populations generated from crosses involving divergent genotypes. In the present study, ten genetic linkage maps constructed from reciprocal F2 and BC1F1 mapping populations derived from the parents Dasanbyeo (indica) and Ilpumbyeo (japonica) were used to identify the distribution, effect, and magnitude of the genetic factors underlying the mechanisms of SD between the two subspecies.ResultsSD loci detected in the present study were affected by male function, female function, and zygotic selection. The most pronounced SD loci were mapped to chromosome 3 (transmitted through male gametes), chromosome 5 (transmitted through male gametes), and chromosome 6 (transmitted through female gametes). The level of SD in BC1F1 populations which defined by chi-square value independence multiple tests was relatively low in comparison to F2 populations. Dasanbyeo alleles were transmitted at a higher frequency in both F2 and BC1F1 populations, suggesting that indic a alleles are strongly favored in inter-subspecific crosses in rice. SD loci in the present study corresponded to previously reported loci for reproductive barriers. In addition, new SD loci were detected on chromosomes 2 and 12.ConclusionThe identification of the distribution of SD and the effect of genetic factors causing SD in genetic mapping populations provides an opportunity to survey the whole genome for new SD loci and their relationships to reproductive barriers. This provides a basis for future research on the elucidation of the genetic mechanisms underlying SD in rice, and will be useful in molecular breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-014-0003-8) contains supplementary material, which is available to authorized users.

Genetic variabiity and character association for quality traits in recombinant inbred lines derived from inter sub-specific crosses of rice (Oryza sativa L.)

The investigation was carried out to study the genetic parameters for quality and nutritional characters in 60 recombinant inbred lines (RIL’s) of rice. Analysis of variance revealed significant differences for all the traits. It was observed that grain yield per plant was positively significant associated with seed width, milling per cent, gelatinization temperature, amylose content and kernel breadth before cooking. Kernel length after cooking, seed width, milling per cent, amylose content and gelatinization temperature had positive direct effect on grain yield. Comprehensive examination of result revealed that the recombinant inbred lines tested for high yield in rice viz., RIL-77, 08, 99, 75, 10 and 13 were identified as superior. DOI: http://dx.doi.org/10.3329/bjb.v43i1.19756 Bangladesh J. Bot. 43(1): 97-99, 2014 (June)

Red pericarp introgression lines derived from interspecific crosses of rice: physicochemical characteristics, antioxidative properties and phenolic content

Antioxidative properties and physicochemical characteristics of introgression lines (ILs) and their recurrent parents were analyzed. In addition, catalase (CAT) and superoxide dismutase (SOD) activities and free radical-scavenging capacity were evaluated, since these are important antioxidative properties for developing nutraceutical and functional foods. Comparative analysis of the brown and milled rice fractions of ILs with their respective recurrent parents revealed 2.26- and 1.22-fold increase in total phenolics, 1.95- and 2.09-fold increase in flavonoids, 8.38- and 6.80-fold increase in proanthocyanidins and 1.55- and 1.20-fold increase in tannins in brown and milled rice fractions respectively. Higher CAT (1.36- and 1.89-fold) and SOD (1.71- and 2.02-fold) activities and Trolox equivalent antioxidant capacity (TEAC, 7.13- and 1.98-fold) were observed in brown and milled rice fractions respectively of ILs compared with their respective recurrent parents. A high and positive correlation was obtained between TEAC and total phenols (0.73, P ≤ 0.01), flavonoids (0.66, P ≤ 0.05) and proanthocyanidins (0.69, P ≤ 0.05). The yield parameters and physicochemical characteristics of the grains, in general, were comparable in the ILs and their respective recurrent parents. The ILs of rice reported in the present study exhibited significant positive differences in the content of phenolic constituents and antioxidant properties with good grain quality characteristics over their recurrent parents, indicating their potential as a natural source of phytochemicals for nutraceutical and functional food development.

Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing

A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing. Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 "high quality" SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.

Natural Variation in OsPRR37 Regulates Heading Date and Contributes to Rice Cultivation at a Wide Range of Latitudes

Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus (QTL) mapping and candidate gene analysis using whole-genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 (OsPRR37; hereafter PRR37) is responsible for the Early heading7-2 (EH7-2)/Heading date2 (Hd2) QTL which was identified from a cross of late-heading rice 'Milyang23 (M23)' and early-heading rice 'H143'. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT (CONSTANS, CO-like, and TOC1) domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day conditions, and are adapted to the northernmost regions of rice cultivation, up to 53° N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and Ghd7/Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.

Heterosis in F1 generations of two Indica rice crosses for growth and yield characteristics

The Journal of Agricultural Sciences is a peer reviewed journal aiming to publish high quality articles on topical issues in Agriculture. The journal provides a forum for Sri Lankan and international scholars especially in Asia and Africa to publish authoritative and well referenced articles in agriculture related areas. The journal publishes original research works, book reviews, short communications and comparative articles. JAS is published by the Faculty of Agricultural Sciences of the Sabaragamuwa University of Sri Lanka.The journal adheres to the publication ethics as portrayed by the Committee on Publication Ethics (COPE) and is a member of this Organisation,The Journal is also available on the Sabaragamuwa University of Sri Lanka website http://www.sab.ac.lk/agri-journalIt is indexed in Web of Science (WoS) as an ESCI journal , Scopus, DOAJ and EBSCO.According to Google Scholar ,Citation years: 3 (2018-2020)Citations/paper: 1.23Hirsch h-index: 4 Egghe g-index: 5

Genetic Analysis and QTL Mapping of Mature Seed Culturability in Indica Rice

Genetic segregation analysis for mature seed culturability was conducted using recombinant inbred lines derived from a cross of indica rice, Yangdao 6 and Pei'ai 64s. Three indices of seed culturability, the frequency of callus induction, the frequency of brown callus and the increase of callus weight were investigated. A combined genetic map constructed with simple sequence repeat (SSR), sequence tag site (STS), cleaved amplified polymorphic sequences (CAPS) and single nucleotide polymorphism (SNP) markers covered a total distance of 1 732.5 cM, averaging approximately 12 cM between two neighboring loci. Three QTLs on chromosomes 7, 7 and 10 were detected for the frequency of callus induction; three QTLs on chromosomes 6, 7 and 9 were detected for the frequency of brown callus; and two QTLs on chromosomes 5 and 7 were detected for the increase of callus weight. Common QTLs mapped at the interval flanking RM5481 and RM6835 on chromosome 7 were identified to be involved in the frequency of callus induction and the frequency of brown callus, explaining 7.29% and 12.52% of phenotypic variation, respectively. A total of 14 epistatic effects were detected for the three indices of mature seed culturability.