Identification of novel QTL contributing resistance to aflatoxin accumulation in maize

The toxic metabolic product aflatoxin produced by the opportunistic fungus Aspergillus flavus (Link:Fr) in maize (Zea mays L.) can cause disease and economic harm when levels exceed very minute quantities. The selection of resistant germplasm has great potential to reduce the problem, but the highly quantitative nature of the trait makes this a difficult endeavor. The identification of aflatoxin accumulation resistance quantitative trait loci (QTL) from resistant donor lines and the discovery of linked markers could speed this task. To identify marker–trait associations for marker-assisted breeding, a genetic mapping population of F_2:3 families was developed from Mp715, a maize inbred line resistant to aflatoxin accumulation, and T173, a susceptible, southern-adapted maize inbred line. QTL, some with large phenotypic effects, were identified in multiple years on chromosomes 1, 3, 5, and 10, and smaller QTL identified in only 1 year were found on chromosomes 4 and 9. The phenotypic effect of each QTL ranged from 2.7 to 18.5%, and models created with multiple QTL could explain up to 45.7% of the phenotypic variation across years, indicating that the variation associated with the trait can be manipulated using molecular markers.     

Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines

Mapping chromosome regions responsible for quantitative phenotypic variation in recombinant populations provides an effective means to characterize the genetic basis of complex traits. We conducted a quantitative trait loci (QTL) analysis of 150 rice recombinant inbred lines (RILs) derived from a cross between two cultivars, Oryza sativa ssp. indica cv. 93-11 and Oryza sativa ssp. japonica cv. Nipponbare. The RILs were genotyped through next-generation sequencing, which accurately determined the recombination breakpoints and provided a new type of genetic markers, recombination bins, for QTL analysis. We detected 49 QTL with phenotypic effect ranging from 3.2 to 46.0% for 14 agronomics traits. Five QTL of relatively large effect (14.6–46.0%) were located on small genomic regions, where strong candidate genes were found. The analysis using sequencing-based genotyping thus offers a powerful solution to map QTL with high resolution. Moreover, the RILs developed in this study serve as an excellent system for mapping and studying genetic basis of agricultural and biological traits of rice.     

Genetic dissection of tocopherol and phytosterol in recombinant inbred lines of sunflower through quantitative trait locus analysis and the candidate gene approach

Sunflower (Helianthus annuus L.) contains tocopherol, a non-enzymatic antioxidant known as lipid-soluble vitamin E, and phytosterol, with interesting properties, which can result in decreased risk of chronic diseases in humans and with several beneficial effects in plants. The genetic control of tocopherol and phytosterol content in a population of 123 recombinant inbred lines of sunflower was studied through quantitative trait loci (QTL) analysis using 190 simple sequence repeats and a gene-based linkage map. Seven experiments were conducted in different environments in France and Iran during 2007 and 2008. Each experiment consisted of three replications. Means over all environments were used for QTL mapping. Five QTL for total tocopherol content on linkage groups 1, 8, 10 and 14 accounted for 45% of phenotypic variation, whereas four QTL for total phytosterol content on linkage groups 1, 2, 16 and 17 explained 27% of the phenotypic variation. GST, PAT2, SFH3 and POD genes showed co-localization with QTL for total phytosterol content. SMT2 is also mapped on linkage group 17 near the QTL of total phytosterol content. Four candidate genes, VTE4, HPPD, GST and Droug1, exhibited co-localization with QTL for total tocopherol content. The candidate genes associated with tocopherol and phytosterol, especially HPPD, VTE4 and SMT2, could be used for alternation of the tocopherol and phytosterol content of sunflower seeds through the development of functional markers.     

Quantitative trait loci for grain moisture at harvest and field grain drying rate in maize (Zea mays, L.)

Hybrids with low grain moisture (GM) at harvest are specially required in mid- to short-season environments. One of the most important factors determining this trait is field grain drying rate (FDR). To produce hybrids with low GM at harvest, inbred lines can be obtained through selection for either GM or FDR. Thus, a single-cross population (181 F _2:3-generation plants) of two divergent inbred lines was evaluated to locate QTL affecting GM at harvest and FDR as a starting point for marker assisted selection (MAS). Moisture measurements were made with a hand-held moisture meter. Detection of QTL was facilitated with interval mapping in one and two dimensions including an interaction term, and a genetic linkage map of 122 SSR loci covering 1,557.8 cM. The markers were arranged in ten linkage groups. QTL mapping was made for the mean trait performance of the F _2:3 population across years. Ten QTL and an interaction were associated with GM. These QTL accounted for 54.8 and 65.2% of the phenotypic and genotypic variation, respectively. Eight QTL and two interactions were associated with FDR accounting for 35.7 and 45.2% of the phenotypic and genotypic variation, respectively. Two regions were in common between traits. The interaction between QTL for GM at harvest had practical implications for MAS. We conclude that MAS per se will not be an efficient method for reducing GM at harvest and/or increasing FDR. A selection index including both molecular marker information and phenotypic values, each appropriately weighted, would be the best selection strategy.     

QTL mapping of yield and fiber traits based on a four-way cross population in <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.

Four-way cross (4WC) involving four different inbred lines frequently appears in the cotton breeding programs. However, linkage analysis and quantitative trait loci (QTL) mapping with molecular markers in cotton has largely been applied to populations derived from a cross between two inbred lines, and few results of QTL dissection were conducted in a 4WC population. In this study, an attempt was made to construct a linkage map and identify QTL for yield and fiber quality traits in 4WC derived from four different inbred lines in Gossypium hirsutum L. A linkage map was constructed with 285 SSR loci and one morphological locus, covering 2113.3 cM, approximately 42% of the total recombination length of the cotton genome. A total of 31 QTL with 5.1–25.8% of the total phenotypic variance explained were detected. Twenty-four common QTL across environments showed high stability, and six QTL were environment-specific. Several genomic segments affecting multiple traits were identified. The advantage of QTL mapping using a 4WC were discussed. This study presents the first example of QTL mapping using a 4WC population in upland cotton. The results presented here will enhance the understanding of the genetic basis of yield and fiber quality traits and enable further marker-assisted selection in cultivar populations in upland cotton.     

Identification of QTL underlying somatic embryogenesis capacity of immature embryos in soybean (Glycine max (L.) Merr.)

High embryogenesis capacity of soybean (Glycine max (L.) Merr.) in vitro possessed potential for effective genetic engineering and tissue culture. The objects of this study were to identify quantitative trait loci (QTL) underlying embryogenesis traits and to identify genotypes with higher somatic embryogenesis capacity. A mapping population, consisting of 126 F_5:6 recombinant inbred lines, was advanced by single-seed-descent from cross between Peking (higher primary and secondary embryogenesis) and Keburi (lower primary and secondary embryogenesis). This population was evaluated for primary embryogenesis capacity from immature embryo cultures by measuring the frequency of somatic embryogenesis (FSE), the somatic embryo number per explant (EPE) and the efficiency of somatic embryogenesis (ESE). A total of 89 simple sequence repeat markers were used to construct a genetic linkage map. Six QTL were associated with somatic embryogenesis. Two QTL for FSE were found, QFSE-1 (Satt307) and QFSE-2 (Satt286), and both were located on linkage group C2 that explained 45.21 and 25.97% of the phenotypic variation, respectively. Four QTL for EPE (QEPE-1 on MLG H, QEPE-2 on MLG G and QEPE-3 on MLG G) were found, which explained 7.11, 7.56 and 6.12% of phenotypic variation, respectively. One QTL for ESE, QESE-1 (Satt427), was found on linkage group G that explained 6.99% of the phenotypic variation. QEPE-2 and QESE-1 were located in the similar region of MLG G. These QTL provide potential for marker assistant selection of genotypes with higher embryogenesis.     

水稻生育后期叶绿素含量的QTLs及其与环境的互作分析

利用Dular和Lemont杂交后代单粒传衍生的123个F12家系所组成的重组自交系（RILs）群体,研究水稻剑叶叶绿素含量的数量性状基因座（QTL）.分别在2005年和2006年考察该RIL群体齐穗期剑叶叶绿素含量,并进行QTL定位和上位性分析及其与环境的互作效应分析.结果表明：在4对染色体上共检测到10个控制叶绿素含量的加性QTLs,共解释了73.51%的遗传变异,单个QTL的表型贡献率为2.08%～20.14%,其中6个和环境存在显著互作;同时也检测到13对影响叶绿素含量的加性×加性上位性互作,其中6对具有显著的上位性环境互作效应.     

玉米杂交种掖单13号的SSR连锁图谱构建与叶夹角和叶向值的QTL定位与分析

为了增加单位面积产量, 玉米育种者已经开始了更密植更紧凑株型的选育。叶夹角和叶向值是评价玉米株型的重要指标。本研究以掖478×丹340的500个F2单株为作图群体, 构建了具有138个位点的SSR标记连锁图谱, 图谱总长度为1 394.9 cM, 平均间距10.1 cM。利用397个F2：3家系对叶夹角和叶向值进行QTL定位分析, 结果表明: 叶夹角和叶向值分别检测到6和8个QTL, 累计解释表型变异41.0%和60.8%, 单个QTL的贡献率在2.9%~13.6%之间。与叶夹角和叶向值有关的基因主要作用方式为加性和部分显性。此外两个性状共检测到9对上位性互作位点, 表明上位性互作在叶夹角和叶向值的遗传中也起较重要的作用。     

Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines

 To detect quantitative trait loci (QTLs) controlling seed dormancy, 98 BC₁F₅ lines (backcross inbred lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare were analyzed genetically. We used 245 RFLP markers to construct a framework linkage map. Five putative QTLs affecting seed dormancy were detected on chromosomes 3, 5, 7 (two regions) and 8, respectively. Phenotypic variations explained by each QTL ranged from 6.7% to 22.5% and the five putative QTLs explained about 48% of the total phenotypic variation in the BC₁F₅ lines. Except for those of the QTLs on chromosome 8, the Nipponbare alleles increased the germination rate. Five putative QTLs controlling heading date were detected on chromosomes 2, 3, 4, 6 and 7, respectively. The phenotypic variation explained by each QTL for heading date ranged from 5.7% to 23.4% and the five putative QTLs explained about 52% of the total phenotypic variation. The Nipponbare alleles increased the number of days to heading, except for those of two QTLs on chromosomes 2 and 3. The map location of a putative QTL for heading date coincided with that of a major QTL for seed dormancy on chromosome 3, although two major heading-date QTLs did not coincide with any seed dormancy QTLs detected in this study. Received: 10 October 1997 / Accepted: 12 January 1998     

Genetic basis of pre-harvest sprouting tolerance using single-locus and two-locus QTL analyses in bread wheat

Quantitative trait loci (QTL) analysis for pre-harvest sprouting tolerance (PHST) in bread wheat was conducted following single-locus and two-locus analyses, using data on a set of 110 recombinant inbred lines (RILs) of the International Triticeae Mapping Initiative population grown in four different environments. Single-locus analysis following composite interval mapping (CIM) resolved a total of five QTLs with one to four QTLs in each of the four individual environments. Four of these five QTLs were also detected following two-locus analysis, which resolved a total of 14 QTLs including 8 main effect QTLs (M-QTLs), 8 epistatic QTLs (E-QTLs) and 5 QTLs involved in QTL × environment (QE) or QTL × QTL × environment (QQE) interactions, some of these QTLs being common. The analysis revealed that a major fraction (76.68%) of the total phenotypic variation explained for PHST is due to M-QTLs (47.95%) and E-QTLs (28.73%), and that only a very small fraction of variation (3.24%) is due to QE and QQE interactions. Thus, more than three-quarters of the genetic variation for PHST is fixable and would contribute directly to gains under selection. Two QTLs that were detected in more than one environment and at LOD scores above the threshold values were located on 3BL and 3DL presumably in the vicinity of the dormancy gene TaVp1. Another QTL was found to be located on 3B, perhaps in close proximity to the R gene for red grain colour. However, these associations of QTLs for PHST with genes for dormancy and grain colour are only suggestive. The results obtained in the present study suggest that PHST is a complex trait controlled by large number of QTLs, some of them interacting among themselves or with the environment. These QTLs can be brought together through marker-aided selection, leading to enhanced PHST.     

Quantitative trait loci for growth traits in C57BL/6J × DBA/2J mice

Quantitative trait loci (QTLs) for body weight and tail length are mapped in an F₂ population of 927 C57BL/6J × DBA/2J mice. We test the concordance between the locations of the mapped QTLs with those detected by changes of marker frequency under artificial selection in a previous experiment with the same base population. The directions of effects of the QTLs are generally in agreement, and in many cases significant QTLs are found in similar map positions, but there are also discrepancies between the two experiments. There are indications of age-specific QTL effects on growth. For body weight traits, the genetic variation in the F₂ appears to result from many loci with relatively small effects. For tail length at 10 weeks, however, a single QTL on Chromosome (Chr) 1 with a peak LOD score of ∼33 contributes most of the genetic variation detected, changes the trait value by about 6%, and explains about 20% of the phenotypic variance of the trait. Received: 4 August 1998 / Accepted: 17 November 1998     

胡萝卜(Daucus carota L.)中主要胡萝卜素和番茄红素含量的QTL分析

以高胡萝卜素自交系P50006和HCM A.C.为亲本构建的F2群体为作图群体,对胡萝卜中α-胡萝卜素、α-胡萝卜素、总胡萝卜素和番茄红素含量进行QTL定位及遗传分析。结果表明,α、β-胡萝卜素、总胡萝卜素和番茄红素含量的广义遗传力分别为0.75、0.50、0.31和0.93。遗传图谱包含91个SRAP(Sequence-related amplified polymorphism)标记,分布于9个连锁群,总长度502.9cM,标记间平均距离5.5cM。除α-胡萝卜素含量外,α-胡萝卜素、总胡萝卜素和番茄红素含量分别检测到1个主效QTL,均为加性遗传效应,分别解释表型变异为12.79%、12.87%和14.61%。此外,α-胡萝卜素和番茄红素含量还分别检测到1对上位性QTL,最大遗传效应分别为显性×加性互作和显性×显性互作,分别解释表型变异为15.1%和6.5%。文章中与QTL连锁的分子标记可用于高胡萝卜素、番茄红素的种质筛选和聚合育种。     

QTLs and epistasis for seminal root length under a different water supply in rice (Oryza sativa L.)

To identify the genetic background of seminal root length under different water-supply conditions, a recombinant inbred (RI) population consisting of 150 lines, derived from a cross between an indica lowland rice, IR1552, and a tropical japonica upland rice, Azucena, was used in both solution culture (lowland condition) and paper culture (upland condition). Quantitative trait loci (QTLs) and epistatic loci for seminal root length were analyzed using 103 restriction fragment length polymorphism (RFLP) markers and 104 amplified fragment length polymorphism (AFLP) markers mapped on 12 chromosomes based on the RI population. One QTL for seminal root length in solution culture (SRLS) and one for seminal root length in paper culture (SRLP) were detected on chromosomes 8 and 1, and about 11% and 10% of total phenotypic variation were explained, respectively. The QTL for SRLP on chromosome 1 was very similar with the QTL for the longest nodal root referred to in a previous report; this QTL may be phenotypically selectable in a breeding program using paper culture. Five pairs of epistatic loci for SRLS were detected, but only one for SRLP, which accounted for about 60% and 20% of the total variation in SRLS and SRLP, respectively. The results indicate that epistasis is a major genetic basis for seminal root length, and there is a different genetic system responsible for seminal root growth under different water supply conditions. Received: 26 May 2000 / Accepted: 19 October 2000     

Environmental and genetic interactions reveal FLOWERING LOCUS C as a modulator of the natural variation for the plasticity of flowering in Arabidopsis

The timing of flowering initiation depends strongly on the environment, a property termed as the plasticity of flowering. Such plasticity determines the adaptive potential of plants because it provides phenotypic buffer against environmental changes, and its natural variation contributes to evolutionary adaptation. We addressed the genetic mechanisms of the natural variation for this plasticity in Arabidopsis thaliana by analysing a population of recombinant inbred lines derived from Don‐0 and Ler accessions collected from distinct climates. Quantitative trait locus (QTL) mapping in four environmental conditions differing in photoperiod, vernalization treatment and ambient temperature detected the folllowing: (i) FLOWERING LOCUS C (FLC) as a large effect QTL affecting flowering time differentially in all environments; (ii) numerous QTL displaying smaller effects specifically in some conditions; and (iii) significant genetic interactions between FLC and other loci. Hence, the variation for the plasticity of flowering is determined by a combination of environmentally sensitive and specific QTL, and epistasis. Analysis of FLC from Don identified a new and more active allele likely caused by a cis‐regulatory deletion covering the non‐coding RNA COLDAIR. Further characterization of four FLC natural alleles showed different environmental and genetic interactions. Thus, FLC appears as a major modulator of the natural variation for the plasticity of flowering to multiple environmental factors.     

Pyramiding QTL for multiple lateral branching in cucumber using inbred backcross lines

Multiple lateral branching (MLB) is a quantitatively inherited trait associated with yield in cucumber (Cucumis sativus L.; 2n = 2x = 14). Although quantitative trait loci (QTL) have been identified for MLB and QTL-marker associations have been verified by marker-assisted selection, the individual effects of these QTL have not been characterized. To test the effects of pyramiding QTL for MLB, molecular genotyping was utilized to create two sets (standard- and little-leaf types) of inbred backcross (IBC) lines possessing various numbers of QTL that promote branching. These IBC lines were evaluated for lateral branch number in two Wisconsin environments at three plant densities. Highly significant differences in the number of primary lateral branches were detected between spacings, leaf types, and lines, but not between locations. Lateral branch number decreased at higher plant densities in all genotypes, while genotype by environment and QTL by environment interactions were marginally non-significant. As the number of QTL increased among IBC lines, the number of branches did not generally change in the little-leaf lines, but decreased in the standard-leaf lines, demonstrating an epistatic effect related to genetic background during lateral branch development. The genomic location with the greatest effect on MLB was confirmed as the QTL that was previously mapped near the little-leaf locus (ll), while the addition of one specific QTL consistently decreased the number of lateral branches in standard-leaf lines. Although pyramiding QTL for MLB did not uniformly increase the number of lateral branches, pyramiding QTL in IBC lines allowed further characterization of individual QTL involved in MLB. Our results, coupled with those of previous studies indicate that lateral branch development in cucumber is determined by growing environment (i.e., plant spacing), genetic background, and QTL composition.     

Inheritance of seed condensed tannins and their relationship with seed-coat color and pattern genes in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Condensed tannins are major flavonoid end products that affect the nutritional quality of many legume seeds. They chelate minerals and interact with proteins, thus reducing their bioavailability. Tannins also contribute to seed coat color and pigment distribution or intensity. The objective of this study was to analyze the relationship between quantitative trait loci (QTL) for seed tannin concentration in common bean and Mendelian genes for seed coat color and pattern. Three populations of recombinant inbred lines, derived from crosses between the Andean and Mesoamerican genepools were used for QTL identification and for mapping STS markers associated with seed color loci. Seed coat condensed tannins were determined with a butanol–HCl method and a total of 12 QTL were identified on separate linkage groups (LGs) in each of the populations with individual QTL explaining from 10 to 64% of the phenotypic variation for this trait. Loci on linkage groups B3 and B10 were associated with the Mendelian genes Z and Bip for partly colored seed coat pattern, while a QTL on linkage group B7 was associated with the P gene which is the primary locus for the control of color expression in beans. In conclusion, this study found that the inheritance of tannin concentration fits an oligogenic model and identifies novel putative alleles at seed coat color and pattern genes that control tannin accumulation. The results will be important for the genetic improvement of nutritionally enhanced or biofortified beans that have health promoting effects from higher polyphenolics or better iron bioavailability.     

A green fluorescent protein-engineered haploid inducer line facilitates haploid mutant screens and doubled haploid breeding in maize

Northern corn leaf blight (NCLB) is a prevalent foliar disease in maize. Deployment of resistant cultivars is an effective way to control NCLB. In this study, 207 recombinant inbred lines derived from a K22 × By815 cross were planted in Yangling, China, in 2012 and 2013. NCLB score and lesion size were investigated after artificial inoculation. Significant phenotypic variation in NCLB resistance was observed in both years. Using a genetic map containing high-density single-nucleotide polymorphisms with average genetic distance of 0.74 cM, quantitative trait loci (QTL) for NCLB score and lesion size were analyzed. For NCLB score, four and three QTL were identified in 2012 and 2013, respectively. Two stable QTL were identified in both years. Of these, qNCLB5.04, located on chromosome 5 (bin 5.04), had the largest resistance effect, accounting for 19 and 20 % of the phenotypic variation in 2012 and 2013, respectively. For lesion size, six QTL were identified. Of these, one consensus QTL was associated with both lesion length and width, and the other five were associated only with lesion width. Among all QTL identified, only qNCLB5.04 was associated with both NCLB score and lesion size. Thus, our mapping results suggest that qNCLB5.04 could be a desirable target for marker-assisted selection for NCLB resistance in maize breeding programs.

     

A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.)

Late leaf spot (LLS) and rust are two major foliar diseases of groundnut (Arachis hypogaea L.) that often occur together leading to 50–70% yield loss in the crop. A total of 268 recombinant inbred lines of a mapping population TAG 24 × GPBD 4 segregating for LLS and rust were used to undertake quantitative trait locus (QTL) analysis. Phenotyping of the population was carried out under artificial disease epiphytotics. Positive correlations between different stages, high to very high heritability and independent nature of inheritance between both the diseases were observed. Parental genotypes were screened with 1,089 simple sequence repeat (SSR) markers, of which 67 (6.15%) were found polymorphic. Segregation data obtained for these markers facilitated development of partial linkage map (14 linkage groups) with 56 SSR loci. Composite interval mapping (CIM) undertaken on genotyping and phenotyping data yielded 11 QTLs for LLS (explaining 1.70–6.50% phenotypic variation) in three environments and 12 QTLs for rust (explaining 1.70–55.20% phenotypic variation). Interestingly a major QTL associated with rust (QTL_rust01), contributing 6.90–55.20% variation, was identified by both CIM and single marker analysis (SMA). A candidate SSR marker (IPAHM 103) linked with this QTL was validated using a wide range of resistant/susceptible breeding lines as well as progeny lines of another mapping population (TG 26 × GPBD 4). Therefore, this marker should be useful for introgressing the major QTL for rust in desired lines/varieties of groundnut through marker-assisted backcrossing.     

Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.)

One hundred and fifty F₂–F₃ families from a cross between two inbred sunflower lines FU and PAZ2 were used to map quantitative trait loci (QTL) for resistance to white rot (Sclerotinia sclerotiorum) attacks of terminal buds and capitula, and black stem (Phoma macdonaldii). A genetic linkage map of 18 linkage groups with 216 molecular markers spanning 1,937 cM was constructed. Disease resistances were measured in field experiments for S. sclerotiorum and under controlled conditions for P. macdonaldii. For resistance to S. sclerotiorum terminal bud attack, seven QTL were identified, each explaining less than 10% of phenotypic variance. For capitulum attack by this parasite, there were four QTL (each explaining up to 20% of variation) and for P. macdonaldii resistance, four QTL were identified, each having effects of up to 16%. The S. sclerotiorum capitulum resistance QTL were compared with those reported previously and it was concluded that resistance to this disease is governed by a considerable number of QTL, located on almost all the sunflower linkage groups.     

Identification of quantitative trait loci for bruchid (Caryedon serratus Olivier) resistance components in cultivated groundnut (Arachis hypogaea L.)

Groundnut bruchid (Caryedon serratus Olivier) is a major storage insect pest that significantly lowers the quality and market acceptance of the produce. Screening for resistance against groundnut bruchid in field conditions is difficult due to the variation in environmental factors and possible occurrence of biotypes. Hence, identification of tightly linked markers or quantitative trait loci (QTLs) is needed for selection and pyramiding of resistance genes for durable resistance. A population of recombinant inbred lines derived from a cross between VG 9514 (resistant) and TAG 24 (susceptible) was screened for five component traits of bruchid resistance in 2 years. The same population was genotyped with 221 polymorphic marker loci. A genetic linkage map covering 1,796.7 cM map distance was constructed with 190 marker loci in cultivated groundnut. QTL analysis detected thirteen main QTLs for four components of bruchid resistance in nine linkage groups and 31 epistatic QTLs for total developmental period (TDP). Screening in 2 years for bruchid resistance identified two common main QTLs. The common QTL for TDP, qTDP-b08, explained 57–82 % of phenotypic variation, while the other common QTL for adult emergence, qAE2010/11-a02, explained 13–21 % of phenotypic variation. Additionally, three QTLs for TDP, adult emergence and number of holes and one QTL for pod weight loss were identified which explained 14–39 % of phenotypic variation. This is the first report on identification of multiple main and epistatic loci for bruchid resistance in groundnut.