Quantitative trait locus mapping using sets of near-isogenic lines: relative power comparisons and technical considerations

 The power to detect QTL using near-isogenic line (NIL) comparisons versus recombinant inbred (RI) populations was assessed. The power to detect QTL was found to be generally greater when using RI populations than when using NIL contrasts. Power to detect QTL with NIL contrasts never exceeded that of RI populations when the number of RI lines is maximized relative to replication of lines for a given number of experimental units. The relative power of NIL contrasts is highest for traits with high heritability and when a gain in precision is realized due to increased replication of entries. Although NIL populations are generally less powerful than RI populations of similar size, some practical considerations may enhance the value of these materials. Availability of NILs allows the genetic effect of a specific chromosome region to be determined by comparing two lines; all RI lines in a population need to be rescored for each new trait even if the effect of a specific chromosome region is suspected. NIL comparisons may allow genetic differences to be detected by visual inspection; genetic effects can only be expressed as means and variances with recombinant inbred populations. In summary, RI populations generally, and in some cases, substantially, provide better power for QTL detection than NIL comparisons. Practical considerations, however, indicate that many factors need to be considered when choosing a population structure to meet an experimental objective. Received: 12 December 1996 / Accepted: 21 March 1997     

QTL mapping of resistance to Fusarium ear rot using a RIL population in maize

Fusarium ear rot is a prevalent disease in maize, reducing grain yields and quality. Resistance breeding is an efficient way to minimize losses caused by the disease. In this study, 187 lines from a RIL population along with the resistant (87-1) and susceptible (Zong 3) parents were planted in Zhengzhou and Beijing with three replications in years 2004 and 2006. Each line was artificially inoculated using the nail-punch method. Significant genotypic variation in response to Fusarium ear rot was detected in both years. Based on a genetic map containing 246 polymorphic SSR markers with average genetic distances of 9.1 cM, the ear-rot resistance QTL were firstly analyzed by composite interval mapping (CIM). Three QTL were detected in both Zhengzhou and Beijing in 2004; and three and four QTL, respectively, were identified in 2006. The resistant parent contributed all resistance QTL. By using composite interval mapping and a mixed model (MCIM), significant epistatic effects on Fusarium ear rot as well as interactions between mapped loci and environments were observed across environments. Two QTL on chromosome 3 (3.04 bin) were consistently identified across all environments by the two methods. The major resistant QTL with the largest effect was flanked by markers umc1025 and umc1742 on chromosome 3 (3.04 bin), explaining 13–22% of the phenotypic variation. The SSR markers closely flanking the major resistance QTL will facilitate marker-assisted selection (MAS) of resistance to Fusarium ear rot in maize breeding programs.     

Use of SSRs for establishing heterotic groups in subtropical maize

Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objectives of our research were to: (1) investigate the relationship of simple sequence repeats (SSR) based genetic distances between populations and panmictic midparent heterosis (PMPH) in a broad range of CIMMYT maize germplasm, (2) evaluate the usefulness of SSR markers for defining heterotic groups and patterns in subtropical germplasm, and (3) examine applications of SSR markers for broadening heterotic groups by systematic introgression of other germplasm. Published data of two diallels and one factorial evaluated for grain yield were re-analyzed to calculate the PMPH in population hybrids. Additionally, 20 pools and populations widely used in CIMMYT's breeding program were assayed with 83 SSR markers covering the entire maize genome. Correlations of squared modified Roger's distance (MRD²) and PMPH were mostly positive and significant, but adaption problems caused deviations in some cases. For intermediate- and early-maturity subtropical germplasm, two heterotic groups could be suggested consisting of a flint and dent composite. We concluded that the relationships between the populations obtained by SSR analyses are in excellent agreement with pedigree information. SSR markers are a valuable complementation to field trials for identifying heterotic groups and can be used to introgress exotic germplasm systematically.Communicated by F. Salamini     

Resistance QTL confirmed through development of QTL-NILs for barley leaf rust resistance

Near-isogenic lines (NILs) differing with regard to disease QTLs provide valuable material for a more detailed study into the genetic basis of quantitative resistance. Previously obtained information on QTLs that show an effect on leaf rust (Puccinia hordei) in barley was used in a marker-assisted backcross programme. The genome origin in backcross plants was controlled through AFLP marker analysis and graphical genotyping. Plants obtained after the third generation of backcrossing sufficiently resembled the recurrent parent. For one QTL, BC₃S₁ plants were evaluated in a disease test and genotyped. NILs containing the desired QTL in homozygous condition in a recipient background were finally obtained. A disease test and verification of the marker genotype confirmed the identity of the NILs. Simultaneous with the backcross programme a simulation study on efficiency of marker-assisted backcrossing was performed.     

Characterization of disease resistance gene-like sequences in near-isogenic lines of tomato

 We examined near-isogenic lines (NILs) carrying either of the tomato mosaic virus (ToMV) resistance genes Tm-1 and Tm-2 for sequences homologous to the isolated disease-resistance genes. DNA fragments were amplified from the genomic DNA of the NILs by the polymerase chain reaction (PCR) using primers designed on the basis of sequences of certain domains conserved among some disease-resistance genes. Of ten PCR products cloned, five were identified as having homology to either of the two classes of disease-resistance genes. The first class encoded proteins containing leucine-rich repeats (LRRs) and a nucleotide-binding site (NBS), such as the RPS2 gene in Arabidopsis and the N gene in tobacco. The second class encoded proteins containing a C-terminal membrane anchor but no NBS, such as the Cf 2 and Cf 9 genes in tomato. In Southern hybridization of the genomic DNAs of the NILs carrying either Tm-1 or Tm-2 and their parental NIL carrying neither of these resistance genes, multiple bands could be detected with most of the clones used as probes. This suggests that the genomes of the NILs contain multiple copies of sequences homologous to some of the known disease-resistance genes. No evidence was obtained to show that the Tm-1 and/or Tm-2 loci encode either class of protein, since no polymorphic band patterns between the NILs were detected by Southern hybridization. Received: 15 August 1997 / Accepted: 2 September 1997     

Genetic diversity of maize inbred lines within and among heterotic groups revealed by RFLPs

Summary The objectives of this study were (1) to investigate genetic diversity for RFLPs in a set of important maize inbreds commonly used in Italian breeding programs, (2) to compare genetic similarities between unrelated lines from the same and different heterotic groups, and (3) to examine the potential of RFLPs for assigning maize inbreds to heterotic groups. Forty inbreds were analyzed for RFLPs with two restriction enzymes (EcoRI and HindIII) and 82 DNA clones uniformly distributed over the maize genome. Seventy clone-enzyme combinations gave single-banded RFLP patterns, and 79 gave multiple-banded RFLP patterns. The average number of RFLP patterns detected per clone-enzyme combination across all inbreds was 5.8. RFLP data revealed a wide range of genetic diversity within the two heterotic groups assayed, Iowa Stiff Stalk Synthetic (BSSS) and Lancaster Sure Crop (LSC). Genetic similarity (GS) between lines was estimated from binary RFLP data according to the method of Nei and Li (1979). The mean GS for line combinations of type BSSS × LSC (0.498) was substantially smaller than for unrelated line combinations or type BSSS × BSSS (0.584) but almost as great as for un-related line combinations of type LSC × LSC (0.506). Principal coordinate and cluster analyses based on GS values resulted in the separate groupings of lines, which is consistent with known pedigree information. A comparison between both methods for multivariate analyses of RFLP data is presented.     

Mapping of QTL associated with waterlogging tolerance during the seedling stage in maize

BACKGROUND AND AIMS: Soil waterlogging is a major environmental stress that suppresses maize (Zea mays) growth and yield. To identify quantitative trait loci (QTL) associated with waterlogging tolerance at the maize seedling stage, a F2 population consisting of 288 F(2:3) lines was created from a cross between two maize genotypes, 'HZ32' (waterlogging-tolerant) and 'K12' (waterlogging-sensitive). METHODS: The F2 population was genotyped and a base-map of 1710.5 cM length was constructed with an average marker space of 11.5 cM based on 177 SSR (simple sequence repeat) markers. QTL associated with root length, root dry weight, plant height, shoot dry weight, total dry weight and waterlogging tolerance coefficient were identified via composite interval mapping (CIM) under waterlogging and control conditions in 2004 (EXP.1) and 2005 (EXP.2), respectively. KEY RESULTS AND CONCLUSIONS: Twenty-five and thirty-four QTL were detected in EXP.1 and EXP.2, respectively. The effects of each QTL were moderate, ranging from 3.9 to 37.3 %. Several major QTL determining shoot dry weight, root dry weight, total dry weight, plant height and their waterlogging tolerance coefficient each mapped on chromosomes 4 and 9. These QTL were detected consistently in both experiments. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 3, 6, 7 and 10. These QTL were specific to particular traits or environments. Although the detected regions need to be mapped more precisely, the findings and QTL found in this study may provide useful information for marker-assisted selection (MAS) and further genetic studies on maize waterlogging tolerance.     

QTL mapping of resistance to Sporisorium reiliana in maize

We mapped and characterized quantitative trait loci (QTL) for resistance to Sporisorium reiliana. A population of 220 F₃ families produced from the cross of two European elite inbreds (D32, D145) was evaluated with two replications at a French location with high natural incidence of S. reiliana and at a Chinese location employing artificial inoculation. The 220 F₃ families were genotyped with 87 RFLP and seven SSR markers. Using composite interval mapping, we identified two different sets of 3 and 8 QTL for the French and the Chinese locations explaining 13% and 44% of respectively. Individual QTL explained up to 14% of σ^² _p. The 11 QTL mapped to eight maize chromosomes and displayed mostly additive or partial dominant gene action. Significant digenic epistatic interactions were detected for one pair of these QTL. Only a few QTL for S. reiliana were in common with QTL for resistance to Ustilago maydis and Puccinia sorghi, identified at a German location for the same population. Consequently, in our materials resistance to these three fungal pathogens of maize seems to be inherited independently. Received: 14. December 1998 / Accepted: 30 January 1999     

Characterization of heterotic quantitative trait loci in maize by evaluation of near-isogenic lines and their crosses at two competition levels

In a previous study on a maize (Zea mays L.) population of recombinant inbreds derived from B73 × H99, we identified several quantitative trait loci (QTL) for agronomic traits with high dominance-additive ratio. Then, for four of these QTL, we developed families of near-isogenic lines (NILs) homozygous either for the QTL allele from B73 (BB) or from H99 (HH); for two of these QTL, the NILs’ families were produced in two different genetic backgrounds. The present study was conducted to: (1) characterize these QTL for agronomic traits and (2) verify whether their effects were influenced by the genetic background, inbreeding level and plant density (PD). The six NILs’ families were tested across 3 years and in three experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two PDs (4.5 and 9.0 plants m⁻²). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance–additive ratio superior to 1 for several traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and PD were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using the NILs’ families and their crosses as base materials.     

Production and genetic characterization of near-isogenic lines in the bread-wheat cultivar Alpe

Two biotypes of the bread-wheat cultivar Alpe were shown to possess contrasting alleles at each of the glutenin (Glu-B1, Glu-D1, Glu-B3 and Glu-D3) and gliadin (Gli-B1 and Gli-D1) loci on chromosomes 1B and 1D. Fourteen near-isogenic lines (NILs) were produced by crossing these biotypes and used to determine the genetic control of both low-molecular-weight (LMW) glutenin subunits and gliadins by means of one-dimensional or two-dimensional electrophoresis. Genes coding for the B, C and D groups of EMW subunits were found to be inherited in clusters tightly linked with those controlling gliadins. Southern-blot analysis of total genomic DNAs hybridized to a -gliadin-specific cDNA clone revealed that seven NILs lack both the Gli-D1 and Glu-D3 loci on chromosome 1D. Segregation data indicated that these null alleles are normally inherited. Comparison of the null NILs with those possessing allele b at the Glu-D3 locus showed one B subunit, seven C subunits and two D subunits, as fractionated by two-dimensional A-PAGExSDS-PAGE, to be encoded by this allele. Alleles b and k at Glu-B3 were found to code for two C subunits plus eight and six B subunits respectively, whereas alleles b and k at Gli-B1 each controlled the synthesis of two -gliadins, one and two -gliadins. The novel Gli-B5 locus coding for two -gliadins was shown to recombine with the Gli-B1 locus on chromosome 1B. The two-dimensional map of glutenin subunits showed -gliadins encoded at the Gli-A2 locus on chromosome 6A. The use of Alpe NILs in the study of the individual and combined effects of glutenin subunits on dough properties is discussed.Research supported by a grant from the Commission of the European Communities, ECLAIR programme, Contract AGRE 0052     

Mapping quantitative trait loci controlling silking date in a diallel cross among four lines of maize

 We describe and apply an interval mapping method for quantitative trait locus (QTL) detection using F₃ and testcross progenies derived from F₂ populations obtained from a diallel cross among four elite lines of maize. Linear model-based procedures were used for the test and estimation of putative QTL effects together with genetic interactions including epistasis. We mapped QTL associated with silking date and explored their genetic effects. Ten QTL were detected, and these explained more than 40% of the phenotypic variance. Most of these QTL had consistent and stable effects among genetic backgrounds and did not show significant epistasis. QTL-by-environment interaction was important for four QTL and was essentially due to changes in magnitude of allelic effects. These results show the efficiency of our method in several genetic situations as well as the power of the diallel design in detecting QTL simultaneously over several populations. Received: 2 September 1996 / Accepted: 20 December 1996     

Effect of selection on the heterozygosity of inbred lines of maize

Although pedigree selection is the most commonly used method for developing inbred lines of maize, there are no studies on its effect on the heterozygosity of the lines. The objective of this work was to study the effect of pedigree selection on their heterozygosity. Thirteen F₅ or F₆ maize inbred lines developed by the pedigree selection method in four breeding programs and their F₁ and F₂ − F₄ ancestors were genotyped with simple sequence repeat markers distributed along the genome. Simulation was also conducted assuming different models of selection to investigate the selective forces needed to explain the data. In the F₂, F₃ and F₄ 40%, 66% and 86% of the markers segregating in the F₁ were fixed; that is, in the F₂ and F₃ fixation was lower than neutral expectation, but higher in the F₄. Due to such opposite apparent directions of selection, the heterozygosity of the lines in the F₅ or F₆ generations did not differ significantly from neutral expectations. The time to fixation differed from that expected with neutrality for most of the chromosomes, indicating that selection is distributed across the genome; but apparent overdominant effects in chromosome 7 were higher than in other chromosomes. In conclusion, the relationship between heterozygosity and vigour may reduce the effectiveness of pedigree selection in its goal of selecting the more vigorous, homozygous individuals. A more effective procedure is proposed using molecular markers for the identification of the more homozygous individuals, the most vigorous of those individuals being selected.     

Estimates of gene frequencies in two heterotic maize populations

Summary The present study was undertaken to obtain information on average gene frequency in two heterotic populations of maize (Zea mays L.), Mezcla Amarillo Selection (MAS) and J607. Sixty-four male plants were taken in each of the populations and each of these were crossed to a different set of eight plants, four of which belonged to the same population and four to the other population. This resulted in two groups of intra-population (within MAS and within J607) and two groups of inter-population (MAS X J607 and J607 X MAS) progenies. Each group consisted of 256 full-sib progenies on the pattern of the North Carolina Design I mating system. The male plants were selfed to produce 64 S₁ prgenies in each population. The materials were evaluated at two diverse locations, Ludhiana and Gurdaspur, for grain yield, ear length, ear girth, number of kernel rows, plant height, ear height and days to silk. An incomplete block design with two replications were used. The plot consisted of a 5 m long row. Ratios of estimated genetic components of variance and covariance were compared with corresponding theoretical ratios computed for a single locus for various gene frequencies and levels of dominance, and approximate ranges of the gene frequencies and their relative magnitude were worked out in the two populations. The average frequency of favourable genes for plant height was estimated as 0.6 in MAS and 0.8 in J607. For grain yield the average gene frequency was 0.8 to 0.9 in MAS and 0.7 to 0.8 in J607 whereas for ear height it was 0.5 to 0.7 in MAS and 0.4 to 0.6 in J607. The gene frequency in the two populations seemed to be similar for days to silk, ear length, ear girth and kernel rows.     

Magnitude of hybrid vigor retained in double haploid lines of some heterotic rice hybrids

Sixty one double haploid (DH) lines were evaluated for yield components and yield and compared with the three corresponding hybrids from which they were derived through anther culture. Analysis of a 6×6 diallel experiment led to the selection of these hybrids based on their high heterosis and revealed the nature of gene action of the characters under evaluation. The DH lines along with the hybrids and parents were planted following a simple lattice design with two replications. The results show that in DH lines the values of the characters expressing predominantly additive genetic effects could reach the heterotic level of the hybrids. For characters including yield showing predominantly dominance effects, values in the DH lines were significantly lower than those of the corresponding hybrids. The promising DH lines, however, possess a higher yield potential than the better parents.     

Validation and characterization of a major QTL affecting leaf ABA concentration in maize

A previous study conducted on a maize (Zea mays L.) mapping population derived from Os420 × IABO78 identified a quantitative trait locus (QTL) for leaf-abscisic acid concentration (L-ABA) on chromosome 2 (bin 2.04). In order to validate this QTL, we analyzed with RFLP markers 16 F₄ lines obtained by divergent selection for L-ABA from the same source. Three RFLPs mapping near bin 2.04 showed skewed allelic frequencies; the L-ABA increasing allele (+) was more frequent within the eight lines selected for high L-ABA, while the decreasing allele (–) was more frequent within the eight lines selected for low L-ABA. To characterize more accurately the direct and associated effects of this QTL, near-isogenic lines were developed by molecular marker-assisted back-crossing; four backcross-derived lines were homozygous (+/+) at the QTL and four were (–/–). A pair of near-isogenic hybrids (+/+) and (–/–) at the QTL were also produced. These materials were field tested under water-stressed and well-watered conditions. Across water regimes, the four (+/+) lines averaged a significantly higher mean value than the four (–/–) lines for L-ABA (494 vs. 396 ng ABA g^–1 DW) and a significantly lower mean value for relative water content (90.6 vs. 92.0%). The (+/+) hybrid exceeded the (–/–) for L-ABA (476 vs. 325 ng g^–1 DW) and was less affected by root lodging (44.6 vs. 66.1%). Our results validate the presence of a major QTL for L-ABA on bin 2.04 and indicate that the QTL also affects root traits and relative water content.     

Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection

Drought is one of the main abiotic constraints in rice. A deep root system contributes efficiently to maintaining the water status of the crop through a stress period. After identifying QTLs affecting root parameters in a doubled-haploid (DH) population of rice derived from the cross IR64/Azucena, we started a marker-assisted backcross program to transfer the Azucena allele at four QTLs for deeper roots (on chromosomes 1, 2, 7 and 9) from selected DH lines into IR64. We selected the backcross progenies strictly on the basis of their genotypes at the marker loci in the target regions up to the BC₃F₂. We assessed the proportion of alleles remaining from Azucena in the non-target areas of the BC₃F₂ plants, which was in the range expected for the backcross stage reached. Twenty nine selected BC₃F₃ near-isogenic lines (NILs) were developed and compared to IR64 for the target root traits and three non-target traits in replicated experiments. Of the three tested NILs carrying target 1, one had significantly improved root traits over IR64. Three of the seven NILs carrying target 7 alone, as well as three of the eigth NILs carrying both targets 1 and 7, showed significantly improved root mass at depth. Four of the six NILs carrying target 9 had significantly improved maximum root length. Five NILs carrying target 2 were phenotyped, but none had a root phenotype significantly different from that of IR64. A re-analysis of the initial data with the composite interval mapping technique revealed two linked QTLs with opposite effects in this area. Some NILs were taller than IR64 and all had a decreased tiller number because of a likely co-introgression of linked QTLs. The usefulness of NILs, the efficiency of marker-aided selection for QTLs and the relationship between root traits are discussed. The NILs with an improved root system will permit testing the importance of root depth for water-limited environments. Received: 17 July 2000 / Accepted: 20 October 2000     

RFLP mapping using near-isogenic lines in the soybean [Glycine max (L.) Merr.]

Summary A molecular marker analysis of a near-isogenic line (NIL), its donor parent (DP), and its recurrent parent (RP) can provide information about linkages between molecular markers and a conventional marker introgressed into the NIL. If the DP and RP possess different alleles for a given molecular marker, and if the NIL possesses the same allele as the DP, then it is reasonable to presume a linkage between that molecular marker and the introgressed marker. In this study, we examined the utility of RFLPs as molecular markers for the NIL genemapping approach. The allelic status of fifteen RFLP loci was determined in 116 soybean RP/NIL/DP line sets; 66 of the Clark RP type and 50 of the Harosoy RP type. Of the 1740 possible allelic comparisons (116 NILs x 15 RFLP loci), 1638 were tested and 462 (33.9%) of those were informative (i.e., the RP and DP had different RFLP alleles). In 15 (3.2%) of these 462 cases the NIL possessed the DP-derived RFLP allele, leading to a presumption of linkage between the RFLP locus and the introgressed conventional marker locus. Two presumptive linkages, pK-3 — and pK-472 — Lf _i, were subsequently confirmed by cosegregation linkage analysis. Although not yet confirmed, two other associations, pk-7 ab and pK-229 — y ₉ seemed to be plausible linkages, primarily because the pk-7 — ab association was detected in two independently derived NILs and both markers of the pK-229 — y ₉ association were known to be linked to Pb. The data obtained in this investigation indicated that RFLP loci were useful molecular markers for the NIL gene-mapping technique.Published as Paper no. 9101, Journal Series, Nebraska Agric. Res. Div. Project no. 12-091. Research partially funded by a grant from the Nebraska Soybean Development, Utilization, and Marketing Board     

Heterogeneous inbred populations are useful as sources of near-isogenic lines for RAPD marker localization

The development and use of RAPD markers for applications in crop improvement has recently generated considerable interest within the plant breeding community. One potential application of RAPDs is their use for tagging simply-inherited (monogenic) pest-resistance genes and enabling more efficient identification and selection of genotypes carrying specific combinations of resistance genes. In this report, we propose and describe the use of heterogeneous inbred populations as sources of near-isogenic lines (NILs) for targeting RAPD markers linked to major pest resistance genes. The development of these NILs for RAPD marker analyses involved a sequence of line and mass selection during successive generations of inbreeding. DNA bulks derived from the NILs were used to identify a RAPD marker (designated OK14₆₂₀, generated by 5-CCCGCTACAC-3 decamer) that was tightly linked (2.23±1.33 centiMorgans) to an important rust [Uromyces appendiculatus (Pers.) Unger var. appendiculatus] resistance gene (Ur-3) in common bean (Phaseolus vulgaris L.). The efficiency of this approach was demonstrated by a low rate of false-positives identified, the tightness of the linkage identified, and the ability to detect polymorphism between genomic regions that are representative of the same gene pool of common bean. This method of deriving NILs should find application by researchers interested in utilizing marker-assisted selection for one or more major pest resistance genes. The identification of OK14₆₂₀ should help to facilitate continued use of the Ur-3 resistance source and will now enable marker-assisted pyramiding of three different bean rust resistance sources (two previously tagged) to provide effective and stable resistance to this important pathogen.Research supported in part by the grant DAN 1310-G-SS-6008-00 from the USAID Bean/Cowpea Collaborative Research Support Program, the Michigan Agricultural Experiment Station, and the USDA-ARS. Mention of a trademark or a proprietary product does not constitute a guarantee or warranty of the product by the USDA and does not imply its approval to the exclusion of other products that may also be suitable     

Mapping of qGL7-2,a grain length QTL on chromosome 7 of rice

A residual heterozygous line(RHL)carrying a heterozygous segment between two SSR loci RM11 and RM134 on the rice chromosome 7 was selected from a set of recombinant inbred lines from the cross D50(javanica)/HB277(indica).The former parent produces much longer grains than the latter.Selfed progenies of this selection were analyzed genotypically(SSRs)and phenotypically(grain length).Grain length was discontinuously variable in the mapping populations,allowing for the placement of this QTL qGL7-2 within a～4.8 cM interval defined by RM351 and RM234.A set of new markers within this region were developed,which narrowed the QTL to a 278 kb region defined by the markers Indel1 and RM21945.This region contains 49 predicted genes.The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.