Relationships among maize inbred lines and populations from European and North-American origins as estimated using RFLP markers

RFLP markers have proven to be a reliable and highly informative tool for characterizing genetic diversity in maize. Joint analysis of inbred lines and populations should provide valuable information with respect to (1) a better understanding of the genetic basis of present elite germplasm and (2) the identification of populations that may prove to be useful sources of genetic diversity for breeding programs. Sixty-two inbred lines of known heterotic groups and ten maize populations, some of them significant contributors to the genetic basis of the heterotic groups, were assayed at 28 RFLP loci. Joint data analyses first underlined that the populations displayed a large number of alleles that were absent in the set of inbred lines. Associations among inbreds and populations further proved consistent with pedigree data of the inbreds and provided new information on the genetical basis of heterotic groups. In particular, European flint inbreds were revealed to be as close to the Northeastern U.S. flint population studied as to the typical European populations. These results advocate the analysis of larger sets of populations by means of molecular markers in order to (1) gain insight into the history of maize germplasm and (2) set up appropriate strategies for the use of genetic resources in breeding programs. Received: 23 February 1998 / Accepted: 5 February 1999     

中国17个优良玉米自交系的分子标记杂合性及其与杂交种性状的关系研究

在玉米单交种育种中 ,鉴定高产杂交种和具有优良特性的自交系是一个重要的问题。研究以 1 7个优良玉米自交系为亲本 ,按照双列杂交配组合 ,利用 RAPD技术分析了 1 7个自交系的多态性以及 RAPD标记与 9个重要农艺性状 (包括产量 )的关系。基于 RAPD标记计算的相似系数聚类将 1 7个自交系分为 5个类群 ,经分析与系谱亲缘关系基本一致。杂交种性状及其特殊配合力与亲本间的遗传距离是高度相关的 ,与聚类前比较 ,聚类后平均遗传距离与平均产量、平均特殊配合力的相关系数显著提高 ,类间平均产量高于类内平均产量。RAPD技术可揭示优良玉米自交系的系谱亲缘关系 ,将自交系划分成不同的类群 ,从而为选择类间自交系杂交 ,进行亲本选配和分子标记辅助育种提供一种方法。     

Identification of trait-improving quantitative trait loci for grain yield components from a dent corn inbred line in an advanced backcross BC<Subscript>2</Subscript>F<Subscript>2</Subscript> population and comparison with its F<Subscript>2:3</Subscript> population in popcorn

Normal maize germplasm could be used to improve the grain yield of popcorn inbreds. Our first objective was to locate genetic factors associated with trait variation and make first assessment on the efficiency of advanced backcross quantitative trait locus (AB-QTL) analysis for the identification and transfer of favorable QTL alleles for grain yield components from the dent corn inbred. A second objective was to compare the detection of QTL in the BC₂F₂ population with results using F_2:3 lines of the same parents. Two hundred and twenty selected BC₂F₂ families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for six grain yield components under two environments, and genotyped by means of 170 SSR markers. Using composite interval mapping (CIM), a total of 19 significant QTL were detected. Eighteen QTL had favorable alleles contributed by the dent corn parent Dan232. Sixteen of these favorable QTL alleles were not in the same or near marker intervals with QTL for popping characteristics. Six QTL were also detected in the F_2:3 population. Improved N04 could be developed from 210 and 208 families with higher grain weight per plant and/or 100-grain weight, respectively, and 35 families with the same or higher popping expansion volume than N04. In addition, near isogenic lines containing detected QTL (QTL-NILs) for grain weight per plant and/or 100-grain weight could be obtained from 12 families. Our study demonstrated that the AB-QTL method can be applied to identify and manipulate favorable QTL alleles from normal corn inbreds and combine QTL detection and popcorn breeding efficiently.     

Molecular marker diversity among current and historical maize inbreds

Advanced-cycle pedigree breeding has caused maize (Zea mays L.) inbreds to become more-elite but more-narrow genetically. Our objectives were to evaluate the genetic distance among current and historical maize inbreds, and to estimate how much genetic diversity has been lost among current inbreds. We selected eight maize inbreds (B14, B37, B73, B84, Mo17, C103, Oh43 and H99) that largely represented the genetic background of current elite inbreds in the U.S. seed industry. A total of 32 other inbreds represented historical inbreds that were once important in maize breeding. Cluster analysis of the inbreds, using data for 83 SSR marker loci, agreed well with pedigree information. Inbreds from Iowa Stiff Stalk Synthetic (BSSS), Reid Yellow Dent, and Lancaster clustered into separate groups with only few exceptions. The average number of alleles per locus was 4.9 among all 40 inbreds and 3.2 among the eight current inbreds. The reduction in the number of alleles per locus was not solely due to sample size. The average genetic distance (D _ij ) was 0.65 among the eight current inbreds, 0.67 among the 32 historical inbreds, and 0.67 among all 40 inbreds. These differences were statistically insignificant. We conclude that genetic diversity among current inbreds has been reduced at the gene level but not at the population level. Hybrid breeding in maize maintained, rather than decreased, genetic diversity, at least during the initial subdivision of inbreds into BSSS and non-BSSS heterotic groups. We speculate, however, that exploiting other germplasm sources is necessary for sustaining long-term breeding progress in maize. Received: 21 August 2000 / Accepted: 5 January 2001     

Confirming quantitative trait loci for aflatoxin resistance from Mp313E in different genetic backgrounds

The fungus Aspergillus flavus (Link:Fr) causes ear rot of maize (Zea mays L.) and produces the toxic metabolic product aflatoxin. One particularly effective method of controlling the fungus is via host plant resistance, but while several resistant breeding lines have been identified, transferring the resistance genes from these lines into elite cultivars has been less effective than needed. A high number of genes involved with resistance, each with a small effect, and some only found under certain environmental conditions, has hampered resistance breeding. The identification of markers linked to genomic regions associated with resistance would aid in this effort. The goals of this study were to identify and characterize quantitative trait loci (QTL) conferring resistance to aflatoxin accumulation from resistant maize donor Mp313E in a background of the susceptible inbred line Va35; to compare them to the QTL identified from Mp313E in a background of B73; and to test the stability of the QTL identified in Mp313E × Va35 in multiple environments by remapping the phenotypic tails of the Mp313E × Va35 mapping population in new locations. Twenty different QTL were found in this study, 11 of which were also found in different environments using the phenotypic tail subset mapping population, and five of which were likely the same as those reported in the Mp313E × B73 mapping population. This indicates that many of the QTL are stable over the environments and genetic backgrounds tested, which will make them more valuable in breeding efforts.     

QTL analysis of shading sensitive related traits in maize under two shading treatments

During maize development and reproduction, shading stress is an important abiotic factor influencing grain yield. To elucidate the genetic basis of shading stress in maize, an F(2:3) population derived from two inbred lines, Zhong72 and 502, was used to evaluate the performance of six traits under shading treatment and full-light treatment at two locations. The results showed that shading treatment significantly decreased plant height and ear height, reduced stem diameter, delayed day-to-tassel (DTT) and day-to-silk (DTS), and increased anthesis-silking interval (ASI). Forty-three different QTLs were identified for the six measured traits under shading and full light treatment at two locations, including seven QTL for plant height, nine QTL for ear height, six QTL for stem diameter, seven QTL for day-to-tassel, six QTL for day-to-silk, and eight QTL for ASI. Interestingly, three QTLs, qPH4, qEH4a, and qDTT1b were detected under full sunlight and shading treatment at two locations simultaneously, these QTL could be used for selecting elite hybrids with high tolerance to shading and high plant density. And the two QTL, qPH10 and qDTS1a, were only detected under shading treatment at two locations, should be quit for selecting insensitive inbred line in maize breeding procedure by using MAS method.     

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.     

Identification of agronomically favorable quantitative trait loci alleles from a dent corn inbred Dan232 using advanced backcross QTL analysis and comparison with the F<Subscript>2:3</Subscript> population in popcorn

Specific traits are an important consideration in plant breeding. In popcorn, inferior agronomic traits could be improved using dent or flint corn backcrossed with popcorn. In this study, we used advanced backcross quantitative trait locus (AB-QTL) analysis to identify trait-improving QTL alleles from a dent maize inbred Dan232, and compared the detection of QTL in the BC₂S₁ population with QTL results using F_2:3 families of the same population. Two hundred and twenty BC₂S₁ families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for nine plant traits in replicated field trials under two environments. Using composite interval mapping (CIM), a total of 28 significant QTL were detected, and of these, 23 (82.14%) had favorable alleles contributed by the dent corn parent Dan232. Nine QTL (32.14%) detected in the BC₂S₁ population were also located in or near the same chromosome intervals in the F_2:3 population. All of the favorable QTL alleles from Dan232 could be used in marker-assisted selection (MAS) to improve the respective plant traits in popcorn breeding. In addition, their near isogenic lines (QTL-NILs) could be obtained through selfing or another 1–2 backcross with N04. Also, N04 improved for the studied plant traits could be developed from the BC₂S₁ families used in this study. This study demonstrated that the AB-QTL method can be applied to identify favorable QTL from dent corn inbred in popcorn breeding and, once identified, the alleles could be used in marker-assisted selection to improve the respective plant traits.     

Improvement of hybrid yield by advanced backcross QTL analysis in elite maize

We applied an advanced backcross breeding strategy to identify quantitative trait loci (QTLs) of agronomic importance in a cross between two elite inbreds of maize, RD6502 (Mo17-type recurrent parent) and RD3013 (Iodent donor parent). Two hundred and four BC(2) families were scored at 106 SSR, 15 AFLP, and 38 Heartbreaker (MITE) loci. BC(2) testcrosses (TC) with B73 were phenotyped at six locations in the Midwest and N.Y. We detected four grain yield, six grain moisture, and three plant height QTLs at which the RD3013 allele had a favorable effect ( p < 0.05). All four yield QTLs were selected as target introgressions in the development of BC(3)TC families. As predicted by BC(2)TC analysis, BC(3)TC entries containing introgressions at yld3.1 and yld10.1 significantly outperformed non-carrier entries by 11.1% (15.6 bu/A at one location) and 6.7% (7.1 bu/A averaged across two locations), respectively, in replicated Midwestern trials ( p < 0.05). Detection of yld10.1 effects in the BC(2)TC by spatial analysis (i.e., incomplete block, response surface, autoregressive, moving average or autoregressive moving average), but not by conventional single point analysis or interval mapping, indicated the utility of local environmental control for QTL mapping in unreplicated maize progeny. This work demonstrated that the advanced backcross QTL method can be applied to identify and manipulate useful QTLs in heterotic inbreds of elite maize. Genetic gains by this approach can be coupled with the maintenance and selection of favorable epistatic gene complexes by traditional hybrid breeding for maize improvement.     

Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines

Background

The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05–5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS).

Methods and Findings

A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives.

Conclusions

The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P = 8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.     

Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.)

Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed >80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

Analysis of genetic diversity and relationships among waxy maize inbred lines in Korea using SSR markers

Information regarding the genetic diversity and genetic relationships among elite inbred lines is necessary to improve new cultivars in maize breeding programs. In this study, genetic diversity and genetic relationships were investigated among 84 waxy maize inbred lines using 50 SSR markers. A total of 269 alleles were identified at all the loci with an average of 5.38 and a range between 2 and 13 alleles per locus. The gene diversity values varied from 0.383 to 0.923 with an average of 0.641. The cluster tree generated using the described SSR markers recognized two major groups at 32% genetic similarity. Group I included 33 inbred lines while group II included 51 inbred lines. The clustering patterns of most of the waxy maize inbred lines did not clearly agree with their source, pedigree or geographic location. The average GS among all inbred lines was 35.7 ± 10.8. Analysis of waxy maize inbred lines collected from Korea and China at 50 SSR loci revealed higher values of average number of alleles (4.9) and gene diversity (0.638) in Korean inbred lines as compared to Chinese inbred lines (3.5 and 0.563, respectively). The information obtained from the present studies would be very useful for maize breeding programs in Korea.     

Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data

Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated.     

Linkage disequilibrium in European elite maize germplasm investigated with SSRs

Information about the extent and genomic distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers. We examined genetic diversity and LD in a cross section of European and US elite breeding material comprising 147 inbred lines genotyped with 100 SSR markers. For gene diversity within each group, significant (P<0.05) differences existed among the groups. The LD was significant (P<0.05) for 49% of the SSR marker pairs in the 80 flint lines and for 56% of the SSR marker pairs in the 57 dent lines. The ratio of linked to unlinked loci in LD was 1.1 for both germplasm groups. The high incidence of LD suggests that the extent of LD between SSR markers should allow the detection of marker-phenotype associations in a genome scan. However, our results also indicate that a high proportion of the observed LD is generated by forces, such as relatedness, population stratification, and genetic drift, which cause a high risk of detecting false positives in association mapping.     

Broadening the genetic base of European maize heterotic pools with US Cornbelt germplasm using field and molecular marker data

Maize (Zea mays L.) breeders are concerned about the narrowing of the genetic base of elite germplasm. To reverse this trend, elite germplasm from other geographic regions can be introgressed, but due to lack of adaptation it is difficult to assess their breeding potential in the targeted environment. The objectives of this study were to (1) investigate the relationship between European and US maize germplasm, (2) examine the suitability of different mega-environments and measures of performance to assess the breeding potential of exotics, and (3) study the relationship of genetic distance with mid-parent heterosis (MPH). Eight European inbreds from the Dent and Flint heterotic groups, 11 US inbreds belonging to Stiff Stalk (SS), non-Stiff Stalk (NSS), and CIMMYT Pool 41, and their 88 factorial crosses in F₁ and F₂ generations were evaluated for grain yield and dry matter concentration. The experiments were conducted in three mega-environments: Central Europe (target mega-environment), US Cornbelt (mega-environment where donor lines were developed), and Southeast Europe (an intermediate mega-environment). The inbreds were also fingerprinted with 266 SSR markers. Suitable criteria to identify promising exotic germplasm were F₁ hybrid performance in the targeted mega-environment and F₁ and parental performance in the intermediate mega-environment. Marker-based genetic distances reflected relatedness among the inbreds, but showed no association with MPH. Based on genetic distance, MPH, and F₁ performance, we suggest to introgress SS germplasm into European Dents and NSS into European Flints, in order to exploit the specific adaptation of European flint germplasm and the excellent combining ability of US germplasm in European maize breeding programs.     

Genetic variation at bx1 controls DIMBOA content in maize

The main hydroxamic acid in maize (Zea mays L.) is 2-4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA). DIMBOA confers resistance to leaf-feeding by several corn borers. Most genes involved in the DIMBOA metabolic pathway are located on the short arm of chromosome 4, and quantitative trait loci (QTLs) involved in maize resistance to leaf-feeding by corn borers have been localized to that region. However, the low resolution of QTL linkage mapping does not allow convincing proof that genetic variation at bx loci was responsible for the variability for resistance. This study addressed the following objectives: to determine the QTLs involved in DIMBOA synthesis across genetically divergent maize inbreds using eight RIL families from the nested association mapping population, to check the stability of QTLs for DIMBOA content across years by evaluating two of those RIL families in 2 years, and to test the involvement of bx1 by performing association mapping with a panel of 281 diverse inbred lines. QTLs were stable across different environments. A genetic model including eight markers explained approximately 34% of phenotypic variability across eight RIL families and the position of the largest QTL co-localizes with the majority of structural genes of the DIMBOA pathway. Candidate association analysis determined that sequence polymorphisms at bx1 greatly affects variation of DIMBOA content in a diverse panel of maize inbreds, but the specific causal polymorphism or polymorphisms responsible for the QTL detected in the region 4.01 were not identified. This result may be because the causal polymorphism(s) were not sequenced, identity is masked by linkage disequilibrium, adjustments for population structure reduce significance of causal polymorphisms or multiple causal polymorphisms affecting bx1 segregate among inbred lines.     

Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Detection of QTL in multiple segregating populations is of high interest as it includes more alleles than mapping in a single biparental population. In addition, such populations are routinely generated in applied plant breeding programs and can thus be used to identify QTL which are of direct relevance for a marker-assisted improvement of elite germplasm. Multiple-line cross QTL mapping and joint linkage association mapping were used for QTL detection. We empirically compared these two different biometrical approaches with regard to QTL detection for important agronomic traits in nine segregating populations of elite rapeseed lines. The plants were intensively phenotyped in multi-location field trials and genotyped with 253 SNP markers. Both approaches detected several additive QTL for diverse traits, including flowering time, plant height, protein content, oil content, glucosinolate content, and grain yield. In addition, we identified one epistatic QTL for flowering time. Consequently, both approaches appear suited for QTL detection in multiple segregating populations.     

Fine mapping a major QTL for kernel number per row under different phosphorus regimes in maize (Zea mays L.)

Phosphorus (P) is one of the essential macronutrients for plant growth and development. Grain yield is the primary trait of interest in maize breeding programs. Maize grain yield and yield-related traits are seriously affected by P deficiency. Kernel number per row (KN), as one of the major components of grain yield, has attracted the attention of more and more breeders. In our previous study, one major QTL (named qKN), controlling KN under different P regimes was mapped to the interval between molecular markers bnlg1360 and umc1645 on chromosome 10 using a F _2:3 population derived from the cross between maize inbreds 178 and 5,003 (107). In order to understand its genetic basis, we developed a population of near isogenic lines (NILs) and two P regimes were used to fine map and characterize qKN. The QTL qKN was finally localized in a region of ~480 kb. A single qKN allele of inbred 178 increased KN by 6.08–10.76 % in the 5,003 (107) background; qKN acted in a partially dominant manner. Our results will be instrumental for the future identification and isolation of the candidate gene underlying qKN. The tightly linked molecular markers that we developed for qKN will be useful in maize breeding programs for improving KN applying the marker-assisted selection.     

Clustered QTL for source leaf size and yield traits in rice (Oryza sativa L.)

Improvement of plant type plays an important role in super-high yield breeding in rice (Oryza sativa L.). In the present study, a set of backcross recombinant inbred lines derived from a cross of 9311 and Zhenshan97, both elite indica hybrid parents, were developed to identify quantitative trait loci (QTL) for flag leaf size, panicle and yield traits. Forty-seven QTL for 14 traits were detected in common in the two environmental trials, of which nine genomic regions contained clustered QTL affecting plant type traits and yield traits. Four co-localized QTL on chromosomes 1, 6, 7 and 8 involving QTL for flag leaf size (flag leaf length, width and area) contained the QTL for yield traits such as panicle weight (PW) and secondary branch number (SBN), and in all cases alleles from 9311 increased source leaf size and were associated with increased sink size and yield (SBN and PW). Using a subset of overlapping substitution lines for the QTL region on chromosome 1, the QTL were validated and narrowed into a 990?kbp interval (RM3746?CRM10435) with pleiotropic effects on flag leaf size, PW, SBN and spikelet number per panicle. These QTL clusters with large effects on source leaf size and yield-related traits provide good targets for marker-assisted breeding for plant type improvement and high-yield potential in rice.