Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench

The productivity of sorghum is mainly determined by quantitative traits such as grain yield and stem sugar-related characteristics. Substantial crop improvement has been achieved by breeding in the last decades. Today, genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement. We have investigated QTL associated with the sugar components (Brix, glucose, sucrose, and total sugar content) and sugar-related agronomic traits (flowering date, plant height, stem diameter, tiller number per plant, fresh panicle weight, and estimated juice weight) in four different environments (two locations) using a population of 188 recombinant inbred lines (RILs) from a cross between grain (M71) and sweet sorghum (SS79). A genetic map with 157 AFLP, SSR, and EST-SSR markers was constructed, and several QTLs were detected using composite interval mapping (CIM). Further, additive × additive interaction and QTL × environmental interaction were estimated. CIM identified more than five additive QTLs in most traits explaining a range of 6.0–26.1% of the phenotypic variation. A total of 24 digenic epistatic locus pairs were identified in seven traits, supporting the hypothesis that QTL analysis without considering epistasis can result in biased estimates. QTLs showing multiple effects were identified, where the major QTL on SBI-06 was significantly associated with most of the traits, i.e., flowering date, plant height, Brix, sucrose, and sugar content. Four out of ten traits studied showed a significant QTL × environmental interaction. Our results are an important step toward marker-assisted selection for sugar-related traits and biofuel yield in sorghum.     

Identification of QTLs with Additive,Epistatic, and QTL × Seed Maturity Interaction Effects for Seed Vigor in Rice

Seed maturity is a critical process of seed vigor establishment. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed vigor, including the germination potential (GP), germination rate (GR), germination index (GI), and time for 50 % of germination (T₅₀), at 4, 5, and 6 weeks after heading in 2 years. Significant differences of seed vigor were observed among two parents and RIL population; the heritability of four traits was more than 90 % at three maturity stages. A total of 19 additive and 2 epistatic quantitative trait loci (QTL) for seed vigor were identified using QTL Cartographer and QTLNetwork program, respectively, in 2012, while 16 simple sequence repeat (SSR) markers associated with seed vigor were detected using bulked segregant analysis (BSA) in 2013. The phenotypic variation explained by each additive, epistatic QTL, and QTL × seed maturity interaction ranged from 9.19 to 22.94 %, 7.23 to 7.75 %, and 0.05 to 0.63 %, respectively. Ten additive QTLs were stably expressed in 2 years which might play important roles in establishment of seed vigor in different environments. By comparing chromosomal positions of ten stably expressed additive QTLs with those previously identified, they might be true QTLs for seed vigor; the regions of QTLs for seed vigor are likely to coincide with QTLs for seed dormancy, seed reserve mobilization, low-temperature germinability, and seedling growth. Using four selected RILs, three cross-combinations were predicted to improve seed vigor; 9 to 10 elite alleles could be pyramided by each combination. The selected RILs and the identified QTLs might be applicable for the improvement of seed vigor by marker-assisted selection (MAS) in rice.     

Locating QTLs controlling several adult root traits in an elite Chinese hybrid rice

This study aimed to elucidate the genetics of the adult root system in elite Chinese hybrid rice. Several adult root traits in a recombinant inbred line (RIL) population of Xieyou 9308 and two backcross F₁ (BCF₁) populations derived from the RILs were phenotyped under hydroponic culture at heading stage for quantitative trait locus (QTL) mapping and other statistical analysis. There a total of eight QTLs detected for the root traits. Among of them, a pleiotropic QTL was repeatedly flanked by RM180 and RM5436 on the short arm of chromosome 7 for multiple traits across RILs and its BCF₁ populations, accounting for 6.88% to 25.26% of the phenotypic variances. Only additive/dominant QTLs were detected for the root traits. These results can serve as a foundation for facilitating future cloning and molecular breeding.     

Quantitative trait loci associated with tipburn, heat stress-induced physiological disorders, and maturity traits in crisphead lettuce

Crisphead lettuce (Lactuca sativa L.) crops exhibit several economically important, physiological disorders when grown in high temperature conditions. These include tipburn, rib discoloration, premature bolting, ribbiness, and internal rib cracking. We evaluated seven physiological disorders and three agronomic traits segregating in a recombinant inbred line (RIL) population consisting of 152 F₇ RILs derived from an intra-specific cross between two crisphead cultivars, L. sativa cv. Emperor x L. sativa cv. El Dorado; evaluations were carried out at each of two parental maturities in one planting and at one intermediate maturity in a second planting in each of 2 years for a total of six evaluations. A genetic map was developed using 449 polymorphic SNP markers; it comprises 807 cM in 20 linkage groups that covered 51 % of the nine lettuce chromosomes. Composite interval mapping revealed a total of 36 significant QTLs for eight out of the ten traits evaluated. Significant QTLs were distributed in 11 linkage groups on seven of the chromosomes and accounted for up to 83 % of the phenotypic variation observed. The three largest QTLs for rib discoloration, which accounted individually for 7–21 % of the variation, were clustered with stem length, two with ribbiness and one with head firmness. Three major clusters of QTLs revealed pleiotropic effects or tight linkage between tipburn incidence and severity, head type, stem length, head firmness and ribbiness. One QTL, qTPB5.2, was detected in multiple trials and described 38–70 % of the variation in tipburn incidence. qTPB5.2 is, therefore, a useful candidate gene for breeding for tipburn resistance using marker-assisted selection.     

Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in <Emphasis Type="Italic">Sinonovacula constricta</Emphasis>

The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F₁ cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156.60-fold in the parents and 20.80-fold in each F₁ population on average). The total distance of the linkage map was 2383.85 cM, covering 19 linkage groups with an average inter-marker distance of 0.32 cM. The proportion of gaps less than 5.0 cM was on average 96.90%. A total of 16 suggestive QTLs for five growth-related traits (five QTLs for shell height, six QTLs for shell length, three QTLs for shell width, one QTL for total body weight, and one QTL for soft body weight) were identified. These QTLs were distributed on five linkage groups, and the regions showed overlapping on LG9 and LG13. In conclusion, the high-density genetic map and QTLs for S. constricta provide a valuable genetic resource and a basis for MAS.     

Identification of QTL for agronomic traits of importance for olive breeding

Development of methodologies for early selection is one of the most important goals of olive breeding programs at present. In this context, the identification of molecular markers associated with beneficial alleles could allow the development of marker-assisted selection (MAS) strategies in olive breeding programs. Fruit-related and plant vigor traits, which are of key importance for olive selection and breeding, were analyzed during two seasons in a progeny derived from the cross ‘Picual’ × ‘Arbequina.’ Quantitative trait loci (QTL) analyses were performed using MapQTL 4.0. A total of 22 putative QTLs were identified in the map of ‘Arbequina.’ QTLs clustered in linkage groups (LG) 1, 10 and 17. QTLs for oil-related traits located in LG 1 and 10 explained around 20–30 % of the phenotypic variability depending on the season and the trait. QTL for moisture-related traits were detected in LG 1, 10 and 17, and QTLs for the ratio pulp to stone were identified in LG 10 and 17 explaining around 15–20 %. Interaction between QTLs for the same trait was investigated. The significance of these results was discussed considering the co-localization of QTLs and Pearson correlations among traits. Five additional QTLs were detected in the map of ‘Picual.’ Four of them clustered in LG 17 indicating the presence of a QTL for fruit weight explaining around 12.7–15.2 % of the variability. Additionally, a QTL for trunk diameter was detected in LG 14 explaining 16 % of the variation. These results represent an important step toward the application of MAS in olive breeding programs.     

QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses

Background

Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis.

Methodology/Principal Findings

In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits.

Conclusions/Significance

The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1–6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.     

Verification of marker–trait associations in biparental winter barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) DH populations

In previous genome-wide association studies, marker–trait associations for grain yield and additional traits of agronomic importance were identified in the German winter barley (Hordeum vulgare L.) breeding gene pool. In the present study, seven doubled haploid populations segregating for the relevant alleles at the associated loci were used to get information whether these marker–trait associations can be verified in biparental populations and reliably used in applied barley breeding. The doubled haploid populations were phenotyped in field trials at two to five locations each in 1 year and genotyped by 40 trait-associated single nucleotide polymorphisms using an Illumina VeraCode GoldenGate assay. Large phenotypic variation was observed for all traits within at least one doubled haploid population. For 19 out of 58 marker–trait associations tested, the phenotypic means of both marker classes were significantly (p ≤ 0.005) different, thus confirming the association of the respective marker and the quantitative trait locus detected. For example, doubled haploid lines derived from a cross of ‘Malta’ × ‘Goldmine’ carrying different marker alleles differed by 0.41 t/ha in mean grain yield. The 19 (out of 58) marker–trait associations verified correspond to 10 (out of 27) genomic regions. Markers that were verified to be associated with a quantitative trait locus can be implemented directly in winter barley breeding for the selection of parental lines and marker-assisted pedigree selection.     

Identification and verification of QTLs for agronomic traits using wild barley introgression lines

A set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs) was subjected to a QTL study to verify genetic effects for agronomic traits, previously detected in the BC₂DH population S42 (von Korff et al. 2006 in Theor Appl Genet 112:1221–1231) and, in addition, to identify new QTLs and favorable wild barley alleles. Each line within the S42IL set contains a single marker-defined chromosomal introgression from wild barley (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is exclusively derived from elite spring barley (H. vulgare ssp. vulgare). Agronomic field data of the S42ILs were collected for seven traits from three different environments during the 2007 growing season. For detection of putative QTLs, a two-factorial mixed model ANOVA and, subsequently, a Dunnett test with the recurrent parent as a control were conducted. The presence of a QTL effect on a wild barley introgression was accepted, if the trait value of a particular S42IL was significantly (P < 0.05) different from the control, either across all environments and/or in a particular environment. A total of 47 QTLs were localized in the S42IL set, among which 39 QTLs were significant across all tested environments. For 19 QTLs (40.4%), the wild barley introgression was associated with a favorable effect on trait performance. Von Korff et al. (2006 in Theor Appl Genet 112:1221–1231) mapped altogether 44 QTLs for six agronomic traits to genomic regions, which are represented by wild barley introgressions of the S42IL set. Here, 18 QTLs (40.9%) revealed a favorable wild barley effect on the trait performance. By means of the S42ILs, 20 out of the 44 QTLs (45.5%) and ten out of the 18 favorable effects (55.6%) were verified. Most QTL effects were confirmed for the traits days until heading and plant height. For the six corresponding traits, a total of 17 new QTLs were identified, where at six QTLs (35.3%) the exotic introgression caused an improved trait performance. In addition, eight QTLs for the newly studied trait grains per ear were detected. Here, no QTL from wild barley exhibited a favorable effect. The introgression line S42IL-107, which carries an introgression on chromosome 2H, 17–42 cM is an example for S42ILs carrying several QTL effects simultaneously. This line exhibited improved performance across all tested environments for the traits days until heading, plant height and thousand grain weight. The line can be directly used to transfer valuable Hsp alleles into modern elite cultivars, and, thus, for breeding of improved varieties.     

Identification of QTLs controlling tissue-culture traits in barley ( Hordeum vulgare L.)

Quantitative trait loci (QTLs) controlling callus growth (CG), subsequent shoot differentiation ratio (SD) and green shoot ratio (GS) in immature embryo culture were identified in barley. A base map was developed from 99 recombinant inbred lines (RILs) of 'Azumamugi' 2 'Kanto Nakate Gold'. The tissue-culture traits were evaluated at the F₇ and F₁₀ generations of the RILs. The RILs showed wide and continuous variations in each of the three tissue-culture traits. Three QTLs for CG, three QTLs for SD and two QTLs for GS were detected by using composite interval mapping. A QTL for SD on chromosome 3H had a large effect, and 'Kanto Nakate Gold', which has a high differentiation ability, contributed to this QTL. The location of this QTL is identical to, or very close to, the uzu locus. We discuss the relationships between tissue-culture loci in 'Azumamugi' 2 'Kanto Nakate Gold' and those in other mapping populations.     

QTLs for agronomic traits in the Mediterranean environment identified in recombinant inbred lines of the cross 'Arta' × <Emphasis Type="Italic">H. spontaneum</Emphasis> 41-1

A genetic linkage map has been developed for recombinant inbred lines (RILs) of the cross 'Arta' × Hordeum spontaneum 41-1. One hundred and ninety four RILs, randomly chosen from a population of 494 RILs, were mapped with 189 markers including one morphological trait (btr = brittle rachis locus). The linkage map extended to 890 cM. Agronomic traits such as grain yield, biological yield, days to heading, plant height, cold tolerance and others were evaluated at the ICARDA research stations Tel Hadya and Breda during the years 1996–97 and 1997–98. QTLs for agronomic traits related to drought resistance were localized. For the most-important character 'plant height under drought stress', QTLs on 2H, 3H and 7H were detected. The 'plant height' QTLs, specially the one on 3H, showed pleiotropic effects on traits such as days to heading, grain yield and biological yield. QTLs were also identified for other traits associated with adaptation to the Mediterranean environment such as cold tolerance, days to heading and tiller number. The identification of QTLs for agronomic traits is a first step to analyze and to dissect complex characters such as adaptation to drought tolerance.Comunicated by R. Hagemann     

Association mapping of six yield-related traits in rapeseed (Brassica napus L.)

Yield is one of the most important traits for rapeseed (Brassica napus L.) breeding, but its genetic basis remains largely ambiguous. Association mapping has provided a robust approach to understand the genetic basis of complex agronomic traits in crops. In this study, a panel of 192 inbred lines of B. napus from all over the world was genotyped using 451 single-locus microsatellite markers and 740 amplified fragment length polymorphism markers. Six yield-related traits of these inbred lines were investigated in three consecutive years with three replications, and genome-wide association studies were conducted for these six traits. Using the model controlling both population structure and relative kinship (Q + K), a total of 43 associations (P < 0.001) were detected using the means of the six yield-related traits across 3 years, with two to fourteen markers associated with individual traits. Among these, 18 markers were repeatedly detected in at least 2 years, and 12 markers were located within or close to QTLs identified in previous studies. Six markers commonly associated with correlated traits. Conditional association analysis indicated that five of the associations between markers and correlated traits are caused by one QTL with pleiotropic effects, and the remaining association is caused by linked but independent QTLs. The combination of favorable alleles of multiple associated markers significantly enhances trait performance, illustrating a great potential of utilization of the associations in rapeseed breeding programs.     

A first step toward the development of a barley NAM population and its utilization to detect QTLs conferring leaf rust seedling resistance

Key message

We suggest multi-parental nested association mapping as a valuable innovation in barley genetics, which increases the power to map quantitative trait loci and assists in extending genetic diversity of the elite barley gene pool.

Abstract

Plant genetic resources are a key asset to further improve crop species. The nested association mapping (NAM) approach was introduced to identify favorable genes in multi-parental populations. Here, we report toward the development of the first explorative barley NAM population and demonstrate its usefulness in a study on mapping quantitative trait loci (QTLs) for leaf rust resistance. The NAM population HEB-5 was developed from crossing and backcrossing five exotic barley donors with the elite barley cultivar ‘Barke,’ resulting in 295 NAM lines in generation BC₁S₁. HEB-5 was genetically characterized with 1,536 barley SNPs. Across HEB-5 and within the NAM families, no deviation from the expected genotype and allele frequencies was detected. Genetic similarity between ‘Barke’ and the NAM families ranged from 78.6 to 83.1 %, confirming the backcrossing step during population development. To explore its usefulness, a screen for leaf rust (Puccinia hordei) seedling resistance was conducted. Resistance QTLs were mapped to six barley chromosomes, applying a mixed model genome-wide association study. In total, four leaf rust QTLs were detected across HEB-5 and four QTLs within family HEB-F23. Favorable exotic QTL alleles reduced leaf rust symptoms on two chromosomes by 33.3 and 36.2 %, respectively. The located QTLs may represent new resistance loci or correspond to new alleles of known resistance genes. We conclude that the exploratory population HEB-5 can be applied to mapping and utilizing exotic QTL alleles of agronomic importance. The NAM concept will foster the evaluation of the genetic diversity, which is present in our primary barley gene pool.     

Mapping and validation of QTLs for resistance to aphids and whiteflies in melon

Aphis gossypii and Bemisia tabaci are severe hemipteran pests of melon crops and breeding for resistance to both insects is required to reduce pesticide use. Resistance was evaluated for its effect on behaviour and biotic potential of both hemipterans in a population of recombinant inbred lines (RILs) derived from the cross Védrantais × PI 161375. Insect variability was considered using two A. gossypii clones and two B. tabaci populations. Two additive QTLs affected the whiteflies. Four additive QTLs and two couples of epistatic QTLs affected the aphids. Amongst them, a major QTL affects both behaviour and biotic potential of A. gossypii and therefore a same R gene induces both antixenosis and antibiosis. This major QTL colocalizes with the Vat gene belonging to the NBS-LRR gene family. No loci affected both aphids and whiteflies contrary to what was observed for the Mi1.2 gene, a NBS-LRR gene in tomato. Original populations with different allelic compositions at QTLs affecting A. gossypii were built by one inter-crossing of RILs used for the mapping process. The genetic background was shown homogeneous between these populations what allowed validating QTLs and investigating the effect of allelic combinations at QTLs. Effects of QTLs were stronger than expected and some QTLs had a wider spectrum than expected. This strategy of validation appeared rapid and low cost.     

Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum

The identification of quantitative trait loci (QTLs) affecting agronomically important traits enable to understand their underlying genetic mechanisms and genetic basis of their complex interactions. The aim of the present study was to detect QTLs for 12 agronomic traits related to staygreen, plant early development, grain yield and its components, and some growth characters by analyzing replicated phenotypic datasets from three crop seasons, using the population of 168 F₇ RILs of the cross 296B × IS18551. In addition, we report mapping of a subset of genic-microsatellite markers. A linkage map was constructed with 152 marker loci comprising 149 microsatellites (100 genomic- and 49 genic-microsatellites) and three morphological markers. QTL analysis was performed by using MQM approach. Forty-nine QTLs were detected, across environments or in individual environments, with 1–9 QTLs for each trait. Individual QTL accounted for 5.2–50.4% of phenotypic variance. Several genomic regions affected multiple traits, suggesting the phenomenon of pleiotropy or tight linkage. Stable QTLs were identified for studied traits across different environments, and genetic backgrounds by comparing the QTLs in the study with previously reported QTLs in sorghum. Of the 49 mapped genic-markers, 18 were detected associating either closely or exactly as the QTL positions of agronomic traits. EST marker Dsenhsbm19, coding for a key regulator (EIL-1) of ethylene biosynthesis, was identified co-located with the QTLs for plant early development and staygreen trait, a probable candidate gene for these traits. Similarly, such exact co-locations between EST markers and QTLs were observed in four other instances. Collectively, the QTLs/markers identified in the study are likely candidates for improving the sorghum performance through MAS and map-based gene isolations.     

Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population

A recombinant inbred population developed from a cross between high-yielding lowland rice (Oryza sativa L.) subspecies indica cv. IR64 and upland tropical rice subspecies japonica cv. Cabacu was used to identify quantitative trait loci (QTLs) for grain yield (GY) and component traits under reproductive-stage drought stress. One hundred fifty-four lines were grown in field trials in Indonesia under aerobic conditions by giving surface irrigation to field capacity every 4 days. Water stress was imposed for a period of 15 days during pre-flowering by withholding irrigation at 65 days after seeding. Leaf rolling was scored at the end of the stress period and eight agronomic traits were evaluated after recovery. The population was also evaluated for root pulling force, and a total of 201 single nucleotide polymorphism markers were used to construct the molecular genetic linkage map and QTL mapping. A QTL for GY under drought stress was identified in a region close to the sd1 locus on chromosome 1. QTL meta-analysis across diverse populations showed that this QTL was conserved across genetic backgrounds and co-localized with QTLs for leaf rolling and osmotic adjustment (OA). A QTL for percent seed set and grains per panicle under drought stress was identified on chromosome 8 in the same region as a QTL for OA previously identified in three different populations.     

Genome-wide association mapping of agronomic traits in relevant barley germplasm in Uruguay

The genetic basis of agronomic traits determining adaptation to specific production conditions is a key factor for the improvement of crops, including malting barley (Hordeum vulgare L.). The aim of this study was to determine the genome-wide genetic components associated with agronomic phenotypes of local and global significance in a population of 76 barley genotypes that have been introduced into Uruguay in different chronological periods. The phenotypic database was obtained from five field experiments, planted in 2 years and in two locations, where a total of 13 agronomic traits were determined. The population was genotyped with 1,033 single nucleotide polymorphisms. We found a total of 41 quantitative trait loci (QTL) in a combined analysis using all datasets and 79 QTL if we considered all the trait/experiment combinations analyzed. The highest concentration of QTL was detected on chromosomes 2H and 4H. Most QTL were detected for grain plumpness and weight. Two linkage disequilibrium (LD) blocks associated with a large number of traits were detected on 2HS. The largest LD block was composed of three haplotypes, possibly derived from three ancestors of different geographical origin. We also detected three genomic regions in different chromosomes (2H, 5H and 7H) in LD between them, associated with agronomic traits. This study provides a contribution to the understanding of the genetics of barley adaptation in the southern cone of South America. Our results showed that elite varieties have favorable alleles at different QTL, indicating that gains can be made through plant breeding.     

Identification of QTLs with additive,epistatic and QTL × development interaction effects for seed dormancy in rice

Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach.     

Identification of QTL for maize grain yield and kernel-related traits

Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea mays L.) breeding practice. Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs). One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were used to genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW), 10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1) per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval between bnlg1893 and chr2-236477 (chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simultaneously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved in chromosomal region at bin 2.03 was detected for HKW; no significant QTL × environment interactions were observed. These results provide the common QTLs and for marker-assisted breeding.     

Quantitative trait loci associated with resistance to Fusarium head blight and kernel discoloration in barley

Resistance to Fusarium head blight (FHB), deoxynivalenol (DON) accumulation, and kernel discoloration (KD) in barley are difficult traits to introgress into elite varieties because current screening methods are laborious and disease levels are strongly influenced by environment. To improve breeding strategies directed toward enhancing these traits, we identified genomic regions containing quantitative trait loci (QTLs) associated with resistance to FHB, DON accumulation, and KD in a breeding population of F_4:7 lines using restriction fragment length polymorphic (RFLP) markers. We evaluated 101 F_4:7 lines, derived from a cross between the cultivar Chevron and an elite breeding line, M69, for each of the traits in three or four environments. We used 94 previously mapped RFLP markers to create a linkage map. Using composite interval mapping, we identified 10, 11, and 4 QTLs associated with resistance to FHB, DON accumulation, and KD, respectively. Markers flanking these QTLs should be useful for introgressing resistance to FHB, DON accumulation, and KD into elite barley cultivars. Received: 8 November 1998 / Accepted: 8 January 1999