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.     

Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.     

水稻穗部性状的QTL与环境互作分析

分别在两年收集珍汕97／明恢63的重组自交系群体的表现数据,运用混合线性模型的QTL定位方法,联合分析穗部5个性状的QTLs7及QTL与环境互作关系。每穗颖花数、每穗实粒数、结实率、穗长和穗着密度分别检测到10、3、6、8和7个QTLs分别解释各性状变异的29．13％、19．2％、29．46％、26．39％和35．76％。对于同一性状,高值亲本和低值亲本中均存在增效和减效QTL。相关性状QTL的位置表现相同或相似,高值亲本和低值亲本中均存在增效和减效QTL。相关性状QTL的位置表现相同或相似,成族分布。1个穗长QTL,2个每穗颖花数QTL3,3个结实率QTLs表现与环境显著互作,QTL与环境互作效应的贡献率比相应的QTL贡献率略大。遗传力稍高的每穗实粒数和穗着粒密度的DQTL与环境不互作。     

直播条件下水稻6个穗部性状的QTL分析

在大田直播条件下,利用来源于＂Lemont/特青＂的重组自交系群体,对水稻6个穗部性状及其相互间遗传相关的分子基础进行了QTL分析,共检测到19个QTL,各性状QTL数为2～4个,单个QTL贡献率为4%～22%。共检测到3个染色体区段能同时影响多个穗部性状,其中第1染色体RM212-RM104和第2染色体RM263-RM221区段的QTL能同时影响单株产量、每穗颖花数、着粒密度和二次枝梗数中的3个或4个性状,且这2个区段的QTL对各性状的效应方向相同,增效等位基因均来自‘特青’,为各性状间表型正相关提供了重要的遗传解释。第11染色体RG1022附近的QTL对着粒密度的效应值为负,来自‘特青’的等位基因增加性状值,而对穗长的效应值为正,来自‘特青’的等位基因降低性状值,为这2个性状间表型负相关也提供了一定的遗传解释。此外,对水稻穗部性状QTL在多种环境和遗传背景下的稳定表达及其在分子标记辅助育种中的应用进行了讨论。     

Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia

Rice double-haploid (DH) lines of an indica and japonica cross were grown at nine different locations across four countries in Asia. Genotype-by-environment (G x E) interaction analysis for 11 growth- and grain yield-related traits in nine locations was estimated by AMMI analysis. Maximum G x E interaction was exhibited for fertility percentage number of spikelets and grain yield. Plant height was least affected by environment, and the AMMI model explained a total of 76.2% of the interaction effect. Mean environment was computed by averaging the nine environments and subsequently analyzed with other environments to map quantitative trait loci (QTL). QTL controlling the 11 traits were detected by interval analysis using mapmaker/qtl. A threshold LOD of >/=3.20 was used to identify significant QTL. A total of 126 QTL were identified for the 11 traits across nine locations. Thirty-four QTL common in more than one environment were identified on ten chromosomes. A maximum of 44 QTL were detected for panicle length, and the maximum number of common QTL were detected for days to heading detected. A single locus for plant height (RZ730-RG810) had QTL common in all ten environments, confirming AMMI results that QTL for plant height were affected the least by environment, indicating the stability of the trait. Two QTL were detected for grain yield and 19 for thousand-grain weight in all DH lines. The number of QTL per trait per location ranged from zero to four. Clustering of the QTL for different traits at the same marker intervals was observed for plant height, panicle number, panicle length and spikelet number suggesting that pleiotropism and or tight linkage of different traits could be the possible reason for the congruence of several QTL. The many QTL detected by the same marker interval across environments indicate that QTL for most traits are stable and not essentially affected by environmental factors.     

Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara

With a small and sequenced genome, rice provides an excellent system for studying the genetics of cereal domestication. We conducted a quantitative trait locus (QTL) analysis of key domestication traits using an F2 population derived from a cross between the cultivated rice, Oryza sativa, and the annual wild species, O. nivara. We found that the QTL of large phenotypic effects were targeted by domestication selection for effective harvest and planting, including a reduction in seed shattering and seed dormancy and the synchronization of seed maturation. Selection for higher yield was probably responsible for the fixation of mutations at a cluster of QTL on chromosome 7 and a few other chromosomal locations that could have substantially improved plant architecture and panicle structure, resulting in fewer erect tillers and longer and more highly branched panicles in cultivated rice. In comparison with the wild perennial species, O. rufipogon, rice domestication from O. nivara would have involved QTL with a greater degree of chromosomal co-localization and required little genetic change associated with life history or mating system transitions. The genetic analyses of domestication traits with both wild relatives will open opportunities for the improvement of rice cultivars utilizing natural germplasm.     

Identification of QTL for flag leaf length in common wheat and their pleiotropic effects

Leaf size is an important factor contributing to the photosynthetic capability of wheat plants. It also significantly affects various agronomic traits. In particular, the flag leaves contribute significantly to grain yield in wheat. A recombinant inbred line (RIL) population developed between varieties with significant differences in flag leaf traits was used to map quantitative trait loci (QTL) of flag leaf length (FLL) and to evaluate its pleiotropic effects on five yield-related traits, including spike length (SL), spikelet number per spike (SPN), kernel number per spike (KN), kernel length (KL), and thousand-kernel weight (TKW). Two additional RIL populations were used to validate the detected QTL and reveal the relationships in different genetic backgrounds. Using the diversity arrays technology (DArT) genetic linkage map, three major QTL for FLL were detected, with single QTL in different environments explaining 8.6–23.3% of the phenotypic variation. All the QTL were detected in at least four environments, and validated in two related populations based on the designed primers. These QTL and the newly developed primers are expected to be valuable for fine mapping and marker-assisted selection in wheat breeding programs.     

Comparative mapping of QTLs for agronomic traits of rice across environments by using a doubled-haploid population

We report here the RFLP mapping of quantitative trait loci (QTLs) which affect some important agronomic traits in cultivated rice. An anther culture-derived doubled-haploid (DH) population was established from a cross between indica and japonica rice varieties. A molecular linkage map comprising 137 markers was constructed based on this population which covered the rice genome at intervals of 14.8 cM on average. The linkage map was used to locate QTLs for such important agronomic traits as heading date, plant height, number of spikelets per panicle, number of grains per panicle, 1 000-grain weight and the percentage of seed set, by interval mapping. Evidence of genotype-by-environment interaction was found by comparing QTL maps of the same population grown in three diverse environments. A total of 22 QTLs for six agronomic traits was detected which were significant in at least one environment, but only seven were significant in all three environments; seven were significant in two environments and eight could only be detected in a single environment. However, QTLs-by-environment interaction was trait dependent. QTLs for spikelets and grains per panicle were common across environments while traits like heading date and plant height were more sensitive to environment. Received: 22 February 1996 / Accepted: 10 May 1996     

Whole-Genome Quantitative Trait Locus Mapping Reveals Major Role of Epistasis on Yield of Rice

Although rice yield has been doubled in most parts of the world since 1960s, thanks to the advancements in breeding technologies, the biological mechanisms controlling yield are largely unknown. To understand the genetic basis of rice yield, a number of quantitative trait locus (QTL) mapping studies have been carried out, but whole-genome QTL mapping incorporating all interaction effects is still lacking. In this paper, we exploited whole-genome markers of an immortalized F₂ population derived from an elite rice hybrid to perform QTL mapping for rice yield characterized by yield per plant and three yield component traits. Our QTL model includes additive and dominance main effects of 1,619 markers and all pair-wise interactions, with a total of more than 5 million possible effects. The QTL mapping identified 54, 5, 28 and 4 significant effects involving 103, 9, 52 and 7 QTLs for the four traits, namely the number of panicles per plant, the number of grains per panicle, grain weight, and yield per plant. Most identified QTLs are involved in digenic interactions. An extensive literature survey of experimentally characterized genes related to crop yield shows that 19 of 54 effects, 4 of 5 effects, 12 of 28 effects and 2 of 4 effects for the four traits, respectively, involve at least one QTL that locates within 2 cM distance to at least one yield-related gene. This study not only reveals the major role of epistasis influencing rice yield, but also provides a set of candidate genetic loci for further experimental investigation.     

Genetic Relationships Among Panicle Characteristics of Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) Using Unconditional and Conditional QTL Analyses

Using mixed-model-based composite interval mapping and conditional statistical methods, we studied quantitative trait loci (QTLs) with epistatic effects and QTLs by environment interaction effects for rice seed set percent (SSP), filled grain number per plant (FGP), and panicle length (PL). A population of 241 recombinant inbred lines was used which was derived from a cross between “Zhenshan 97” and “Minghui 63.” Its linkage map included 221 molecular markers. Our QTL analysis detected 28, 25, and 32 QTLs for SSP, FGP, and PL, respectively. Each QTL explained 1.37%∼13.19% of the mean phenotypic variation. A comparison of conventional and conditional mapping provided information about the genetic control system involved in the synthetic process of SSP, FGP, and PL at the level of individual QTLs. Conditional QTLs with reduced (or increased) effects were identified for SSP, which were significantly influenced by FGP or PL. Some QTLs could express independently for the given traits, thereby providing possibilities for simultaneous improvement of SSR and PL, and SSR and FGP. Epistasis was more sensitive to environmental conditions than were additive effects.     

Seed and agronomic QTL in low linolenic acid, lipoxygenase-free soybean (Glycine max (L.) Merrill) germplasm.

Linolenic acid and seed lipoxygenases are associated with off flavours in soybean products. F5 recombinant inbred lines (RILs) from a cross between a low linolenic acid line (RG10) and a seed lipoxygenase-free line (OX948) were genotyped for simple sequence repeats (SSR), random amplified polymorphic DNA (RAPD), sequence-tagged sites (STS), and cleaved amplified polymorphic sequence (CAPS) markers and evaluated for seed and agronomic traits at 3 Ontario locations in 2 years. One hundred twenty markers covering 1247.5 cM were mapped to 18 linkage groups (LGs) in the soybean composite genetic map. Seed lipoxygenases L-1 and L-2 mapped as single major genes to the same location on LG G13-F. L-3 mapped to LG G11-E. This is the first report of a map position for L-3. A major quantitative trait locus (QTL) associated with reduced linolenic acid content was identified on LG G3-B2. QTLs for 12 additional seed and agronomic traits were detected. Linolenic acid content, linoleic acid content, yield, seed mass, protein content, and plant height QTL were present in at least 4 of 6 environments. Three to 8 QTLs per trait were detected that accounted for up to 78% of total variation. Linolenic acid and lipoxygenase loci did not overlap yield QTL, suggesting that it should be possible to develop high-yielding lines resistant to oxidative degradation by marker-assisted selection (MAS).     

QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross

Advanced backcross QTL analysis was used to identify quantitative trait loci (QTL) for agronomic performance in a population of BC₂F_3:5 introgression lines created from the cross of a Colombian large red-seeded commercial cultivar, ICA Cerinza, and a wild common bean accession, G24404. A total of 157 lines were evaluated for phenological traits, plant architecture, seed weight, yield and yield components in replicated trials in three environments in Colombia and genotyped with microsatellite, SCAR, and phaseolin markers that were used to create a genetic map that covered all 11 linkage groups of the common bean genome with markers spaced at an average distance of every 10.4 cM. Segregation distortion was most significant in regions orthologous for a seed coat color locus (R-C) on linkage group b08 and two domestication syndrome genes, one on linkage group b01 at the determinacy (fin) locus and the other on linkage group b02 at the seed-shattering (st) locus. Composite interval mapping analysis identified a total of 41 significant QTL for the eight traits measured of which five for seed weight, two for days to flowering, and one for yield were consistent across two or more environments. QTL were located on every linkage group with b06 showing the greatest number of independent loci. A total of 13 QTL for plant height, yield and yield components along with a single QTL for seed size showed positive alleles from the wild parent while the remaining QTL showed positive alleles from the cultivated parent. Some QTL co-localized with regions that had previously been described to be important for these traits. Compensation was observed between greater pod and seed production and smaller seed size and may have resulted from QTL for these traits being linked or pleiotropic. Although wild beans have been used before to transfer biotic stress resistance traits, this study is the first to attempt to simultaneously obtain a higher yield potential from wild beans and to analyze this trait with single-copy markers. The wild accession was notable for being from a unique center of diversity and for contributing positive alleles for yield and other traits to the introgression lines showing the potential that advanced backcrossing has in common bean improvement.     

Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population

We report here the RFLP mapping of quantitative triat loci (QTLs) that affect some important agronomic traits in cultivated rice. An anther culturederived doubled haploid (DH) population was established from a cross between an indica and a japonica rice variety. On the basis of this population a molecular linkage map comprising 137 markers was constructed that covered the rice genome at intervals of 14.8cM on average. Interval mapping of the linkage map was used to locate QTLs for such important agronomic traits as heading date, plant height, number of spikelets per panicle, number of grains Per panicle, 1000-grain weight and percentage of seed set. Evidence of genotype-byenvironment interaction was found by comparing QTL maps of the same population grown in three diverse environments. A total of 22 QTLs for six agronomic traits were detected that were significant in at least one environment, but only 7 were significant in all three environments, 7 were significant in two environments and 8 could only be detected in a single environment. However, QTL-by-environment interaction was traitdependent. QTLs for spikelets and grains per panicle were common across environments, while traits like heading date and plant height were more sensitive to environment.     

Identification of quantitative trait loci controlling winter hardiness in an annual × perennial ryegrass interspecific hybrid population

Winter hardiness is a quantitative trait and the lack of it limits geographic distribution of ryegrass. Improving winter hardiness is an important breeding goal in ryegrass breeding programs. An understanding of the genetic basis for the component traits of winter hardiness would allow more efficient selection. A three-generation interspecific population of an annual × perennial ryegrass consisting of 152 progenies was used to map quantitative trait loci (QTL) that control winter hardiness-related traits including fall growth (FG), freezing tolerance (FT), and winter survival (WS) over 2 years. A total of 39 QTL were identified for the three traits from both the female parental (MFA) and the male parental (MFB) maps, of which 13 were for FG, 6 for FT, and 20 for WS. The proportion of phenotypic variation explained by individual QTL ranged from 10.4 to 22.1%. Both FG and FT were positively correlated with WS. Common QTL were detected between FG, FT, and WS. The QTL associated with WS on linkage groups (LGs) 4 and 5, and the QTL for FT on LG 5 were consistently identified over years and maps. These consistent QTL might serve as potential tools for marker-assisted selection to improve ryegrass winter hardiness.     

QTL mapping of resistance to gray leaf spot in ryegrass

Gray leaf spot (GLS) is a serious fungal disease caused by Magnaporthe grisea, recently reported on perennial ryegrass (Lolium perenne L.), an important turfgrass and forage species. This fungus also causes rice blast and many other grass diseases. Rice blast is usually controlled by host resistance, but durability of resistance is a problem. Little GLS resistance has been reported in perennial ryegrass. However, greenhouse inoculations in our lab using one ryegrass isolate and one rice-infecting lab strain suggest presence of partial resistance. A high density linkage map of a three generation Italian × perennial ryegrass mapping population was used to identify quantitative trait loci (QTL) for GLS resistance. Potential QTL of varying effect were detected on four linkage groups, and resistance to the ryegrass isolate and the lab strain appeared to be controlled by different QTL. Of three potential QTL detected using the ryegrass isolate, the one with strongest effect for resistance was located on linkage group 3 of the MFB parent, explaining between 20% and 37% of the phenotypic variance depending on experiment. Another QTL was detected on linkage group 6 of the MFA parent, explaining between 5% and 10% of the phenotypic variance. The two QTL with strongest effect for resistance to the lab strain were located on linkage groups MFA 2 and MFB 4, each explaining about 10% of the phenotypic variance. Further, the QTL on linkage groups 3 and 4 appear syntenic to blast resistance loci in rice. This work will likely benefit users and growers of perennial ryegrass, by setting the stage for improvement of GLS resistance in perennial ryegrass through marker-assisted selection.     

Genetic dissection of the source-sink relationship affecting fecundity and yield in rice (shape Oryza sativa L.)

The genetic basis underlying the relationship between the source leaves (the top two leaves) and the sink capacity in rice was investigated in a replicated trial of 2418 F₂ derived F₄ progeny from an inter-subspecific cross between cv. Lemont (japonica) and cv. Teqing (indica) and a complete linkage map with 115 well distributed RFLP markers. Path analysis indicated that 50% of the phenotypic variation in the primary sink capacity-grain weight per panicle was attributable to variation of the flag leaf area. Thirteen QTL and 30 pairs of epistatic loci were identified, which influence the length, width and area of the source leaves and the size of the primary sink (panicles) panicle length, floret density and floret number per panicle. Two QTL (QLl3b and QLw4) and 7 pairs of epistatic loci are largely responsible for the observed relationship between the source leaves and the sink capacity. The others appear to primarily influence the shape of the source leaves or panicle length/branching, and contribute little to the observed source-sink relationship and partially explain the yield component compensation. Our results suggest that important QTL affecting the source leaves can be manipulated through marker-assisted selection to increase sink capacity, which might result in improved yield potential in rice.     

Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars

The thousand-grain weight and spikelets per panicle directly contribute to rice yield. Heading date and plant height also greatly influence the yield. Dissection of genetic bases of yield-related traits would provide tools for yield improvement. In this study, quantitative trait loci (QTL) mapping for spikelets per panicle, thousand-grain weight, heading date and plant height was performed using recombinant inbred lines derived from a cross between two diverse cultivars, Nanyangzhan and Chuan7. In total, 20 QTLs were identified for four traits. They were located to 11 chromosomes except on chromosome 4. Seven and five QTLs were detected for thousand-grain weight and spikelets per panicle, respectively. Four QTLs were identified for both heading date and plant height. About half the QTLs were commonly detected in both years, 2006 and 2007. Six QTLs are being reported for the first time. Two QTL clusters were identified in regions flanked by RM22065 and RM5720 on chromosome 7 and by RM502 and RM264 on chromosome 8, respectively. The parent, Nanyangzhan with heavy thousand-grain weight, carried alleles with increased effects on all seven thousand-grain weight QTL, which explained why there was no transgressive segregation for thousand-grain weight in the population. In contrast, Chuan7 with more spikelets per panicle carried positive alleles at all five spikelets per panicle QTL except qspp5. Further work on distinction between pleiotropic QTL and linked QTL is needed in two yield-related QTL clusters.     

Interval mapping of quantitative trait loci for reproductive,morphological, and seed traits of soybean (Glycine max L.)

Quantitative trait loci (QTL) were mapped in segregating progeny from a cross between two soybean (Glycine max (L.) Merr.) cultivars: Minsoy (PI 27.890) and Noir 1 (PI 290.136). The 15 traits analyzed included reproductive, morphological, and seed traits, seed yield and carbon isotope discrimination ratios (¹³C/¹²C). Genetic variation was detected for all of the traits, and transgressive segregation was a common phenomenon. One hundred and thirty-two linked genetic markers and 24 additional unlinked markers were used to locate QTL by interval mapping and one-way analysis of variance, respectively. Quantitative trait loci controlling 11 of the 15 traits studied were localized to intervals in 6 linkage groups. Quantitative trait loci for developmental and morphological traits (R1, R5, R8, plant height, canopy height, leaf area, etc.) tended to be clustered in three intervals, two of which were also associated with seed yield. Quantitative trait loci for seed oil were separated from all the other QTL. Major QTL for maturity and plant height were linked to RFLP markers R79 (31% variation) and G173 (53% variation). Quantitative trait loci associated with unlinked markers included possible loci for seed protein and weight. Linkage between QTL is discussed in relation to the heritability and genetic correlation of the traits.