Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm

Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm

The introgression of winter germplasm into spring canola (Brassica napus L.) represents a novel approach to improve seed yield of hybrid spring canola. In this study, quantitative trait loci (QTL) for seed yield and other traits were genetically mapped to determine the effects of genomic regions introgressed from winter germplasm into spring canola. Plant materials used comprised of two populations of doubled haploid (DH) lines having winter germplasm introgression from two related French winter cultivars and their testcrosses with a spring line used in commercial hybrids. These populations were evaluated for 2 years at two locations (Wisconsin, USA and Saskatchewan, Canada). Genetic linkage maps based on RFLP loci were constructed for each DH population. Six QTL were detected in the testcross populations for which the winter alleles increased seed yield. One of these QTL explained 11 and 19% of the phenotypic variation in the two Canadian environments. The winter allele for another QTL that increased seed yield was linked in coupling to a QTL allele for high glucosinolate content, suggesting that the transition of rapeseed into canola could have resulted in the loss of favorable seed yield alleles. Most QTL for which the introgressed allele decreased seed yield of hybrids mapped to genomic regions having homoeologous non-reciprocal transpositions. This suggests that allelic configurations created by these rearrangements might make an important contribution to genetic variation for complex traits in oilseed B. napus and could account for a portion of the heterotic effects in hybrids. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under field and controlled conditions

To increase yield in pea (Pisum sativum L.), autumn sowing would be preferable. Hence, frost tolerance of pea became a major trait of interest for breeders. In order to better understand the cold acclimation in pea, Champagne a frost tolerant line and Terese, a frost sensitive line, and their recombinant inbred lines (RIL) were studied. RIL frost tolerance was evaluated by a frost damage scale under field as well as controlled conditions. A quantitative trait loci (QTL) approach was used to identify chromosomal regions linked to frost tolerance. The detected QTL explained from 6.5 to 46.5% of the phenotypic variance. Amongst them, those located on linkage groups 5 and 6 were consistent with over all experiments, in field as well as in controlled environments. In order to improve the understanding of the frost tolerance mechanisms, several cold acclimation key characters such as concentration of sugars, electrolyte leakage, osmotic pressure, and activity of RuBisCO were assessed. Some of these physiological QTL colocalised with QTL for frost damage, in particular two raffinose QTL on LG5 and LG6 and one RuBisCO activity QTL on LG6, explaining 8.8 to 27.0% of the phenotypic variance. In addition, protein quantitative loci were mapped; some of them colocalised with frost damage and physiological QTL on LG5 and LG6, explaining 16.0–43.6% of the phenotypic variance. Raffinose metabolism and RuBisCO activity and its effect on photosynthesis might play a major role in cold acclimation of pea. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance

Key message

Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea.

Abstract

The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9–71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.     

Mapping and characterisation of QTL × E interactions for traits determining grain and stover yield in pearl millet

A mapping population of 104 F(3) lines of pearl millet, derived from a cross between two inbred lines H 77/833-2 x PRLT 2/89-33, was evaluated, as testcrosses on a common tester, for traits determining grain and stover yield in seven different field trials, distributed over 3 years and two seasons. The total genetic variation was partitioned into effects due to season (S), genotype (G), genotype x season interaction (G x S), and genotype x environment-within-season interaction [G x E(S)]. QTLs were determined for traits for their G, G x S, and G x E(S) effects, to assess the magnitude and the nature (cross over/non-crossover) of environmental interaction effects on individual QTLs. QTLs for some traits were associated with G effects only, while others were associated with the effects of both G and G x S and/or G, G x S and G x E(S) effects. The major G x S QTLs detected were for flowering time (on LG 4 and LG 6), and mapped to the same intervals as G x S QTLs for several other traits (including stover yield, harvest index, biomass yield and panicle number m(-2)). All three QTLs detected for grain yield were unaffected by G x S interaction however. All three QTLs for stover yield (mapping on LG 2, LG 4 and LG 6) and one of the three QTLs for grain yield (mapping on LG 4) were also free of QTL x E(S) interactions. The grain yield QTLs that were affected by QTL x E(S) interactions (mapping on LG 2 and LG 6), appeared to be linked to parallel QTL x E(S) interactions of the QTLs for panicle number m(-2) on (LG 2) and of QTLs for both panicle number m(-2) and harvest index (LG 6). In general, QTL x E(S) interactions were more frequently observed for component traits of grain and stover yield, than for grain or stover yield per se.     

Exploring new alleles for frost tolerance in winter rye

Key message

Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs.

Abstract

Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr–2) in Triticeae. The Puma allele at the Fr–R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr–R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

     

Genetic analysis of physiological components of salt tolerance conferred by Solanum rootstocks. What is the rootstock doing for the scion?

Grafting desirable crop varieties on stress-tolerant rootstocks provides an opportunity to increase crop salt tolerance. Here, a commercial hybrid tomato variety was grafted on two populations of recombinant inbred lines developed from a salt-sensitive genotype of Solanum lycopersicum var. cerasiforme, as female parent, and two salt-tolerant lines, as male parents, from S. pimpinellifolium, the P population, and S. cheesmaniae, the C population, to identify an easy screening method for identifying rootstocks conferring salt tolerance in terms of fruit yield. Potential physiological components of salt tolerance were assessed in the scion: leaf biomass, [Na⁺], nutrition, water relations and xylem ABA concentration. A significant correlation between scion fruit yield and scion leaf fresh weight, water potential or the ABA concentration was found in the C population under salinity, but the only detected QTL did not support this relationship. The rootstocks of the P population clearly affected seven traits related to the sodium, phosphorous and copper concentrations and water content of the scion leaf, showing heritability estimates around 0.4 or higher. According to heritability estimates in the P population, up to five QTLs were detected per trait. QTLs contributing over 15% to the total variance were found for P and Cu concentrations and water content of the scion leaf, and the proportion of fresh root weight. Correlation and QTL analysis suggests that rootstock-mediated improvement of fruit yield in the P population under salinity is mainly explained by the rootstock’s ability to minimise perturbations in scion water status.     

QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice

Agricultural environments deteriorate due to excess nitrogen application.Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input.Rice genotypes respond variably to soil available nitrogen.The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits.Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena.Three nitrogen regimes namely,native (0 kg/ha; no nitrogen applied),optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments.The parents and DH lines were significantly varying for all traits under different nitrogen regimes.All traits except plant height recorded significant genotype x environment interaction.Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake.Sixteen QTLs were detected by composite interval mapping.Eleven QTLs showed significant QTL x environment interactions.On chromosome 3,seven QTLs were detected associated with nitrogen use,plant yield and associated traits.A QTL region between markers RZ678,RZ574 and RZ284 was associated with nitrogen use and yield.This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.     

Identification of QTL involved in field resistance to light leaf spot (Pyrenopeziza brassicae) and blackleg resistance (Leptosphaeria maculans) in winter rapeseed (Brassica napus L.)

 Quantitative trait loci (QTL), involved in the polygenic field resistance of rapeseed (Brassica napus L.) to light leaf spot disease, were mapped using 288 DNA markers on 152 doubled-haploid (DH) lines derived from the cross ‘Darmor-bzh’בYudal’. Over two years (1995 and 1996), the DH population was evaluated for light leaf spot resistance on leaves (L) and stems (S), and for blackleg disease resistance in same field trials. For the L resistance criterion, a total of five and seven QTL were detected in 1995 and in 1996 respectively, accounting for 53% and 57% of the genotypic variation. For the S criterion, three and five QTL were identified in 1995 and in 1996 respectively, explaining 29% and 43% of the genotypic variation. The locations of the QTL detected were quite consistent over the two years (4- and 2-year common QTL for L and S, respectively). Three genomic regions, located on the DY5, DY10 and DY11 groups, were common to the resistance on leaves and stems. In comparison with the QTL for blackleg resistance described by Pilet et al. (1998), two regions on the DY6 and DY10 groups, were associated with the two disease resistances. These ‘multiple disease resistance’ (‘MDR’) QTL may correspond to genes involved in common resistance mechanisms towards the two pathogens or else to clusters of resistance genes. Received: 21 November 1997 / Accepted: 3 March 1998     

QTL Mapping for Fiber and Yield Traits in Upland Cotton under Multiple Environments

A population of 178 recombinant inbred lines (RILs) was developed using a single seed descendant from a cross between G. hirsutum. acc DH962 and G. hirsutum. cv Jimian5, was used to construct a genetic map and to map QTL for fiber and yield traits. A total of 644 polymorphic loci were used to construct a final genetic map, containing 616 loci and spanning 2016.44 cM, with an average of 3.27 cM between adjacent markers. Statistical analysis revealed that segregation distortion in the intraspecific population was more serious than that in the interspecific population. The RIL population and the two parents were phenotyped under 8 environments (two locations, six years), revealing a total of 134 QTL, including 64 for fiber qualities and 70 for yield components, independently detected in seven environments, explaining 4.40–15.28% of phenotypic variation (PV). Among the 134 QTL, 9 common QTL were detected in more than one environment, and 22 QTL and 19 new QTL were detected in combined analysis (E9). A total of 26 QTL hotspot regions were observed on 13 chromosomes and 2 larger linkage groups, and some QTL clusters related to fiber qualities or yield components were also observed. The results obtained in the present study suggested that to map accurate QTL in crops with larger plant types, such as cotton, phenotyping under multiple environments is necessary to effectively apply the obtained results in molecular marker-assisted selection breeding and QTL cloning.     

A QTL on chromosome 6A in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis>) is associated with longer coleoptiles,greater seedling vigour and final plant height

Wheat crops with greater early vigour shade the soil surface more rapidly and reduce water loss. Evaporative losses affect water-use efficiency particularly in drier regions where most of the rainfall occurs early in the growing season before canopy closure. Greater seedling leaf area and longer coleoptiles are major determinants of increased vigour and better crop establishment. A previously developed high vigour breeding line ‘Vigour 18’ was used to establish a large recombinant inbred family and framework map to identify a QTL on chromosome 6A that accounted for up to 8% of the variation for coleoptile length, 14% of seedling leaf width and was associated with increased plant height. The SSR marker NW3106, nearest to the 6A QTL, was also associated with greater leaf width in a breeding population that was also derived from a cross involving the high vigour donor line ‘Vigour18’. The association between the NW3106 marker and coleoptile length was validated in a second breeding population which was developed using an unrelated long coleoptile donor line. The ‘Vigour18’ allele of the QTL on chromosome 6A promoted coleoptile length and leaf width during early plant growth but was also associated with increased plant height at maturity. Markers linked to the QTL are being used to increase the frequency of increased vigour and long coleoptile alleles in early generations of breeding populations.     

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.     

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.     

Genotypic variation of quantitative trait loci controlling in vitro androgenesis in maize.

A quantitative trait loci (QTL) analysis for androgenetic capability has been conducted on three different crosses in maize, including very high and nonresponding lines for androgenesis. The doubled haploid lines derived by anther culture from the crosses DH5 x DH7, A188 x DH7, and R6 x DH99 showed a range of 0-70%, 0-40%, and 0-50% androgenetic responding anthers, respectively. The genotypic heritability of means for this trait is close to 0.90 for A188 x DH7 and 0.78 for R6 x DH99. The QTL analysis involved in each population the mapping of more than 100 loci covering a large part of the genome with reasonably spaced markers averaging 12 cM. Different measurements describing the androgenetic process were studied: AC, percentage of responding anthers; ELS, number of androgenetic embryos produced per 100 plated anthers; PLE, number of plantlets regenerated per 100 embryos; PLA, number of plantlets per 100 plated anthers. In each cross, three to four QTLs were found for AC, explaining 30-40% of the phenotypic variation. The QTL detected for PLA was also strong QTL for AC or ELS. This agrees with the observation that these last two traits are good predictors for final plantlet yield. The QTLs found were specific, although the same line DH7 was used in two crosses and DH99 derived from DH5 and DH7 in the third cross. These results suggest that the transfer of the androgenetic capabilities in elite germplasm will still involve a phenotypic evaluation of the androgenetic performances. A backcross-assisted selection based only on the genotype at the QTL is probably possible but only within the crosses used for this QTL analysis.     

Molecular breeding for grain yield in barley: an evaluation of QTL effects in a spring barley cross

 We report results from a breeding strategy designed to accumulate favorable QTL alleles for grain yield identified in the SteptoeבMorex’ (SM) barley germplasm. Two map lines (SM73 and SM145) from the original mapping population were selected based on their marker genotype and QTL structure. When crossed, these lines would be expected to produce progeny with most favorable QTL alleles. One hundred doubled haploid (DH) lines from the F₁ hybrid of this cross were genotyped with ten RFLP markers and one morphological marker defining grain yield to monitor QTL segregation. A subset of 24 lines representing various combinations of putatively favorable and unfavorable QTL alleles, together with Steptoe, ‘Morex’, SM73, and SM145, were phenotyped for grain yield in five environments. Multiple regression procedures were used to explore phenotype and genotype relationships. Most target QTLs showed significant effects. However, significance and magnitude of QTL effects and favorable QTL allele phase varied across environments. All target QTLs showed significant QTL-by-environment interaction (QTL×E), and the QTL on chromosome 2 expressed alternative favorable QTL alleles in different environments. Digenic epistatic effects were also detected between some QTL loci. For traits such as grain yield, marker-assisted selection efforts may be better targeted at determining optimum combinations of QTL alleles rather than pyramiding alleles detected in a reference mapping population. Received: 2 June 1998 / Accepted: 17 September 1998     

New insights into the genetics of in vivo induction of maternal haploids, the backbone of doubled haploid technology in maize

Haploids and doubled haploid (DH) inbred lines have become an invaluable tool for maize genetic research and hybrid breeding, but the genetic basis of in vivo induction of maternal haploids is still unknown. This is the first study reporting comparative quantitative trait locus (QTL) analyses of this trait in maize. We determined haploid induction rates (HIR) in testcrosses of a total of 1061 progenies of four segregating populations involving two temperate haploid inducers, UH400 (HIR = 8%) and CAUHOI (HIR = 2%), one temperate and two tropical inbreds with HIR = 0%, and up to three generations per population. Mean HIR of the populations ranged from 0.6 to 5.2% and strongly deviated from the midparent values. One QTL (qhir1) explaining up to p = 66% of the genetic variance was detected in bin 1.04 in the three populations involving a noninducer parent and the HIR-enhancing allele was contributed by UH400. Segregation ratios of loci in bin 1.04 were highly distorted against the UH400 allele in these three populations, suggesting that transmission failure of the inducer gamete and haploid induction ability are related phenomena. In the CAUHOI × UH400 population, seven QTL were identified on five chromosomes, with qhir8 on chromosome 9 having p > 20% in three generations of this cross. The large-effect QTL qhir1 and qhir8 will likely become fixed quickly during inducer development due to strong selection pressure applied for high HIR. Hence, marker-based pyramiding of small-effect and/or modifier QTL influencing qhir1 and qhir8 may help to further increase HIR in maize. We propose a conceptual genetic framework for inheritance of haploid induction ability, which is also applicable to other dichotomous traits requiring progeny testing, and discuss the implications of our results for haploid inducer development.     

Confirmation of QTL controlling seed yield in spring canola (Brassica napus L.) hybrids

Allelic effects observed in QTL discovery experiments must be confirmed to be useful in subsequent breeding efforts. Two QTL affecting seed yield of spring hybrid canola (Brassica napus L.) were previously identified in two populations of inbred backcross lines (IBLs) containing germplasm introgressed from a winter cultivar. The effects of favorable alleles at these QTL were retested by crossing two selected IBLs (M5 and M31) to three spring canola lines having different genetic backgrounds. Doubled haploid (DH) lines derived from each F₁ were genotyped with RFLP markers flanking the QTL and grouped into the four possible QTL genotypes. For the first field experiment, DH lines derived by crossing the M5 line to one spring line were crossed to two female testers and evaluated as individual testcross progenies in one environment. QTL genotypes had large variances and were not significantly different. A second field experiment was conducted using the DH lines from the first experiment and two other sets of DH lines derived from the M31 line crossed to two different spring canola lines. Individual lines within each QTL genotype of each set were bulked and crossed to the same testers used in Experiment 1. Bulked hybrid seeds of each QTL genotype were planted in a split-split plot randomized block design and 12 replicates. QTL genotypes had smaller variances in this experiment, and the effects of one QTL were confirmed in some genetic backgrounds. These results suggest that bulking of QTL genotypes and use of an appropriate experimental design with many replicates are needed to detect small differences between QTL genotypes.     

Identification of QTLs for grain yield and grain-related traits of maize (Zeamays L.) using an AFLP map, different testers, and cofactor analysis

We exploited the AFLP®¹(AFLP® is a registered trademark of Keygene, N.V.) technique to map and characterise quantitative trait loci (QTLs) for grain yield and two grain-related traits of a maize segregating population. Two maize elite inbred lines were crossed to produce 229 F₂ individuals which were genotyped with 66 RFLP and 246 AFLP marker loci. By selfing the F₂ plants 229 F₃ lines were produced and subsequently crossed to two inbred testers (T1 and T2). Each series of testcrosses was evaluated in field trials for grain yield, dry matter concentration, and test weight. The efficiency of generating AFLP markers was substantially higher relative to RFLP markers in the same population, and the speed at which they were generated showed a great potential for application in marker-assisted selection. AFLP markers covered linkage group regions left uncovered by RFLPs; in particular at telomeric regions, previously almost devoided of markers. This increase of genome coverage afforded by the inclusion of the AFLPs revealed new QTL locations for all the traits investigated and allowed us to map telomeric QTLs with higher precision. The present study has also provided an opportunity to compare simple (SIM) and composite interval mapping (CIM) for QTL analysis. Our results indicated that the method of CIM employed in this study has greater power in the detection of QTLs, and provided more precise and accurate estimates of QTL positions and effects than SIM. For all traits and both testers we detected a total of 36 QTLs, of which only two were in common between testers. This suggested that the choice of a tester for identifying QTL alleles for use in improving an inbred is critical and that the expression of QTL alleles identified may be tester-specific.     

A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat.

A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat x maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis. Among the 28 linkage groups identified, 25 were assigned to the 21 chromosomes of wheat. The total map length was 3948 cM, including the three unassigned linkage groups (88 cM), and the mean interval between loci was 12.0 cM. Loci with segregation distortion were clustered on chromosomes 1A, 4B, 4D, 5A, 6A, 6B, and 6D. After vernalization, the DH lines were evaluated for spike number per plant (SN) and spike length (SL) in a greenhouse under 24-h daylength to assess the "gigas" features (extremely large spikes and leaves) of 'Oligoculm'. The DH lines were also autumn-sown in the field in two seasons (1990-1991 and 1997-1998) for SN and SL evaluation. QTL analysis was performed by composite interval mapping (CIM) with the framework map to detect QTLs for SN and SL. A major QTL on 1AS, which was stable in both greenhouse and field conditions, was found to control SN. This QTL was close to the glume pubescence locus (Hg) and explained up to 62.9% of the total phenotypic variation. The 'Oligoculm' allele restricted spike number. The SSR locus Xpsp2999 was the closest locus to this QTL and is considered to be a possible marker for restricted tillering derived from 'Oligoculm'. Eight QTLs were detected for SL. The largest QTL detected on 2DS was common to the greenhouse and field environments. It explained up to 33.3% of the total phenotypic variation. The second largest QTL on 1AS was common to the greenhouse and the 1997-1998 season. The position of this QTL was close to that for the SN detected on 1AS. The association between SN and SL is discussed.     

QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions

Heat and drought adaptive quantitative trait loci (QTL) in a spring bread wheat population resulting from the Seri/Babax cross designed to minimize confounding agronomic traits have been identified previously in trials conducted in Mexico. The same population was grown across a wide range of environments where heat and drought stress are naturally experienced including environments in Mexico, West Asia, North Africa (WANA), and South Asia regions. A molecular genetic linkage map including 475 marker loci associated to 29 linkage groups was used for QTL analysis of yield, days to heading (DH) and to maturity (DM), grain number (GM2), thousand kernel weight (TKW), plant height (PH), canopy temperature at the vegetative and grain filling stages (CTvg and CTgf), and early ground cover. A QTL for yield on chromosome 4A was confirmed across several environments, in subsets of lines with uniform allelic expression of a major phenology QTL, but not independently from PH. With terminal stress, TKW QTL was linked or pleiotropic to DH and DM. The link between phenology and TKW suggested that early maturity would favor the post—anthesis grain growth periods resulting in increased grain size and yields under terminal stress. GM2 and TKW were partially associated with markers at different positions suggesting different genetic regulation and room for improvement of both traits. Prediction accuracy of yield was improved by 5 % when using marker scores of component traits (GM2 and DH) together with yield in multiple regression. This procedure may provide accumulation of more favorable alleles during selection.