Minor Quantitative Trait Loci Research Articles

The major quantitative trait locus for mungbean yellow mosaic Indian virus resistance is tightly linked in repulsion phase to the major bruchid resistance locus in a cross between mungbean [Vigna radiata (L.) Wilczek] and its wild relative Vigna radiata ssp. sublobata

Mungbean yellow mosaic Indian virus (MYMIV) and bruchid infestation are severe production constraints of mungbean in South Asia, a major global mungbean production area. Marker-assisted selection for resistance against these disorders while maintaining or even improving agronomic traits is an important step toward breeding elite mungbean varieties. This study employed recombinant inbred lines (F12) derived from a cross between MYMIV-tolerant Vigna radiata NM92 and bruchid-resistant V. radiata ssp. sublobata TC1966 to identify chromosomal locations associated with disease and insect pest resistance and seed traits. A linkage map comprising 11 linkage groups was constructed with random amplified polymorphic DNA (RAPD), sequence characterized amplified regions (SCAR), cleaved amplified polymorphic DNA (CAP), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Quantitative trait loci (QTLs) for MYMIV and bruchid resistance, 100 seed weight and seed germination rate were identified. Three major QTLs for MYMIV and one major bruchid resistance locus were mapped on LG 9. The resistance alleles were contributed by the MYMIV tolerant parent NM92 and the bruchid resistant parent TC1966 respectively. One of the MYMIV QTLs was tightly linked in repulsion phase to the bruchid resistance locus. In addition, three minor QTLs for MYMIV resistance were found, where the resistance alleles were contributed by TC1966. Lines combining MYMV resistance alleles from both parents have greater resistance to MYMIV than the tolerant parent. Two minor bruchid resistance QTLs were identified in TC1966. Furthermore, three QTLs each for 100 seed weight and germination rate were detected. The markers defining the QTLs identified in this study will be useful in marker-assisted breeding of improved mungbean varieties in the future.

QTL for spot blotch resistance in bread wheat line Saar co-locate to the biotrophic disease resistance loci Lr34 and Lr46

Spot blotch caused by Bipolaris sorokiniana is a major disease of wheat in warm and humid wheat growing regions of the world including south Asian countries such as India, Nepal and Bangladesh. The CIMMYT bread wheat line Saar which carries the leaf tip necrosis (LTN)-associated rust resistance genes Lr34 and Lr46 has exhibited a low level of spot blotch disease in field trials conducted in Asia and South America. One hundred and fourteen recombinant inbred lines (RILs) of Avocet (Susceptible)×Saar, were evaluated along with parents in two dates of sowing in India for 3years (2007-2008 to 2009-2010) to identify quantitative trait loci (QTL) associated with spot blotch resistance, and to determine the potential association of Lr34 and Lr46 with resistance to this disease. Lr34 was found to constitute the main locus for spot blotch resistance, and explained as much as 55% of the phenotypic variation in the mean disease data across the six environments. Based on the large effect, the spot blotch resistance at this locus has been given the gene designation Sb1. Two further, minor QTL were detected in the sub-population of RILs not containing Lr34. The first of these was located about 40cM distal to Lr34 on 7DS, and the other corresponded to Lr46 on 1BL. A major implication for wheat breeding is that Lr34 and Lr46, which are widely used in wheat breeding to improve resistance to rust diseases and powdery mildew, also have a beneficial effect on spot blotch.

Genetic Architecture of Seed Dormancy in U.S. Weedy Rice in Different Genetic Backgrounds

ABSTRACTSeed dormancy (SD) is a key domestication trait closely related to preharvest sprouting tolerance. Wild and weedy rices (Oryza spp.) exhibit higher degrees of seed dormancy compared to the cultivated rice. Red rice (Oryza sativa L.), a major weed in the rice growing areas of the southern United States, was used to elucidate the genetic architecture of SD. Quantitative trait loci (QTL) analysis conducted in two recombinant inbred line (RIL) populations developed from the crosses involving two rice cultivars (Bengal and Cypress) and a red rice accession (PSRR‐1) revealed six to seven QTL for seed dormancy, which accounted for 49 to 52% of the total phenotypic variance. The magnitude of the QTL contribution to phenotypic variance was influenced by genetic backgrounds. The majority of QTL had minor effects, except the QTL linked to Rc and Sdr4. The genetic architecture for seed dormancy in U.S. red rice was distinct compared with the earlier reported weedy accessions. Four QTL were mapped onto similar positions in both populations. Both cultivars and red rice contributed alleles for increased SD. Most of the digenic epistatic interactions involved loci other than the QTL with main effects. The nucleotide polymorphisms at the Sdr4 locus could not explain the phenotypic variation for seed dormancy in our materials. The variation in SD among the rice cultivars could be attributed to segregation of minor QTL, which may be exploited to improve preharvest sprouting tolerance.

Genomic collinearity and the genetic architecture of floral differences between the homoploid hybrid species Iris nelsonii and one of its progenitors, Iris hexagona

Hybrid speciation represents a relatively rapid form of diversification. Early models of homoploid hybrid speciation suggested that reproductive isolation between the hybrid species and progenitors primarily resulted from karyotypic differences between the species. However, genic incompatibilities and ecological divergence may also be responsible for isolation. Iris nelsonii is an example of a homoploid hybrid species that is likely isolated from its progenitors primarily by strong prezygotic isolation, including habitat divergence, floral isolation and post-pollination prezygotic barriers. Here, we used linkage mapping and quantitative trait locus (QTL) mapping approaches to investigate genomic collinearity and the genetic architecture of floral differences between I. nelsonii and one of its progenitor species I. hexagona. The linkage map produced from this cross is highly collinear with another linkage map produced between I. fulva and I. brevicaulis (the two other species shown to have contributed to the genomic makeup of I. nelsonii), suggesting that karyotypic differences do not contribute substantially to isolation in this homoploid hybrid species. Similar to other studies of the genetic architecture of floral characteristics, at least one QTL was found that explained >20% variance in each color trait, while minor QTLs were detected for each morphological trait. These QTLs will serve as hypotheses for regions under selection by pollinators.

Genetic analysis of phenylpropanoid metabolites associated with resistance against Verticillium longisporum in Brassica napus

Verticillium longisporum is a major threat to production of oilseed rape (Brassica napus) in Europe. The aim of the study was to develop new markers and obtain insights into putative mechanisms and pathways involved in the resistance reaction. A genetic approach was used to identify quantitative trait loci (QTL) for V. longisporum resistance and metabolic traits potentially influencing resistance in a B. napus mapping population. Resistance to V. longisporum was mapped in a doubled haploid (DH) population from a cross between the partially resistant winter oilseed rape variety Express 617 and a resistant resynthesized B. napus line, R53. One major resistance QTL contributed by R53 was identified on chromosome C5, while a further, minor QTL contributed by Express 617 was detected on chromosome C1. Markers flanking the QTL also significantly correlated with V. longisporum resistance in four further DH populations derived from crosses between elite oilseed rape cultivars and other resynthesized B. napus lines originating from genetically and geographically diverse brassica A and C genome donors. The tightly-linked markers developed enable the combination of favorable alleles for novel resistance loci from resynthesized B. napus materials with existing resistance loci from commercial breeding lines. HPLC analysis of hypocotyls from infected DH lines revealed that concentrations of a number of phenylpropanoids were correlated with V. longisporum resistance. QTL for some of these phenylpropanoids were also found to co-localize with the QTL for V. longisporum resistance. Genes from the phenylpropanoid pathway are suggested as candidates for V. longisporum resistance.

Novel Septoria Speckled Leaf Blotch Resistance Loci in a Barley Doubled-Haploid Population

The genetics of resistance to Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, was studied in the Leger × CIho9831 barley doubled-haploid population. The 140 lines in the population segregated as 102 resistant and 38 susceptible, approximating a 3:1 ratio. A recombination map was developed using diversity arrays technology and other molecular markers. Quantitative trait locus (QTL) analysis demonstrated that resistance is primarily conferred either by having the CIho9831 allele at a QTL on 6HS or by having the CIho9831 allele at both of two QTLs on 3H and 2HL. In addition, ≈1/16 of the lines were resistant for unidentified reasons. This model predicts a resistant/susceptible ratio of 11:5, which fits the phenotypic observations. Minor QTLs were detected on 2HS and 1H. DNA sequences of linked markers suggest that the 6HS, 3H, and 2HS QTLs are part of resistance gene clusters and that the 6HS and 3H QTLs share homology. The 6HS QTL is identical to or closely linked to the SSLB resistance locus Rsp4 and the 1H QTL to the Rsp2 or Rsp3 locus. The 3H and 2HS QTLs are unique and offer new opportunities for pyramiding resistance genes through marker-assisted breeding for resistance to S. passerinii.

Identification of Quantitative Trait Loci for Bacterial Blight Resistance Derived from Oryza meyeriana and Agronomic Traits in Recombinant Inbred Lines of Oryza sativa

AbstractBacterial blight (BB) is one of the major diseases that affect rice productivity. In previous studies, BB resistance was transferred to cultivated rice Oryza sativa from wild rice Oryza meyeriana using asymmetric somatic hybridization. One of the resistant hybrid progenies (Y73) has also been shown to possess novel resistance gene(s) different from any of those previously associated with BB resistance. We have mapped quantitative trait loci (QTLs) for BB resistance in a recombinant inbred line (RIL) population derived from a cross between Y73 and a BB‐susceptible cv. IR24. Five QTLs were detected where Y73 alleles contributed to increased BB resistance. Three minor QTLs were identified on chromosomes 3, 10 and 11, and two major QTLs on chromosomes 1 and 5, respectively. QTL on chromosome 5, designated qBBR5, had the strongest effect on BB resistance, explaining approximately 37% of the phenotypic variance. Using the same RIL population, we also mapped QTLs for agronomic traits including plant height (PH), heading date (HD), plant yield (PYD) and PYD component traits. A total of 21 QTLs were identified, of which four were detected for PH, six for HD, three for panicle number per plant (PNPP), one for spikelets per panicle (SPP), six for 1000‐grain weight (TGW) and one for PYD. qPH1 (a QTL for PH) was found in the same interval as qBBR1 for BB resistance, and qHD11 for HD and qBBR11 for BB resistance also shared a similar interval. Additionally, BB resistance was significantly correlated with PH or HD in the RIL population. This suggests that the resistance genes may have pleiotropic effects on, or close linkage to, genes controlling PH or HD. These results will help deduce the resistance mechanisms of the novel resistance gene(s) and provide the basis for cloning them and using them in marker‐assisted breeding.

Characterization of QTL for oil content in maize kernel

Kernel oil content in maize is a complex quantitative trait. Phenotypic variation in kernel oil content can be dissected into its component traits such as oil metabolism and physical characteristics of the kernel, including embryo size and embryo-to-endosperm weight ratio (EEWR). To characterize quantitative trait loci (QTL) for kernel oil content, a recombinant inbred population derived from a cross between normal line B73 and high-oil line By804 was genotyped using 228 molecular markers and phenotyped for kernel oil content and its component traits [embryo oil content, embryo oil concentration, EEWR, embryo volume, embryo width, embryo length, and embryo width-to-length ratio (EWLR)]. A total of 58 QTL were identified for kernel oil content and its component traits in 26 genomic regions across all chromosomes. Eight main-effect QTL were identified for kernel oil content, embryo oil content, embryo oil concentration, EEWR, embryo weight, and EWLR, each accounting for over 10% of the phenotypic variation in six genomic regions. Over 90% of QTL identified for kernel oil content co-localized with QTL for component traits, validating their molecular contribution to kernel oil content. On chromosome 1, the QTL that had the largest effect on kernel oil content (qKO1-1) was associated with embryo width; on chromosome 9, the QTL for kernel oil content (qKO9) was related to EEWR (qEEWR9). Embryo oil concentration and embryo width were identified as the most important component traits controlling the second largest QTL for kernel oil content on chromosome 6 (qKO6) and a minor QTL for kernel oil content on chromosome 5 (qKO5-2), respectively. The dissection of kernel oil QTL will facilitate future cloning and/or functional validation of kernel oil content, and help to elucidate the genetic basis of kernel oil content in maize.

Genetic components and major QTL confer resistance to bean pyralid (Lamprosema indicata Fabricius) under multiple environments in four RIL populations of soybean

Bean pyralid (BP; Lamprosema indicata Fabricius) is one of the major leaf-feeding insects that affect soybean crops in central and southern China. Four recombinant inbred line populations (KY, WT, XG and SX) were tested during 2004-2006 in Nanjing, China, to identify quantitative trait loci (QTL) for resistance to BP on the basis of data for rolled leaflet percentage under field infestation conditions. The mapping was performed using QTL Network V2.0 and checked with Windows QTL Cartographer V2.5 and IciMapping V2.2. The results showed that 81-92 % of the phenotypic variation was accounted for by additive QTL (27-43 %), epistatic QTL pairs (5-13 %), and collective unmapped minor QTL (38-58 %). In total, 17 QTL were detected on 11 linkage groups, of which two had additive effects, six had both additive and epistatic effects, and nine had only epistatic effects. Eight epistatic QTL pairs were observed, of which three pairs involved two QTL with additive effects, one involved one QTL with additive effect, and four involved no QTL with additive effects. Different genetic structures for BP resistance were found among the populations. Eight QTL (five additive and three epistatic pairs) were detected in KY, ten QTL (four additive and five epistatic pairs) were detected in WT, and only one additive QTL was detected in both the XG and the SX populations. BP12-1 and BP1-1 are major QTL, with the former accounting for 15, 31, and 50 % of the total genetic variation (including epistasis) in KY, WT, and XG, respectively, and the latter accounting for 13 and 32 % of the total genetic variation in KY and SX, respectively. The additive × year and epistasis × year interaction effects were negligible, indicating that the QTL were stable over the years. Because 41-68 % of the total genetic variation could not be accounted for by these QTL, the use of both identified QTL and unmapped minor QTL in breeding for BP resistance should be considered.

Mapping of DNA Sex-Specific Markers and Genes Related to Sex Differentiation in Turbot (Scophthalmus maximus)

Production of all-female populations in turbot can increase farmer's benefits since sexual dimorphism in growth in this species is among the highest within marine fish, turbot females reaching commercial size 3-6months earlier than males. Puberty in males occurs earlier than in females, which additionally slows their growth. Thus, elucidating the mechanisms of sex determination and gonad differentiation is a relevant goal for turbot production. A ZZ/ZW sex determination mechanism has been suggested for this species, and four sex-related quantitative trait loci (QTL) were detected, the major one located in linkage group (LG) 5 and the three minor ones in LG6, LG8, and LG21. In the present work, we carried out a linkage analysis for several sex-related markers: (1) three anonymous sex-associated RAPD and (2) several candidate genes related to sex determination and gonad differentiation in other species (Sox3, Sox6, Sox8, Sox9, Sox17, Sox19, Amh, Dmrta2, Cyp19a, Cyp19b). We focused our attention on their co-localization with the major and minor sex-related QTL trying to approach to the master sex-determining gene of this species. Previously described growth-related QTL were also considered since the association observed between growth and sex determination in fish. Amh, Dmrta2, and one RAPD were located in LG5, while Sox9 and Sox17 (LG21), Cyp19b (LG6), and a second RAPD (LG8) co-mapped with suggestive sex-related QTL, thus supporting further analyses on these genes to elucidate the genetic basis of this relevant trait for turbot farming.

Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat–Triticum militinae introgression line

Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. Tähti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL.

Mapping of a gene that confers short lateral branching (slb) in melon (Cucumis melo L.)

Plant architecture plays an important role in the yield, product quality, and cultivation practices of many crops. Branching pattern is one of the most important components in the plant architecture of melon (Cucumis melo L.). ‘Melon Chukanbohon Nou 4 Go’ (Nou-4) has a short-lateral-branching trait derived from a weedy melon, LB-1. This trait is reported to be controlled by a single recessive or incompletely dominant major gene called short lateral branching (slb). To find molecular markers for marker-assisted selection of this gene, we first constructed a linkage map using 94 F2 plants derived from a cross between Nou-4 and ‘Earl’s Favourite (Harukei-3)’, a cultivar with normal branching. We then conducted quantitative trait locus (QTL) analysis and identified two loci for short lateral branching. A major QTL in linkage group (LG) XI, at which the Nou-4 allele is associated with short lateral branching, explained 50.9 % of the phenotypic variance, with a LOD score of 12.5. We suggest that this QTL corresponds to slb because of the magnitude of its effect. Another minor QTL in LG III, at which the Harukei-3 allele is associated with short lateral branching, explained 9.9 % of the phenotypic variance, with a LOD score of 4.2. Using an independent population, we demonstrated that an SSR marker linked to the QTL in LG XI (slb) could be used to select for short lateral branching. This is the first report of mapping a gene regulating the plant architecture of melon.

Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L.)

Silique length (SL) and seed weight (SW) are two important yield-related traits controlled by quantitative trait loci (QTL) in oilseed rape (Brassica napus L.). The genetic bases underlying these two traits are largely unknown at present. In this study, we conducted QTL analyses for SL and SW using 186 recombinant inbred lines (RILs) derived from a cross between S1, an EMS mutant with extremely long siliques and large seeds, and S2, an inbred line with regular silique length and seed size. RILs were grown in Wuhan in the 2008/09 (SS09) and 2009/10 (SS10) growing seasons, and mean SL and SW for each line were investigated. Ten non-redundant QTL were identified for SL. Of these, a major QTL, cqSLA9, consistently explained as much as 53.4% of SL variation across environments. The others are minor QTL and individually explained less than 10% of the SL variation. Nine non-redundant QTL were identified for SW. Of which, one major QTL, cqSWA9, explained as much as 28.2% of the total SW variation in the SS09 and SS10 environments. In addition, three additive by additive interactions with small effects were detected for SL, and no interactions were detected for SW. Interestingly, the two major QTL, cqSLA9 for SL and cqSWA9 for SW colocalized in the same chromosomal region and were integrated into a unique QTL, uqA9. The S1 allele at this locus increases both SL and SW, suggesting that uqA9 has pleiotropic effects on both SL and SW. The existence and effect of uqA9 was confirmed in genetically different RILs derived from the cross between S1 and No2127, a resynthesized DH line having regular silique length and seed size. Individuals in one residual heterozygous line for cqSLA9 showed significant difference in silique length. The results in this study revealed that silique length in the S1 mutant is mainly controlled by the cqSLA9 locus, which will be suitable for fine mapping and marker-assisted selection in rapeseed breeding for high yield.

QTL analysis of main and epistatic effects for flour color traits in durum wheat

The aim of this work was to map quantitative trait loci (QTLs) associated with flour yellow color (Fb*) and yellow pigment content (YPC) in durum wheat (Triticum turgidum L. var. durum). Additionally, QTLs affecting flour redness (Fa*) and brightness (FL*) color parameters were investigated. A population of 93 RILs (UC1113 × Kofa) was evaluated in three locations of Argentina over 2 years. High heritability values (>94%) were obtained for Fb* and YPC, whereas FL* and Fa* showed intermediate to high values. The main QTLs affecting Fb* and YPC overlapped on chromosome arms 4AL (4AL.2), 6AL (6AL.2), 7AS, 7AL, 7BS (7BS.2) and 7BL (7BL.2). The 7BL.1 QTL included the Psy-B1 locus, but one additional linked QTL was detected. A novel minor QTL located on 7AS affected Fb*, with an epistatic effect on YPC. An epistatic interaction occurred between the 7AL and 7BL.2 QTLs. The 4AL.2 QTL showed a strong effect on Fb* and was involved in two digenic epistatic interactions. The 6AL.2 QTL explained most of the variation for Fb* and YPC. The main QTLs affecting FL* and Fa* were located on 2BS and 7BL, respectively. These results confirm the complex inheritance of flour color traits and open the possibility of developing perfect markers to improve pasta quality in Argentinean breeding programs.

Quantitative trait loci for resistance to Fusarium head blight in the Chinese wheat landrace Huangfangzhu

The Chinese wheat landrace Huangfangzhu (HFZ) has a high level of resistance to Fusarium head blight (FHB). To identify chromosomal regions that are responsible for FHB resistance in HFZ, F8 recombinant inbred lines (RIL) were developed from a cross between HFZ and Wheaton, a U.S. hard spring wheat. FHB was evaluated by single floret inoculation in both greenhouse and field environments. Two quantitative trait loci (QTL) with major effects were identified. One QTL was located on the short arm of chromosome 3B, and explained 35.4% of the phenotypic variation; the other QTL was assigned to 7AL and explained 18.0% of the phenotypic variation for FHB response. In addition, three minor QTL were detected on chromosomes 1AS, 1B and 5AS by single marker regression. HFZ contributed all favorable alleles. The RIL with HFZ alleles at the QTL on 3BS and 7AL displayed significantly lower percentages of infected spikelets than RIL without these alleles in both greenhouse and field environments. HFZ combined several alleles from germplasm reported previously and is a promising alternative source for improving wheat FHB resistance.

Preliminary study on ‘genomewide selection’ for maize (Zea mays L.) breeding in Japanese public sectors: Estimated selection response in the first selfing cycle of single‐cross progeny

AbstractJapanese public sectors are now expected to breed high‐yielding silage maize varieties highly adapted to the Japanese climates in order to support the governmental policy to raise the feed self‐sufficiency ratio from 26% (in 2008) to 38% by 2020. ‘Genomewide selection (GwS)’ is a technique to substitute a part of phenotyping with molecular marker genotyping, and is thought to be suitable to accumulate favorable genes in many minor quantitative trait loci (QTLs) whereby yield is thought to be controlled. The purpose of this study was to use computer simulations to evaluate the potential of GwS from the viewpoint of maize breeding sections of Japanese public sectors interested in rapider yield improvement through selection at early breeding stages. It was assumed in each repeat of the simulation experiments that eight S1 (first selfing generation) candidates were selected from 1000 solely on their molecular marker information obtained from testcross investigation with GwS. The experiments indicated that (i) shorter intervals of molecular marker loci led to moderately larger selection response (SR) when the intervals were more than 20 cM, but not when they were less than 20 cM, (ii) higher heritability unexceptionally led to larger SR, and (iii) larger training population size led to slightly larger SR in most cases. The results suggest that it is important for the success of GwS to obtain high heritability in the field for testcross investigation, and that GwS will be a powerful tool for maize breeding sections of Japanese public sectors targeting rapider yield improvement.

Genetic studies on saline and sodic tolerances in soybean

Salt-affected soils are generally classified into two main categories: saline and sodic (alkaline). Developing and using soybean (Glycine max (L.) Merr) cultivars with high salt tolerance is an effective way of maintaining sustainable production in areas where soybean growth is threatened by salt stress. Early classical genetics studies revealed that saline tolerance was conditioned by a single dominant gene. Recently, a series of studies consistently revealed a major quantitative trait locus (QTL) for saline tolerance located on linkage group N (chromosome 3) around the SSR markers Satt255 and Sat_091; other minor QTLs were also reported. In the case of sodic tolerance, most studies focused on iron deficiency caused by a high soil pH, and several QTLs associated with iron deficiency were identified. A wild soybean (Glycine soja Sieb. & Zucc.) accession with high sodic tolerance was recently identified, and a significant QTL for sodic tolerance was detected on linkage group D2 (chromosome 17). These studies demonstrated that saline and sodic tolerances were controlled by different genes in soybean. DNA markers closely associated with these QTLs can be used for marker-assisted selection to pyramid tolerance genes in soybean for both saline and sodic stresses.

Mapping quantitative trait loci (QTL) for clubroot resistance in Brassica rapa L.

SummaryThe genes related to clubroot resistance (CR) from a new genetic resource of European turnip (Brassica rapa ssp. rapifera) were identified, and their chromosomal locations were determined using quantitative trait loci (QTL) analysis. One hundred and ninety F2 plants derived from a cross between a clubroot-resistant inbred turnip line (IT033820) and a susceptible inbred Chinese cabbage (B. rapa ssp. pekinensis) line (BP079) were used to construct a genetic linkage map. The map contained 477 markers, including 401 amplified fragment length polymorphism (AFLP) and 56 simple sequence repeat (SSR) markers, in ten linkage groups (LGs). It covered a total length of 1,149.1 cM, with an average interval of 2.53 cM between markers. The majority of individual F2 plants were found to be highly resistant to clubroot disease based on phenotypic evaluations following inoculation with race 4 of Plasmodiophora brassicae. Using composite interval mapping analysis, two major QTLs (Pb-Br3 and Pb-Br8) and one minor QTL associated with resistance to race 4 of P. brassicae were detected. Pb-Br3 and the minor QTL were located on LG3, while Pb-Br8 was on LG8. Most of the markers identified by bulk segregant analysis (BSA) were located in the region of the two major QTLs. Along with the markers developed in the present study, the Pb-Br3 region included the previously published markers HC352b-SCAR and TCR08, for the loci CRa and CRb, respectively. Five markers, including OPW06_297 identified by BSA, were located in the Pb-Br8 region, spanning 5.9 cM. The QTL Pb-Br8 differed from previously reported CR genes. The two major QTLs explained 85.4% of the total phenotypic variation. The QTLs Pb-Br3 and Pb-Br8 were marked by two convenient co-dominant sequence characterised amplified region (SCAR) and cleaved amplified polymorphic sequence (CAPS) markers, CRW06_297 and CRU12_SspI, respectively. These markers will assist in future marker-assisted selection to accelerate the breeding of clubroot-resistant Brassica crops.

Mapping and use of QTLs controlling pod dehiscence in soybean.

While the cultivated soybean, Glycine max (L.) Merr., is more recalcitrant to pod dehiscence (shattering-resistant) than wild soybean, Glycine soja Sieb. & Zucc., there is also significant genetic variation in shattering resistance among cultivated soybean cultivars. To reveal the genetic basis and develop DNA markers for pod dehiscence, several research groups have conducted quantitative trait locus (QTL) analysis using segregated populations derived from crosses between G. max accessions or between a G. max and G. soja accession. In the populations of G. max, a major QTL was repeatedly identified near SSR marker Sat_366 on linkage group J (chromosome 16). Minor QTLs were also detected in several studies, although less commonality was found for the magnitudes of effect and location. In G. max × G. soja populations, only QTLs with a relatively small effect were detected. The major QTL found in G. max was further fine-mapped, leading to the development of specific markers for the shattering resistance allele at this locus. The markers were used in a breeding program, resulting in the production of near-isogenic lines with shattering resistance and genetic backgrounds of Japanese elite cultivars. The markers and lines developed will hopefully contribute to the rapid production of a variety of shattering-resistant soybean cultivars.

A major QTL for resistance to soil-borne cereal mosaic virus derived from an old Italian durum wheat cultivar

The genetic basis of resistance to soil-borne cereal mosaic virus (SBCMV) in the Triticum turgidum L. var. durum cv. Neodur was analyzed in this study, using a linkage mapping approach. We performed phenotypic and molecular analyses of 146 recombinant inbred lines derived from the cross Cirillo (highly susceptible)×Neodur (highly resistant). A major quantitative trait locus (QTL) that explained up to 87% of the observed variability for symptom severity was identified on the short arm of chromosome 2B, within the 40-cM interval between the markers Xwmc764 and Xgwm1128, with wPt-2106 as the peak marker. Three minor QTLs were found on chromosomes 3B and 7B. Two markers coding for resistance proteins co-segregate with the major QTL on chromosome 2B and the minor QTL on chromosome 3B, representing potential candidate genes for the two resistance loci. Microsatellite markers flanking the major QTL were evaluated on a set of 25 durum wheat genotypes that were previously characterized for SBCMV resistance. The allelic composition of the genotypes at these loci, together with pedigree data, suggests that the old Italian cultivar Cappelli provided the SBCMV-resistance determinants to durum cultivars that have been independently bred in different countries over the last century.