Molecular mapping and location of QTLs for drought-resistance traits in <Emphasis Type="Italic">indica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) lines adapted to target environments

Drought is a major limitation for rice production in rainfed ecosystems. Identifying quantitative trait loci (QTLs) linked to drought resistance provides opportunity to breed high yielding rice varieties suitable for drought-prone areas. Although considerable efforts were made in mapping QTLs associated with drought-resistance traits in rice, most of the studies involved indica × japonica crosses and hence, the drought-resistance alleles were contributed mostly by japonica ecotypes. It is desirable to look for genetic variation within indica ecotypes adapted to target environment (TE) as the alleles from japonica ecotype may not be expressed under lowland conditions. A subset of 250 recombinant inbred lines (RILs) of F₈ generation derived from two indica rice lines (IR20 and Nootripathu) with contrasting drought-resistance traits were used to map the QTLs for morpho-physiological and plant production traits under drought stress in the field in TE. A genetic linkage map was constructed using 101 polymorphic PCR-based markers distributed over the 12 chromosomes covering a total length of 1,529 cM in 17 linkage groups with an average distance of 15.1 cM. Composite interval mapping analysis identified 22 QTLs, which individually explained 4.8–32.2% of the phenotypic variation. Consistent QTLs for drought-resistance traits were detected using locally adapted indica ecotypes, which may be useful for rainfed rice improvement.     

QTL Mapping of Downy Mildew Resistance in an Introgression Line Derived from Interspecific Hybridization Between Cucumber and Cucumis hystrix

Downy mildew (DM), caused by Pseudoperonospora cubensis (Berk. & M.A. Curtis) Rostovzev, is a worldwide major disease of cucumbers (Cucumis sativus L.). By screening 10 introgression lines (ILs) derived from interspecific hybridization between cucumber and the wild Cucumis, C. hystrix, through a whole plant assay, one introgression line (IL52) was identified with high DM‐resistance. IL52 was further used as a resistant parent to make an F₂ population with ‘changchunmici’ (susceptible parent). The F₂ population (300 plants) was investigated for DM‐yellowing, DM‐necrosis and DM‐resistance in the adult stage. A genetic map spanning 642.5 cM with 104 markers was constructed and used for QTL analysis from the population. Three QTL regions were identified on chromosome 5 and chromosome 6. By interval mapping analysis, two QTLs for DM‐resistance were determined on chromosome 5 (DM_5.1 and DM_5.2), which explained 17.9% and 14.2% of the variation, respectively. QTLs for DM‐yellowing were in the same regions as DM‐resistance. For DM‐necrosis, by interval mapping analysis, one QTL was determined on chromosome 5 (Necr_5.1) that explained 18.3% of the variation and one on chromosome 6 (Necr_6.1) that explained 13.9% of the variation. Our results indicated that the identification of molecular markers linked to the QTLs could be further applied for marker‐assisted selection (MAS) of downy mildew resistance in cucumber.     

Isolate-specific and broad-spectrum QTLs are involved in the control of clubroot in<Emphasis Type="Italic"> Brassica oleracea</Emphasis>

Clubroot, caused by Plasmodiophora brassicae, is one of the most damaging diseases of vegetable Brassica crops in the world. In this study, genetic control and mapping of loci implied in quantitative resistance against five isolates of P. brassicae were studied in the F₁ and F_2/3 progenies of the cross C10 (resistant kale)×HDEM (susceptible broccoli). A genetic map was constructed using RFLP, random and specific PCR-based markers. The 199 loci were assembled into nine linkage groups covering 1,226.3 cM. The F₃ families were assessed for resistance under controlled conditions with four single-spore isolates and one field isolate. A total of nine genomic regions were detected for clubroot resistance. Depending on the isolate, two to five QTLs were identified. The total phenotypic variation accounted for by QTLs ranged from 70% to 88% depending on the isolate. One of the QTLs (Pb-Bo1) was detected in all isolates and explained 20.7–80.7% of the phenotypic variation. Pb-Bo1 had a major effect on three isolates but this effect was weaker for the last two. Five QTLs with minor effect were identified in only one isolate. To construct clubroot resistant varieties, the existence of both broad-spectrum and isolate-specific QTLs should be taken into account for the choice of genomic regions to use in a marker-assisted selection strategy.Communicated by C. Möllers     

Targeted discovery of quantitative trait loci for resistance to northern leaf blight and other diseases of maize

To capture diverse alleles at a set of loci associated with disease resistance in maize, heterogeneous inbred family (HIF) analysis was applied for targeted QTL mapping and near-isogenic line (NIL) development. Tropical maize lines CML52 and DK888 were chosen as donors of alleles based on their known resistance to multiple diseases. Chromosomal regions (“bins”; n = 39) associated with multiple disease resistance (MDR) were targeted based on a consensus map of disease QTLs in maize. We generated HIFs segregating for the targeted loci but isogenic at ~97% of the genome. To test the hypothesis that CML52 and DK888 alleles at MDR hotspots condition broad-spectrum resistance, HIFs and derived NILs were tested for resistance to northern leaf blight (NLB), southern leaf blight (SLB), gray leaf spot (GLS), anthracnose leaf blight (ALB), anthracnose stalk rot (ASR), common rust, common smut, and Stewart’s wilt. Four NLB QTLs, two ASR QTLs, and one Stewart’s wilt QTL were identified. In parallel, a population of 196 recombinant inbred lines (RILs) derived from B73 × CML52 was evaluated for resistance to NLB, GLS, SLB, and ASR. The QTLs mapped (four for NLB, five for SLB, two for GLS, and two for ASR) mostly corresponded to those found using the NILs. Combining HIF- and RIL-based analyses, we discovered two disease QTLs at which CML52 alleles were favorable for more than one disease. A QTL in bin 1.06–1.07 conferred resistance to NLB and Stewart’s wilt, and a QTL in 6.05 conferred resistance to NLB and ASR.     

Genetic linkage maps of two interspecific grape crosses (Vitis spp.) used to localize quantitative trait loci for downy mildew resistance

Two populations (Pop) segregating quantitatively for resistance to downy mildew (DM), caused by Plasmopara viticola, were used to construct genetic maps and to carry out quantitative trait locus (QTL) analysis. Pop1 comprised of 174 F₁ individuals from a cross of ‘Moscato Bianco’, a susceptible Vitis vinifera cultivar, and a resistant individual of Vitis riparia. Pop2 consisted of 94 progeny from a cross of two interspecific hybrids, ‘VRH3082 1-42’ and ‘SK77 5/3’, with resistance traits inherited from Vitis rotundifolia and Vitis amurensis, respectively. Resistance of progeny was measured in field and greenhouse conditions by visual evaluation of disease symptoms on leaves. Linkage maps of 1037.2 and 651 cM were built essentially with simple sequence repeat markers and were enriched with gene-derived single-strand conformational polymorphism and single-nucleotide polymorphism markers. Simple interval mapping and Kruskall–Wallis analysis detected a stable QTL involved in field resistance to DM on linkage group (LG) 7 of the Pop1 integrated map co-localized with a putative Caffeoyl-CoA O-methyltransferase-derived marker. Additional QTLs were detected on LGs 8, 12 and 17. We were able to identify genetic factors correlated with resistance to P. viticola with lower statistical significance on LGs 1, 6 and 7 of the Pop2 map. Finally, no common QTLs were found between the two crosses analyzed. A search of the grapevine genome sequence revealed either homologues to non-host-, host- or defense-signalling genes within the QTL intervals. These positional candidate genes may provide new information about chromosomal regions hosting phenotypic loci.     

Mapping QTLs conferring early blight (Alternaria solani) resistance in a Lycopersicon esculentum×L. hirsutum cross by selective genotyping

Most commercial cultivars of tomato, Lycopersicon esculentum Mill., are susceptible to early blight (EB), a devastating fungal (Alternaria solani Sorauer) disease of tomato in the U.S. and elsewhere in the world. Currently, sanitation, long crop rotation, and routine application of fungicides are the most common disease control measures. Although no source of genetic resistance is known within the cultivated species of tomato, resistant resources have been identified within related wild species. The purpose of this study was to identify and validate quantitative trait loci (QTLs) conferring EB resistance in an accession (PI126445) of the tomato wild species L. hirsutum Humb. and Bonpl. by using a selective genotyping approach. A total of 820 BC₁ plants of a cross between an EB susceptible tomato breeding line (NC84173; maternal and recurrent parent) and PI126445 were grown in a greenhouse. During late seedling stage, plants were inoculated with mixed isolates of A. solani and subsequently evaluated for EB symptoms. The most resistant (75 plants = 9.1%) and most susceptible (80 = 9.8%) plants were selected and subsequently transplanted into a field where natural infestation of EB was severe. Plants were grown to maturity and evaluated for final disease severity. From among the 75 resistant plants, 46 (5.6% of the total) that exhibited the highest resistance, and from among the 80 susceptible plants, 30 (3.7% of the total) that exhibited the highest susceptibility, were selected. The 76 selected plants, representing the two extreme tails of the response distribution, were genotyped for 145 restriction fragment length polymorphism (RFLP) markers and 34 resistance gene analogs (RGAs). A genetic linkage map, spanning approximately 1298 cM of the 12 tomato chromosomes with an average marker distance of 7.3 cM, was constructed. A trait-based marker analysis (TBA), which measures differences in marker allele frequencies between extreme tails of a population, detected seven QTLs for EB resistance, one on each of chromosomes 3, 4, 5, 6, 8, 10 and 11. Of these, all but the QTL on chromosome 3 were contributed from the resistant wild parent, PI126445. The standardized effects of the QTLs ranged from 0.45 to 0.81 phenotypic standard deviations. Four of the seven QTLs were previously identified in a study where different populations and mapping strategy were used. The high level of correspondence between the two studies indicated the reliability of the detected QTLs and their potential use for marker-assisted breeding for EB resistance. The location of several RGAs coincided with locations of EB QTLs or known tomato resistance genes (R genes), suggesting that these RGAs could be associated with disease resistance. Furthermore, similar to that for many R gene families, several RGA loci were identified in clusters, suggesting their potential evolutionary relationship with R genes.     

QTLs for resistance to Setosphaeria turcica in an early maturing Dent×Flint maize population

Quantitative trait loci (QTLs) for resistance to the fungal pathogen Setosphaeria turcica, the cause of northern corn leaf blight (NCLB), were mapped in a population of 220 F₃ families derived from a cross between two moderately resistant European inbred lines, D32 (dent) and D145 (flint). The population was genotyped with 87 RFLP and 7 SSR markers. Trials were conducted in the field in Switzerland, and in the greenhouse with selected F₃ families in Germany. The F₃ population segregated widely for resistance with transgression of the parents. By composite interval mapping, a total of 13 QTLs were detected with two disease ratings (0 and 3 weeks after flowering). Together these QTLs explained 48% and 62% of the phenotypic variation. Gene action at most QTLs was partially dominant. Eight out of the 13 QTL alleles for resistance were contributed by the more-resistant parent, D145. On chromosomes 3, 5 and 8, QTLs were located in the same chromosomal regions as QTLs in tropical and U.S. Corn Belt germplasm. Some QTLs affected NCLB, head smut and common rust at the same time, with alleles at these loci acting isodirectionally. Received: 25 January 1999 / Accepted: 20 Februar 1999     

QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice

Field resistance is defined as the resistance that allows effective control of a parasite under natural field conditions and is durable when exposed to new races of that parasite. To identify the genes for field resistance to rice blast, quantitative trait loci (QTLs) conferring field resistance to rice blast in Japanese upland rice were detected and mapped using RFLP and SSR markers. QTL analysis was carried out in F₄ progeny lines from the cross between Nipponbare (moderately susceptible, lowland) and Owarihatamochi (resistant, upland). Two QTLs were detected on chromosome 4 and one QTL was detected on each of chromosomes 9 and 12. The phenotypic variation explained by each QTL ranged from 7.9 to 45.7% and the four QTLs explained 66.3% of the total phenotypic variation. Backcrossed progeny lines were developed to transfer the QTL with largest effect using the susceptible cultivar Aichiasahi as a recurrent parent. Among 82 F₃ lines derived from the backcross, resistance segregated in the expected ratio of resistant 1 : heterozygous 2 : susceptible 1. The average score for blast resistance measured in the field was 4.2 ± 0.67, 7.5 ± 0.51and 8.2 ± 0.66, for resistant, heterozygous and susceptible groups, respectively. The resistance gene, designated pi21, was mapped on chromosome 4 as a single recessive gene between RFLP marker loci G271 and G317 at a distance of 5.0 cM and 8.5 cM, respectively. The relationship to previously reported major genes and QTLs conferring resistance to blasts, and the significance of marker-assisted selection to improve field resistance, are discussed. Received: 8 June 2000 / Accepted: 24 November 2000     

Mapping quantitative trait loci associated with chlorophyll a fluorescence parameters in soybean (Glycine max (L.) Merr.)

Chlorophyll a fluorescence parameters can provide qualitative and quantitative information about photosynthetic processes in chloroplasts. JIP-test and modulated fluorescence (MF) parameters are commonly used chlorophyll a fluorescence parameters. This study was conducted to identify quantitative trait loci (QTLs) associated with JIP-test parameters, MF parameters, and photosynthetic rate (P_N), and to examine the relationships among them in soybean (Glycine max (L.) Merr.). Pot and field experiments were performed to evaluate 184 recombinant inbred lines (RILs) for five JIP-test parameters (ABS/RC, TR_o/ABS, ET_o/TR_o, RE_o/ET_o, and PI_ABS), four MF parameters (Fv/Fm, Fv′/Fm′, ΦPSII, and qP), and P_N. Significant correlations were commonly observed among JIP-test parameters, MF parameters, and P_N. QTL mapping analysis identified 13, 9, and 4 QTLs for JIP-test parameters, MF parameters, and P_N, respectively, of which 13 were stable. Four major genomic regions were detected: LG A2 (19.81 cM) for JIP-test parameters, LG C1 (94.31 and 97.61 cM) for P_N and MF parameters, LG M (100.51 cM) for JIP-test and MF parameters, and LG O (30.61–49.91 cM) for P_N, JIP-test, and MF parameters. These results indicate that chlorophyll fluorescence parameters, especially ΦPSII and qP, could play an important role in regulating P_N, and that JIP-test and MF parameters could be controlled by the same or different genes. The QTLs identified in this study will help in the understanding of the genetic basis of photosynthetic processes in plants. They will also contribute to the development of marker-assisted selection breeding programs for photosynthetic capacity in soybean.     

Mapping of quantitative trait loci for partial resistance to<Emphasis Type="Italic"> Mycosphaerella pinodes</Emphasis> in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.), at the seedling and adult plant stages

The inheritance of resistance to Ascochyta blight, an economically important foliar disease of field pea (Pisum sativum L.) worldwide, was investigated. Breeding resistant pea varieties to this disease, caused by Mycosphaerella pinodes, is difficult due to the availability of only partial resistance. We mapped and characterized quantitative trait loci (QTLs) for resistance to M. pinodes in pea. A population of 135 recombinant inbred lines (RILs), derived from the cross between DP (partially resistant) and JI296 (susceptible), was genotyped with morphological, RAPD, SSR and STS markers. A genetic map was elaborated, comprising 206 markers distributed over eight linkage groups and covering 1,061 cM. The RILs were assessed under growth chamber and field conditions at the seedling and adult plant stages, respectively. Six QTLs were detected at the seedling stage, which together explained up to 74% of the variance. Ten QTLs were identified at the adult plant stage in the field, and together these explained 56.6–67.1% of the variance, depending on the resistance criteria and the organ considered. Four QTLs were detected under both growth chamber and field conditions, suggesting they were not plant-stage dependent. Three QTLs for flowering date and three QTLs for plant height were also identified in the RIL population, some of which co-located with QTLs for resistance. The relationship between QTLs for resistance to M. pinodes, plant height and flowering date is discussed.Communicated by H.C. Becker     

Construction of a comparative RFLP map of<Emphasis Type="Italic"> Echinochloa crus-galli</Emphasis> toward QTL analysis of flooding tolerance

To analyze quantitative trait loci (QTLs) affecting flooding tolerance and other physiological and morphological traits in Echinochloa crus-galli, a restriction fragment length polymorphism (RFLP) map was constructed using 55 plants of the F₂ population (E. crus-galli var. praticola × E. crus-galli var. formosensis). One hundred forty-one loci formed 41 linkage groups. The total map size was 1,468 cM and the average size of linkage groups was 35.8 cM. The average distance between markers was 14.7 cM and the range was 0–37.2 cM. Early comparisons to the genetic maps of other taxa suggest appreciable synteny with buffelgrass (Pennisetum spp.) and sorghum (Sorghum spp.). One hundred ninty-one F₂ plants were used to analyze QTLs of flooding tolerance, plant morphology, heading date, number of leaves, and plant height. For flooding tolerance, two QTLs were detected and one was mapped on linkage group 24. Other traits, including plant morphology, heading date, number of leaves, and plant height were highly correlated. Three genomic regions accounted for most of the mapped QTLs, each explaining 2–4 of the significant marker-trait associations. The high observed correlation between the traits appears to result from QTLs with a large contribution to the phenotypic variance at the same or nearby locations.Communicated by D.J. Mackill     

Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust

A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0–85 cM and 4H, 125–170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166–181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.     

Molecular mapping of soybean aphid resistance genes in PI 567541B

The soybean aphid (Aphis glycines Matsumura) is an important pest of soybean [Glycine max (L.) Merr.] in North America since it was first reported in 2000. PI 567541B is a newly discovered aphid resistance germplasm with early maturity characteristics. The objectives of this study were to map and validate the aphid resistance genes in PI 567541B using molecular markers. A mapping population of 228 F₃ derived lines was investigated for the aphid resistance in both field and greenhouse trials. Two quantitative trait loci (QTLs) controlling the aphid resistance were found using the composite interval mapping method. These two QTLs were localized on linkage groups (LGs) F and M. PI 567541B conferred resistant alleles at both loci. An additive × additive interaction between these two QTLs was identified using the multiple interval mapping method. These two QTLs combined with their interaction explained most of the phenotypic variation in both field and greenhouse trials. In general, the QTL on LG F had less effect than the one on LG M, especially in the greenhouse trial. These two QTLs were further validated using an independent population. The effects of these two QTLs were also confirmed using 50 advanced breeding lines, which were all derived from PI 567541B and had various genetic backgrounds. Hence, these two QTLs identified and validated in this study could be useful in improving soybean aphid resistance by marker-assisted selection.     

Restriction fragment length polymorphism analysis of loci associated with disease resistance genes and developmental traits in Pisum sativum L.

An F₂ population of pea (Pisum sativum L.) consisting of 174 plants was analysed by restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) techniques. Ascochyta pisi race C resistance, plant height, flowering earliness and number of nodes were measured in order to map the genes responsible for their variation. We have constructed a partial linkage map including 3 morphological character genes, 4 disease resistance genes, 56 RFLP loci, 4 microsatellite loci and 2 RAPD loci. Molecular markers linked to each resistance gene were found: Fusarium wilt (6 cM from Fw), powdery mildew (11 cM from er) and pea common Mosaic virus (15 cM from mo). QTLs (quantitative traits loci) for Ascochyta pisi race C resistance were mapped, with most of the variation explained by only three chromosomal regions. The QTL with the largest effect, on chromosome 4, was also mapped using a qualitative, Mendelian approach. Another QTL displayed a transgressive segregation, i.e. the parental line that was susceptible to Ascochyta blight had a resistance allele at this QTL. Analysis of correlations between developmental traits in terms of QTL effects and positions suggested a common genetic control of the number of nodes and earliness, and a loose relationship between these traits and height.     

Pear scab resistance QTLs via a European pear (Pyrus communis) linkage map

Pear scab caused by Venturia pyrina is an economically important disease throughout the world and can cause severe crop loss in susceptible cultivars. The varying range of susceptibility to pear scab in F1 populations has made it possible to identify quantitative trait loci (QTLs). Ninety-five seedlings derived from the cross ‘Abbè Fétel’ (AF) × ‘Max Red Bartlett’ (MRB) were evaluated for scab resistance in greenhouse tests, with 39% being classified as resistant, 33 as moderately susceptible and 28 as highly susceptible. Amplified fragment length polymorphisms (157) and simple sequence repeats (41) were used to construct two maps, one of 908.1 cM (AF) and the other of 879.8 cM (MRB). The analysis of the resistance data collected made it possible to identify two major QTLs on linkage groups 3 and 7 associated with resistance to V. pyrina. Both QTLs explained 88% of the phenotypic variance and the log of odds values were higher than 10, suggesting the involvement of two major genes in pear scab resistance. L. Pierantoni and L. Dondini have contributed equally to this work.     

Identification of QTLs related to cocoa resistance to three species of<Emphasis Type="Italic"> Phytophthora</Emphasis>

This study aimed to compare the genetic control of cacao resistance to three species of Phytophthora: Phytophthora palmivora, Phytophthora megakarya and Phytophthora capsici. The study was conducted on 151 hybrid progenies created in Côte d'Ivoire and grown in a green-house in Montpellier. Phytophthora resistance was screened by leaf-test inoculation with two different strains per species. Selection of the best individuals for resistance to P. palmivora at a 10% selection rate, would lead to a genetic progress of 47% in the disease evaluation for this species and a genetic progress of 42% and 21% for the two other species. A genetic map with a total length of 682 cM was built with 213 markers, 190 AFLPs and 23 microsatellites. QTLs were identified using composite interval mapping. QTLs were found located in six genomic regions. One of these was detected with five strains belonging to the three Phytophthora species. Two other regions were detected with two or three strains of two different species. Three additional QTLs were detected for only one species of Phytophthora. Each QTL explained between 8 to 12% of the phenotypic variation. For each strain, between 11.5% to 27.5% of the total phenotypic variation could be explained by the QTLs identified. The identification of multiple QTLs involved in resistance to Phytophthora offers the possibility to improve durability of resistance in cocoa by a possible cumulation of many different resistance genes located in different chromosome regions using marker-aided selection.Communicated by H.F. Linskens     

Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs

An earlier study identified quantitative trait loci (QTLs) lb4, lb5b, and lb11b for quantitative resistance to Phytophthora infestans (late blight) in a backcross population derived from crossing susceptible cultivated tomato (Lycopersicon esculentum) with resistant L. hirsutum. The QTLs were located in intervals spanning 28–47 cM. Subsequently, near-isogenic lines (NILs) were developed for lb4, lb5b, and lb11b by marker-assisted backcrossing to L. esculentum. Sub-NILs containing overlapping L. hirsutum segments across each QTL region were selected and used to validate the QTL effects, fine-map QTLs, and evaluate potential linkage drag between resistance QTLs and QTLs for horticultural traits. The NILs and sub-NILs were evaluated for disease resistance and eight horticultural traits at three field locations. Resistance QTLs were detected in all three sets of NIL lines, confirming the BC₁ mapping results. Lb4 mapped near TG609, and between TG182 and CT194, on chromosome 4, a 6.9-cM interval; lb5b mapped to an 8.8-cM interval between TG69a and TG413 on chromosome 5, with the most likely position near TG23; and lb11b mapped to a 15.1-cM interval on chromosome 11 between TG194 and TG400, with the peak centered between CT182 and TG147. Most QTLs for horticultural traits were identified in intervals adjacent to those containing the late blight resistance QTLs. Fine mapping of these QTLs permits the use of marker-assisted selection for the precise introgression of L. hirsutum segments containing late blight resistance alleles separately from those containing deleterious alleles at horticulturally important QTLs.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by D.B. Neale     

Genetic Mapping and QTL Analysis of Growth-Related Traits in the Pacific Oyster

The Pacific oyster (Crassostrea gigas) is one of the most important oysters cultured worldwide. To analyze the oyster genome and dissect growth-related traits, we constructed a sex-averaged linkage map by combining 64 genomic simple sequence repeats, 42 expressed sequence tag-derived SSRs, and 320 amplified fragment length polymorphism markers in an F₁ full-sib family. A total of 426 markers were assigned to 11 linkage groups, spanning 558.2 cM with an average interval of 1.3 cM and 94.7% of genome coverage. Segregation distortion was significant for 18.8% of the markers (P < 0.05), and distorted markers tended to occur on some genetic regions or linkage groups. Most growth-related quantitative traits were highly significantly (P < 0.01) correlated, and principal component analysis obtained four principal components. Quantitative trait locus (QTL) analysis identified three significant QTLs for two principal components, which explained 0.6–13.9% of the phenotypic variation. One QTL for sex was detected on linkage group 6, and the inheritabilities of sex for parental alleles and maternal alleles on that locus C15 are 39.8% and 0.01%, respectively. The constructed linkage map and determined QTLs can provide a tool for further genetic analysis of the traits and be potential for marker-assisted selection in C. gigas breeding.     

Identification and introgression of QTLs implicated in resistance to sorghum downy mildew (Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw) in maize through marker-assisted selection

Sorghum downy mildew caused by Peronosclerospora sorghi is a major disease of maize and resistance is under the control of polygenes which necessitated identification of quantitative-trait loci (QTLs) for initiating marker-assisted introgression of resistant QTLs in elite susceptible inbred lines. In the present study, QTLs for sorghum downy mildew (SDM) resistance in maize were identified based on cosegregation with linked simple sequence repeats in 185 F₂ progeny from a cross between susceptible (CM500-19) and resistant (MAI105) parents. F₃ families were screened in the National Sorghum Downy Mildew Screening Nursery during 2010 and 2011. High heritability was observed for the disease reaction. The final map generated using 87 SSR markers had 10 linkage groups, spanning a length of 1210.3 cM. Although, we used only 87 SSR markers for mapping, the per cent of genome within 20 cM to the nearest marker was 88.5. Three putative QTLs for SDM resistance were located on chromosomes 3 (bin 3.01), 6 (bin 6.01) and 2 (bin 2.02) using composite interval mapping. The locus on chromosome 3 had a major effect and explained up to 12.6% of the phenotypic variation. The other two QTLs on chromosomes 6 and 2 had minor effects with phenotypic variation of 7.1 and 2%. The three QTLs appeared to have additive effects on resistance. The QTLs on chromosomes 3 and 6 were successfully used in the marker-assisted selection programme for introgression of resistance to SDM in eight susceptible maize lines.     

Detection of two quantitative trait loci for resistance to ascochyta blight in an intra-specific cross of chickpea (Cicer arietinum L.): development of SCAR markers associated with resistance

Two quantitative trait loci (QTLs), (QTL_AR1 and QTL_AR2) associated with resistance to ascochyta blight, caused by Ascochyta rabiei, have been identified in a recombinant inbred line population derived from a cross of kabuli×desi chickpea. The population was evaluated in two cropping seasons under field conditions and the QTLs were found to be located in two different linkage groups (LG4a and LG4b). LG4b was saturated with RAPD markers and four of them associated with resistance were sequenced to give sequence characterized amplified regions (SCARs) that segregated with QTL_AR2. This QTL explained 21% of the total phenotypic variation. However, QTL_AR1, located in LG4a, explained around 34% of the total phenotypic variation in reaction to ascochyta blight when scored in the second cropping season. This LG4a region only includes a few markers, the flower colour locus (B/b), STMS GAA47, a RAPD marker and an inter-simple-sequence-repeat and corresponds with a previously reported QTL. From the four SCARs tagging QTL_AR2, SCAR (SCY17₅₉₀) was co-dominant, and the other three were dominant. All SCARs segregated in a 1:1 (presence:absence) ratio and the scoring co-segregated with their respective RAPD markers. QTL_AR2 on LG4b was mapped in a highly saturated genomic region covering a genetic distance of 0.8 cM with a cluster of nine markers (three SCARs, two sequence-tagged microsatellite sites (STMS) and four RAPDs). Two of the four SCARs showed significant alignment with genes or proteins related to disease resistance in other species and one of them (SCK13₆₀₃) was sited in the highly saturated region linked to QTL_AR2. STMS TA72 and TA146 located in LG4b were described in previous maps where QTL for blight resistance were also localized in both inter and intraspecific crosses. These findings may improve the precision of molecular breeding for QTL_AR2 as they will allow the choice of as much polymorphism as possible in any population and could be the starting point for finding a candidate resistant gene for ascochyta blight resistance in chickpea.