A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds

Key message

We detected a QTL for single seed weight in soybean that was stable across multiple environments and genetic backgrounds with the use of two recombinant inbred line populations.

Abstract

Single seed weight (SSW) in soybean is a key determinant of both seed yield and the quality of soy food products, and it exhibits wide variation. SSW is under genetic control, but the molecular mechanisms of such control remain unclear. We have now investigated quantitative trait loci (QTLs) for SSW in soybean and have identified such a QTL that is stable across multiple environments and genetic backgrounds. Two populations of 225 and 250 recombinant inbred lines were developed from crosses between Japanese and US cultivars of soybean that differ in SSW by a factor of ~2, and these populations were grown in at least three different environments. A whole-genome panel comprising 304 simple sequence repeat (SSR) loci was applied to mapping in each population. We identified 15 significant QTLs for SSW dispersed among 11 chromosomes in the two populations. One QTL located between Sat_284 and Sat_292 on chromosome 17 was detected (3.6 < LOD < 14.1) in both populations grown in all environments. This QTL, tentatively designated qSw17-1, accounted for 9.4–20.9 % of phenotypic variation in SSW, with a dominant allele being associated with increased SSW. Given its substantial effect on SSW, qSw17-1 is an attractive target for positional cloning, and SSR markers closely associated with this locus may prove useful for marker-assisted selection for SSW control in soybean.     

QTL mapping of fire blight resistance in apple

Fire blight caused by the bacterium Erwinia amylovora is a severe threat to apple and pear orchards worldwide. Apple varieties exhibit a wide range of relative susceptibility/tolerance to fire blight. Although, no monogenic resistance against fire blight has been identified yet, recent evidence indicates the existence of quantitative resistance. Potential sources of fire blight resistance include several wild Malus species and some apple cultivars. F1 progenies of ‘Fiesta’בDiscovery’ were inoculated with the Swiss strain Ea 610 and studied under controlled conditions to identify quantitative trait loci (QTLs) for fire blight resistance. Disease was evaluated at four time points after inoculation. Shoot lesion length and the area under disease progress curve (AUDPC) values were used for QTL analysis. One significant (LOD score of 7.5–8.1, p<0.001) QTL was identified on the linkage group 7 of ‘Fiesta’ (F7). The F7 QTL explained about 37.5–38.6% of the phenotypic variation.     

QTL analysis of soybean seed weight across multi-genetic backgrounds and environments

Seed weight, measured as mass per seed, is an important yield component of soybean and is generally positively correlated with seed yield (Burton et al, Crop Sci 27:1093, 1987). In previous reports, quantitative trait loci (QTL) associated with seed weight, were identified in single genetic background. The objective of the present study was to identify QTL and epistatic QTL underlying soybean seed weight in three RIL populations (with one common male parent 'Hefeng25') and across three different environments. Overall, 18, 11, and 17 seed weight QTL were identified in HC ('Hefeng25' × 'Conrad'), HM ('Hefeng25' × 'Maple Arrow'), and HB ('Hefeng25' × 'Bayfield') populations, respectively. The amount of phenotypic variation explained by a single QTL underlying seed weight was usually less than 10 %. The environment and background-independent QTL often had higher additive (a) effects. In contrast, the environment or background-dependent QTL were probably due to weak expression of QTL. QTL by environment interaction effects were in the opposite direction of a effects and/or epistasis effects. Four QTL and one QTL could be identified (2.0 < LOD < 9.06) in the HC and HB populations, respectively, across three environments (swHCA2-1, swHCC2-1, swHCD1b-1, swHCA2-2 (linked to Satt233, Satt424, Satt460, Satt428, respectively) and swHBA1-1(Satt449). Seven QTL could be identified in all three RIL populations in at least one location. Two QTL could be identified in the three RIL populations across three environments. These two QTL may have greater potential for use in marker-assisted selection of seed weight in soybean.     

A QTL for rice grain yield in aerobic environments with large effects in three genetic backgrounds

A large-effect QTL associated with grain yield in aerobic environments was identified in three genetic backgrounds, Apo/²*Swarna, Apo/²*IR72, and Vandana/²*IR72, using bulk-segregant analysis (BSA). Apo and Vandana are drought-tolerant aerobic-adapted varieties, while Swarna and IR72 are important lowland rice varieties grown on millions of hectares in Asia but perform poorly in aerobic conditions. Two closely linked rice microsatellite (RM) markers, RM510 and RM19367, located on chromosome 6, were found to be associated with yield under aerobic soil conditions in all three backgrounds. The QTL linked to this marker, qDTY6.1 (DTY, grain yield under drought), was mapped to a 2.2 cM region between RM19367 and RM3805 at a peak LOD score of 32 in the Apo/²*Swarna population. The effect of qDTY6.1 was tested in a total of 20 hydrological environments over a period of five seasons and in five populations in the three genetic backgrounds. In the Apo/²*Swarna population, qDTY6.1 had a large effect on grain yield under favorable aerobic (R ² ≤ 66%) and irrigated lowland (R ² < 39%) conditions but not under drought stress; Apo contributed the favorable allele in all the conditions where an effect was observed. In the Apo/IR72 cross, Apo contributed the favorable allele in almost all the aerobic environments in RIL and BC₁-derived populations. In the Vandana/IR72 RIL and BC₁-derived populations, qDTY6.1 had a strong effect on yield in aerobic drought stress, aerobic non-stress, and irrigated lowland conditions; the Vandana allele was favorable in aerobic environments and the IR72 allele was favorable in irrigated lowland environments. We conclude that qDTY6.1 is a large-effect QTL for rice grain yield under aerobic environments and could potentially be used in molecular breeding of rice for aerobic environments.     

Conditional QTL underlying resistance to late blight in a diploid potato population

A large number of quantitative trait loci (QTL) for resistance to late blight of potato have been reported with a "conventional" method in which each phenotypic trait reflects the cumulative genetic effects for the duration of the disease process. However, as genes controlling response to disease may have unique contributions with specific temporal features, it is important to consider the phenotype as dynamic. Here, using the net genetic effects evidenced at consecutive time points during disease development, we report the first conditional mapping of QTL underlying late blight resistance in potato under five environments in Peru. Six conditional QTL were mapped, one each on chromosome 2, 7 and 12 and three on chromosome 9. These QTL represent distinct contributions to the phenotypic variation at different stages of disease development. By comparison, when conventional mapping was conducted, only one QTL was detected on chromosome 9. This QTL was the same as one of the conditional QTL. The results imply that conditional QTL reflect genes that function at particular stages during the host-pathogen interaction. The dynamics revealed by conditional QTL mapping could contribute to the understanding of the molecular mechanism of late blight resistance and these QTL could be used to target genes for marker development or manipulation to improve resistance.     

A functional genetic marker for apple red skin coloration across different environments

The red skin color desired by most apple consumers is not easy to achieve in warm climates, as the expression of MYB10, which regulates red pigmentation in apple, is influenced negatively by high temperatures. We describe the development and validation of a genetic marker for red skin coloration that effectively predicts color in a warm summer environment in Spain, as well as more temperate climates in New Zealand and Italy. Following the determination of a major-effect quantitative trait locus (QTL) controlling red skin coloration on linkage group (LG)9, using four segregating populations grown in New Zealand, and screened using the IRSC apple 8-K single-nucleotide polymorphism (SNP) array, the most significant SNP marker (ss475879531) was transformed into a marker suitable for use in a real-time PCR assay. This marker was validated using five apple seedling populations growing in a warm summer environment in Spain, demonstrating that the marker system efficiently predicts red skin coloration and can be used for marker assisted selection, even under conditions considered adverse for skin color development.     

Detection of Fusarium head blight resistance QTL in a wheat population using bulked segregant analysis

A population of 218 recombinant inbred lines (RILs) was developed from the cross of two wheat (Triticum aestivum L.) cultivars, 'Ning 894037' and 'Alondra'. Ning 894037 has resistance to Fusarium head blight (FHB) and Alondra is moderately susceptible. Response of the RILs and their parental lines to FHB infection was evaluated with point inoculation in four experiments both in greenhouse and in field conditions. Distribution of disease severity in the population is continuous, indicating quantitative inheritance of resistance to FHB. Bulked segregant analysis and QTL mapping based on simple sequence repeat (SSR) markers revealed three chromosome regions that are responsible for FHB resistance. A chromosome region on 3BS accounted for 42.5% of the phenotypic variation for FHB resistance. Additional QTLs were located on chromosomes 2D and 6B. These three QTLs jointly accounted for 51.6% of the phenotypic variation. SSR markers linked to the QTLs influencing resistance to FHB have potential for use in breeding programs.     

Powdery mildew resistance in roses: QTL mapping in different environments using selective genotyping

Podosphaera pannosa, the causal agent of rose powdery mildew, hampers the production of cut roses throughout the world. A major tool to control this disease is the use of resistant plant material. Single resistance genes, like Rpp1, may be overcome within a few years by high risk pathogens like powdery mildews. Durable resistance could be achieved using quantitative resistances. Here we describe mapping of QTLs for resistance to P. pannosa in six different environments (artificial and natural infections in the greenhouse over 3 years and natural infections in the field over 2 years). AFLPs, RGAs and other marker types were used to construct an integrated linkage map for the diploid population 97/7 containing 233 markers. In a selective genotyping procedure, marker segregation was analysed for 170 of the up to 270 phenotyped individuals. We identified seven linkage groups with an average length of 60 cM, corresponding to seven rose chromosomes in the haploid set. Using an LOD significance threshold of 3.9 we detected a total of 28 QTLs for the nine powdery mildew disease scores under analysis. Using the data from artificial inoculations with powdery mildew race 9, three resistance QTLs explaining about 84% of the variability were mapped. Twelve and 15 QTLs were detected for resistance to naturally occurring infections in the greenhouse and in the field, respectively, over several years.     

A major QTL for resistance against Fusarium head blight in European winter wheat

We report on the verification of a resistance quantitative trait locus (QTL) on chromosome 1BL (now designated Qfhs.lfl-1BL) which had been previously identified in the winter wheat cultivar Cansas. For a more precise estimation of the QTL effect and its influence on plant height and heading date lines with a more homogeneous genetic background were created and evaluated in four environments after spray inoculation with Fusarium culmorum. Qfhs.lfl-1BL reduced FHB severity by 42% relative to lines without the resistance allele. This QTL did not influence plant height, but significantly delayed heading date by one day. All of the most resistant genotypes of the verification population carried this major QTL displaying its importance for disease resistance. This resistance QTL has not only been found in the cultivar Cansas, but also in the three European winter wheat cultivars Biscay, History and Pirat. A subsequent meta-analysis confirmed the presence of a single QTL on the long arm of chromosome 1B originating from the four mentioned cultivars. Altogether, the results of the present study indicate that Qfhs.lfl-1BL is an important component of FHB resistance in European winter wheat and support the view that this QTL would be effective and valuable in backcross breeding programmes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic characterization of QTL associated with resistance to Fusarium head blight in a doubled-haploid spring wheat population.

Fusarium head blight (FHB) is one of the most important fungal wheat diseases worldwide. Understanding the genetics of FHB resistance is the key to facilitating the introgression of different FHB resistance genes into adapted wheat. The objectives of the present study were to detect and map quantitative trait loci (QTL) associated with FHB resistance genes and characterize the genetic components of the QTL in a doubled-haploid (DH) spring wheat population using both single-locus and two-locus analysis. A mapping population, consisting of 174 DH lines from the cross between DH181 (resistant) and AC Foremost (susceptible), was evaluated for type I resistance to initial infection during a 2-year period in spray-inoculated field trials, for Type II resistance to fungal spread within the spike in 3 greenhouse experiments using single-floret inoculation, and for resistance to kernel infection in a 2001 field trial. One-locus QTL analysis revealed 7 QTL for type I resistance on chromosome arms 2DS, 3AS, 3BS, 3BC (centromeric), 4DL, 5AS, and 6BS, 4 QTL for type II resistance on chromosomes 2DS, 3BS, 6BS, and 7BL, and 6 QTL for resistance to kernel infection on chromosomes 1DL, 2DS, 3BS, 3BC, 4DL, and 6BS. Two-locus QTL analysis detected 8 QTL with main effects and 4 additive by additive epistatic interactions for FHB resistance and identified novel FHB resistance genes for the first time on chromosomes 1DL, 4AL, and 4DL. Neither significant QTL by environment interactions nor epistatic QTL by environment interactions were found for either type I or type II resistance. The additive effects of QTL explained most of the phenotypic variance for FHB resistance. Marker-assisted selection for the favored alleles at multiple genomic regions appears to be a promising tool to accelerate the introgression and pyramiding of different FHB resistance genes into adapted wheat genetic backgrounds.     

Confirming quantitative trait loci for aflatoxin resistance from Mp313E in different genetic backgrounds

The fungus Aspergillus flavus (Link:Fr) causes ear rot of maize (Zea mays L.) and produces the toxic metabolic product aflatoxin. One particularly effective method of controlling the fungus is via host plant resistance, but while several resistant breeding lines have been identified, transferring the resistance genes from these lines into elite cultivars has been less effective than needed. A high number of genes involved with resistance, each with a small effect, and some only found under certain environmental conditions, has hampered resistance breeding. The identification of markers linked to genomic regions associated with resistance would aid in this effort. The goals of this study were to identify and characterize quantitative trait loci (QTL) conferring resistance to aflatoxin accumulation from resistant maize donor Mp313E in a background of the susceptible inbred line Va35; to compare them to the QTL identified from Mp313E in a background of B73; and to test the stability of the QTL identified in Mp313E × Va35 in multiple environments by remapping the phenotypic tails of the Mp313E × Va35 mapping population in new locations. Twenty different QTL were found in this study, 11 of which were also found in different environments using the phenotypic tail subset mapping population, and five of which were likely the same as those reported in the Mp313E × B73 mapping population. This indicates that many of the QTL are stable over the environments and genetic backgrounds tested, which will make them more valuable in breeding efforts.     

Single and multiple phenotype QTL analyses of downy mildew resistance in interspecific grapevines

Key message

Downy mildew resistance across days post-inoculation, experiments, and years in two interspecific grapevine F₁ families was investigated using linear mixed models and Bayesian networks, and five new QTL were identified.

Abstract

Breeding grapevines for downy mildew disease resistance has traditionally relied on qualitative gene resistance, which can be overcome by pathogen evolution. Analyzing two interspecific F₁ families, both having ancestry derived from Vitis vinifera and wild North American Vitis species, across 2 years and multiple experiments, we found multiple loci associated with downy mildew sporulation and hypersensitive response in both families using a single phenotype model. The loci explained between 7 and 17% of the variance for either phenotype, suggesting a complex genetic architecture for these traits in the two families studied. For two loci, we used RNA-Seq to detect differentially transcribed genes and found that the candidate genes at these loci were likely not NBS-LRR genes. Additionally, using a multiple phenotype Bayesian network analysis, we found effects between the leaf trichome density, hypersensitive response, and sporulation phenotypes. Moderate–high heritabilities were found for all three phenotypes, suggesting that selection for downy mildew resistance is an achievable goal by breeding for either physical- or non-physical-based resistance mechanisms, with the combination of the two possibly providing durable resistance.

     

A substitution mutation in OsPELOTA confers bacterial blight resistance by activating the salicylic acid pathway

We previously reported a spotted-leaf mutant pelota(originally termed HM_(47)) in rice displaying arrested growth and enhanced resistance to multiple races of Xanthomonas oryzae pv. oryzae. Here, we report the mapbased cloning of the causal gene OsPELOTA(originally termed spl~(HM47)). We identified a single base substitution from T to A at position 556 in the coding sequence of OsPELOTA, effectively mutating phenylalanine to isoleucine at position 186 in the translated protein sequence. Both functional complementation and over-expression could rescue the spotted-leaf phenotype. OsPELOTA, a paralogue to eukaryotic release factor 1(eRF_1), shows high sequence similarity to Drosophila Pelota and also localizes to the endoplasmic reticulum and plasma membrane.OsPELOTA is constitutively expressed in roots, leaves,sheaths, stems, and panicles. Elevated levels of salicylic acid and decreased level of jasmonate were detected in the pelota mutant. RNA-seq analysis confirmed that genes responding to salicylic acid were upregulated in the mutant. Our results indicate that the rice PELOTA protein is involved in bacterial leaf blight resistance by activating the salicylic acid metabolic pathway.     

Inheritance and QTL mapping of resistance to gummy stem blight in cucumber stem

Gummy stem blight (GSB), a common disease of all major cucurbits, is caused by the fungus Didymella bryoniae. It results in serious losses in fruit production, which in cucumber can be up to 80% or more. Because the severity of the disease varies from season to season and also because of the harm to the environment caused by using pesticides to control the disease, the best method for overcoming GSB in cucumber is to develop more resistant cultivars by molecular breeding. There are no reports on molecular markers for use in breeding GSB resistance and no studies on chromosomal mapping of resistance. In this paper, a set of 160 F₉ recombinant inbred lines (RILs) were derived from the cross between the wild-type GSB-resistant cucumber accession PI 183967 and the cultivated GSB-susceptible accession 931. A total of 2112 pairs of SSR primers were used to study the inheritance of GSB resistance and to detect quantitative trait loci (QTLs) conferring resistance in the cucumber stem. Genetic analysis indicated that resistance to GSB in PI 183967 was quantitative and mainly governed by three pairs of additive epistatic major genes. Five QTLs, gsb-s1.1, gsb-s2.1, gsb-s6.1, gsb-s6.2, and gsb-s6.3, for resistance to GSB in cucumber stems were detected. The loci gsb-s1.1 and gsb-s2.1 with phenotypic variations of 8.7 and 6.7% were mapped to chromosomes (Chr.) 1 and 2, respectively. The loci gsb-s6.1, gsb-s6.2, and gsb-s6.3 were linked on Chr.6. Locus gsb-s6.2 accounted for the highest phenotypic variation of 22.7% and was flanked by markers SSR04083 and SSR02940 with genetic distances of 5.0 and 1.8 cM, respectively. There were 117 candidate genes predicted between SSR04083 and SSR02940, of which 14 were related to disease resistance.     

Host‐induced gene silencing of an essential chitin synthase gene confers durable resistance to Fusarium head blight and seedling blight in wheat

Fusarium head blight (FHB) and Fusarium seedling blight (FSB) of wheat, caused by Fusarium pathogens, are devastating diseases worldwide. We report the expression of RNA interference (RNAi) sequences derived from an essential Fusarium graminearum (Fg) virulence gene, chitin synthase (Chs) 3b, as a method to enhance resistance of wheat plants to fungal pathogens. Deletion of Chs3b was lethal to Fg; disruption of the other Chs gene family members generated knockout mutants with diverse impacts on Fg. Comparative expression analyses revealed that among the Chs gene family members, Chs3b had the highest expression levels during Fg colonization of wheat. Three hairpin RNAi constructs corresponding to the different regions of Chs3b were found to silence Chs3b in transgenic Fg strains. Co‐expression of these three RNAi constructs in two independent elite wheat cultivar transgenic lines conferred high levels of stable, consistent resistance (combined type I and II resistance) to both FHB and FSB throughout the T₃ to T₅ generations. Confocal microscopy revealed profoundly restricted mycelia in Fg‐infected transgenic wheat plants. Presence of the three specific short interfering RNAs in transgenic wheat plants was confirmed by Northern blotting, and these RNAs efficiently down‐regulated Chs3b in the colonizing Fusarium pathogens on wheat seedlings and spikes. Our results demonstrate that host‐induced gene silencing of an essential fungal chitin synthase gene is an effective strategy for enhancing resistance in crop plants under field test conditions.     

Quantitative trait dissection analysis in Eucalyptus using RAPD markers: 1. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages

 The objective of this study was to use random amplified polymorphic DNA (RAPD) to determine the genetic location and effects of genomic regions controlling wood density, stem growth and stem form in two species of Eucalyptus. Two hundred F₁ trees generated from an interspecific cross E. urophylla×E. grandis between two elite trees were used. Genetic maps were constructed for each parent with markers segregating in the 1:1 ratio in FS progeny. A total of 86 and 92 markers distributed among 11 linkage groups covered 1295 cM and 1312 cM for the E. urophylla and E. grandis parent, respectively. Traits were measured three times up to selection age (38 months). The magnitude of the phenotypic variation explained by the joint action of the segregating quantitative trait alleles indicated that genetic factors of large effect were involved in the control of the studied characters. Several regions controlling part of the variation for the studied traits were identified by interval mapping. Some regions of the genome exerted effects on more than one trait, providing a genetic explanation for at least some of the correlation between the traits. On the basis of an age-by-age analysis, a partial stability of QTL expression was observed with 68% of the QTL being expressed at two ages and 32% being age-specific. No QTL were significant for all three ages. Taking advantage of repeated measurements on the same material across different ages, we investigated with a maximum statistical power, the effect of marker genotype on traits, with age and QTL×age interaction effects being removed. A two-way analysis of variance made it possible to detect significant marker-trait associations over the period studied. Most of them had already been detected in the annual analysis. This result is very encouraging for the application of marker information to the early selection of hybrid trees to be vegetatively propagated for the production of clonal varieties. Received: 2 December 1996/Accepted: 4 April 1997     

QTL mapping for fiber quality traits across multiple generations and environments in upland cotton

Identification of quantitative trait loci (QTL) for fiber quality traits that are stable across multiple generations and environments could facilitate marker-assisted selection for improving cotton strains. In the present study, F₂, F_2:3, and recombinant inbred lines (RILs, F _6:8 ) populations derived from an upland cotton (Gossypium hirsutum L.) cross between strain 0-153, which has excellent fiber quality, and strain sGK9708, a commercial transgenic cultivar, were constructed for QTL tagging of fiber quality. We used 5,742 simple sequence repeat primer pairs to screen for polymorphisms between the two parent strains. Linkage maps of F₂ and RILs were constructed, containing 155 and 190 loci and with a total map distance of 959.4 centimorgans (cM) and 700.9?cM, respectively. We screened fiber quality QTL across multiple generations and environments through composite interval mapping of fiber quality data. Specifically, we studied F₂ and F_2:3 family lines from Anyang (Henan Province) in 2003 and 2004 and RILs in Anyang in 2007 and Anyang, Quzhou (Hebei Province), and Linqing (Shandong Province) in 2008. We identified 50 QTL for fiber quality: 10 for fiber strength, 10 for fiber length, 10 for micronaire, eight for fiber uniformity, and 12 for fiber elongation. Nine of these fiber quality QTL were identified in F₂, F_2:3 and RILs simultaneously. Two QTL for fiber strength on chromosomes C7 and C25 were detected in all three generations and all four environments and explained 16.67?C27.86% and 9.43?C21.36% of the phenotypic variation, respectively. These stable QTL for fiber quality traits could be used for marker assisted selection.