SUMMARY - Gluten strength is the main determinant of the end-use quality in durum. Wheat gluten strength is affected by genetic variation at genes coding for gliadins and glutenins, and by environmental factors. We grew 110 recombinant... more
SUMMARY - Gluten strength is the main determinant of the end-use quality in durum. Wheat gluten strength is affected by genetic variation at genes coding for gliadins and glutenins, and by environmental factors. We grew 110 recombinant inbred lines of the cross Jennah Khetifa x Cham1 in 13 environments (sites and years), and analyzed gluten strength in the resulting grain
A number of clubroot resistant (CR) Chinese cabbage cultivars have been developed in Japan using resistant genes from CR European fodder turnips (B. rapa ssp. rapifera). Clubroot resistance in European fodder turnips are known to be... more
A number of clubroot resistant (CR) Chinese cabbage cultivars have been developed in Japan using resistant genes from CR European fodder turnips (B. rapa ssp. rapifera). Clubroot resistance in European fodder turnips are known to be controlled by the combined action of several dominant resistance genes. We have developed three Chinese cabbage clubroot-resistant doubled haploid (DH) lines—T136-8, K10, and C9—which express resistance in different manners against two isolates of Plasmodiophora brassicae, M85 and K04. Depending on the isolates, we identified two CR loci, CRk and CRc. CRk was identified by quantitative trait loci (QTL) analysis of an F2 population derived from a cross between K10 and Q5. This locus showed resistance to both isolates and is located close to Crr3 in linkage group R3. The other locus, CRc was identified by QTL analysis of an F2 population derived from a cross between C9 and susceptible DH line, 6R. This locus was mapped to linkage group R2 and is independent from any published CR loci. We developed sequence-tagged site markers linked to this locus.
Although F2s are the most informative populations for genetic analysis, it has been difficult to use F2 populations directly for QTL analysis because it is usually difficult to assess the reliability of the data, due to an inability to... more
Although F2s are the most informative populations for genetic analysis, it has been difficult to use F2 populations directly for QTL analysis because it is usually difficult to assess the reliability of the data, due to an inability to estimate the experimental errors. In this study, we performed a QTL analysis for yield and yield-component traits of an F2 population based on data from replicated field trials over 2 years using vegetative shoots of ratooned plants, making use of the ratooning habit of rice. The objective of this study was to explore the possibility of conducting QTL analyses directly based on an F2 population by means of ratooning plants. The experimental population was from a cross between ’Zhenshan 97’ and ’Minghui 63’, the parents of ’Shanyou 63’, an elite rice hybrid widely grown in China. A genetic linkage map containing 151 molecular markers was constructed for QTL mapping. A total of 20 distinct QTLs were detected; eight of these were detected in both years and remaining 12 in only 1 year. Compared with the results of our previous analysis of the F2:3 families from the same cross, it was shown that most of the QTLs detected in the ratooned F2 population were also detected in the F2:3 population. However, the estimates of both additive and dominant types of genetic effects for many of the QTLs based on F2 ratoons were substantially larger than those based on F2:3 families. The results indicate that vegetatively ratooned F2 populations may have considerable utility in the mapping of QTLs, especially if dominant types of gene actions are of concern, although there were certain technical limitations in making use of such populations in the experiments.
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could... more
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We report here the construction of the first genetic linkage map of bambara groundnut using a F 3 population derived from a " narrow " cross between two domesticated landraces (Tiga Nicuru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 linkage groups with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a quantitative trait loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be useful for marker-assisted selection in bambara groundnut breeding programmes. Résumé : Le pois bambara (Vigna subterranea (L.) Verdc.) est une légumineuse indigène sous-utilisée qui a le potentiel de contribuer a ` la sécurité alimentaire dans les régions semi-arides de l'Afrique. À ce jour, peu d'études ont décrit des populations issues de croisements contrôlés qui pourraient être employées pour des fins de dével-oppement variétal et des études génétiques. Les auteurs rapportent la production d'une première carte génétique pour le pois bambara au moyen d'une population F 3 dérivée d'un croisement « proche » entre deux variétés de pays cultivées (Tiga Nicaru et DipC) qui présentent une divergence marquée en matière de caractères phénotypiques. La carte est composée de 238 marqueurs DArT et SSR qui définissent 21 groupes de liaison totalisant une distance génétique de 608,3 cM. De plus, les caractères phénotypiques ont été mesurés sur deux générations pour réaliser une analyse QTL (locus de caractère quantitatif). Au total, 36 QTL significatifs ont été détectés pour 19 caractères. La contribution au phénotype faite par un seul QTL variait entre 11,6 % et 49,9 %. Deux QTL stables ont été identifiés pour la longueur des entre-noeuds et le port de la plante. Les QTL identifiés pourront servir a ` des fins de sélection assistée de marqueurs dans le cadre de programmes d'amélioration génétique du pois bambara. [Traduit par la Rédaction]
The breeding of sugar beet varieties that combine resistance to Cercospora and high yield under non-diseased conditions is a major challenge to the breeder. The understanding of the quantitative trait loci (QTLs) contributing to... more
The breeding of sugar beet varieties that combine resistance to Cercospora and high yield under non-diseased conditions is a major challenge to the breeder. The understanding of the quantitative trait loci (QTLs) contributing to Cercospora resistance offers one route to solving this problem. A QTL analysis of Cercospora resistance in sugar beet was carried out using a linkage map based on AFLP and RFLP markers. Two different screening methods for Cercospora resistance (a field test at Copparo, Italy, under natural infection, and a newly-developed leaf disc test) were used to estimate the level of Cercospora resistance; the correlation between scores from the field (at 162 days after sowing) and the leaf disc test was significant. QTL analysis was based on F2 and F3 (half-sib family) generations derived from crosses between diploid single plants of 93164P (resistant to Cercospora leaf spot disease) and 95098P (susceptible). Four QTLs associated with Cercospora resistance (based on Lsmean data of the leaf disc test) on chromosomes III, IV, VII and IX were revealed using Composite interval mapping. To produce populations segregating for leaf spot resistance as a single Mendelian factor, we selected for plants heterozygous for only one of the QTLs (on chromosome IV or IX) but homozygous for the others.
Barley genotypes, in particular landraces and wild species, represent an important source of variation for adaptive traits that may contribute to increase yield and yield stability under drought conditions, and that could be introgressed... more
Barley genotypes, in particular landraces and wild species, represent an important source of variation for adaptive traits that may contribute to increase yield and yield stability under drought conditions, and that could be introgressed into improved varieties. Traits that have been investigated include physiological/biochemical and developmental/ morphological traits. Yield performance under drought is particularly a complex phenomenon, and plants exhibit a diverse range of genetically complex mechanisms for drought resistance. Quantitative trait loci (QTL) studies with and without H. spontaneum have shown that developmental genes, notably those involved in flowering time and plant stature show pleiotropic effects on abiotic stress tolerance and ultimately determine yield. Problems associated with the hybridization of H. spontaneum such as alleles with deleterious effects on field performance could be best addressed in the advanced backcross (AB-) QTL analysis. It was interesting to see that in AB-QTL populations like in balanced populations major QTL overshadowed minor QTL-alleles. Nevertheless, crosses with H. spontaneum, AB-QTL populations and association studies with H. spontaneum have also identified new alleles and genes that are related to abiotic stress tolerance. In order to identify genes that are related to drought tolerance microarrays analysis to monitor gene expression profiles for plants exposed to limited water environment is performed. Several studies with rapid dehydration treatment have shown that osmotic-stress-inducible genes could explain the response to drought stress in plants. Another development is the identification and use of nucleotide polymorphisms (SNP) in genes related to abiotic stress tolerance. An understanding of the combined function and expression of genes involved in various abiotic stresses, could help identify candidate genes underlying QTL of interest.
The beet cyst nematode (Heterodera schachtii Schmidt) can be controlled biologically in highly infected soils of sugar beet rotations using resistant varieties of oil radish (Raphanus sativus L. ssp. oleiferus DC.) as a green crop.... more
The beet cyst nematode (Heterodera schachtii Schmidt) can be controlled biologically in highly infected soils of sugar beet rotations using resistant varieties of oil radish (Raphanus sativus L. ssp. oleiferus DC.) as a green crop. Resistant plants stimulate infective juveniles to invade roots, but prevent them after their penetration to complete the life cycle. The resistance trait has been transferred successfully to susceptible rapeseed by the addition of a complete radish chromosome. The aim of the study was to construct a genetic map for radish and to develop resistance-associated markers. The map with 545 RAPD, dpRAPD, AFLP and SSR markers had a length of 1,517 cM, a mean distance of 2.8 cM and consisted of nine linkage groups having sizes between 120 and 232 cM. Chromosome-specific markers for the resistance-bearing chromosome d and the other eight radish chromosomes, developed previously from a series of rapeseed-radish addition lines, were enclosed as anchor markers. Each of the extra chromosomes in the addition lines could be unambiguously assigned to one of the radish linkage groups. The QTL analysis of nematode resistance was realized in the intraspecific F2 mapping population derived from a cross between varieties ‘Pegletta’ (nematode resistant) x ‘Siletta Nova’ (susceptible). A dominant major QTL Hs1Rph explaining 46.4% of the phenotypic variability was detected in a proximal position of chromosome d. Radish chromosome-specific anchor markers with known map positions were made available for future recombination experiments to incorporate segments carrying desired genes as Hs1Rph from radish into rapeseed by means of chromosome addition lines.
Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic analysis of natural variation in the... more
Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana. Instead of focusing on specific metabolites, we have applied empirical untargeted metabolomics using liquid chromatography-time of flight mass spectrometry (LC-QTOF MS). This uncovered many qualitative and quantitative differences in metabolite accumulation between A. thaliana accessions. Only 13.4% of the mass peaks were detected in all 14 accessions analyzed. Quantitative trait locus (QTL) analysis of more than 2,000 mass peaks, detected in a recombinant inbred line (RIL) population derived from the two most divergent accessions, enabled the identification of QTLs for about 75% of the mass signals. More than one-third of the signals were not detected in either parent, indicating the large potential for modifi...
QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can... more
QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can be used to locate QTLs. In autopolyploid Saccharum, 36 significant associations between variation in sugar content and unlinked loci detected by 31
Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted... more
Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appro...
Cercospora leaf spot (CLS) caused by the fungus Cercospora canescens Illis & Martin is a serious disease in mungbean (Vigna radiata (L.) Wilczek), and disease can reduce seed yield by up to 50%. We report here for the first time... more
Cercospora leaf spot (CLS) caused by the fungus Cercospora canescens Illis & Martin is a serious disease in mungbean (Vigna radiata (L.) Wilczek), and disease can reduce seed yield by up to 50%. We report here for the first time quantitative trait loci (QTL) mapping for CLS resistance in mungbean. The QTL analysis was conducted using F2 (KPS1 × V4718) and BC1F1 [(KPS1 × V4718) × KPS1] populations developed from crosses between the CLS-resistant mungbean V4718 and CLS-susceptible cultivar Kamphaeng Saen 1 (KPS1). CLS resistance in F2 populations was evaluated under field conditions during the wet seasons of 2008 and 2009, and resistance in BC1F1 was evaluated under field conditions during the wet season in 2008. Seven hundred and fifty-three simple sequence repeat (SSR) markers from various legumes were used to assess polymorphism between KPS1 and V4718. Subsequently, 69 polymorphic markers were analyzed in the F2 and BC1F1 populations. The results of segregation analysis indicated that resistance to CLS is controlled by a single dominant gene, while composite interval mapping consistently identified one major QTL (qCLS) for CLS resistance on linkage group 3 in both F2 and BC1F1 populations. qCLS was located between markers CEDG117 and VR393, and accounted for 65.5–80.53% of the disease score variation depending on seasons and populations. An allele from V4718 increased the resistance. The SSR markers flanking qCLS will facilitate transferral of the CLS resistance allele from V4718 into elite mungbean cultivars.
The high-throughput analytical techniques used in genome, proteome and metabolome studies produce large sets of data that must be studied using appropriate tools. The construction of networks linking different genetic elements and/or... more
The high-throughput analytical techniques used in genome, proteome and metabolome studies produce large sets of data that must be studied using appropriate tools. The construction of networks linking different genetic elements and/or functions makes it possible to obtain an integrated view of the cell molecular biology and will eventually help us to predict complex phenotypes from molecular data. Genetic networks can be constructed using different types of data such as genes involved in the control of complex phenotypic traits, genes controlling global gene expression, genetic elements involved in the same metabolic process, gene products interacting physically between them. The connections linking these genetic elements in the network reflect the genetic, physical and/or functional interaction among them. All these networks share common properties and reflect the different layers of the cell's complexity. In this review, we will study how different types of networks can be cons...
Perennial ryegrass (Lolium perenne L.) is one of the important forage and turf grasses in temperate zones in the world. Gray leaf spot caused by the fungus Pyricularia oryzae has recently become a serious problem on perennial ryegrass for... more
Perennial ryegrass (Lolium perenne L.) is one of the important forage and turf grasses in temperate zones in the world. Gray leaf spot caused by the fungus Pyricularia oryzae has recently become a serious problem on perennial ryegrass for golf course fairways. The causal agent also causes rice blast disease on rice, as well as foliar diseases on wheat and barley. Crown and stem rust caused by Puccinia spp. are also important for forage- and turf-type perennial ryegrass and seed production. In addition, foliar diseases caused by Bipolaris species, are common and widespread on graminaceous plants. Despite a recent advancement of molecular markers for forage and turf grasses, effective utilization of genetic information available in cereal crops will significantly lead to better understanding of the genetic architecture of disease resistance in ryegrass. Quantitative trait loci (QTL) analysis based on a three-generation interspecific ryegrass population detected a total of 16 QTLs for resistance to the four pathogens. Those QTL were compared with 45 resistance loci for the same or related pathogens previously identified in cereal crops, based on comparative genome analysis using a ryegrass genetic map and a rice physical map. Some pathogen-specific QTLs identified in ryegrass were conserved at corresponding genome regions in cereals but coincidence of QTLs for disease resistance in ryegrass and cereals was not statistically significant at the genome-wide comparison. In conclusion, the conserved synteny of disease resistance loci will facilitate transferring genetic resources for disease resistance between ryegrass and cereals to accommodate breeding needs for developing multiple disease resistance cultivars in ryegrass.
Double haploid (DH) plants of Brassica spp. can be produced via anther culture or culture of microspores. This paper reviews the uses of double haploids in crop improvement research in vegetable brassicas (B. oleracea). Applications of DH... more
Double haploid (DH) plants of Brassica spp. can be produced via anther culture or culture of microspores. This paper reviews the uses of double haploids in crop improvement research in vegetable brassicas (B. oleracea). Applications of DH lines are described for breeding; construction of linkage maps; genetic analysis of quantitative traits and capturing genetic variation. The advantages and disadvantages of DH lines are discussed
