Flowering time quantitative trait Loci analysis of oilseed brassica in multiple environments and genomewide alignment with Arabidopsis

Most agronomical traits exhibit quantitative variation, which is controlled by multiple genes and are environmentally dependent. To study the genetic variation of flowering time in Brassica napus, a DH population and its derived reconstructed F(2) population were planted in 11 field environments. The flowering time varied greatly with environments; 60% of the phenotypic variation was attributed to genetic effects. Five to 18 QTL at a statistically significant level (SL-QTL) were detected in each environment and, on average, two new SL-QTL were discovered with each added environment. Another type of QTL, micro-real QTL (MR-QTL), was detected repeatedly from at least 2 of the 11 environments; resulting in a total of 36 SL-QTL and 6 MR-QTL. Sixty-three interacting pairs of loci were found; 50% of them were involved in QTL. Hundreds of floral transition genes in Arabidopsis were aligned with the linkage map of B. napus by in silico mapping; 28% of them aligned with QTL regions and 9% were consistent with interacting loci. One locus, BnFLC10, in N10 and a QTL cluster in N16 were specific to spring- and winter-cropped environments respectively. The number of QTL, interacting loci, and aligned functional genes revealed a complex genetic network controlling flowering time in B. napus.     

Comparative mapping reveals similar linkage of functional genes to QTL of yield-related traits between <Emphasis Type="Italic">Brassica napus</Emphasis> and <Emphasis Type="Italic">Oryza sativa</Emphasis>

Oryza sativa and Brassica napus-two important crops for food and oil, respectively-share high seed yield as a common breeding goal. As a model plant, O. sativa genomics have been intensively investigated and its agronomic traits have been advanced. In the present study, we used the available information on O. sativa to conduct comparative mapping between O. sativa and B. napus, with the aim of advancing research on seed-yield and yield-related traits in B. napus. Firstly, functional markers (from 55 differentially expressed genes between a hybrid and its parents) were used to detect B. napus genes that co-localized with yield-related traits in an F(2:3) population. Referring to publicly available sequences of 55 B. napus genes, 53 homologous O. sativa genes were subsequently detected by screening, and their chromosomal locations were determined using silico mapping. Comparative location of yield-related QTL between the two species showed that a total of 37 O. sativa and B. napus homologues were located in similar yield-related QTL between species. Our results indicate that homologous genes between O. sativa and B. napus may have consistent function and control similar traits, which may be helpful for agronomic gene characterization in B. napus based on what is known in O. sativa.     

Comparative mapping of human chromosome 10 to pig chromosomes 10 and 14

Identification of predictive markers in QTL regions that impact production traits in commercial populations of swine is dependent on construction of dense comparative maps with human and mouse genomes. Chromosomal painting in swine suggests that large genomic blocks are conserved between pig and human, while mapping of individual genes reveals that gene order can be quite divergent. High-resolution comparative maps in regions affecting traits of interest are necessary for selection of positional candidate genes to evaluate nucleotide variation causing phenotypic differences. The objective of this study was to construct an ordered comparative map of human chromosome 10 and pig chromosomes 10 and 14. As a large portion of both pig chromosomes are represented by HSA10, genes at regularly spaced intervals along this chromosome were targeted for placement in the porcine genome. A total of 29 genes from human chromosome 10 were mapped to porcine chromosomes 10 (SSC10) and 14 (SSC14) averaging about 5 Mb distance of human DNA per marker. Eighteen genes were assigned by linkage in the MARC mapping population, five genes were physically assigned with the IMpRH mapping panel and seven genes were assigned on both maps. Seventeen genes from human 10p mapped to SSC10, and 12 genes from human 10q mapped to SSC14. Comparative maps of mammalian species indicate that chromosomal segments are conserved across several species and represent syntenic blocks with distinct breakpoints. Development of comparative maps containing several species should reveal conserved syntenic blocks that will allow us to better define QTL regions in livestock.     

Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific markers for high oleic and low linolenic acid contents

Modification of oleic acid (C18:1) and linolenic acid (C18:3) contents in seeds is one of the major goals for quality breeding after removal of erucic acid in oilseed rape (Brassica napus). The fatty acid desaturase genes FAD2 and FAD3 have been shown as the major genes for the control of C18:1 and C18:3 contents. However, the genome structure and locus distributions of the two gene families in amphidiploid B. napus are still not completely understood to date. In the present study, all copies of FAD2 and FAD3 genes in the A- and C-genome of B. napus and its two diploid progenitor species, Brassica rapa and Brassica oleracea, were identified through bioinformatic analysis and extensive molecular cloning. Two FAD2 genes exist in B. rapa and B. oleracea, and four copies of FAD2 genes exist in B. napus. Three and six copies of FAD3 genes were identified in diploid species and amphidiploid species, respectively. The genetic control of high C18:1 and low C18:3 contents in a double haploid population was investigated through mapping of the quantitative trait loci (QTL) for the traits and the molecular cloning of the underlying genes. One major QTL of BnaA.FAD2.a located on A5 chromosome was responsible for the high C18:1 content. A deleted mutation in the BnaA.FAD2.a locus was uncovered, which represented a previously unidentified allele for the high oleic variation in B. napus species. Two major QTLs on A4 and C4 chromosomes were found to be responsible for the low C18:3 content in the DH population as well as in SW Hickory. Furthermore, several single base pair changes in BnaA.FAD3.b and BnaC.FAD3.b were identified to cause the phenotype of low C18:3 content. Based on the results of genetic mapping and identified sequences, allele-specific markers were developed for FAD2 and FAD3 genes. Particularly, single-nucleotide amplified polymorphisms markers for FAD3 alleles were demonstrated to be a reliable type of SNP markers for unambiguous identification of genotypes with different content of C18:3 in amphidiploid B. napus.     

Regional association analysis delineates a sequenced chromosome region influencing antinutritive seed meal compounds in oilseed rape

This study describes the use of regional association analyses to delineate a sequenced region of a Brassica napus chromosome with a significant effect on antinutritive seed meal compounds in oilseed rape. A major quantitative trait locus (QTL) influencing seed colour, fibre content, and phenolic compounds was mapped to the same position on B. napus chromosome A9 in biparental mapping populations from two different yellow-seeded × black-seeded B. napus crosses. Sequences of markers spanning the QTL region identified synteny to a sequence contig from the corresponding chromosome A9 in Brassica rapa. Remapping of sequence-derived markers originating from the B. rapa sequence contig confirmed their position within the QTL. One of these markers also mapped to a seed colour and fibre QTL on the same chromosome in a black-seeded × black-seeded B. napus cross. Consequently, regional association analysis was performed in a genetically diverse panel of dark-seeded, winter-type oilseed rape accessions. For this we used closely spaced simple sequence repeat (SSR) markers spanning the sequence contig covering the QTL region. Correction for population structure was performed using a set of genome-wide SSR markers. The identification of QTL-derived markers with significant associations to seed colour, fibre content, and phenolic compounds in the association panel enabled the identification of positional and functional candidate genes for B. napus seed meal quality within a small segment of the B. rapa genome sequence.     

Treatment- and population-dependent activity patterns of behavioral and expression QTLs

Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol.     

Molecular mapping of Arabidopsis thaliana lipid-related orthologous genes in Brassica napus

Quantitative Trait Loci (QTL) for oil content has been previously analyzed in a SG-DH population from a cross between a Chinese cultivar and a European cultivar of Brassica napus. Eight QTL with additive and epistatic effects, and with environmental interactions were evaluated. Here we present an integrated linkage map of this population predominantly based on informative markers derived from Brassica sequences, including 249 orthologous A. thaliana genes, where nearly half (112) are acyl lipid metabolism related genes. Comparative genomic analysis between B. napus and A. thaliana revealed 33 colinearity regions. Each of the conserved A. thaliana segments is present two to six?times in the B. napus genome. Approximately half of the mapped lipid-related orthologous gene loci (76/137) were assigned in these conserved colinearity regions. QTL analysis for seed oil content was performed using the new map and phenotypic data from 11 different field trials. Nine significant QTL were identified on linkage groups A1, A5, A7, A9, C2, C3, C6 and C8, together explaining 57.79% of the total phenotypic variation. A total of 14 lipid related candidate gene loci were located in the confidence intervals of six of these QTL, of which ten were assigned in the conserved colinearity regions and felled in the most frequently overlapped QTL intervals. The information obtained from this study demonstrates the potential role of the suggested candidate genes in rapeseed kernel oil accumulation.     

Identification of quantitative trait loci for resistance to shoot fly in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench]

The shoot fly is one of the most destructive insect pests of sorghum at the seedling stage. Deployment of cultivars with improved shoot fly resistance would be facilitated by the use of molecular markers linked to QTL. The objective of this study was to dissect the genetic basis of resistance into QTL, using replicated phenotypic data sets obtained from four test environments, and a 162 microsatellite marker-based linkage map constructed using 168 RILs of the cross 296B (susceptible) × IS18551 (resistant). Considering five component traits and four environments, a total of 29 QTL were detected by multiple QTL mapping (MQM) viz., four each for leaf glossiness and seedling vigor, seven for oviposition, six for deadhearts, two for adaxial trichome density and six for abaxial trichome density. The LOD and R ² (%) values of QTL ranged from 2.6 to 15.0 and 5.0 to 33%, respectively. For most of the QTL, IS18551 contributed resistance alleles; however, at six QTL, alleles from 296B also contributed to resistance. QTL of the related component traits were co-localized, suggesting pleiotropy or tight linkage of genes. The new morphological marker Trit for trichome type was associated with the major QTL for component traits of resistance. Interestingly, QTL identified in this study correspond to QTL/genes for insect resistance at the syntenic maize genomic regions, suggesting the conservation of insect resistance loci between these crops. For majority of the QTL, possible candidate genes lie within or very near the ascribed confidence intervals in sorghum. Finally, the QTL identified in the study should provide a foundation for marker-assisted selection (MAS) programs for improving shoot fly resistance in sorghum.     

Identification and characterization of candidate Rlm4 blackleg resistance genes in Brassica napus using next-generation sequencing

A thorough understanding of the relationships between plants and pathogens is essential if we are to continue to meet the agricultural needs of the world's growing population. The identification of genes underlying important quantitative trait loci is extremely challenging in complex genomes such as Brassica napus (canola, oilseed rape or rapeseed). However, recent advances in next-generation sequencing (NGS) enable much quicker identification of candidate genes for traits of interest. Here, we demonstrate this with the identification of candidate disease resistance genes from B.?napus for its most devastating fungal pathogen, Leptosphaeria maculans (blackleg fungus). These two species are locked in an evolutionary arms race whereby a gene-for-gene interaction confers either resistance or susceptibility in the plant depending on the genotype of the plant and pathogen. Preliminary analysis of the complete genome sequence of Brassica rapa, the diploid progenitor of B.?napus, identified numerous candidate genes with disease resistance characteristics, several of which were clustered around a region syntenic with a major locus (Rlm4) for blackleg resistance on A7 of B.?napus. Molecular analyses of the candidate genes using B.?napus NGS data are presented, and the difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome are discussed.     

QTL mapping of fruit-related traits in pepper (Capsicum annuum)

QTL analysis of pepper fruit characters was performed in an F₃ population derived from a cross between two Capsicum annuum genotypes, the bell-type cultivar Maor and the Indian small-fruited line Perennial. RFLP, AFLP^®1, RAPD and morphological markers (a total of 177) were used to construct a comparative pepper-tomato genetic map for this cross, and 14 quantitatively inherited traits were evaluated in 180 F₃ families. A total of 55 QTL were identified by interval analysis using LOD 3.0 as the threshold for QTL detection. QTL for several traits including fruit diameter and weight, pericarp thickness and pedicel diameter were often located in similar chromosomal regions, thus reflecting high genetic correlations among these traits. A major QTL that accounts for more than 60% of the phenotypic variation for fruit shape (ratio of fruit length to fruit diameter) was detected in chromosome 3. This chromosome also contained QTL for most of the traits scored in the population. Markers in linkage groups 2, 3, 8 and 10 were associated with QTL for multiple traits, thereby suggesting their importance as loci that control developmental processes in pepper. Several QTL in pepper appeared to correspond to positions in tomato for loci controlling the same traits, suggesting the hypothesis that these QTL may be orthologous in the two species.     

Quantitative trait loci and comparative genomics of cereal cell wall composition

Quantitative trait loci (QTLs) affecting sugar composition of the cell walls of maize (Zea mays) pericarp were mapped as an approach to the identification of genes involved in cereal wall biosynthesis. Mapping was performed using the IBM (B73 x Mo17) recombinant inbred line population. There were statistically significant differences between B73 and Mo17 in content of xylose (Xyl), arabinose (Ara), galactose (Gal), and glucose. Thirteen QTLs were found, affecting the content of Xyl (two QTLs), Ara (two QTLs), Gal (five QTLs), Glc (two QTLs), Ara + Gal (one QTL), and Xyl + Glc (one QTL). The chromosomal regions corresponding to two of these, affecting Ara + Gal and Ara on maize chromosome 3, could be aligned with a syntenic region on rice (Oryza sativa) chromosome 1, which has been completely sequenced and annotated. The contiguous P1-derived artificial chromosome rice clones covering the QTLs were predicted to encode 117 and 125 proteins, respectively. Two of these genes encode putative glycosyltransferases, displaying similarity to carbohydrate-active enzyme database family GT4 (galactosyltransferases) or to family GT64 (C-terminal domain of animal heparan synthases). The results illustrate the potential of using natural variation, emerging genomic resources, and homeology within the Poaceae to identify candidate genes involved in the essential process of cell wall biosynthesis.     

Identification and validation of genomic regions that affect shoot fly resistance in sorghum [<Emphasis Type="Italic">Sorghum bicolor</Emphasis> (L.) Moench]

Shoot fly is one of the most important pests affecting the sorghum production. The identification of quantitative trait loci (QTL) affecting shoot fly resistance enables to understand the underlying genetic mechanisms and genetic basis of complex interactions among the component traits. The aim of the present study was to detect QTL for shoot fly resistance and the associated traits using a population of 210 RILs of the cross 27B (susceptible) × IS2122 (resistant). RIL population was phenotyped in eight environments for shoot fly resistance (deadheart percentage), and in three environments for the component traits, such as glossiness, seedling vigor and trichome density. Linkage map was constructed with 149 marker loci comprising 127 genomic-microsatellite, 21 genic-microsatellite and one morphological marker. QTL analysis was performed by using MQM approach. 25 QTL (five each for leaf glossiness and seedling vigor, 10 for deadhearts, two for adaxial trichome density and three for abaxial trichome density) were detected in individual and across environments. The LOD and R ² (%) values of QTL ranged from 2.44 to 24.1 and 4.3 to 44.1%, respectively. For most of the QTLs, the resistant parent, IS2122 contributed alleles for resistance; while at two QTL regions, the susceptible parent 27B also contributed for resistance traits. Three genomic regions affected multiple traits, suggesting the phenomenon of pleiotrophy or tight linkage. Stable QTL were identified for the traits across different environments, and genetic backgrounds by comparing the QTL in the study with previously reported QTL in sorghum. For majority of the QTLs, possible candidate genes were identified. The QTLs identified will enable marker assisted breeding for shoot fly resistance in sorghum.     

Genetic and QTL analysis of maize tassel and ear inflorescence architecture

Maize (Zea mays L.) ear inflorescence architecture is directly relevant to grain yield components, and tassel architecture is relevant to hybrid seed production. The objectives of this study were to (1) determine heritabilities and correlations of a comprehensive set of tassel and ear inflorescence architecture traits in a set of (Illinois Low Protein×B73) B73 S₁ families, (2) identify chromosomal positions of QTL affecting tassel and ear architecture, and (3) identify possible candidate genes associated with these QTL. For tassel traits, the number of detected QTL ranged from one to five, and explained between 6.5 and 35.9% of phenotypic variation. For ear traits, the number of detected QTL ranged from one to nine and phenotypic variation explained by those QTL varied between 7.9 and 53.0%. We detected QTL for tassel architecture traits that required calculation of ratios from measured traits. Some of these calculated traits QTL were detected in regions that did not show QTL for the measured traits, suggesting that calculation of ratios may reveal developmentally relevant patterns of tassel architecture. We detected a QTL on chromosome 7 for tassel branch number near the gene ramosa1 (ra1), which is known to control tassel branch number, making ra1 a candidate gene for tassel branch number. We detected QTL for several traits on chromosomes 6, 8, and 9, where no inflorescence architecture genes have been mapped, thus providing initial information towards new gene discovery for control of inflorescence architecture.     

Quantitative trait loci influencing endosperm texture, dough-mixing strength, and bread-making properties of the hard red spring wheat breeding lines

Wheat end product quality is determined by a complex group of traits including dough viscoelastic characteristics and bread-making properties. Quantitative trait loci (QTL) mapping and analysis were conducted for endosperm texture, dough-mixing strength, and bread-making properties in a population of 139 (MN99394 × MN98550) recombinant inbred lines that were evaluated at three environments in 2006. Based on the genetic map of 534 loci, six QTL were identified for endosperm texture, with the main QTL on chromosomes 1A (R(2) = 6.6%-17.3%), 5A (R(2) = 6.1%-17.1%), and 5D (R(2) = 15.8%-22%). Thirty-four QTL were identified for eight dough-mixing strength and bread-making properties. Major QTL clusters were associated with the low-molecular weight glutenin gene Glu-A3, the two high-molecular weight glutenin genes Glu-B1 and Glu-D1, and two regions on chromosome 6D. Alleles at these QTL clusters have previously been proven useful for wheat quality, except one of the QTL clusters on chromosome 6D. A QTL cluster on chromosome 6D is one of the novel chromosome regions influencing dough-mixing strength and bread-making properties. The QTL for endosperm texture on chromosomes 1A, 5A, and 5B also influenced flour ash content (12.4%-23.3%), flour protein content (10.5%-12.5%), and flour colour (7.7%-13.5%), respectively.     

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.     

Quantitative trait locus mapping of pyrethroid resistance in Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae)

Quantitative trait locus (QTL) mapping is a valuable new tool for locating genomic regions that underlie variation in important traits such as insecticide resistance. Because QTL mapping complements a candidate gene strategy for understanding the genetic architecture of important traits, it may also facilitate the identification of genes causing important variation. After mapping the QTL locations, markers closely linked to QTL can be used for genetic analysis of population structure and to measure the spread and increase of resistance-causing QTL alleles. In this study, QTL influencing resistance to the pyrethroid insecticide esfenvalerate were mapped in the Colorado potato beetle Leptinotarsa decemlineata (Say) (CPB). Three QTL contributing to esfenvalerate resistance were identified from a mapping population of 79 individuals analyzed at 90 marker loci. One QTL had a large effect and two QTL had smaller effects. The major QTL occurs on the X chromosome, overlapping the position of a candidate gene (Leptinotarsa decemlineata Voltage sensitive sodium channel [LdVssc1]) previously implicated in pyrethroid resistance. Resistance-increasing alleles at the two minor-effect QTL originated with the susceptible parent, suggesting that alleles of small effect may be segregating in susceptible populations. Comparison of the New York population from which the susceptible parent originated with a more-susceptible population from North Carolina suggests that the minor-effect loci identified here may explain some of the variation in tolerance observed among susceptible populations. DNA sequencing of a portion of LdVssc1 shows that the resistance-conferring allele from the resistant parent does not contain the kdr mutation previously found in CPB and typically observed in other insects that are resistant to pyrethroid insecticides because of changes in this gene.     

直播条件下水稻6个穗部性状的QTL分析

在大田直播条件下,利用来源于＂Lemont/特青＂的重组自交系群体,对水稻6个穗部性状及其相互间遗传相关的分子基础进行了QTL分析,共检测到19个QTL,各性状QTL数为2～4个,单个QTL贡献率为4%～22%。共检测到3个染色体区段能同时影响多个穗部性状,其中第1染色体RM212-RM104和第2染色体RM263-RM221区段的QTL能同时影响单株产量、每穗颖花数、着粒密度和二次枝梗数中的3个或4个性状,且这2个区段的QTL对各性状的效应方向相同,增效等位基因均来自‘特青’,为各性状间表型正相关提供了重要的遗传解释。第11染色体RG1022附近的QTL对着粒密度的效应值为负,来自‘特青’的等位基因增加性状值,而对穗长的效应值为正,来自‘特青’的等位基因降低性状值,为这2个性状间表型负相关也提供了一定的遗传解释。此外,对水稻穗部性状QTL在多种环境和遗传背景下的稳定表达及其在分子标记辅助育种中的应用进行了讨论。     

Validation of quantitative trait loci for Fusarium head blight and kernel discoloration in barley

Validation of quantitative trait loci (QTLs) is a prerequisite to marker assisted selection (MAS), however, only a fraction of QTLs identified for important plant traits have been independently tested for validation. Resistance to the diseases kernel discoloration (KD) and Fusarium head blight (FHB) in barley is complex and technically difficult to assess, and therefore QTLs for these traits are suitable targets for MAS. We selected two lines, from a QTL mapping population created using the resistant variety Chevron, and crossed them to susceptible parents to generate two validation populations. Genetic maps of both populations were developed for five chromosomes covering 15 selected regions containing QTLs for FHB severity, KD score and concentration of deoxynivalenol (DON), a mycotoxin produced by the FHB pathogen. QTL analyses using these validation populations confirmed that five of the possible 15 QTL regions were associated with at least one of the three traits. While some QTL were detected inconsistently across environments, QTL that could be subjected to validation in both populations were confirmed in both populations in seven out of eight instances. A QTL for KD score on chromosome 6(6H) was confirmed in both validation populations in eight of nine environments and was also associated with FHB in three of six environments. A QTL for FHB on chromosome 2(2H) was confirmed and was also associated with KD and heading date. Marker assisted selection at these two QTLs should enhance disease resistance, however, the QTL on chromosome 2(2H) will also delay heading date.     

Fine mapping and comparative genomics integration of two quantitative trait loci controlling resistance to powdery mildew in a Spanish barley landrace

The intervals containing two major quantitative trait loci (QTL) from a Spanish barley landrace conferring broad spectrum resistance to Blumeria graminis were subjected to marker saturation. First, all the available information on recently developed marker resources for barley was exploited. Then, a comparative genomic analysis of the QTL regions with other sequenced grass model species was performed. As a result of the first step, 32 new markers were added to the previous map and new flanking markers closer to both QTL were identified. Next, syntenic integration revealed that the barley target regions showed homology with regions on chromosome 6 of rice (Oryza sativa), chromosome 10 of Sorghum bicolor and chromosome 1 of Brachypodium distachyon. A nested insertion of ancestral syntenic blocks on Brachypodium chromosome 1 was confirmed. Based on sequence information of the most likely candidate orthologous genes, 23 new barley unigene-derived markers were developed and mapped within the barley target regions. The assessment of colinearity revealed an inversion on chromosome 7HL of barley compared to the other three grass species, and nearly perfect colinearity on chromosome 7HS. This two-step marker enrichment allowed for the refinement of the two QTL into much smaller intervals. Inspection of all predicted proteins for the barley unigenes identified within the QTL intervals did not reveal the presence of resistance gene candidates. This study demonstrates the usefulness of sequenced genomes for fine mapping and paves the way for the use of these two loci in barley breeding programs.     

Comparison of Flowering Time Genes in Brassica Rapa, B. Napus and Arabidopsis Thaliana

The major difference between annual and biennial cultivars of oilseed Brassica napus and B. rapa is conferred by genes controlling vernalization-responsive flowering time. These genes were compared between the species by aligning the map positions of flowering time quantitative trait loci (QTLs) detected in a segregating population of each species. The results suggest that two major QTLs identified in B. rapa correspond to two major QTLs identified in B. napus. Since B. rapa is one of the hypothesized diploid parents of the amphidiploid B. napus, the vernalization requirement of B. napus probably originated from B. rapa. Brassica genes also were compared to flowering time genes in Arabidopsis thaliana by mapping RFLP loci with the same probes in both B. napus and Arabidopsis. The region containing one pair of Brassica QTLs was collinear with the top of chromosome 5 in A. thaliana where flowering time genes FLC, FY and CO are located. The region containing the second pair of QTLs showed fractured collinearity with several regions of the Arabidopsis genome, including the top of chromosome 4 where FRI is located. Thus, these Brassica genes may correspond to two genes (FLC and FRI) that regulate flowering time in the latest flowering ecotypes of Arabidopsis.