Dissection of a major QTL for seed colour and fibre content in Brassica napus reveals colocalization with candidate genes for phenylpropanoid biosynthesis and flavonoid deposition

A major quantitative trait locus (QTL) influencing seed fibre and colour in Brassica napus was dissected by marker saturation in a doubled haploid (DH) population from the black‐seeded oilseed rape line ‘Express 617’ crossed with a yellow‐seeded B. napus line, ‘1012–98’. The marker at the peak of a sub‐QTL with a strong effect on both seed colour and acid detergent lignin content lay only 4 kb away from a Brassica (H+)‐ATPase gene orthologous to the transparent testa gene AHA10. Near the peak of a second sub‐QTL, we mapped a copy of the key phenylpropanoid biosynthesis gene cinnamyl alcohol dehydrogenase, while another key phenylpropanoid biosynthesis gene, cinnamoyl co‐a reductase 1, was found nearby. In a cross between ‘Express 617’ and another dark‐seeded parent, ‘V8’, Bna.CCR1 was localized in silico near the peak of a corresponding seed fibre QTL, whereas in this case Bna.CAD2/CAD3 lay nearby. Re‐sequencing of the two phenylpropanoid genes via next‐generation amplicon sequencing revealed intragenic rearrangements and functionally relevant allelic variation in the three parents.     

Genetic mapping within the wheat D genome reveals QTL for germination, seed vigour and longevity, and early seedling growth

Quantitative trait loci (QTL) controlling germination, seed vigour and longevity, and early seedling growth were identified using a set of common wheat lines carrying known D genome introgression segments. Seed germination (capacity, timing, rate and synchronicity) was characterized by a standard germination test, based either on the 1 mm root protrusion (germination sensu stricto) or the development of normal seedlings. To quantify seed vigour, the same traits were measured from batches of seed exposed for 72 h at 43°C and high (ca. 100%) humidity. Seed longevity was evaluated from the relative trait values. Seedling growth was assessed both under non-stressed and under osmotic stress conditions. Twenty QTL were mapped to chromosomes 1D, 2D, 4D, 5D, and 7D. Most of the QTL for germination sensu stricto clustered on chromosome 1DS in the region Xgwm1291–Xgwm337. A region on chromosome 7DS associated with Xgwm1002 harboured loci controlling the development of normal seedlings. Seed vigour-related QTL were present in a region of chromosome 5DL linked to Xgwm960. QTL for seed longevity were coincident with those for germination or seed vigour on chromosomes 1D or 5D. QTL for seedling growth were identified on chromosomes 4D and 5D. A candidate homologues search suggested the putative functions of the genes within the respective regions. These results offer perspectives for the selection of favourable alleles to improve certain vigour traits in wheat, although the negative effects of the same chromosome regions on other traits may limit their practical use.     

Quantitative trait loci mapping of seed colour,hairy leaf,seedling anthocyanin,leaf chlorosis and days to flowering in F2 population of Brassica rapa L.

A diversity arrays technology (DArT) map was constructed to identify quantitative trait loci (QTL) affecting seed colour, hairy leaf, seedling anthocyanin, leaf chlorosis and days to flowering in Brassica rapa using a F₂ population from a cross between two parents with contrasting traits. Two genes with dominant epistatic interaction were responsible for seed colour. One major dominant gene controls the hairy leaf trait. Seedling anthocyanin was controlled by a major single dominant gene. The parents did not exhibit leaf chlorosis; however, 32% F₂ plants showed leaf chlorosis in the population. A distorted segregation was observed for days to flowering in the F₂ population. A linkage map was constructed with 376 DArT markers distributed over 12 linkage groups covering 579.7 cM. The DArT markers were assigned on different chromosomes of B. rapa using B. rapa genome sequences and DArT consensus map of B. napus. Two QTL (RSC1‐2 and RSC12‐56) located on chromosome A8 and chromosome A9 were identified for seed colour, which explained 19.4% and 18.2% of the phenotypic variation, respectively. The seed colour marker located in the ortholog to Arabidopsis thaliana Transparent Testa2 (AtTT2). Two QTL RLH6‐0 and RLH9‐16 were identified for hairy leaf, which explained 31.6% and 20.7% phenotypic variation, respectively. A single QTL (RSAn‐12‐157) on chromosome A7, which explained 12.8% of phenotypic variation was detected for seedling anthocyanin. The seedling anthocyanin marker is found within the A. thaliana Transparent Testa12 (AtTT12) ortholog. A QTL (RLC6‐04) for leaf chlorosis was identified, which explained 55.3% of phenotypic variation. QTL for hairy leaf and leaf chlorosis were located 0–4 cM apart on the same chromosome A1. A single QTL (RDF‐10‐0) for days to flowering was identified, which explained 21.4% phenotypic variation.     

A major quantitative trait locus for resistance to Turnip Yellows Virus (TuYV, syn. beet western yellows virus, BWYV) in rapeseed

Turnip yellows virus (TuYV) is responsible for a recognizable loss of yield in European winter oilseed rape cultivation. To map genes involved in TuYV resistance, a double haploid population was established by crossing a resynthesized rapeseed line (R54) as donor for TuYV resistance with an elite rapeseed line (‘Express’). Resistance was determined with 10 plants per line by double antibody sandwich‐enzyme‐linked immunosorbent assay. After screening 17 primer combinations (Pstl/Msel and EcoRI/Msel), 143 amplified fragment length polymorphism markers were mapped to 20 linkage groups representing 15 chromosomes of the rapeseed genome. Quantitative trait loci (QTL) were mapped using the composite interval mapping approach. As a result, one major quantitative trait locus was found on linkage group MS17, explaining up to 50% of the phenotypic variation. Because no other factors displaying a significant effect on the expression of resistance could be identified, a simple mode of inheritance for TuYV resistance is suggested, thus enabling marker‐assisted selection during rapeseed breeding.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

Identification of QTL for oil content,seed yield,and flowering time in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis>)

A genetic map was constructed with 353 sequence-related amplified polymorphism and 34 simple sequence repeat markers in oilseed rape (Brassica napus L.). The map consists of 19 linkage groups and covers 1,868 cM of the rapeseed genome. A recombinant doubled haploid (DH) population consisting of 150 lines segregating for oil content and other agronomic traits was produced using standard microspore culture techniques. The DH lines were phenotyped for days to flowering, oil content in the seed, and seed yield at three locations for 3 years, generating nine environments. Data from each of the environments were analyzed separately to detect quantitative trait loci (QTL) for these three phenotypic traits. For oil content, 27 QTL were identified on 14 linkage groups; individual QTL for oil content explained 4.20–30.20% of the total phenotypic variance. For seed yield, 18 QTL on 11 linkage groups were identified, and the phenotypic variance for seed yield, as explained by a single locus, ranged from 4.61 to 24.44%. Twenty-two QTL were also detected for days to flowering, and individual loci explained 4.41–48.28% of the total phenotypic variance.     

Genetic variation for secondary seed dormancy and seed longevity in a set of black‐seeded European winter oilseed rape cultivars

Secondary seed dormancy in oilseed rape is a phenomenon that allows seeds to survive in the soil for many years without germination. Following soil cultivation, dormant seeds may germinate in subsequent years, and they are the main reason for the occurrence of volunteer oilseed rape plants in successive crops. Inheritance of secondary dormancy may be related to seed longevity (SL) in the soil. Genetic reduction in secondary dormancy and SL could provide a mean to reduce the frequency of volunteer plants and especially the dispersal of transgenic oilseed rape. The aim of the present study was to analyse secondary dormancy, germination rate and SL of 28 black‐seeded winter oilseed rape cultivars using in vitro laboratory tests. The material was tested in field experiments at six different locations in Germany in 2008/2009. Significant effects of the genotype and the location on all traits were found. Heritability was high for secondary dormancy (0.97) and moderate for germination rate (0.70) and SL (0.71). Results indicate that a selection for low secondary dormancy would be effective.     

Identification of QTLs for phenolic compounds in oilseed rape (<Emphasis Type="Italic">Brassica napus L.</Emphasis>) by association mapping using SSR markers

Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. In this study, association mapping was performed to detect QTL-linked and genome wide SSR markers linked to phenolic compounds of extraction meal in a population of 49 genetically diverse oilseed rape cultivars of dark-seeded, winter-type oilseed rape accessions. Correction for population structure was performed using 559 genome wide SSR markers. Results showed that seed colour is an important contributor to seed meal quality. Totally, 52 SSR markers linked to phenolic compounds were detected, five of them being QTL linked markers. Some of these markers were already mapped on Brassica napus chromosomes that contain known QTL controlling oilseed rape meal quality traits. Our results demonstrate that association mapping is a useful approach to complement and enhance previous QTL information for marker-assisted selection.     

Marker-assisted increase of genetic diversity in a double-low seed quality winter oilseed rape genetic background

Generation of novel genetic diversity for maximization of heterosis in hybrid production is a significant goal in winter oilseed rape breeding. Here, we demonstrate that doubled haploid (DH) production using microspore cultivation can simultaneously introgress favourable alleles for double‐low seed quality (low erucic acid and low‐glucosinolate content) into a genetically diverse Brassica napus genetic background. The DH lines were derived from a cross between a double‐low quality winter rapeseed variety and a genetically diverse semisynthetic B. napus line with high erucic acid and high glucosinolates (++ quality). Twenty‐three low‐glucosinolate lines were identified with a genome component of 50–67% derived from the ++ parent. Four of these lines, with a genome component of 50–55% derived from the ++ parent, also contained low erucic acid. Heterosis for seed yield was confirmed in test‐crosses using these genetically diverse lines as pollinator. The results demonstrate the potential of marker‐assisted identification of novel genetic pools for breeding of double‐low quality winter oilseed rape hybrids.     

Flooding tolerance of spelt (Triticum spelta L.) compared to wheat (Triticum aestivum L.) – A physiological and genetic approach

In marginal, agroclimatic zones, yield is often affected by flooding, but the effect is much less for winter spelt (Triticum spelta L.) than for winter wheat (Triticum aestivum L.). This study evaluates the reaction of a wheat x spelt population (F₅ RILs of Forno x Oberkulmer) to flooding stress in the early phase of germination. Lines with greater tolerance to 48 h flooding just after imbibition showed less electrolyte leakage (r = -0.79) indicating greater membrane integrity and better survival. Five QTL explaining 40.6% of the phenotypic variance for survival to flooding were found, and localized on the chromosomes 2B, 3B,5A, and 7S. The tolerance to 48 h flooding four days after sowing was best correlated with the mean germination time (r = 0.8), indicating that the plants with a fast coleoptile growth during flooding are less susceptible to flooding. Ten QTL were found for seedling growth index after flooding explaining 35.5% of the phenotypic variance. They were localized on chromosomes 2A, 2B, 2D, 3A, 4B, 5A, 5B, 6A, and 7S. Standard varieties of spelt and wheat showed the same tolerance characteristics. The possibility to use marker assisted selection for flooding tolerance is discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Heat stress during seed development affects forage brassica (Brassica napus L.) seed quality

In two consecutive seasons, forage rape (Brassica napus L.) plants were exposed to short periods (240°C hr) of heat stress (30°C day/25°C night) during seed filling (80% seed moisture content = S1), at physiological maturity (50% seed moisture content = S2) and at both S1 plus S2 (=S3) in a Biotron before being returned to the field until seed harvest. Seeds were hand harvested at 14% seed moisture content and their quality assessed by measuring germination, seed vigour (using the accelerated ageing and conductivity tests) and seed mass (as determined by thousand seed weight). Heat stress at both S1 and S2 caused a small (<10%) but significant reduction in germination in both seasons. There was a significant heat stress timing interaction in the first but not the second season. Reductions in germination were a result of increased abnormal seedling production not seed death. All three heat stress treatments significantly reduced seed vigour, with S3>S2>S1. Seed mass was reduced by heat stress at S1 but not at S2. Variable seed vigour in high‐germinating New Zealand‐produced forage rapeseed lots is most likely explained by short periods of heat stress during seed development.     

Molecular mapping of quantitative trait loci for grain moisture at harvest in maize

In maize, high grain moisture (GM) at harvest causes problems in harvesting, threshing, artificial drying, storage, transportation and processing. Understanding the genetic basis of GM will be useful for breeding low‐GM varieties. A quantitative genetics approach was used to identify quantitative trait loci (QTL) related to GM at harvest in field‐grown maize. The GM of a double haploid population consisting of 240 lines derived from Xianyu335 was evaluated in three planting seasons and a high‐density genetic linkage map covering 1546.4 cM was constructed. The broad‐sense heritability of GM at harvest was 71.0%. Using composite interval mapping, six QTL for GM at harvest were identified on five chromosomes (Chr). Two QTL located on Chr1, qgm1‐1 and qgm1‐2, explained 5.0% and 10.8% of the phenotypic variation in GM at harvest, respectively. The QTL qgm2, qgm3, qgm4 and qgm5 accounted for 3.3%, 8.3%, 5.4% and 11.0% of the mean phenotypic variation, respectively. Because of their consistent detection over multiple planting seasons, the detected QTL appear to be robust and reliable for the breeding of low‐GM varieties.     

QTL mapping of a partial resistance to the corn delphacid‐transmitted viruses in Lepidopteran‐resistant maize line Mp705

A partial resistance to maize mosaic virus (MMV) and maize stripe virus (MStV) was mapped in a RILs population derived from a cross between lines MP705 (resistant) and B73 (susceptible). A genetic map constructed from 131 SSR markers spanned 1399 cM with an average distance of 9.6 cM. A total of 10 QTL were detected for resistance to MMV and MStV, using composite interval mapping. A major QTL explaining 34–41% of the phenotypic variance for early resistance to MMV was detected on chromosome 1. Another major QTL explaining up to 30% of the phenotypic variation for all traits of resistance to MStV was detected in the centromeric region of chromosome 3 (3.05 bin). After adding supplementary SSR markers, this region was found to correspond well to the one where a QTL of resistance to MStV already was located in a previous mapping study using an F₂ population derived from a cross between Rev81 and B73. These results suggested that these QTL of resistance to MStV detected on chromosome 3 could be allelic in maize genome.     

Molecular mapping of soybean seed tocopherols in the cross ‘OAC Bayfield’ × ‘OAC Shire’

Soybean (Glycine max [L.] Merr.) is cultivated primarily for its protein and oil in the seed. In addition, soybean seeds contain nutraceutical compounds such as tocopherols (vitamin E), which are powerful antioxidants with health benefits. The objective of this study was to identify molecular markers linked to quantitative trait loci (QTL) that affect accumulation of soybean seed tocopherols. A recombinant inbred line (RIL) population derived from the cross ‘OAC Bayfield’ × ‘OAC Shire’ was grown in three locations over 2 years. A total of 151 SSR markers were polymorphic of which a one‐way analysis of variance identified 42 markers whereas composite interval mapping identified 26 markers linked to tocopherol QTL across 17 chromosomes. Individual QTL explained from 7% to 42% of the total phenotypic variation. Significant two‐locus epistatic interactions were identified for a total of 122 combinations in 2009 and 152 in 2010. The multiple‐locus models explained 18.4–72.2% of the total phenotypic variation. The reported QTL may be used in marker‐assisted selection (MAS) to develop high tocopherol soybean cultivars.     

Oligogenic control of resistance to soil‐borne viruses SBCMV and WSSMV in rye (Secale cereale L.)

Rye production in European growing areas is constrained by the soilborne cereal mosaic virus (SBCMV) and the wheat spindle streak mosaic virus (WSSMV). To date, no European rye cultivars are known to exhibit resistance against these viruses. In this study, we pursued a quantitative trait locus (QTL) mapping strategy to identify genomic regions for resistance to SBCMV and WSSMV in rye. Three populations, each comprising 100 lines segregating for resistance to SBCMV and/or WSSMV, were evaluated for disease response at two years in three locations in Germany where soils are naturally infested with SBCMV and WSSMV. In the combined analysis across environments, one QTL for SBCMV resistance on chromosome 5R explained 31.9% of the phenotypic variation in one of the populations. For WSSMV resistance, one QTL explaining up to 64.0% of the phenotypic variation was detected on chromosome 7R in each of the three populations. On the Triticeae homoeologous group 5, we found evidence for synteny of the major QTL for SBCMV resistance between the wheat and rye genomes.     

QTL analysis for cooking traits of super rice with a high‐density SNP genetic map and fine mapping of a novel boiled grain length locus

Hybrid rice has contributed substantially to the improvement of grain production worldwide, yet its poor cooking and tasting characteristics have long been recognized. In this study, 132 recombinant inbred lines derived from LYPJ were used to identify quantitative trait loci (QTLs) for 12 cooking traits with the high‐density SNP linkage map recently developed by our team. We identified 17 QTLs on chromosomes 1, 2, 4, 5, 6, 7, 8, 9 and 11, which accounted for 7.50% to 23.50% of the phenotypic variations. A novel major QTL qBGL7 for boiled grain length was further fine‐mapped to an interval of 440 Kb between the two markers RM21906 and gl3 using a BC₃F₂ population. Two near‐isogenic lines with extreme boiled grain length, GX5‐176 and GX5‐101, could be directly used in improving cooking quality. We also identified a QTL for soaked grain width expansion rate, qSGWE6, in the Wx gene region on chromosome 6. The Wx differential regulation coincided with sequential variation between the two parents. Our work offered a theoretical basis for molecular breeding of high‐quality hybrid rice.     

Characterization of Brassica nigra chromosomes and of blackleg resistance in B. napus–B. nigra addition lines

Brassica napus-B. nigra addition lines were previously created using the variety ‘Darmor’ as the oilseed rape genetic background. Two isozyme loci and 46 RAPD markers were added on five different B. nigra chromosomes. The oilseed rape variety used was highly susceptible to blackleg at the cotyledon stage and only the addition of chromosome 4 gave the same level of blackleg resistance as B. nigra. This resistance was efficient whatever the isolates used. A significant effect on the development of stem canker under field conditions was observed only for the line carrying chromosome 4 which was more resistant than the susceptible control. The potential effects of two other chromosomes have to be confirmed. F1 hybrids obtained by crosses between two highly susceptible lines and the monosomic addition line carrying chromosome 4 were examined under field conditions. No effect of the oilseed rape genetic background on the expression of resistance was detected. The introduction of this resistance and mapping of the gene(s) into oilseed rape varieties are discussed.     

The potential of genomic‐assisted breeding to improve Fusarium head blight resistance in winter durum wheat

Durum wheat is the most important tetraploid wheat mainly used for semolina and pasta production, but is notorious for its high susceptibility to Fusarium head blight (FHB). Our objectives were to identify and characterize quantitative trait loci (QTL) in winter durum and to evaluate the potential of genomic approaches for the improvement of FHB resistance. Here, we employed an international panel of 170 winter and 14 spring durum lines, phenotyped for Fusarium culmorum resistance at five environments. Heading date, plant height and mean FHB severity showed significant genotypic variation with high heritabilities and FHB resistance was negatively correlated with both heading date and plant height. The dwarfing gene Rht‐B1 significantly affected FHB resistance and the genome‐wide association scan identified eight additional QTL affecting FHB resistance, explaining between 1% and 14% of the genotypic variation. A genome‐wide prediction approach yielded only a slightly improved predictive ability compared to marker‐assisted selection based on the four strongest QTL. In conclusion, FHB resistance in durum wheat is a highly quantitative trait and in breeding programmes may best be tackled by classical high‐throughput recurrent phenotypic selection that can be assisted by genomic prediction if marker profiles are available.     

Creating favourable morphological and yield variations for rapeseed by interspecific crosses between Brassica rapa and Brassica oleracea

Brassica napus is a most important oilseed grown worldwide with a limited genetic background, due to the short history of speciation, domestication and cultivation. To create novel germplasm for rapeseed breeding, we made interspecific crosses followed with chromosome doubling between B. rapa and B. oleracea to generate novel B. napus with favourable agronomic traits. The resynthesized (S0) hybrids were confirmed by SSR and cytogenetic analysis, and the fertility was increased from 32.7% in S0 generation to ~97.31% in S1 generation. The plant shapes of the progeny were dramatically improved compared to the diploid parents and B. napus cv. ‘Yangyou 6’, especially for the branch initiation height, branch number and pod number. The single‐plant yield was significantly improved in S1 progeny for the variations in branching sites and number. Significant improvement in plant shape and yield was observed on S2 generation compared to the local elite commercial open‐pollinated cultivar, which would be further fixed by intensive selection and pyramiding breeding. Such variation is of great value for breeding rapeseed with improved plant architecture and harvest index.