Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

Two previously described QTL mapping methods, which combine linkage analysis (LA) and linkage disequilibrium analysis (LD), were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA) gave good results as long as the distance between the QTL was large (> 90 cM). When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA) gave good results for all evaluated distances between the QTL. For the large distances between the QTL (> 90 cM) the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown

The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

<p>Abstract</p> <p>Background</p> <p>Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD) test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets.</p> <p>Methods</p> <p>The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5^th, 10^thand 50^thhighest T_CLDvalue from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively.</p> <p>Results</p> <p>In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001), where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001). In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05), i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position.</p> <p>Conclusions</p> <p>The CLD test can provide evidence for a causative SNP, but its power may be low in situations with closely linked markers. In such situations, also functional evidence will be needed to definitely conclude whether the SNP is causative or not.</p

Nutritional composition of bilberries (<i>Vaccinium myrtillus</i> L.) from forest fields in Norway – Effects of geographic origin, climate, fertilization and soil properties

Effects of different environmental factors (origin, climate, fertilization and soil properties) on berry nutritional quality were studied in eight forest fields of bilberry (Vaccinium myrtillus) in Northern-, Mid- and Southern Norway. No clear trend between locations could be found, however untargeted multivariate analysis of metabolite profiles revealed clear segregation patterns between locations. Anthocyanin, and phenolics content, and titratable acidity were significantly affected by mineral fertilization (Mid-Norway), while organic fertilization did not show any significant effects (Northern Norway). Bilberry chemical composition was affected by harvest time point, as indicated by a potentially higher nutritional quality regarding the content of phytochemicals when harvesting at mid or towards the end of the production season (Southern Norway). Regional and annual climate had strongest impact on the nutritious content of bilberries. Significant differences were found between locations, however previous findings on increasing anthocyanin content with latitude were not confirmed due to environmental impacts confounding the population effects

Landbruk i nord-norge – tilpasning til endret klima

VIKTIGE ENDRINGER I NORD-NORGE -Lengre vekstsesong -Varmere, særlig i vintermånedene -Mer nedbør, spesielt om høsten, hyppigere episoder med sterk nedbør -Mindre nedbør som snø, kortere periode med snødekke -Lengre perioder med vannmetta jordpublishedVersio

Effect of combined seasonal coverage on northern production of strawberry (Fragaria ananassa Duch)

Two field trials with five strawberry cultivars planted on a woven black polyfibre ground cover sheet with or without translucent sheet plant coverage during winter and the growing season as combined treatments were started in 2004 and 2005. In total, nine different cultivars were included in the two fields. One early cv. ‘Polka’ and one late cv. ‘Korona’ acted as standard cultivars, while the other cultivars were new, named or labelled selections from Norwegian, Finnish and Swedish breeding programs. Winter survival, spring vigour, earliness, saleable and total berry yield, berry size and berry quality were registered for three years. The cultivars differed in earliness, berry size, yield (gram per plant) and total production (sum of all years). A combination of fibre sheet winter and spring coverage and more open net sheet harvest season coverage showed favourable results for overwintering, earliness and berry yield, and enhanced the ripening process in all cultivars.Effect of combined seasonal coverage on northern production of strawberry (Fragaria ananassa Duch)publishedVersio

Klimaendringenes påvirkning på landbruket i Norge innenfor ulike klimasoner

Klimaendringer vil ha stor påvirkning på fremtidig landbruksproduksjon i Norge og tilpasning vil være nødvendig både for å utnytte muligheter og håndtere utfordringer som følger av det nye klimaet. Klimaprojeksjoner fram mot slutten av dette århundret viser at klimaet kan endres betydelig, men det er fortsatt stor usikkerhet rundt nivået på disse endringene. Det er likevel slik at mange aktuelle tilpasninger i landbrukssektoren vil ha positiv effekt uavhengig av klimaendringene. I landbruket brukes 6 agroklimatiske klimasoner for å beskrive dyrkingsforholdene i de forskjellige delene av landet. De beste sonene finnes i hovedsak på Østlandet, Sør-Vestlandet og i Trøndelag og samsvarer i stor grad med korndyrkingsområdene. I Buskerud er 75 % av dagens dyrka arealer innenfor de to beste klimasonene og dette gjenspeiles i en variert jordbruksproduksjon innen fylket, med mye korn, grønnsaker, frukt og bær. I Troms finnes det dyrka arealet innen sonene 4 og 5 og brukes i all hovedsak til produksjon av grovfôr. Forskjellene i produksjoner innebærer også noe forskjeller i sårbarhet for forskjellige klimaeffekter. For Buskerud vil handtering av overflatevann være viktig fremover. Flom og ekstreme nedbørshendelser vil ha stor potensiell skadeeffekt på arealer med ettårige vekster. For Troms vil særlig vinteroverlevelse av fôrvekster kunne bli et viktig tema fremover. Felles for fylkene er behovet for fokus på overvåking av flom og skred samt behov for oppgradering av hydrotekniske løsninger.publishedVersio

Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – A comparison of single QTL and multi QTL methods

Two previously described QTL mapping methods, which combine linkage analysis (LA) and linkage disequilibrium analysis (LD), were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA) gave good results as long as the distance between the QTL was large ($>90$ cM). When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a “ghost” QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA) gave good results for all evaluated distances between the QTL. For the large distances between the QTL ($>90$ cM) the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown

Effect of fertilization, tiller cutting and environment on plant growth and yield of European Blueberry (Vaccinium myrtillus L.) in Norwegian forest fields.

-BACKGROUND: European blueberry (E. blueberry; Vaccinium myrtillus L.) is a natural resource demanded by the processing industry with potential of domestication. Therefore an investigation of the possibilities of partial cultivation of native stands was started. OBJECTIVE: To increase knowledge of how E. blueberry react to soil types, climate, mineral nutrition, organic amendments and cutting of tillers. METHODE: Five forest fields with E.blueberry stands in Norway were examined. Besides natural development influenced by soil parameters and climate, effect of fertilization and plant pruning were examined in the municipalities of Bardu in Troms county (68◦N) and of Sn°asa and Lierne in Nord-Trøndelag county (64◦N). Experiments were executed in randomized block designs in forest fields of native E. blueberry stands. RESULTS: The fields that performed best had O-layers close to 7 cm or thicker. The C/N ratios indicate that N was not easily available in any field, and addition of mineral fertilizer containing nitrogen and phosphor show that especially N increased elongation of long shoots and more nodes were developed. However, the effect on number of short shoots per long shoot initiated a growth gain only the last of two years. The positive growth effect of fertilizer was not followed by higher yields throughout the years, and strongest fertilization level (N60P40) reduced yield in average of four years. Adding composted wood chips or wood chips alone increased tiller growth in the birch-field in Bardu both years, but only the first year in the pine-field; this was not reflected in higher yield. Cutting of shoots to the ground reduced yield and full yield potential was not recovered before the third year after cutting. CONCLUSION: The results suggest that by improving growth conditions, especially by securing a thick natural O-layer and adjusting soil macro nutrient composition, growth conditions could be improved; and that fruit yield were down the two first years after pruning

Arktisk kvalitet – En beskrivelse av nordlige natur- og klimaforhold og virkning på egenskaper hos nordnorske matprodukter

Unike nordlige klimaforhold med lange dager og lave temperaturer, kan påvirke egenskaper hos mat, fôr og beitevekster. En gjennomgang av vitenskapelige studier av slik Arktisk kvalitet viser effekter for både sensorisk kvalitet og ulike innholdsstoffer for flere produkter. Innen kålvekster påvirker klimaet utseende (brokkoli) og reduserer glukosinolatinnhold og bittersmak (brokkoli og kålrot). Gulrot og kålrot får tydeligere søtsmak på grunn av lavere innhold av bitterstoffer, selv om sukkerinnholdet er uendret. På den annen side får gulrot i nord lavere innhold av karoten og lysere farge enn i varmere klima. Resultatene for kålrot, brokkoli og gulrot tyder også på mer sprø og saftig konsistens, og friskere smak, ved lave dyrkingstemperaturer. Ville bær i nordlig klima har litt høyere innhold av enkelte antioksidanter enn i sørligere områder, men lokale forskjeller i vekstforhold (fjell, kyst) kan ha like stor betydning. Hagebær i nordlig klima kan smake søtere (jordbær) eller mindre søte (solbær) på grunn av forskjellige klimaresponser. Jordbær og bringebær får noe svekket rødfarge ved lave dyrkingstemperaturer. Klimatiske og geografiske effekter på kvalitet i potet, urter til mat og krydder, fôrvekster og kjøtt- og melkeprodukter er per idag for lite undersøkt til å gi entydige konklusjoner.....publishedVersio