QTL mapping of net blotch resistance genes in a doubled-haploid population of six-rowed barley

Net blotch, caused by Pyrenophora teres f. teres, is a damaging foliar disease of barley worldwide. It is important to identify resistance germplasm and study their genetics. 'Chevron', a six-rowed barley used as a parent for the production of a doubled haploid (DH) population for mapping of Fusarium head blight (FHB) resistance, was also found to be resistant to net blotch. To map the resistance genes, the population was evaluated for resistance at the seedling stage in a greenhouse. The resistance data showed a two-peak distribution. Through linkage mapping, one resistance gene, tentatively called Rpt, was located on chromosome 6HS flanked by Xksua3b-Xwg719d, which was also detected by QTL mapping. This QTL explained 64% of the phenotypic variance for the resistance in this DH population. In addition, a minor QTL was found on chromosome 2HS defined by Xcdo786-Xabc156a. 'Chevron' and 'Stander' contributed the resistant alleles of Rpt and the 2HS QTL, respectively. Both QTLs together explained nearly 70% of the phenotypic variance. The markers for these QTLs are useful for marker-assisted selection of net blotch resistance in barley breeding.     

Inheritance of cabbage head formation in crosses of cabbage × ornamental cabbage and cabbage × kale

We investigated the inheritance of head formation in Brassica oleracea by using two crosses, cabbage × ornamental cabbage and cabbage × kale. The degree of head formation (DHF) was classified into nine grades ranging from non‐heading to full heading. DHF in the two F₂ populations showed a continuous distribution. The variance of F₃ offspring selected for full heading or non‐heading was large. The DHF distributions in the F₃ offspring selected for moderate heading or randomly selected F₃ populations were similar to those of the respective F₂ populations, but had smaller average values and variance. However, the realized heritability in F₃ offspring was similar in full‐heading and non‐heading selections. Our findings suggest that head formation is a quantitative trait controlled additively with low dominance effects. In comparisons of leaf developmental patterns among the parents, only cabbage showed a change in leaf shape becoming wider because of the shorter petiole length with increasing leaf position. These findings suggest that cabbage acquired the developmental changes in leaves required to form a head during the process of domestication.     

Identification and mapping of adult‐plant stripe rust resistance in soft red winter wheat cultivar ‘USG 3555’

Little is known about the extent or diversity of resistance in soft red winter wheat (Triticum aestivum L.) to stripe rust, caused by the fungal pathogen Puccinia striiformis f.sp. tritici. The soft red winter (SRW) wheat cultivar ‘USG 3555’ has effective adult‐plant resistance to stripe rust, which was characterized in a population derived from ‘USG 3555’/‘Neuse’. The mapping population consisted of 99 recombinant inbred lines, which were evaluated for stripe rust infection type (IT) and severity to race PST‐100 in field trials in North Carolina in 2010 and 2011. Genome‐wide molecular‐marker screenings with 119 simple sequence repeats and 560 Diversity Arrays Technology (DArT) markers were employed to identify quantitative trait loci (QTL) for stripe rust resistance. QTL on chromosomes 1AS, 4BL and 7D of ‘USG 3555’ explained 12.8, 73.0 and 13.6% of the variation in stripe rust IT, and 13.5, 72.3 and 10.5% of the variation in stripe rust severity, respectively. Use of these and additional diagnostic markers for these QTL will facilitate the introgression of this source of stripe rust resistance into SRW wheat lines via marker‐assisted selection.     

Mature plant resistance of barley to barley leaf rust,another type of resistance

Summary Seedling and flag leaves of three barley cultivars were simultaneously inoculated with urediospores of barley leaf rust, race 1-2-1, and incubated at the same greenhouse bench. The inoculated leaves were harvested before urediospore formation was initiated. The volume of a large number of colonies was estimated by measuring colony area and colony depth by embedding the colony containing leaf segments into paraffin for microtome cutting. The colony volume was considerably smaller in flag leaves than in seedling leaves even in the extremely susceptible cultivar. On average the difference was about tenfold.     

SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal–Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.E.S. Mace and D.T. Phong contributed equally to this work.     

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.     

Genomewide association study reveals novel quantitative trait loci associated with resistance towards Septoria tritici blotch in North European winter wheat

Fungal diseases are a major constraint for wheat production. Effective disease resistance is essential for ensuring a high production quality and yield. One of the most severe fungal diseases of wheat is Septoria tritici blotch (STB), which influences wheat production across the world. In this study, genomewide association mapping was used to identify new chromosomal regions on the wheat genome conferring effective resistance towards STB. A winter wheat population of 164 North European varieties and breeding lines was genotyped with 15K single nucleotide polymorphism (SNP) wheat array. The varieties were evaluated for STB in field trials at three locations in Denmark and across 3 years. The association analysis revealed four quantitative trait loci, on chromosomes 1B, 2A, 5D and 7A, highly associated with STB resistance. By comparing varieties containing several quantitative trait loci (QTL) with varieties containing none of the found QTL, a significant difference was found in the mean disease score. This indicates that an effective resistance can be obtained by pyramiding several QTL.     

Quantitative trait locus mapping of floral and related traits using an F2 population of Aquilegia

The objective of this study was to determine quantitative trait loci (QTL) underlying ten floral and related traits in Aquilegia. The traits assessed were calyx diameter, corolla diameter, petal length, petal blade length, sepal length, sepal width, spur length, spur width, plant height and flower number. These are important traits for ornamental value and reproductive isolation of Aquilegia. QTL analysis of these traits was conducted using single‐marker analysis and composite interval mapping (CIM). We used an F₂ population consisting of 148 individuals derived from a cross between the Chinese wild species Aquilegia oxysepala and the cultivar Aquilegia flabellata ‘pumila’. Resulting CIM analysis identified 39 QTLs associated with these traits, which were mapped on seven linkage groups. These QTLs could explain 1.22–53.28% of the phenotypic variance. Thirty‐one QTLs, which explained more than 10% of the phenotypic variation, were classified as major QTLs. Graphical representations of the QTLs on seven linkage groups were made. Our research provides the potential for future molecular assisted selection breeding programmes and the cloning of target genes through fine mapping.     

Race-specific effects in major genic and polygenic resistance of barley to barley leaf rust in the field: identification and distinction

Summary Six partially resistant spring barley cultivars were exposed to four barley leaf rust (Puccinia hordei) races in the field and in the greenhouse. The 24 cultivar-race combinations were tested in field plots of 1.5×1.5 m² in two replications over two years. To reduce the interplot exchange of urediospores each plot was surrounded by winter rye.The level of barley leaf rust varied among cultivars, races and years. In both years the variance for cultivar-race interactions was highly significant and originating largely from the cultivar-race combinations Berac-22. Armelle-22, Armelle-A and Tyra-A. The Berac-22 interaction was towards higher, the other three interactions towards a lower level of barley leaf rust. The reduced rust levels of these three combinations were not due to interactions between the partial resistance of these cultivars and the aggressiveness of the races but to major genes for hypersensitivity not effective to the races 1-2-1 and F, common in Western Europe, but effective against the rare races 22 and A. This was revealed in the greenhouse experiments where all combinations had a susceptible infection type except Armelle-22, Armelle-A and Tyra-A, which showed low infection types in both the seedling and adult plant stages. The urediosori present in the field plots of these three combinations apparently arose from spores derived from other plots; this interplot interchange suggesting partial resistance.The interaction of Berac with race 22 truly was a small race-specific effect within the polygenic, partial resistance of barley to barley leaf rust like the one reported before between Julia and race 18.     

Quantitative trait loci underlying soybean seed tocopherol content with main additive,epistatic and QTL × environment effects

Soybean (Glycine max [L.] Merrill) seeds are a major source of tocopherols (Toc), which could significantly improve immune system health of human and prevent or treat many serious diseases. Selection for higher Toc contents of seeds could increase nutritional value of soybean‐derived food, laying on an important breeding goal for many soybean breeders. The present objectives of the work were to evaluate various genetic effects of QTL associated with individual and total Toc content based on a RIL population (“Beifeng 9” × “Freeborn”) in six environments to improve the efficiency of molecular marker‐assisted selection (MAS) for high‐Toc breeding. The results described that eighteen, thirteen, eleven and thirteen QTL were associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc content, respectively, and have additive main effects (a) and/or additive × environment interaction effects (ae) in certain environments. Among them, four QTL for α‐Toc, two QTL for γ‐Toc, one QTL for δ‐Toc and four QTL for total Toc could increase α‐Toc, γ‐Toc, δ‐Toc and total Toc content via significant a effect, respectively, which have stronger stability in different years and locations. It implied a value for MAS. Additionally, twenty‐five, fifteen, eleven and twenty epistatic pairwise QTL associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc contents, respectively, were detected. The genetic information of the QTL effects obtained here would be beneficial for breeding soybean variety with high‐Toc content by MAS.     

Quantitative trait loci mapping of adult‐plant resistance to leaf rust in a Fundulea 900 × ‘Thatcher’ wheat cross

Wheat leaf rust (LR), caused by the obligate biotrophic fungus Puccinia triticina (Pt), is a destructive foliar disease of common wheat (Triticum aestivum L.) worldwide. The most effective, economic means to control the disease is resistant cultivars. The Romanian wheat line Fundulea 900 showed high resistance to LR in the field. To identify the basis of resistance to LR in Fundulea 900, a population of 188 F_2:3 lines from the cross Fundulea 900/‘Thatcher’ was phenotyped for LR severity during the 2010–2011, 2011–2012 and 2012–2013 cropping seasons in the field at Baoding, Hebei Province. Bulked segregant analysis and simple sequence repeat markers were used to identify the quantitative trait loci (QTLs) for LR adult‐plant resistance in the population. Three QTLs were detected and designated as QLr.hebau‐1BL, QLr.hebau‐2DS and QLr.hebau‐7DS. Based on the chromosome positions and molecular marker tests, QLr.hebau‐1BL is Lr46, and QLr.hebau‐7DS is Lr34. QLr.hebau‐2DS was derived from ‘Thatcher’ and was close to Lr22. This result suggests that Lr22b may confer residual resistance on field nurseries when challenged with isolates virulent on Lr22b, or another gene linked to Lr22b confers this resistance from ‘Thatcher’. This study confirms the value of Lr34 and Lr46 in breeding for LR resistance in China; the contribution of the QTL to chromosome 2D needs further validation.     

QTL mapping for capsaicin and dihydrocapsaicin content in a population of Capsicum annuum ‘NB1’ × Capsicum chinense ‘Bhut Jolokia’

Capsaicinoids are pungent compounds used for industrial and medical purposes including food, medicine and cosmetics. The Indian local variety ‘Bhut Jolokia’ (Capsicum chinense Jacq.) is one of the world's hottest chilli peppers. It produces more than one million Scoville heat units (SHUs) in total capsaicinoids. In this study, our goal was to identify quantitative trait loci (QTLs) responsible for the high content of capsaicin and dihydrocapsaicin in ‘Bhut Jolokia’. Capsicum annuum ‘NB1’, a Korean pepper inbred line containing 14 000 SHUs, was used as a maternal line. An F₂ population derived by crossing between ‘NB1’ and ‘Bhut Jolokia’ was generated to map QTLs for capsaicinoids content. A total of 234 markers, including 201 HRM, 21 SSR, 2 CAPS and 10 gene‐based markers of the capsaicinoid synthesis pathway, were mapped. The final map covered a total distance of 1175.2 cM and contained 12 linkage groups corresponding to the basic chromosome number of chilli pepper. Capsaicin and dihydrocapsaicin content were analysed in 175 F₂ pepper fruits using the HPLC method. The maximum total capsaicinoids content was 1389 mg per 100g DW (dry weight), and the minimum content was 11 mg per 100g DW. Two QTLs (qcap3.1 and qcap6.1) for capsaicin content were identified on LG3 and LG6, and two QTLs (qhdc2.1 and qdhc2.2) for dihydrocapsaicin content were located on LG2. We did not detect QTLs for total capsaicinoids content. The QTL positions for capsaicin content were different from those for dihydrocapsaicin content. These results indicate that the complexity of selecting for more pungent chilli peppers must be considered in a chilli pepper breeding programme. The QTL‐linked markers identified here will be helpful to develop more pungent pepper varieties from ‘Bhut Jolokia’, a very hot pepper.     

Co-localization of quantitative trait loci for foliar disease resistance in sorghum

Quantitative trait loci (QTL) analysis of resistance to three foliar diseases, viz. target leaf spot, zonate leaf spot and drechstera leaf blight was undertaken in sorghum using 168 F₇ recombinant inbred lines derived from a cross between '296B' (resistant) and 'IS18551' (susceptible) parents. The genomic region flanked by plant colour locus ( Plcor ) and simple sequence repeat marker Xtxp95 on chromosome SBI-06 harboured disease-response QTL for all the three diseases caused by different fungal pathogens. It is hypothesized that this region on sorghum chromosome SBI-06 could harbour a cluster of disease-response loci to different pathogens as observed in the syntenic regions on rice chromosome 4 and maize chromosome 2. The information gained in this study can be used in deploying marker-assisted selection for foliar resistance and map-based isolation of important disease resistance genes in sorghum.     

Accumulating polygenes for partial resistance in barley to barley leaf rust,Puccinia hordei. II. Field evaluation

Summary Eight lines from the cross between Vada and Cebada Capa with long to very long latent periods and four barley cultivars representing the known range of partial resistance to barley leaf rust, caused by Puccinia hordei, were evaluated in the field for partial resistance and in the greenhouse for the latent period (LP) in the young flag leaf.Each of the 12 entries was sown (15-4-1983) on a plot of 1.0 m². There were four replicates. To reduce interplot interference the plots were separated from each other by 4.0 m of spring rye. The number of urediosori per tiller was evaluated at 27-6, 4-7, 12-7 and ten days after heading. The LP was measured on 10 to 15 plants per entry in 1982 and on 10 plants in 1983.The levels of partial resistance varied greatly. The difference in number of sori per tiller between the most susceptible cultivar, Akka, and the most resistant cultivar, Vada, was about 50 times. Between Akka and the most resistant line this was approximately 5000 times. The LP's varied similarly. Vada had a LP 64% longer than that of Akka, the LP of line 26-6-11 was 15% longer. The range of partial resistance has been extended more than twofold.The correlation coefficients between LP and the level of barley leaf rust, expressed in transformed scale units, varied from -0.99 for the first sampling date to -0.97 for the third sampling date. Sampling the same development stage, ten days after heading, did not improve the r-value (r=–0.98). The LP evaluated in the young flag leaf is shown to be a very reliable criterion for partial resistance in the barley-Puccinia hordei pathosystem.Earliness tends to be associated with susceptibility. The correlation of days to heading with LP was 0.63, and with the level of barley leaf rust in the field 0.64.     

Interplot interference and the assessment of barley cultivars for partial resistance to leaf rust,Puccinia hordei

Summary The barley cultivars Akka, highly susceptible, and Vada, partially resistant to barley leaf rust, Puccinia hordei, were evaluated for the amount of leaf rust in five experimental field plot situations over three successive years. The field plot situations were: A) plots well isolated from each other by distance and non-leaf rust contributing host plants; B) adjacent plots of 4×41/2 m (18 rows); C) adjacent plots of 4×11/2 m (6 rows); D) adjacent plots of 4×1/4 m (1 row); E) adjacent plots of only one plant (cultivar mixtures).The sporulating leaf area of each plot was measured from samples of 20 tillers taken at random from each plot. In each year the difference in sporulating area between Akka and Vada was large to very large in the absence of interplot interference in the isolated plots, ranging from 150 to 2100 times. In the adjacent plots the partial resistance of Vada was greatly underestimated, 5 to 16 times in the situation B, 14 to 30 times in C, and 75 to 130 times in D and E.Testing lines or cultivars in adjacent plots is the standard procedure in use in breeding programs and in tests of cultivars for their agricultural value. To avoid such under estimation the following procedure is suggested. A few cultivars representing the known range of partial resistance and whose level of partial resistance is well known are evaluated together with the lines and cultivars whose partial resistance has to be assessed. This is demonstrated with a number of cultivars of which resistance values are know from the recommended variety lists for England and Wales. Cultivars have been assessed in Wageningen over four years together with the check cultivars Akka, Sultan, Julia and Vada representing the range of partial resistance with values (on a 1 to 10 scale) of 1, 3–4, 7 and 8 respectively, based on isolated plots experiments.     

Investigation and genetic mapping of a Glomerella leaf spot resistance locus in apple

Apple Glomerella leaf spot (GLS) is a severe fungal disease that damages apple leaves during the summer in China. Breeding new apple varieties that are resistant to the disease is considered the best way of controlling GLS. Fine mapping and tightly linked marker are critically essential for the preselection of resistant seedlings. In this study, a population of 207 F₁ individuals derived from a cross between ‘Golden Delicious’ and ‘Fuji’ was used to construct a fine simple sequence repeat (SSR)‐based genetic linkage map. The position of R_gls, a locus responsible for resistance to GLS, was identified on apple linkage group (LG) 15 using SSR markers CH05g05 and CH01d08, which was adapted from a published set of 300 SSR markers that were developed using the bulked segregant analysis (BSA) method. These two SSR markers flanked the gene, and its recombination rate was 8.7% and 23.2%, respectively. A total of 276 newly developed SSR markers around the target region and designed from the genome apple assembly contig of LG15 were screened. Only nine of these were determined to be linked to the R_gls locus. Thus, a total of 11 SSR markers were in linkage with R_gls, and mapped at distances ranging from 0.5 to 33.8 cM. The closest marker to the R_gls locus was S0405127, which showed a genetic distance of approximately 0.5 cM. The first mapping of the gene R_gls was constructed, and the locations of the 11 effective primers in the ‘Golden Delicious’ apple genome sequence were anchored. This result facilitates better understanding of the molecular mechanisms underlying the trait of resistance to GLS and could be used in improving the breeding efficiency of GLS‐resistant apple varieties.     

QTL mapping of adult‐plant resistance to stripe rust in a ‘Lumai 21 × Jingshuang 16’ wheat population

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a devastating fungal disease in common wheat (Triticum aestivum L.) worldwide. Chinese wheat cultivars ‘Lumai 21’ and ‘Jingshuang 16’ show moderate levels of adult‐plant resistance (APR) to stripe rust in the field, and they showed a mean maximum disease severity (MDS) ranging from 24 to 56.7% and 26 to 59%, respectively, across different environments. The aim of this study was to identify quantitative trait loci (QTL) for resistance to stripe rust in an F₃ population of 199 lines derived from ‘Lumai 21’ × ‘Jingshuang 16’. The F₃ lines were evaluated for MDS in Qingshui, Gansu province, and Chengdu, Sichuan province, in the 2009–2010 and 2010–2011 cropping seasons. Five QTL for APR were detected on chromosomes 2B (2 QTL), 2DS, 4DL and 5DS based on mean MDS in each environment and averaged values from all three environments. These QTL were designated QYr.caas‐2BS.2, QYr.caas‐2BL.2, QYr.caas‐2DS.2, QYr.caas‐4DL.2 and QYr.caas‐5DS, respectively. QYr.caas‐2DS.2 and QYr.caas‐5DS were detected in all three environments, explaining 2.3–18.2% and 5.1–18.0% of the phenotypic variance, respectively. In addition, QYr.caas‐2BS.2 and QYr.caas‐2BL.2 colocated with QTL for powdery mildew resistance reported in a previous study. These APR genes and their linked molecular markers are potentially useful for improving stripe rust and powdery mildew resistances in wheat breeding.